### FWRI Technical Report TR-11 2007 

# TECHNICAL REPORTS

Florida Fish and Wildlife Conservation Commission Florida Bay Science Program: A Synthesis of Research on Florida Bay

John Hunt and William Nuttle Editors 

# FISH AND WILDLIFE RESEARCH INSTITUTE 

# TECHNICAL REPORTS ISSN 1930-1448

### Charlie Crist **Governor of Florida**



## Florida Fish and Wildlife Conservation Commission

**K enneth D. Haddad** 

**E xecutive Director** 

**T he Fish and Wildlife Research Institute (FWRI) is a division of the Florida Fish and Wildlife**  **Conservation Commission (FWC). The FWC is “managing fish and wildlife resources for their long-term well-being and the benefit of people.” The FWRI conducts applied research perti**  **nent to managing marine-fishery resources and marine species of special concern in Florida.**

**Programs at the FWRI focus on resource-management topics such as managing gamefish and shellfish populations, restoring depleted fish stocks and the habitats that support them,**  **protecting coral reefs, preventing and mitigating oil-spill damage, protecting endangered and threatened species, and managing coastal-resource information.** 

**T he FWRI publishes three series:**  **Memoirs of the Hourglass Cruises, Florida Marine Research Pub lications,**  **and FWRI Technical Reports. FWRI Technical Reports**  **contain information relevant to immediate resource-management needs.** 

**Gil McRae, FWRI Director** 

**J ames F. Quinn, Jr.,**  **Science Editor**

**J udith G. Leiby,**  **Copy Editor**

**Llyn C. French, Publications Production** 

# Florida Bay Science Program: A Synthesis of Research on Florida Bay

John H. Hunt Editor

Florida Fish and Wildlife Conservation Commission Fish and Wildlife Research Institute South Florida Regional Laboratory 2796 Overseas Highway, Suite 119 Marathon, Florida 33050 USA



# W illiam Nuttle Editor

Eco-hydrology.com

Ottawa, Ontario Canada K1S 4B6



# Florida Fish and Wildlife Conservation Commission FWRI Technical Report TR-11

2007

### Cover Photographs

**Center: T** **he Crocodile Dragover pass, below Terrapin Bay and Madeira Bay (Bill Perry, Everglades**  **National Park). Clockwise from upper left: Sampling in seagrass**  **(Florida Fish and Wildlife Conservation Commission);**  **Anhinga with spotted sea trout, Florida Bay (Bill Perry, Everglades National Park);**  **Florida Bay hardbottom habitat (**  **Florida Fish and Wildlife Conservation Commission); W**  **hite Pelicans and Black Skimmers at low tide, Flamingo, Florida Bay**  **(Bill Perry, Everglades National Park).**



### Copies of this document may be obtained from

**Florida Fish and Wildlife Conservation Commission Fish and Wildlife Research Institute**  **100 Eighth Avenue SE St. Petersburg, FL 33701-5020 USA**  **Attention: Librarian**



### Document Citation

**Hunt, J. H., and W. Nuttle, eds. 2007. Florida Bay Science Program: A Synthesis of Research on Florida Bay. Fish and Wildlife Research Institute Technical Report TR-11. iv + 148 p.** 



### Document Production

**T**

**his document was composed in Microsoft Word ®**  **and produced using QuarkXPress ®**  **on Apple Macintosh ®**  **computers.The headline font is Adobe ®**  **Av ant Garde, the text font is Adobe**  **® P**  **alatino, and the cover headline is Adobe**  **® Gill Sans.** 

**T he cover and text papers used in this publication meet the minimum requirements of the American**  **National Standard for Permanence of Paper for Printed Library Materials Z39.48—1992.**

# Ta ble of Contents

Chapter 1 Florida Bay Science **............................ 1** 

### Chapter 2 Executive Summary **............................ 2 PURPOSE OF THIS REPORT**  **................................ 2 ECOSYSTEM HISTORY**  **.................................. 3 PHYSICAL PROCESSES**  **.................................. 4 NUTRIENT DYNAMICS**  **.................................. 4 PLANKTON BLOOMS**  **................................... 5 Northeast Region**  **..................................... 5 Central Region**  **...................................... 5 W** 

**est Region ....................................... 6**  **SEAGRASS ECOLOGY .................................. 6**  **HIGHER–TROPHIC–LEVEL SPECIES ............................ 7**  

### Chapter 3 Ecosystem History **............................. 9 INTRODUCTION**  **..................................... 9 Methodology**  **...................................... 9 Previous Work**  **. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10 Summary of Ecosystem History and Paleoecology Research**  **. . . . . . . . . . . . . . . . . . . . 12 SALINITY PATTERNS AND TRENDS**  **. . . . . . . . . . . . . . . . . . . . . . . . . . . . 15 Methods**  **. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16 F** 

**indings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16**  **Status of Research . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19**  **NUTRIENT PATTERNS AND TRENDS . . . . . . . . . . . . . . . . . . . . . . . . . . . 21**  **Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21**  **F**

**indings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21**  **Status of Research . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22**  **OCCURRENCE AND PATTERN OF ALGAL BLOOMS . . . . . . . . . . . . . . . . . . . . 23**  **Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23**  **F**

**indings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23**  **Status of Research . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23**  **SEAGRASS TRENDS AND PATTERNS . . . . . . . . . . . . . . . . . . . . . . . . . . . 24**  **Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24**  **F**

**indings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24**  **Status of Research . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26**  **HIGHER–TROPHIC–LEVEL SPECIES . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27**  **Status of Research . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27**  **LITERATURE CITED . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27**  

### Chapter 4 Physical Processes **. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30 INTRODUCTION**  **. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30 Background**  **. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30 Research Summary**  **. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32 DRIVING PROCESSES**  **. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35 W** 

**inds and Storms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35**  **Precipitation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36**  **Evaporation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36**  **Surface-Water Input . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36**  **Groundwater Input . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37**  **Sea Level and Tides . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38**  **Boundary Currents . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38** 

iii **INFLUENCE OF DRIVING PROCESSES . . . . . . . . . . . . . . . . . . . . . . . . . . 38**  **Salinity . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38**  **Circulation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40**  **Exchanges with Adjacent Waters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42**  **PREDICTION . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43**  **F**

**resh Water Inflow . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43**  **Exchanges with Adjacent Waters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45**  **Circulation Models . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46**  **Salinity Models . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47**  **UNRESOLVED QUESTIONS AND ONGOING RESEARCH . . . . . . . . . . . . . . . . . . 48**  **Driving Processes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48**  **System Characteristics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49**  **Hydrodynamic Models . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50**  **LITERATURE CITED . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51**  

### Chapter 5 Nutrient Dynamics **. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55 INTRODUCTION**  **. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55 Summary of Knowledge**  **. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56 PA**  **TTERNS AND TRENDS IN WATER QUALITY . . . . . . . . . . . . . . . . . . . . . . . 57**  **P**

**eriod of Study . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58**  **Recent Conditions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58**  **EXOGENOUS SOURCES OF NUTRIENTS . . . . . . . . . . . . . . . . . . . . . . . . . 59**  **Nutrient Inputs from the Everglades: Taylor Slough–C-111 and Shark River . . . . . . . . . . . . . 60**  **Ground Water . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62**  **Atmospheric, Keys Waste Water, Keys Storm Water, and the Gulf of Mexico Nutrient Inputs . . . . . . 66**  **Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66**  **INTERNAL NUTRIENT CYCLING . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66**  **Benthic Nutrient Fluxes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66**  **Internal Nutrient Cycling: Carbonate–Phosphorus–Iron Relations . . . . . . . . . . . . . . . . . 67**  **Role of Sediment Resuspension in Phosphorus Cycling . . . . . . . . . . . . . . . . . . . . . 67**  **Nutrient Flux at the Sediment–Water Interface . . . . . . . . . . . . . . . . . . . . . . . . . 68**  **Seagrass Modeling . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68**  **INFLUENCE OF FLORIDA BAY WATER QUALITY ON THE REEF TRACT . . . . . . . . . . . 69**  **Nutrient Export Through Keys Passes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69**  **WA TER–QUALITY MODELING**  **. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69 CURRENT AND ONGOING RESEARCH**  **. . . . . . . . . . . . . . . . . . . . . . . . . . 71 Unresolved Questions**  **. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71 Summary of Ongoing Research**  **. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73 LITERATURE CITED**  **. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73** 

### Chapter 6 Plankton Blooms **. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77 INTRODUCTION**  **. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77 Regional Differences**  **. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77 Summary of Research**  **. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79 EASTERN FLORIDA BAY**  **. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81 CENTRAL FLORIDA BAY**  **. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 82 Cause of Blooms in the Central Region**  **. . . . . . . . . . . . . . . . . . . . . . . . . . . . 82 Domination by Cyanobacteria**  **. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85 WESTERN FLORIDA BAY**  **. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 86 LITERATURE CITED**  **. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89** 

### Chapter 7 Seagrass Ecology **. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 92 INTRODUCTION**  **. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 92 Seagrass Communities in Florida Bay**  **. . . . . . . . . . . . . . . . . . . . . . . . . . . . 92 Recent and Historical Changes**  **. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 93 Conceptual Models for Seagrass Die-off**  **. . . . . . . . . . . . . . . . . . . . . . . . . . . 98 Summary of Research**  **. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 99 EFFECT OF ECOSYSTEM CHARACTERISTICS ON GROWTH AND SURVIVAL**  **. . . . . . . 101 Temp**  **erature . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101**  **Salinity . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 102**  **Light . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 102**  **Nutrients . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 103**  **Sulfide . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 103**  **Labyrinthula Infection**  **. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 103 Sediment Characteristics**  **. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 104 EFFECT OF ECOSYSTEM CHARACTERISTICS ON COMMUNITY STRUCTURE**  **AND DISTRIBUTION . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 104**  **Correlation with Patterns of Water Quality . . . . . . . . . . . . . . . . . . . . . . . . . 104**  **Geographic Variation in Seagrass Die-off . . . . . . . . . . . . . . . . . . . . . . . . . . 104**  **MODELING CHANGE IN BENTHIC COMMUNITIES . . . . . . . . . . . . . . . . . . . 106**  **CURRENT RESEARCH . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 106**  **F**

**ield Assessment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 106**  **Experimental . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 106**  **LITERATURE CITED . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 106**  

### Chapter 8 Higher-Trophic-Level Species **. . . . . . . . . . . . . . . . . . . . . . 110 INTRODUCTION**  **. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 110 Description of Higher-Trophic-Level Species in Florida Bay**  **. . . . . . . . . . . . . . . . . . 110 Processes Driving Change in the Ecosystem**  **. . . . . . . . . . . . . . . . . . . . . . . . . 113 Research Approaches**  **. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 115 Summary of Recent Results**  **. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 116 DISTRIBUTION OF SPECIES AND PATTERNS OF ABUNDANCE**  **. . . . . . . . . . . . . . 119 EFFECT OF ECOSYSTEM CHARACTERISTICS ON GROWTH AND SURVIVAL**  **. . . . . . . 120 Effect of Salinity on Growth and Survival**  **. . . . . . . . . . . . . . . . . . . . . . . . . . 120 Effect of Water Quality on Growth and Survival**  **. . . . . . . . . . . . . . . . . . . . . . . 121 Effect of Benthic Habitat on Growth and Survival**  **. . . . . . . . . . . . . . . . . . . . . . 122 Immigration, Growth, and Survival of Offshore-Spawning Fishes that Use Florida Bay as a Nursery**  **. 122 EFFECT OF ECOSYSTEM CHARACTERISTICS ON SPECIES DISTRIBUTION AND**  **COMMUNITY AND TROPHIC STRUCTURE . . . . . . . . . . . . . . . . . . . . . . 123**  **Effect of Salinity on Species Abundance and Community Structure . . . . . . . . . . . . . . . 123**  **Effect of Water Quality on Species Abundance and Community Structure . . . . . . . . . . . . . 124**  **Effect of Benthic Habitat on Species Abundance and Community Structure . . . . . . . . . . . . 124**  **V**

**ARIATION IN ECOSYSTEM CHARACTERISTICS . . . . . . . . . . . . . . . . . . . . 127** 

**Effects of Animals on the Ecosystem . . . . . . . . . . . . . . . . . . . . . . . . . . . . 127**  **Oceanographic Effects on Larval Transport and Recruitment . . . . . . . . . . . . . . . . . . 128**  **Effect of Human Activities . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 132**  **MODELING CHANGE IN HIGHER–TROPHIC–LEVEL SPECIES . . . . . . . . . . . . . . 134**  **Statistical Models . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 134**  **Simulation Models . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 135**  **ONGOING RESEARCH . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 137**  **Projects . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 137**  **Unresolved Issues and Questions: Research Needs . . . . . . . . . . . . . . . . . . . . . . 138**  **LITERATURE CITED . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 141** 

iii

# About This Report

**T his report draws its material directly from syntheses compiled for the 2001 Florida Bay Science**  **Conference. The Florida Bay Science Program organizes itself around five strategic research questions. T** 

**opical teams associated with each question consist of modelers and researchers working in the Bay and adjacent marine systems.These teams compiled the original synthesis documents.**  **In preparation for the 2003 Florida Bay Science Conference, the research teams have modified the existing synthesis documents to bring them up to date and implement a more uniform, common format.**  **In some cases, entirely new documents have been drafted, such as the information here on ecosystem history and on nutrient dynamics. The present report compiles these separate documents into one and**  **provides the reader with summary material as a guide to the contents.**



### T eam Leaders
Ecosystem History **G. L ynn Wingard (USGS, Reston)**  Physical Processes **T homas Lee (University of Miami), Elizabeth Johns (NOAA/AOML), Peter Ortner and Dawn Boyer**  **(NOAA/AOML, PMC)** Nutrient Dynamics **J oseph Boyer (Florida International University), Brian Keller ( Florida Keys National Marine Sanctuary,**  **PMC)** Algal Blooms **Gary Hitchcock (University of Miami), Ed Phlips (University of Florida), Larry Brand (University of Miami), Douglas Morrison (ENP, PMC)**  Seagrass Ecology **Michael Durako (University of North Carolina at Wilmington), Joseph Zieman (University of Virginia), Michael Robblee (USGS, PMC)**  Higher-Trophic-Level Species **J oan Browder (NOAA/NMFS), John Lamkin (NOAA/NMFS, PMC)** 



### Editors

**W illiam Nuttle (Eco-hydrology.com) and John Hunt (Florida FWC, PMC)** 

iv**Florida Bay lies between the southern tip of the Florida mainland and the island chain known as the Florida**  **Ke ys. More than 85% of the bay’s 2,200-km**  **2 area lies**  **within Everglades National Park, and the Florida Keys National Marine Sanctuary contains much of the rest.**  **T he bay includes more than 200 small islands, many**  **of which are rimmed with mangroves. Florida Bay supports numerous protected species, including the** **Roseate Spoonbill, the bottlenose dolphin, the Amer ican crocodile, the West Indian manatee, and several**  **species of sea turtles. Moreover, Florida Bay provides critical habitat for commercially important species,** **such as spiny lobsters, stone crabs, and many impor tant finfish species. It also serves as the principal nurs**  **ery for the offshore Tortugas pink shrimp, which supports an important fishery.**  **Florida Bay is an important component of the much larger south Florida region that is the focus of**  **the Comprehensive Everglades Restoration Plan (CERP). The bay receives freshwater runoff from the** **Everglades, a large portion of which is managed dis**

**c harge from canals in the region. Decisions guiding the**  **restoration of the Everglades carry implications for future conditions in Florida Bay, just as the develop**  **ment of the regional water management system over the past fifty years influences present conditions. Al** **though a specific restoration target has not yet been de fined for Florida Bay, many expect that restoration of**  **more natural hydrologic conditions in the Everglades will move the bay toward an ecological state more typ**  **ical of the period prior to the time of engineered**

**c hanges imposed on the regional south Florida system.**  **Rapid ecological changes occurred in Florida Bay between 1987 and 1991. These changes came at the**  **end of a multiyear drought that had elevated salinity**

**v**

**alues in the central portion of the bay to nearly 70 prac tical salinity units (psu), almost double the typical**  **salinity of seawater. Large areas of seagrasses began to die late in 1987. Concurrently, the shrimp harvest on**  **the Tortugas Grounds declined to record lows. In 1991, turbidity and plankton concentrations increased dra** **matically, reducing the supply of light to the remain ing seagrass beds through the previously “gin-clear”**  **bay waters. Mass mortality of sponges, which help to filter the bay’s waters and provide habitat for juvenile**  **lobster, followed in the path of the plankton blooms. By the end of 1991, there was widespread concern**  **among the public for the health of the Florida Bay ecosystem, yet very little scientific information existed**  **that resource managers could use in response to this**

**concern. T** **he Florida Bay Science Program emerged in 1994 as a coordinated effort by state and federal agencies to** **identify the mechanisms and underlying causes re sponsible for the recent ecological changes. Its objec**  **tives were to implement an interagency program of research aimed at developing the knowledge needed**  **to guide ecosystem restoration and to communicate this scientific knowledge to restoration managers, scientists,**  **policy makers, and the informed public. Currently 11 state and federal agencies participate in the program**  **through representatives on the Program Management Committee. This committee formulated a Strategic** **Plan, which was revised in 1997, to coordinate the re search supported independently by the separate agen**  **cies.The committee also provides for occasional review of the program by the independent Science Oversight**  **P**

**anel and for dissemination of its findings through a series of science conferences.This report is part of the**  **Strategic Plan’s effort. T** **he CERP was established in 2000 with the over arching goal of restoring and preserving the ecosystems**  **of south Florida, including Florida Bay.This plan relies on scientific information to document the condition of**  **south Florida’s ecosystems and evaluate the effects of human activities on them. Human activities influence**  **the structure and function of ecosystems both directly, by**  **altering the ecosystems themselves, and indirectly, by**  **altering the climatic, hydrologic, and geologic processes that drive the ecosystems and maintain their** **structure.This has probably occurred throughout his tory. However, the extent and intensity of human ac**  **tivities and their influence on ecosystems has increased greatly with the expansion of agriculture and urban de** 

**v elopment in the past 100 years. In order to guide**  **restoration efforts, resource managers now require scientific information on the bay’s ecosystem, how it has** 

**c hanged during the past 100 years, how it works, and** **how it likely will respond to planned restoration ac tivities. Since its inception, the Florida Bay Science** **Program has pursued the goal of developing this in formation and providing it to resource managers.** 

FWRI Technical Report TR-11 1 

# Chapter 1 Florida Bay Science2 FWRI Technical Report TR-11 

## Purpose of This Report

**T his report documents the progress made toward the**  **objectives established in the Strategic Plan revised in 1997 for the agencies cooperating in the program.**  **T hese objectives are expressed as five questions (see**  **box below) that organized the research on the Florida Bay ecosystem. Each question examines different char** **acteristics of the Florida Bay ecosystem and the rela tion of these to the geomorphological setting of the bay**  **and to processes linking the bay with adjacent systems and driving change.This report also examines the ad**  **ditional question of what changes have occurred in Florida Bay over the past 150 years.** **Preparation of this report coincided with the reeval uation of the strategy for organizing ecosystem re**  **search in Florida Bay around these five central questions. This strategy originated in response to the**  **need by resource managers for basic information about startling changes in the ecosystem that occurred in** **the late 1980s and early 1990s. Since 1994, the pro gram, focused by the central questions, has sought to**  **identify the underlying mechanisms and causes of these decade-old events. Resource managers now ask** **a different set of questions.The inception of the Com prehensive Everglades Restoration Plan (CERP) in**  **2000 signals a shift in resource management away from the reactive stance of protecting natural resources**  **toward the proactive pursuit of restoring south Florida’s ecosystems. In general, ecosystem restoration chal**  **lenges us to look ahead. Can we predict future conditions in the Florida Bay**  **ecosystem that will follow from resource-management decisions made today? The 1997 Strategic Plan de**  **scribes a set of interrelated predictive models for this**
**purpose, i.e.,**  **for circulation, water quality, and eco logical models.This activity has been pursued at sev**  **eral levels. The most visible has been the ongoing effort to identify and implement an appropriate set of**  **numerical simulation models to describe circulation and water quality within the bay and the interaction**  **of the bay with the Everglades, the Florida Shelf, the reef tract, and waters of the Florida Keys. Research** **has spawned the development of other types of pre dictive models,**  **i.e., historical analogs, correlative mod**  **els, and mechanistically based empirical models. Some of these models can be used to peer into the future, al**  **beit through somewhat narrow windows focused on specific elements of the bay.**  **T he concluding chapter examines progress toward**  **answering the original central questions and explores some of the new challenges for research on Florida Bay.**  **By maintaining focus on the central questions to serve the programmatic purposes described above, this re**  **port addresses most directly past concerns of resource managers. However, scientific information developed**  **by the Florida Bay Science Program is also relevant to** **the present management goal of restoring the ecosys** 

# Chapter 2 Executive Summary

Ecosystem History **W hat was the Florida Bay ecosystem like 50, 100, and 150 years ago?**  Question 1—Physical Processes **How and at what rates do storms, changing freshwater flows, sea level rise, and local evaporation and precipitation influence circulation and salinity patterns within Florida Bay and**  **exchange between the bay and adjacent waters?** Question 2—Nutrient Dynamics **Wh at is the relative importance of the influx of external nutrients and**  **of internal nutrient cycling in determining the nutrient budget for Florida Bay? What mechanisms control the sources and sinks of the bay’s nutrients?**  Question 3—Plankton Blooms **Wh at regulates the onset, persistence, and fate of planktonic algal blooms**  **in Florida Bay?** Question 4—Seagrass Ecology **W hat are the causes and mechanisms for the observed changes in the sea**  **grass community of Florida Bay? What is the effect of changing salinity, light, and nutrient regimes on these communities?**  Question 5—Higher Trophic Levels **Wh at is the relationship between environmental and habitat change**  **and the recruitment, growth, and survivorship of animals in Florida Bay? tems of south Florida. For both the program and for ef** **forts to restore Florida Bay, knowledge of the past of fers the best perspective for looking ahead.** 



## Ecosystem History

**T he alarming ecological changes witnessed in Florida**  **Bay during the late 1980s and early 1990s precipitated a shift in natural-resource management in south**  **Florida that culminated in the CERP. For many in the public-at-large, and among scientists as well, the** **restoration of Florida Bay will mean a return to con ditions remembered from immediately prior to these** 

**c hanges—clear water, lush beds of seagrass, and good**  **fishing. Resource managers must be concerned with whether these conditions can be sustained by the**  **ecosystem given the variety of processes driving change in the ecosystem. Perhaps if viewed over a time span**  **longer than only the past twenty years, the natural state of Florida Bay will be revealed as something**  **quite different from what is remembered. An objective of the program shared across the five**  **central questions has been to construct a history of past conditions in the bay based principally on objective,**  **quantitative data. Quantitative observations on the state of the Florida Bay ecosystem date back to the**  **1950s, when systematic surveys were conducted by Finucane, Dragovich, and Tabb. Although invaluable,**  **these observations provide an incomplete and biased representation of the bay’s natural state. Major changes** **had already occurred in the hydrology of the Ever glades by the time these studies took place. Fortu**  **nately, through analysis of coral and sediment cores we can read the history of the Florida Bay ecosystem**  **recorded in the skeletons of organisms that resided here during the past 150 years.This work leads to the**  **following conclusions:**

**• Salinity in Florida Bay is more strongly correlated to** 

**rainfall than any other single factor. A periodicity in salinity and rainfall data suggests linkages to the El** **Niño/Southern Oscillation climatic patterns. Al though anthropogenic influences play a secondary**  **role to rainfall in determining salinity for Florida Bay as a whole, they may be a factor in the magnitude of**  **salinity variations seen in recent times. Additionally, anthropogenic factors may act on a local basis to**  **influence salinity patterns.**

**• Seagrass has been more abundant in the past 50** 

**y ears than in the first half of the 20th century. Prior**  **to the mid-20th century, epiphytal ostracodes were relatively rare at sites in central and northeastern**  **Florida Bay, suggesting a greater abundance and/or density of seagrass over the past 50 years than in the**  **first half of the century. Epiphytal mollusks, although not rare, increased significantly at most sites from ap**  **proximately 1940 on.These data suggest that dense and abundant seagrass beds may not have been the**  **long-term normal state of the ecosystem, and they carry implications for restoration.**  **• Do wncore profiles of dated cores from central Florida** 

**Bay show that productivity events ( i.e.,**  **blooms) have occurred historically in Florida Bay. A large multi**  **decadal productivity event characterized by greatly elevated levels of organic carbon and nitrogen, dated**  **to about the mid 1700s, was observed in two cores from Whipray Basin. Interestingly, total phosphorus** 

**w as not elevated during this time span.This time pe**  **riod (the Little Ice Age) may correspond to a period of higher rainfall in the Everglades and more ex**  **tensive land runoff into Florida Bay, which may have triggered the productivity event.** 

**• Sediments from northeastern Florida Bay (espe** 

**cially from sites near Pass Key and Russell Key banks) show indications of recent nutrient (carbon, nitrogen,**  **and phosphorous) enrichment (1980 to present). T** **his nutrient enrichment could be related to recent microalgal blooms and seagrass die-off within**  **Florida Bay. • N**  **ortheastern Florida Bay appears to be a source of**

**nutrients to the mangrove zone at the southern end of Taylor Slough. Uranium-isotope studies indicate**  **that the phosphorus contamination at the northern end of Taylor Slough appears to be fertilizer-de** **rived. However, phosphorus contamination in Tay lor Slough diminishes to background by midslough;**  **therefore, Taylor Slough does not appear to be a source of nutrients to northeastern Florida Bay.**  **• M acroalgae have increased. Relative abundance of** 

**mollusks with a strong preference for T**  **halassia has**  **declined since approximately 1970 in northeastern Florida Bay and since 1910 in Whipray, whereas**  **more generally epiphytic organisms have generally increased. This may indicate an increase in the**  **amount of macrobenthic algae relative to T**  **halassia. • A**  **t Bob Allen, seagrass abundance appears to have**

**been increasing since a recent minimum around 1960. Downcore profiles of lignin phenols from Pass**  **Ke y core show large variations in lignin-phenol dis**  **tributions over short time intervals, reflecting the proximity of this site to the mangrove zone along the**  **coast and the outlet of Taylor Creek.**

**• Changes also occurred in circulation and exchange** 

**with adjacent waters during the early part of the 20th century. Geochemical changes recorded in coral** **bands suggest that construction of the overseas rail road altered exchange by blocking passes between**  **the Keys. Other changes appear to be the result of** Hunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 3 Executive SummaryFlorida Bay Synthesis Hunt and Nuttle

4 FWRI Technical Report TR-11 **decreased freshwater inflow from the Everglades that resulted from “reclamation” activities on the**  **mainland.**


## Physical Processes

**Research on physical processes aims to identify the main external factors that control the movement of** 

**w ater and solutes within Florida Bay and their ex** 

**c hange with the Everglades and adjacent marine sys**  **tems.The difficulty is estimating the relative influence of the various physical driving processes, even though**  **the identities of the physical processes themselves are known from the study of other estuaries. The two** **physical characteristics of Florida Bay that distin guish it from most other estuaries in the U.S. are the**  **restricted exchange across the shallow but otherwise open boundary with the Florida Shelf and the rela**  **tively small amount of terrestrial freshwater discharge to the bay.** 

**• Historical data from the salinity-synthesis database** 

**(Robblee et al.,**  **2001) show that Florida Bay has be haved as a marine lagoon for the past several** **decades. Salinity has reached as high as 70 in the cen tral bay on a few occasions and typically exceeded**  **40 during drought years like 1989–1990. For example, following the wet period of 1994–1995, salinity in**  **creased, tropical storms in 1999 induced a decrease, and data from the drought years of 2000 and 2001 in**  **dicated another increase. More recent data from 2002 and early 2003 indicate another general fresh**  **ening trend. • T**  **he south Florida coastal region is surrounded by an intense, large-scale, oceanic boundary current (the** **Loop Current–Florida Current system) and its evolv ing eddies that link local coastal waters to remote**  **river discharges upstream in the Gulf of Mexico.**

**• Seasonal cycles in local wind-forcing produce sea** 

**sonal patterns in circulation pathways, connecting south Florida coastal waters through western Florida**  **Bay and transporting Everglades freshwater discharges. Southward flows through the Keys pas** **sages predominate in winter and spring, north-north**

**w est flows in summer, and southwest flow toward the**  **T**

**ortugas in the fall. Large-volume, wind-forced flows through the Keys passages provide linkage for gulf**  **to-Atlantic exchange through the southwestern shelf region adjacent to western Florida Bay.** 

**• Seasonal cycles in south Florida coastal current sys** 

**tems provide seasonal pathways for local larval re cruitment. They also furnish opportunities for**  **recruitment from remote sources.**

**• Shallow bank configurations that restrict water ex**  **c hange tend to separate the bay’s interior into three**  **distinct regions with different salinity regimes.The northeastern region is the most isolated from oceanic**  **influences, receives most of the surface runoff, and has the largest seasonal cycle of salinity.The central**  **region receives little runoff and has the maximum salinity. The basins in the western region have the**  **greatest oceanic exchange and the smallest seasonal**

**c hange in salinity.**  **• V ariability of Florida Bay average salinity is directly** **related to the net flux of fresh water from the com bined influence of evaporation, precipitation, and**  **runoff. For the bay as a whole, on seasonal or annual time scales, evaporation is approximately equal to** **precipitation, and runoff is roughly 10% of either. His torical salinity data and salinity proxy data show**  **that Florida Bay salinity has commonly undergone large changes on time scales of seasonal, interannual**  **(ENSO), decadal (NAO), and even longer periods that are not understood.** 

**• Stable-isotopic markers indicate that runoff from** 

**the Everglades is the dominant source of fresh water to the northeastern region of Florida Bay, whereas**  **for the western region, precipitation shows a strong signal. In the central region, a mixture of runoff and**  **precipitation provides the fresh water.**

**• Since 1985, freshwater discharge from Taylor Slough** 

**and the C-111 canal have increased as a consequence of changes in water management.Trout Creek con** 

**ve ys the largest volume of fresh water to northeast**  **ern Florida Bay, varying from –6 to 32 m 3**  **/s. By contrast, the flow from each of another eight creeks**  **where discharge is metered ranges from –1.4 to 6**

**m 3**  **/s. Negative flows can occur during the dry sea son and during storm events.**  **• Lo w-salinity Shark River plume waters are advected** 

**southward around Cape Sable to western Florida Bay and the Keys reef tract by seasonal, wind-driven**  **coastal flows. For the Ten Thousand Island region of the western Everglades, the mean annual river dis** 

**c harge is estimated to be 13.3 m**  **3 /s for Harney River,**  **11 m 3**  **/s for Broad River, and 12.4 m 3**  **/s for Shark River.** 

**• Groundwater inflows are believed to be most influ** 

**ential along the northern boundary of the bay. How**

**ev er, estimates for the rate of groundwater discharge**  **are highly uncertain, ranging over four orders of magnitude.** 


## Nutrient Dynamics

**In contrast to water movement and salinity, which re flect the influence of outside processes, both external**  Executive SummaryHunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 5**and internal processes combine to determine charac teristics of water quality. Research on this question**  **has concentrated on quantifying external sources and sinks of nitrogen and phosphorus. More recently, the**  **focus has been on internal exchanges between the sediment and the water column. The major external**  **sources of nutrients have proven difficult to quantify. As a result it has been challenging to resolve the ques**  **tion of whether the seagrass die-off and subsequent plankton blooms were triggered by the onset of eu**  **trophication of Florida Bay. • Ov**  **er a thirteen-year period of record, temporal**

**trends have shown bay-wide declines in total phos phorus (P), total nitrogen (N), and chlorophyll**  **a (CHLA), with an overall increase in turbidity.** 

**• Objective analysis shows that there are three zones** 

**in Florida Bay that exhibit significant differences in**

**w ater-quality characteristics due to nutrient inputs,**  **tidal advection, and water residence time. These zones correspond generally to the northeast, central,**  **and west regions, which are defined by variation in other ecosystem characteristics. In general, dissolved**  **phosphorus concentrations increase and nitrogen concentrations decrease from east to west, resulting**  **in a shift from phosphorous limitation to nitrogen limitation. Central bay waters have high ammonium**  **concentrations, which may indicate a bottleneck in the process of nitrification.** 

**• Atmospheric input of nutrients is large relative to** 

**other sources. • T** **here is a measurable effect of water management**

**on nutrient loading in the Taylor Slough system.Ter restrial nutrient loading fluctuates in phase with** **freshwater flow; however, flow-weighted concen trations decrease with increasing flow. A serious** **disconnect exists between upland/canal loading es timates and actual input to the bay because of un**  **measured nutrient processing in the intervening**

**w etland/mangrove areas.**  **• H igh rates of organic carbon and nitrogen fluxes** 

**occur, both into and out of sediments, over diel cycles. Benthic denitrification is higher than predicted from**  **nitrogen-loading rates.There are times when benthic N** **2 fixation in Florida Bay balances denitrification but**  **the system overall shows a net loss of nitrogen.**

**• Sediment flux of ammonium decreases with an in** 

**crease in sediment chlorophyll a**  **concentration, which indicates that the microphytobenthos is im** **portant in regulating water column nitrogen con centrations.**  **• T here is very little, if any, inorganic phosphorous flux** **out of the sediments with the exception of the west ern bay/shelf area.**  

## Plankton Blooms

**F or Florida Bay as a whole, plankton blooms can be** **viewed as a distinct mode of variation in the ecosys tem that arises from a consequence of external drivers** **and internal processes. On a mechanistic level, plank ton blooms form whenever plankton growth exceeds**  **the combined effect of grazing and dispersion (the processes that reduce plankton concentrations). Stud**  **ies of other estuaries link plankton blooms to increased nutrient loads in runoff. Research on plankton blooms**  **in Florida Bay has been directed at describing the combination of internal and external conditions asso**  **ciated with the onset, persistence and fate of blooms in this ecosystem. Research to date indicates that there**  **are three ecologically distinct regions within the bay from the standpoint of algal blooms: the Northeast**  **Region, the Central Region, and the West Region.The nature and causes of blooms can be most appropriately**  **summarized within the context of these three regions.**


### Northeast Region

**• Algal blooms are largely absent from the Northeast** 

**Region of Florida Bay. The phytoplankton commu nity of the Northeast Region is a diverse mixture of** 
**cya nobacteria, dinoflagellates, diatoms, and mi**  **croflagellates, none of which form blooms. • T** **he lack of algal blooms in the Northeast Region of**

**Florida Bay is largely attributable to the severe phos phorus limitation characteristic of the region. Despite** **significant water inflows to the region from the Ever glades, the very low phosphorus levels in these in**  **puts combined with the calcium carbonate-rich**

**w aters of the region result in nutrient-limited con**  **ditions.** 

### Central Region

**• Large algal blooms have been a common feature of** 

**the central region since at least 1992.The focal point for blooms is in the north-central part of the region,**  **extending from Rankin Basin and into Whipray Basin.The greatest bloom activity is generally in the**  **summer and early fall, although blooms have been observed in other seasons. In the fall and early sum**  **mer, blooms originating in the north-central part of the Central Region are pushed southward by the** **prevailing, wind-driven circulation into the south ern part of the Central region, where they can spread**  **out into the Atlantic reef tract through cuts in the Florida Keys. The dominant bloom-forming alga in** **the central region is the picoplanktonic cyanobac** Executive SummaryFlorida Bay Synthesis Hunt and Nuttle

6 FWRI Technical Report TR-11

**terium Synechococcus elongatus,**  **although several species of diatom and dinoflagellate do occasionally**  **occur in bloom proportions. • N**  **utrient limitation of phytoplankton growth in the**

**central region appears to switch back and forth from phosphorus to nitrogen.The nature of the sources of**  **nutrients for blooms in the central region has been a subject of considerable debate, yielding several**  **hy potheses:** 



## ° **A significant supply of nutrients for algal pro**

**duction is available from the flocculent muddy sediments within the region;** 



## ° **A groundwater source of phosphorus is present**

**within the region that, in combination with nitro gen from the northeast region, feeds algal blooms;** 



## ° **Nutrients from the shelf region west of the bay are**

**av ailable to blooms in the central region via tidal**  **exchange;**



## ° **Atmospheric deposition is a significant source of**

**nutrients (particularly N) for algal primary pro duction.**  **T hese hypotheses are not mutually exclusive, and**  **several mechanisms may be operational at the same time.**  **• T he domination of blooms in the Central Region by** 

**Synechococcus elongatus is attributable to the unique**  **ecophysiological characteristics of this species of**
**cy anobacterium.These characteristics include** 



## ° **wide tolerance to salinity,**



## ° **superior ability to compete for phosphorus at low**

**concentrations,**



## ° **ability to regulate buoyancy and thereby take ad**

**v**

**antage of nutrients available in the sediments, and**



## ° **lower susceptibility to grazing losses.**



### W

est Region

**• A lgal blooms are also a common feature of the West** 

**Region of Florida Bay.The West Region, in contrast to the cyanobacterial blooms in the Central Region,** **is dominated by diatoms.The blooms in the West Re gion are mainly**  **Rhizosolenia spp.,**  **Chaetoceros spp.,** **and pinnate diatoms, which dominate in terms of cel lular biomass. Diatom blooms in the west region**  **begin in late summer and are advected into the bay from shallow coastal waters off Cape Sable.**  **• T he diatom-dominated blooms in western Florida** 

**Bay are mainly limited in their growth by nitrogen, either singly or in combination with phosphorus**  **and/or silicon supply. Temperature, salinity, and light do not appear to be important factors in the ini**  **tiation or maintenance of diatom blooms. Maximum growth rates of the diatom community during bloom**  **initiation in the West Region range from 1 to 2 day –1**  **(first-order rate constant), based on increases in net plankton (>5 μm size fraction), chlorophyll**  **a , o**  **r bio genic silica. The onset of diatom blooms on the** 

**w estern Florida Shelf appears to be associated with**  **enhanced riverine outflow, predominantly from the Shark River.The onset of increased diatom biomass**  **occurs within the riverine, low-salinity plume near Cape Sable.** 



## Seagrass Ecology

**Seagrasses account for a major portion of the primary production in the Florida Bay ecosystem.Therefore, it**  **is particularly important to understand the mechanism for the die-off observed in the late 1980s and the re**  **lation of this event to the algal blooms that occurred subsequently. The loss of seagrass observed in other** **estuaries has been explained as a consequence of eu trophication increasing algal growth and reducing** **the amount of light available to the seagrasses.The sea grass die-off in Florida Bay did not follow this pattern,**  **and its cause may be unique to Florida Bay. Research on this topic has focused on the influence of both in**  **ternal conditions and external driving factors on plant growth and metabolism and on documenting the se**  **quence and patterns of seagrass die-off and recovery in Florida Bay.** 

**• Geographic variation in patterns of seagrass loss** 

**suggests multiple causes and a distinction between primary die-off and secondary mortality.There is a**  **high spatial coincidence among the distribution of T** 

**halassia loss,**  **Labyrinthula abundance, high sedi**  **ment sulfide levels, and turbidity. Determining the relative contributions of these factors to die-off ver**  **sus secondary mortality has been problematic.**

**• Primary die-off is associated with high-density**  **Tha**

**lassia beds. High-density beds result in conditions**  **that increase stress on T**  **halassia: high sediment sul** **fide levels (>2–4 mmol), self-shading of shoots, night time or early morning anoxia/hypoxia in meristems,** **and increased susceptibility for leaf-to-leaf trans mission of the**  **Labyrinthula disease organism. Recent**  **die-off in the Barnes Key area occurred where Tha**  **lassia densities and standing crop were among the**  **highest in Florida Bay.**

**• Recent bay-scale changes in seagrass distribution and** 

**abundance, following the region-scale primary sea grass die-off (1987–1991), are largely due to sec**  **ondary mortality of Thalassia,**  **which is associated with areas of chronic turbidity (since 1994) in the West**  **Region. These changes are most likely due to light limitation as indicated by stand-thinning in**  **T halas**  **sia beds and concommitant increases in low-light**  Executive SummaryHunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 7

**adapted species such as Halodule wrightii**  **and Halophila engelmanii.**  **T here has also been a loss of**  **T**

**halassia in northern Little Madeira Bay, near the**  **mouth of the Taylor River, followed by recolonization by**  **Halodule and**  **Ruppia. T** **he cause of this loss is un known. Primary acute die-off (rapidly developing**  **dead patches within dense beds) is known to be currently occurring (initiated in 1999) only in the**  **high-density T**  **halassia beds of the Barnes Key area.** **A chronic die-off is occurring in dense beds in Sun set Cove. However, the etiologies of these two sites**  **are different.**

**• In central basins that periodically have low salinities,** 

**shallow sediments and low overall densities of Tha**  **lassia, there has been little net change in seagrass dis**  **tribution since 1995. These conditions may reduce density-related stresses and allow for development**  **of robust species communities. Low salinity may also provide refugia from disease since**  **Labyrinthula has never been observed in Florida Bay in salinities**  **below 15 practical salinity units (psu).**

**• Unique characteristics of the Florida Bay ecosystem** 

**make it susceptible to conditions that contribute to primary die-off. Other marine areas with high**  **Tha lassia**  **densities and carbonate sediments, such as the Lakes Region of the Lower Keys, did not expe**  **rience extensive die-off in the late 1980s. Relative to these other areas, the central basins in Florida Bay**  **are isolated from tidal influences and are subject to relatively high terrestrial influence.**  **• A statistical, disciminant-function model of seagrass** 

**species occurrence has been developed.The model predicts that an increase in freshwater delivery to**  **Florida Bay will result in an expansion of Ruppia**  **maritima and**  **Halodule wrightii distribution into the**  **Northeast Region and a concomitant loss of T** **halas sia**  **in this region.**



## Higher-Trophic-Level Species

**T he value placed on Florida Bay derives largely from** **its role supporting ecologically and commercially im portant animal species. These species and the com**  **munities they create depend on and integrate the net ecosystem metabolism at lower trophic levels. As well,**  **the structure of the ecosystem at higher trophic levels can feed back to influence the structure and function**  **at lower levels, i.e.,**  **top-down control. Research in this area focuses on the influence of internal conditions of** 

**w ater quality and benthic habitat on both the growth**  **and survival of individual organisms and on whole populations and communities. A key objective in this** 

**w ork has been to formulate models that can predict how**  **v alued species can be expected to respond to changes**  **in the supply of fresh water and water quality. • S**  **alinity patterns and variability directly affect re**

**cruitment, survival, and growth of many animals that live in Florida Bay and that use Florida Bay as**  **a nursery ground.We have sufficient information on about a dozen key species to predict how they will**  **respond to future salinity conditions that might arise from altered freshwater inflow into Florida Bay.**  **• H abitat, tidal amplitude, freshwater inflow to Florida** 

**Bay, and salinity were the most widely influential**

**v ariables explaining density in 11 forage species in** **a meta-analysis of data from historical surveys. Sea grass density and tidal amplitude were significant for**  **10 species, seagrass type and freshwater inflow were significant for nine species, and salinity was signif**  **icant for seven species.**

**• Analysis of historical data indicates that water man** 

**agement affects the productive capacity of Florida Bay. This information has been used to predict the**  **annual catch of pink shrimp in the Dry Tortugas fishery based on upstream hydrologic conditions in**  **the Everglades.**

**• Recent findings discount earlier concerns that sea** 

**grass die-off and subsequent plankton blooms sig naled a fundamental change in the food web. The**  **abundance of bay anchovy in the West Region, one signal of a possible shift, has fluctuated since it** **reached a maximum in 1995.The diversity and over all abundance of canopy-dwelling fauna has in**  **creased since 1995 without a return to the original T** 

**halassia -dominated seagrass canopy.** 

**• Seagrass diversity may determine faunal density. A** 

**principal components analysis suggested that fau nal species have affinities to certain seagrass types—**  **T**

**halassia, Halodule, Syringodium, or macroalgae.** **Seagrass type was significant in explaining a meta analysis of faunal density in Florida Bay. Faunal den**  **sity in relation to seagrass type varied differently depending on faunal species. No species favored** 
**pure T**  **halassia.**

**• Characteristics of the bottom and shoreline habitats** 

**affect abundance and community composition. Man grove prop root habitats in northeastern Florida Bay**  **have significantly more fish larvae than nearby, open-water sites or nearshore areas without man** 
**groves. • F**  **ishing affects fish populations. According to a com**

**parison of the length-frequency distribution inside and outside of an area in Everglades National Park**  **protected from recreational fishing affects the size structure of gray snapper. Evidence of overfishing is**  **seen in gray snapper and other species on the reef**
**tract.** Executive Summary**• Spatial variation in influencing factors (**  **e.g., fresh** 

**w ater inflow, tidal mixing) is reflected in distinct re**  **gional patterns of species distributions, community composition, and trophic composition. Postlarval**  **shrimp enter the bay preferentially where tidal flows are greatest. Peak concentrations of postlarval pink**  **shrimp are roughly an order of magnitude greater in passes leading into the West Region from the**  **Gulf of Mexico than in channels to Florida Bay through the Florida Keys.**  **• T he food web shows the same regional structure as** 

**seen in the variation of circulation, salinity, and**

**w ater quality. Based on stable isotope analyses, the**  **central region has a strongly seagrass-based trophic structure, whereas the northwestern bay has a more** **plankton-dominated trophic structure. The North east Region has a non-seagrass-based diet (more**  **likely water-column based). The trophic structure of the southwestern bay is supported by macroalgae.**  **• T emporal variation in recruitment strength of spiny** **lobster, snapper, and pink shrimp is related to re gional oceanographic processes, especially the Tor**  **tugas gyres. •**  **High methylmercury in Florida Bay and its biota may have a local source in the bay. Sources of ele** 

**v ated mercury concentrations in fish from north**  **eastern Florida Bay include (1) methylmercury in runoff from the Everglades and (2)**  **in situ mercury**  **methylation in sediments from both the mangrove transition zone and the open bay itself. Mercury**  **concentrations seem to be higher along a Taylor River–Little Madeira Bay sampling transect than**  **along a C-111 canal–Joe Bay transect. These data suggest that the urban and agricultural runoff that**  **more strongly influences the C-111 canal–Joe Bay transect is not the most important source of mercury**  **to the bay and its biota.**

**Loss of sponges may have reduced water clarity and affected seagrass recovery. Recovery of the largest**  **and most abundant species has been extremely slow following a die-off in the early 1990s. Sponges are ef**  **ficient filters of small (<5 μm) planktonic particles. At pre-die-off (pre-1992) densities, sponges in Florida**  **Bay may have been capable of filtering the entire water column in one day. At present densities, filtering takes**  **an estimated four days.** Florida Bay Synthesis Hunt and Nuttle

8 FWRI Technical Report TR-11 Executive SummaryFWRI Technical Report TR-11 9 

## Introduction

Question**—What was the Florida Bay ecosystem like 50, 100, and 150 years ago?** 
**A critical part of understanding an ecosystem as a whole is to understand the natural patterns and cycles**  **of change. However, changes in ecosystems take place at many time scales, from diurnal to millennial, and it**  **is not practical or even possible to directly observe**

**c hange at the longer time scales. The ability to accu**  **rately understand natural conditions and cycles of**

**c hange within Florida Bay is crucial to successfully re**  **store and preserve the bay and to meet the goals of the Comprehensive Everglades Restoration Plan (CERP).** **Information on the historical and current natural sys tem allows restoration planners to establish realistic** **baseline conditions, restoration goals, and perfor mance measures; create predictive models; and mon**  **itor the success of restoration efforts. Understanding past conditions and cycles of change also allows for bet**  **ter-informed planning, project implementation, and land-management decisions.** **Although the ecosystem history and paleoecol ogy of Florida Bay was not specifically identified by the**  **Florida Bay Science Program as a strategic research question, these types of studies contribute to all five**  **strategic questions. By their very nature, these studies are multidisciplinary and integrate data to provide a** **holistic picture of the environment over biologically sig nificant time scales.This chapter summarizes ecosys**  **tem history research that has contributed to the Florida Bay Science Program.** 


### Methodology

**T he history of an ecosystem may be recorded in two** **distinct modes: (1) human records, in the form of his torical accounts, reports, or archived data; and (2) nat**  **ural records preserved in the sediments. Both methods can provide valuable information, but the sediment** **record and associated paleoecologic data can be es pecially important because few monitoring programs**  **have been in place long enough to provide sufficient data to establish the range of variability in ecosystem** **parameters over a significant period of time. Further more, monitoring or experimental data are absent**  **prior to human influence on the environment. Ideally, both human records and natural records are retrieved,** **compiled, and compared to develop the most com plete picture possible of the configuration of an ecosys**  **tem over time and of the spatial and temporal scale of**

**c hanges to the system.** 

HUMAN RECORDS**Significant efforts have been made by a number of in dividuals and groups to compile data sets and histor**  **ical records for the south Florida ecosystem and Florida Bay. It is not the purpose of this summary to list all of**  **these compilations, but the following illustrate the**

**v ariety of records available:**  **Robblee, M. B., et al.**  **(2000, 2001) —A compilation of**  **more than 34,000 historical salinity measurements from Florida Bay, beginning in 1947 and extending**  **through 1995. DeMaria, K. (1996)**  **—Changes in the Florida Keys Marine Ecosystem Based upon Interviews with Expe** **rienced Residents—A compilation of “eyewitness”ac counts of 75 individuals with more than 10 years’**  **experience on Florida Keys and Florida Bay waters. Smith,T. J. (2002a and unpublished data)**  **—Historical reconstruction of vegetation from aerial photographs**  **of selected islands within Florida Bay, dating from 1927. Areas of interest include the entirety of Ever** **glades NP, Big Cypress NP, and the Water Conserva tion Areas.**  **Smith,T. J., et al.**  **(2002b) —Digitally compiled set of** **scanned historical topographic sheets from the Ever glades and south Florida available on CD–ROM.** 

SEDIMENT RECORDS**Retrieving historical information recorded in sedi ments involves basic principals of geology (principally**  **the laws of superposition and “the present is the key to the past”) and using a number of paleoecological and**  **geochemical tools:** 

# Chapter 3 Ecosystem History

Lead Author G. Lynn Wingard (USGS, Reston) Contributors To m Cronin (USGS) and William Orem (USGS)Florida Bay Synthesis Hunt and Nuttle

10 FWRI Technical Report TR-11 **Assemblage analyses —the faunal and floral remains**  **found in a sediment core allow inferences to be made about past environments, including salinity, substrate,**  **and water quality, based on analoguous data from the present.**  **Biochemical analyses —organisms with calcareous**  **skeletons record information about the water in which they secrete their skeletons. Stable isotope analyses and** **metal:calcium ratios in shells or coral skeletons can pro vide information on salinities and sources of water.**  **Geochemical analyses —radiogenic isotopes are used**  **to determine the chronology of cores,and analyses of the geochemistry of the sediments (carbon, nitrogen, sulfur,**  **and phosphorus, for example) provide data on changes in nutrient supply and sediment influx over time.**  **Each of these methods is limited by the resolution of the age model for sediment deposition. Typical** **geochronologic methods used on late Holocene sedi ments involve analyses of**  **210 Pb (lead),**  **137 Cs (cesium),** 

**7 Be (beryllium), and**  **14 C (carbon) (see Holmes**  **et al., 2001,**  **for explanation).The error term increases down-core, so that a typical core from eastern Florida Bay with a**  **sedimentation rate of 1.0 cm/year and an error of ±0.08 cm/year will have an average age of 1900 years (±8** 
**y ears) at a depth of one meter. Because of the error as** **sociated with increasingly older sediments, the an nual banding of corals provides the most accurate age**  **control, but only a few large corals have been found within Florida Bay that can be used to reconstruct past**  **conditions. Analyses of sediment cores from Florida Bay have**  **been conducted principally by two different groups of researchers during the past ten years (Table 3.1): (1) the**  **University of Miami/NOAA group ( C. A. Alvarez Zarikian, P. L. Blackwelder,T. Hood,T. A. Nelson, P. K.**  **Swart, L. P. Tedesco, H. R. Wanless, et al.**  **) and (2) the USGS group (T. M. Cronin, G. S. Dwyer, R. B. Halley,**  **C. W. Holmes, J. K. Huvane, S. E. Ishman, W. Orem, E. Shinn, D. A.Willard, G. L.Wingard,**  **et al. ). Both groups** **have sought out areas of sediment accretion with min imal sediment disturbance; however, they diverge in**  **terms of benthic habitats (Holmes et al.,**  **2001; Nelsen et al.,**  **2002).The University of Miami/NOAA group has sought out cores from bare-bottom habitats in order**  **to ensure the presence of well-laminated sediments undisturbed by roots. The USGS group has collected**  **cores from banks stabilized by seagrass beds because these areas are subjected to minimal erosion during**  **storms, so that the organisms being analyzed are trapped**  **in situ. Both groups X-ray and physically ex**  **amine the cores for signs of sediment disruption and use the radiogenic isotope profiles as assurance of**  **minimal disturbance. These two divergent strategies have been beneficial by providing data from different**  **regions and different environmental settings within Florida Bay. A comparison of the findings and results**  **will be discussed below.**



### Previous Work

**Prior to 1990, few paleoecological analyses of sedi ment cores had been conducted in Florida Bay. The**  **Holocene core studies that had been done focused on the sediments themselves and the diagenesis of the** **sediments (Fleece, 1962), the mineralogy of the sedi ments (Taft and Harbaugh, 1964), and the origins of the**  **material composing the sediments (Enos, 1977). In their study of the molluscan fauna of Florida Bay,Tur**  **ney and Perkins (1972) examined cores to determine the persistence of subenvironments over time.They discuss**  **the growth and migration of mudbanks based on their analyses. Wanless and Tagett (1989) performed an ex** **tensive study of cores to determine the depositional his tory of the mudbanks within Florida Bay. All of these** **studies provide important information on the sedi mentation and geologic history of Florida Bay and**  **allow the history of the late Holocene ecosystem to be more accurately interpreted.**  **Tw o studies were done in the 1980s on a coral from**  **Lignumvitae Basin. Hudson et al.**  **(1989) compared the growth of a 1-m-diameter**  **Solenastrea to rainfall, tem**  **perature records, and human perturbations.They found a significant correlation between poor coral growth and**  **construction of the Flagler Railroad. Smith et al.**  **(1989) investigated the relationship between the fluorescent**  **banding (a result of terrestrial runoff) of the same Lignumvitae Basin coral and the flow of water in Shark**  **River and Taylor sloughs. A decline in freshwater flow (as indicated by the fluorescence) began around 1912,**  **a date that corresponds to the construction of drainage canals carrying water from Lake Okeechobee to the At**  **lantic. Smith et al.**  **(1989) found a statistically significant difference between mean fluorescence in the pre-canal** **segment (pre-1932) of the coral and in the post-canal seg ment (post-1932) of the coral. In addition, Smith**  **et al. (1989) found evidence for a 4- to 6-year periodicity in the** **historical annual flow regimes that was no longer ap parent in the Shark River Slough flow record.This pe**  **riodicity corresponds to south Florida rainfall records. Th**  **ey concluded that prior to canal construction, the** **flow of fresh water in Shark River Slough was con trolled by rainfall, but that as early as 1940, flow through** **the slough was reduced substantially and that the nat ural periodicity in flow regimes had been lost.**  Ecosystem HistoryHunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 11

T able 3.1A **List of sediment cores analyzed in Florida Bay between 1990 and present. Abbreviations in square brackets following core location correspond to abbreviations on Figure 3.1 and were used by the original authors.** 

General Core Location Researchers Analyses Done Status/References (Core ID)

1 **Jo e Bay [JB]**  **Holmes 210**  **Pb Geochronology Holmes**  **et al., 1999;**  **W illard**  **Pollen Assemblages Willard**  **et al., 1997**  **W ingard**  **Molluscan Assemblages Ishman**  **Foraminferal Assemblages**

2 **Ta ylor Creek [TC] Ishman**  **Foraminferal Assemblages Brewster-Wingard (T24)**  **Wingard Molluscan Assemblages**  **et al., 2001; Cronin**  **(TC-1,TC-1a, Cronin**  **Ostracode Assemblages et al.,**  **2001; Dwyer TC-2,TC2br)**  **Holmes 210**  **Pb Geochronology and Cronin, 2001;**  **Dwyer Ostracode Biochemistry Holmes**  **et al., 2001;**  **W illard**  **Pollen Assemblages Ishman**  **et al., 1996**  **Edwards Dinoflagellate Assemblages**  **Orem Sediment Geochemistry** 

3 **P ass Key [PAK]**  **Wingard Molluscan Assemblages Brewster-Wingard**  **(PK17D, PK37) Cronin**  **Ostracode Assemblages et al.,**  **1998a; Brewster- (FB-1 Pass Key)**  **Ishman Foraminferal Assemblages Wingard**  **et al., 2001;**  **Halley Molluscan Biochemistry Cronin**  **et al., 2001;**  **Holmes 210**  **Pb Geochronology Halley and Roulier,**  **Huvane Diatom Assemblages**  **1999; Huvane and W**  **illard Pollen Assemblages**  **Cooper, 2001; Orem Edwards**  **Dinoflagellate Assemblages et al.,**  **1999a Orem**  **Sediment Geochemistry**

4 **Russel Bank [RB] Wingard Molluscan Assemblages Brewster-Wingard and**  **(RB19A, RB19B) Cronin**  **Ostracode Assemblages Ishman, 1999; Brewster- (RB19C) (FB-2)**  **Ishman Foraminferal Assemblages Wingard**  **et al., 2001;**  **Holmes 210**  **Pb Geochronology Cronin**  **et al., 2001;**  **Dwyer Ostracode Biochemistry Cronin**  **et al., 2002;**  **W illard**  **Pollen Assemblages Dwyer and Cronin,**  **Halley Molluscan Biochemistry 2001; Halley and**  **Edwards Dinoflagellate Assemblages Roulier, 1999; Holmes**  **Orem Sediment Geochemistry**  **et al., 2001; Huvane and** **Cooper, 2001; Brewster W**  **ingard et al.,**  **1997; Orem**  **et al., 1999a** 

5 **P ark Key [PKK]**  **Cronin, Dwyer Ostracode Biochemistry Cronin et al.,**  **2001 (PKK23A)**  **Holmes 210**  **Pb Geochronolgy Dwyer and Cronin, 2001;**  **Holmes et al.,**  **2001**

6 **Bob Allen [BA] Wingard**  **Molluscan Assemblages Brewster-Wingard and (BA6A) (FB-3)**  **Cronin Ostracode Assemblages Ishman, 1999; Brewster**  **Ishman Foraminferal Assemblages Wingard**  **et al., 2001;**  **Holmes 210**  **Pb Geochronology Cronin**  **et al., 2001;**  **Halley Molluscan Biochemistry Dwyer and Cronin, 2001;**  **W illard**  **Pollen Assemblages Halley and Roulier,**  **Edwards Dinoflagellate Assemblages 1999; Wingard**  **et al., Orem**  **Sediment Geochemistry 1995; Orem et al.,**  **1999a** Ecosystem HistoryFlorida Bay Synthesis Hunt and Nuttle

12 FWRI Technical Report TR-11

T able 3.1A **List of sediment cores analyzed in Florida Bay between 1990 and present. Abbreviations in square brackets following core location correspond to abbreviations on Figure 3.1 and were used by the original authors. (continued)** 

General Core Location Researchers Analyses Done Status/References (Core ID)

7 **Wh ipray [WH]**  **Wingard Molluscan Assemblages Trappe and Wingard,**  **(25B) (FB-4, FB-5) Cronin, Dwyer Ostracode Geochemistry 2001; Cronin**  **et al., 2001;**  **Holmes 210**  **Pb Geochronology Holmes**  **et al., 2001;**  **Orem Sediment Geochemistry Orem**  **et al., 1999a** 

8 **Rankin [RA] Wingard**  **Molluscan Assemblages Unpublished data; report Cronin, Dwyer Ostracode Geochemistry in progress**  **Holmes 210**  **Pb Geochronology Orem Sediment Geochemistry,**  **Lignin Phenols Shinn, Reich Sediment Trace**  **Element Geochemistry**

9 **Jimmy Key [JK] Wanless, Nelsen Sedimentology, Nelsen et al.,**  **2002 Geochronology**  **(JK) Hood**  **Foraminferal Assemblages Zarikian**  **Ostracode Assemblages, Ostracode Geochemistry**  **Swart Stable Isotope Geochemistry**  **T**

**refry and Metz Geochemistry Blackwelder, Capps**  **O’Neal, Garte, F**  **eatherstone, Kang, Ellis** 

10 **Oyster Bay [OB] Wanless, Nelsen Sedimentology, Alvarez Zarikian**  **et al., Geochronology**  **2001; Nelsen et al.,**  **2002 (OB)**  **Hood Foraminferal Assemblages**  **Zarikian Ostracode Assemblages,**  **Ostracode Geochemistry Swart**  **Stable Isotope Geochemistry T** 

**edesco Pollen Assemblages**  **T**

**refry and Metz Geochemistry Blackwelder, Capps**  **O’Neal, Garte, F**  **eatherstone, Kang, Ellis** 

11 **Coot Bay [CB] Wanless, Nelsen Sedimentology,**  **Nelsen et al.,**  **2002 Geochronology**  **T**

**refry and Metz Geochemistry Blackwelder, Capps**  **O’Neal, Garte**



### Summary of Ecosystem History and Paleoecology Research

**F ollowing are the significant research findings to date**  **of the Ecosystem History-Paleoecology research groups, organized into the five principal Florida Bay**  **research questions (Table 3.2).**

Question 1 **—How and at what rates do storms, changing freshwater flows, sea level rise, and local evaporation and**  Ecosystem HistoryHunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 13 T able 3.1B **List of corals analyzed in Florida Bay between 1990 and present. Numbers in parentheses following the location are shown in Figure 3.1 and were used by the original authors.** 

Location Researchers Analyses Done References
**Lignumvitae (SFB-5) Swart, Healy,**  **et al. Stable isotopes (C and O) Swart**  **et al. , 1996;**  **Fluorescence, trace elements Swart et al.,**  **1999 (Ba)** 
**Lignumvitae Basin Smith, Hudson Fluorescence, growth bands Smith**  **et al., 1989;**  **(referred to as Peterson Hudson**  **et al., 1989**  **Ke y Basin by Smith**  **et al. )**  **(SFB-6)**

**Blackwater Sound Swart, Healy,**  **et al. Stable isotopes (C and O) Swart**  **et al., 1999**  **(SFB-3) Arsenicker Keys**  **Swart, Healy, et al.**  **Stable isotopes (C and O) Swart et al.,**  **1999 (SFB-7)**  **Rabbit Key Swart, Healy,**  **et al. Stable isotopes (C and O) Swart**  **et al., 1999**  **(SFB-14) Bob Allen Key Basin/**  **Swart, Healy, et al.**  **Stable isotopes (C and O) Swart et al.,**  **1999 Calusa Key (SFB-16)**  **Duck Key Basin/The Swart, Healy,**  **et al. Stable isotopes (C and O) Swart**  **et al., 1999**  **Bogies (SFB-23) Lignumvitae Basin (SFB-40) Swart, Healy,**  **et al. Stable isotopes (C and O) Swart**  **et al., 1999**  **Lignumvitae Basin (SFB-42) Swart, Healy, et al.**  **Stable isotopes (C and O) Swart et al.,**  **1999 Manatee Key (SFB-45) Swart, Healy,**  **et al. Stable isotopes (C and O) Swart**  **et al., 1999** 

**precipitation influence circulation and salinity patterns within Florida Bay and outflows from the bay to adjacent** 

**w aters?** 

**• Salinity in Florida Bay is more strongly correlated** 

**with rainfall than with any other single factor, and the periodicity in salinity and rainfall data suggests**  **linkages to El Niño/Southern Oscillation (ENSO) climatic patterns.** 

**• Anthropogenic influences play a secondary role to** 

**rainfall in determining salinity for Florida Bay as a whole, but they may be a factor in the magnitudes** **of salinity variations seen in recent times. Addi tionally, anthropogenic factors may act on a local**  **basis to influence salinity patterns.**

**• Declines in diversity and increases in dominance of** 

**salinity-tolerant species have occurred since the 1980s in several benthic invertebrate groups in dif**  **ferent regions of Florida Bay.**

Question 2 **—What is the relative importance of the influx of external nutrients and of internal nutrient cycling in de** **termining the nutrient budget for Florida Bay? What mech anisms control the sources and sinks of the bay’s nutrients?** 

**• Uranium isotope studies indicate that the phos** 

**phorus contamination at the northern end of Taylor Slough appears to be fertilizer-derived. However,** **phosphorus contamination in Taylor Slough dimin ishes to background by mid slough; therefore, Tay**  **lor Slough does not appear to be a source of nutrients to eastern Florida Bay.** 

**• Eastern Florida Bay does appear to be a source of nu** 

**trients to the mangrove zone at the southern end of Ta** **ylor Slough.**

**• Sediments from eastern Florida Bay (especially from** 

**sites near Pass Key and Russell Key banks) show in dications of recent nutrient (carbon [C], nitrogen** **[N], and phosphorus [P]) enrichment (1980 to pre sent). This nutrient enrichment could be related to**  **recent microalgal blooms and seagrass die-off within Florida Bay.**  **• D ow** **ncore profiles of dated cores from central Florida**

**Bay (Whipray Basin) show that productivity events have occurred historically in Florida Bay.**  **• A large, multidecadal productivity event in the**  Ecosystem HistoryFlorida Bay Synthesis Hunt and Nuttle

14 FWRI Technical Report TR-11 T able 3.2 **Summary of research on ecosystem history by topic.**

T

ype of Analysis
Faunal and Floral Biochemical Geochemical Research Questions Assemblage Analysis Analysis Analysis

1 **How and at what rates Wingard et al.,**  **1995; Smith et al.,**  **1989; Holmes**  **et al., 2001;**  **do storms, changing Ishman**  **et al., 1996; Halley**  **et al., 1994;**  **Nelsen et al.,**  **2002 freshwater flows, sea Brewster-Wingard**  **et al., Healy, 1996; Swart**  **levels, and local 1997; Brewster-**  **et al., 1996; Halley and** 

**ev aporation/precipitation Wingard**  **et al., 1998a,b; Roulier, 1999; Swart**  **et influence circulation and Brewster-Wingard and**  **al., 1999; Alvarez**  **salinity patterns within Ishman, 1999; Zarikian**  **et al., 2001;**  **Florida Bay and outflows Alvarez Zarikian Dwyer and Cronin,**  **from the bay to adjacent et al.,**  **2001; Brewster- 2001; Cronin et al.,** 

**w aters?**  **Wingard et al.,**  **2001; 2002; Nelsen**  **et al., 2002**  **Cronin et al.,**  **2001; Huvane and Cooper,**  **2001; Trappe and Wingard, 2001; Cronin**  **et al., 2002; Nelsen**  **et al.,**  **2002**

2 **Wh at is the relative**  **Swart et al.,**  **1999 Orem**  **et al., 1997;**  **importance of the influx of Orem, 1998; Orem**  **external nutrients and of et al.,**  **1999a; Gough internal nutrient cycling in**  **et al., 2000; Nelsen**  **determining the nutrient et al.,**  **2002 budget for Florida Bay?**  **Wh at mechanisms control**  **the sources and sinks of the bay’s nutrients?** 

3 **W hat regulates the Huvane and Cooper, Swart**  **et al., 1999**  **Orem et al.,**  **1999a onset, persistence, and fate 2001**  **Holmes et al.,**  **2001 of planktonic algal blooms**  **in Florida Bay?**

4 **W hat are the causes Brewster-Wingard**  **et al., Dwyer and Cronin, Orem**  **et al., 1999a,**  **and mechanisms for the 1998b; Brewster- 2001**  **b; Holmes et al.,**  **observed changes in Wingard and Ishman, 2001** **seagrass communities of 1999; Brewster Florida Bay? What are Wingard**  **et al., 2001;**  **the effects of changing Cronin et al.,**  **2001; salinity, light, and**  **Trappe and Brewster nutrient regimes on these Wingard, 2001**  **communities?**

5 **Wh at are the**  **Brewster-Wingard et al.,**  **Holmes et al.,**  **2001 relationships between 2001 (mollusks only)**  **environmental and habitat**

**c hanges and the**  **recruitment, growth, and survivorship of**  **animals in Florida Bay?** Ecosystem HistoryHunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 15**mid-1700s, which was characterized by greatly el**

**ev ated levels of organic carbon and nitrogen, was** **observed in two cores from Whipray Basin. Inter estingly, although organic carbon and total nitro**  **gen were high, total phosphorus was not elevated during this time span. This time period (the Little** **Ice Age) may correspond to a period of higher rain fall in the Everglades and more extensive land**  **runoff into Florida Bay, which may have triggered the productivity event.** 

**• Organic carbon records from Jimmy Key indicate that** 

**hurricanes help flush organic carbon out of Florida Bay.** 

Question 3**—What regulates the onset, persistence, and fate of planktonic algal blooms in Florida Bay?** 

**• Surface sediments from eastern Florida Bay show in** 

**dications of nutrient (carbon, nitrogen, and phos phorus) enrichment from 1980 to the present, which**  **could be related to recent microalgal blooms within Florida Bay.**  **• T he multidecadal productivity event of the 1700s** 

**noted in sediment geochemical analyses from Wh**  **ipray Basin cores may represent a period of ex tensive algal blooms.**  **• Do wncore changes in abundance and assemblages** 

**of dinoflagellates and diatoms have been examined at some sites in Florida Bay. Additional studies of the**  **ecology of dinoflagellates and diatoms are needed to interpret the findings in terms of bloom conditions.** 

Question 4 **—What are the causes and mechanisms for the observed changes in seagrass community of Florida Bay?** **What are the effects of changing salinity, light, and nutri ent regimes on these communities?**  **• F requent changes have occurred in the relative abun** 

**dance of epiphytal species of ostracodes and mol lusks over the past century.**  **• P rior to mid-20th century, epiphytal ostracodes were** 

**relatively rare at sites in central and eastern Florida Bay, suggesting a greater abundance and/or density**  **of subaquatic vegetation (SAV) over the past 50 years than in the first half of the 20th century. Epiphytal**  **mollusks, although not rare, increased significantly in relative abundance from approximately 1940 on**  **ward at most sites.These data raise the question of** **whether dense and abundant seagrass beds are nat ural in Florida Bay; if the answer is no, these results**  **have very significant implications for restoration. • A**  **decline occurred in SAV-dwelling ostracodes and**

**mollusks in cores from Whipray, Russell, Bob Allen, and Pass keys between the 1970s and 1980s.**  **• T he relative abundance of mollusks with a strong**  **preference for T**  **halassia has declined since approx**  **imately 1970 in eastern Florida Bay and since 1910 in Whipray, whereas SAV generalists have increased.**  **T hese findings may indicate an increase in the**  **amount of macrobenthic algae relative to T**  **halassia. • Do** **wncore profiles of lignin phenols from a Pass Key**

**core show large variations in lignin phenol distrib utions over short time intervals.These variations re**  **flect the proximity of this site to the mangrove zone along the coast and the outlet of Taylor Creek.** 

**• At Bob Allen Keys, the lignin-phenol distributions** 

**show downcore variations in the abundance of sea grass over time. At Bob Allen, seagrass abundance** **appears to have been increasing since a recent min imum around 1960.** 

Question 5**—What are the relationships between envi ronmental and habitat changes and the recruitment, growth,**  **and survivorship of animals in Florida Bay?**

**• Declines in molluscan faunal diversity have occurred** 

**during the latter half of the 20th century.** 

## Salinity Patterns and Trends

**T**

**he majority of the ecosystem history-paleoecology re search since 1994 has been focused on addressing the**  **question of salinity patterns and influx of fresh water into Florida Bay.The most critical issue in the CERP is**  **to restore more natural patterns of freshwater flow through the terrestrial ecosystem and into the estuar**  **ies and coastal areas. Restoring natural flow to Florida Bay includes restoring the timing, delivery, quantity,** **and quality of the water to the bay. In order to re-cre ate natural freshwater flow patterns, it is essential to**  **understand both the natural patterns of freshwater flow and the natural sources of water prior to signifi** **cant human alteration of the system. Changing salin ity patterns, whether natural or anthropogenically**  **induced, affect the fauna and flora of the bay.The first step in restoration is to understand the natural patterns**  **and be able to set targets and performance measures for restoration.** **An important tool in the restoration effort is mod eling the freshwater flow from the Everglades to Florida**  **Bay under different restoration scenarios.The “Natural System Model” (NSM) of the South Florida Water**  **Management District (SFWMD) was developed in part to meet these needs. The NSM is driven by rainfall.**  **Efforts to calibrate model-simulated freshwater flow in the Everglades using historical rainfall records have** **only been partially successful due to the lack of his torical data on natural conditions prior to water**  **diversion activities. A similar lack of long-term** Ecosystem HistoryFlorida Bay Synthesis Hunt and Nuttle

16 FWRI Technical Report TR-11 **instrumental records of salinity in adjacent Florida Bay has limited our ability to set restoration targets for**  **aquatic ecosystems. T** **he research projects summarized below have ad dressed the lack of historical data on Florida Bay salin**  **ity and freshwater influx. One goal of these studies has been to determine the natural patterns of salinity** 

**c hange and freshwater influx. A second goal has been**  **to distinguish the natural patterns of change from**

**c hanges in the salinity regime caused by water diver** **sion in the Everglades during the 20th century.This sec tion summarizes the methodology applied and the**  **progress made towards these goals.**



### Methods

**Both the University of Miami/NOAA and USGS re search groups have used basic assemblage analyses**  **and biochemical analyses. They use these forms of analysis to extract salinity information from sediment**  **cores dated using 210**  **Pb and other methods of estab lishing chronology (Table 3.1). Interpretations of fau**  **nal and floral assemblages are based on observations of the modern ecology of the organisms being studied.**  **T hese assemblages represent a death assemblage and**  **are therefore time-averaged. However, decadal-scale resolution can be obtained from the assemblages be**  **cause the Florida Bay environment has relatively rapid sedimentation rates, little erosion, and low transport**  **of silt and sand-sized sediments (Turney and Perkins, 1972; Halley**  **et al., 1997). Additional support that a** **death assemblage accurately represents a life assem blage, and therefore a discrete environment, is ob**  **tained when several faunal groups are analyzed and compared from a single sample and the condition of**  **the shell material is considered. Biochemical methods are based on the analyses of**  **individual shells and therefore capture the salinity record of the time during which that shell was se** **creted. Although these analyses can provide an al most instantaneous record, the data are still limited by**  **the temporal resolution of the dating-method for the sample from which the shell was extracted.**  **Dwyer and Cronin (2001) and Cronin et al.**  **(2001, 2002) have used the ratio of magnesium to calcium** **(Mg:Ca) ions in ostracode shells to reconstruct salin ity from Florida Bay cores. They have examined the**  **ecology and shell chemistry of modern ostracodes in Florida Bay and have demonstrated that the Mg:Ca ra**  **tios in the calcium carbonate shells of ostracodes are strongly influenced by the salinity and temperature in**  **which the organism secretes its shell.They have focused the shell biochemical studies on the epiphytal species**  **Loxoconcha matagordensis, although in some cores,**  **Per atocytheridea setipunctata**  **is analyzed. Based on their ecological studies, it appears that adult**  **L. matagorden sis**  **secrete their shells principally during spring or summer seasons (Cronin**  **et al., 2001). In Florida Bay,** 

**w arm-season temperatures vary little over interan** **nual timescales, so temperature is considered less im portant than salinity in influencing ostracode Mg/Ca.**  **However, additional research is warranted. Alvarez Zarikian**  **et al. (2001) and Nelsen**  **et al. (2002)**  **have conducted stable isotopic analyses (** δ **18 O and**  δ **13 C)** **on ostracodes and benthic foraminifera to extract in formation on rainfall, freshwater influx, and evapora**  **tion to infer salinity conditions. Changes in** δ **18 O can**  **be correlated to changes in salinity, and those in** δ **13 C**  **can indicate changes in the influx of organic material. Evaporation of marine and brackish water preferen**  **tially removes the lighter isotopes ( 16**  **O) and enriches the water with heavier isotopes (**  **18 O). An increase in**  δ **18 O indicates increased evaporation and therefore,** **increased salinity. In Florida Bay, however, interpre tation of the**  δ **18 O value is complicated by the influx of** **fresh water from the terrestrial Everglades. Interpre tation of**  δ **13 C is also complicated in coastal waters.**  **Under normal marine conditions, the** δ **13 C of calcare** **ous organisms is principally controlled by physiolog ical processes However, in areas where fresh and**  **marine waters mix, variations in the dissolved inorganic carbon are probably the dominant factor. Freshwater**  **from the Everglades is typically isotopically depleted in**  δ **18 O and**  δ **13 C, whereas the marine waters from the**  **gulf or Atlantic are enriched in** δ **18 O and**  δ **13 C. By com**  **paring and correlating** δ **18 O to**  δ **13 C, researchers can in**  **terpret the relative influence of fresh and marine**

**w aters at the core site. (See Halley**  **et al., 1994; Swart**  **et al.,**  **1996, 1999; and Alvarez Zarikian et al.,**  **2001, for a de tailed explanation of the environmental factors that in**  **fluence** δ **18 O and**  δ **13 C.)** **Stable isotopic analyses have also been used to an alyze corals within Florida Bay (Healy, 1996; Swart**  **et al.,**  **1996, 1999) and on a reef affected by Florida Bay wa ters (Halley**  **et al., 1994).The annual banding of corals**  **provides a very accurate means of determining the age of the isotopic samples being analyzed. Halley**  **and Roulier (1999) used whole mollusk shells ( Brachi**  **dontes exustus and**  **T ransennella**  **spp.) from radiometri cally dated cores for**  δ **18 O and**  δ **13 C analyses.** 


### Findings

**T he following summary is intended to synthesize** **briefly the key results from paleoecologic studies com pleted in the past 10 years.The reader is referred to the** **original papers for detailed results, methods, and ev idence supporting the conclusions.**  Ecosystem HistoryHunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 17 **• Salinity in Florida Bay is more strongly correlated** 

**with rainfall than with any other single factor, and a periodicity in salinity and rainfall data suggests**  **linkages to El Niño/Southern Oscillation climatic patterns.** 

**Nelsen et al.**  **(2002) and Alvarez Zarikian et al.**  **(2001) concluded on the basis of multidisciplinary studies of** **cores from Oyster Bay and Jimmy Key (Table 3.1, Fig ure 3.1) that “anthropogenic influences play a sec**  **ondary role to natural influences such as regional rainfall”(Nelsen**  **et al., 2002: 445).Their analyses showed**  **that salinity responded directly to regional rainfall and that “microfaunal data also indicate direct corre**  **lation to rainfall patterns for temporal scales ranging from decadal down to the limit-of-resolution of**  **geochronology”(Nelsen et al.,**  **2002). Even at the mouth of Shark River Slough they found rainfall to be the dom**  **inant driver. Dwyer and Cronin (2001) compared downcore**  **salinity trends derived from Mg:Ca ratios from Russell Bank, Park Key, and Bob Allen Key mudbank (Table 3.1;**  **Figure 3.1) to historical rainfall records. They found good correspondence between rainfall and the pale** **osalinity data. In addition, they found four extreme low salinity periods that corresponded to strongly negative** 

**v alues in the El Niño/Southern Oscillation (ENSO)**  **index. Cronin**  **et al. (2002) conducted time-series analyses**  **on ostracode Mg:Ca ratios and ostracode abundance data from the Russell Bank core (Table 3.1, Figure 3.1).**  **Th ey**  **determined that based on the Mg:Ca ratio, a 5.6-**
**y ear salinity periodicity existed and that all salinity**  **proxy data analyzed showed 6- to 7-year, 8- to 9-year, and 13- to 14-year periods of variability. They com**  **pared the paleosalinity data to climatic factors and conducted a time-series analysis on south Florida win**  **ter rainfall and the Southern Oscillation Index (SOI), which suggested ~5-, 6- to 7-, 8- to 9-, and 13- to 14-year** 

**c ycles. Paleoproxies and climate data were compared**  **using cross-spectral analyses.The results suggest “that** Figure 3.1 **Location of sites within Florida Bay where cores and corals have been analyzed for paleoecologic information. Table 3.1 lists details about the investigations. Sediment cores listed in Table 3.1A are identified as follows on the map: Bob Allen = BA; Coot Bay = CB;**  **Jimmy Key = JK; Joe Bay = JB; Oyster Bay = OB; Park Key = PKK; Pass Key = PAK; Rankin Basin = RA; Russell Bank = RB; Taylor Cre ek**  **= TC; Whipray Basin = WH. Coral collection sites (SFB) are listed in Table 3.1B.** Ecosystem HistoryFlorida Bay Synthesis Hunt and Nuttle

18 FWRI Technical Report TR-11**regional rainfall variability influences Florida Bay salin ity over interannual and decadal timescales and that**  **much of this variability may have its origin in climate**

**v ariability in the Pacific Ocean/atmosphere system.”It**  **may also be related to ENSO (Cronin et al.,**  **2002). Swart**  **et al. (1999), in an analysis of coral records** **from Florida Bay (Table 3.1), mentioned that “a super ficial comparison between precipitation from the lower**  **east coastal region of south Florida appears to indicate that periods of lowest rainfall relate to times when the**  **salinity was highest.”However, a comparison of the** δ **18 O** **of the coral skeleton from Lignumvitae Basin indi cates no statistically significant correlation. Perhaps**  **this is due to miscalculations in the age of the coral bands or to the lack of accurate rainfall data for that** **basin.They conducted spectral analyses on the salin ity values calculated from the corals and found three**  **statistically significant signals at 4–7 years, 28 years, and 12–14 years.They pointed out that the most significant**  **periodicity, the 4–7-year cycle, which accounts for greater than 20% of the variance, may be related to**  **ENSO cycles (Swart et al.,**  **1999: 392–393). T** **hese short-term cycles in salinity that have been found in recent research are consistent with the find**  **ings of Smith et al.**  **(1989) in their examination of flu orescent banding in the Lignumvitae Basin coral.They** **found “strong evidence for a regular 4- to 6-year peri odicity in the historical annual flow regimes: years of**  **low flow alternated with years of high flow.”(Smith et**  **al., 1989: 280)** 

**• Anthropogenic influences play a secondary role to** 

**rainfall in determining salinity for Florida Bay as a whole, but they may be a factor in the magnitude of**  **salinity variations seen in recent times. Additionally, anthropogenic factors may act on a local basis to**  **influence salinity patterns.**

**Dwyer and Cronin (2001) noted a shift to high-am plitude salinity oscillations after 1950 as indicated by**  **the Mg:Ca ratio from cores in eastern Florida Bay (Table 3.1, Figure 3.1).These high-amplitude oscillations**  **corresponded to a period of increased variability in rainfall, but human alteration of freshwater flow may**  **also have been a factor. Brewster-Wingard and Ishman (1999) noted sim**  **ilar increases in the amplitude of salinity oscillations after ~1940, as indicated by foraminiferal and mollus**  **can assemblages in cores from Bob Allen and Russell banks (also examined by Dwyer and Cronin; Table 3.1,** **Figure 3.1). They did not conduct any statistical com parisons but they did note that the cause could be**  **meteorological patterns, anthropogenic changes to freshwater flow, or a combination of factors.**  **Clear evidence of decreasing freshwater influence during the 20th century was found in the northern**  **transition zone at the mouth of Taylor Creek and at Mud Creek near Joe Bay by Holmes**  **et al. (1999) and Willard**  **et al. (1997) (Table 3.1, Figure 3.1). The changes in the** **molluscan assemblage from an oligohaline-mesoha line fauna to a predominantly polyhaline fauna could** **be explained by the local alteration of flow through Tay lor Slough, by changes in rainfall that ultimately af**  **fected the flow, or by a combination of both. Alvarez Zarikian**  **et al. (2001) and Nelsen**  **et al. (2002)** **presented evidence of the local effects of water-man agement practices in their detailed analyses of the** **Oyster Bay core (Table 3.1, Figure 3.1). Several an thropogenic factors affected Oyster and Whitewater**  **bays during the 1980s: the beginning of SFWMD’s “Rainfall Plan” for managing flow, the shift of water**  **from Shark River Slough basin into Taylor Slough basin, and the closing of Buttonwood Canal. Alvarez**  **Zarikian et al.**  **(2001) noted that a significant decline in ostracode diversity and abundance occurred around** **1980, which could have been linked to these anthro pogenic changes or could have been due to the mid**  **1980s drought. Nelsen et al.**  **(2002) illustrated that regardless of the cause of the faunal changes in Oys**  **ter Bay, a comparison of rainfall and flow records showed that the most significant correlations were**  **prior to 1960, during the “pre-management period,”and after 1983, during implementation of the Rainfall Plan.** 

**• Declines in diversity and increases in dominance of** 

**salinity-tolerant species have occurred since the 1980s in several benthic invertebrate groups in dif**  **ferent regions of Florida Bay.**

**Alvarez Zarikian et al.**  **(2001) and Nelsen et al.** **(2002) saw two periods of reduced diversity in the ben thic microfauna at Oyster Bay: mid-1930s to late 1940s**  **and late 1970s to the time of core recovery in 1994. Nelsen**  **et al. (2002: 444) related the faunal changes to**  **“the changing nature of the salinity field at Oyster Bay after ~1980.”At Jimmy Key, the periods of reduced**  **diversity were from the mid to late 1930s and late 1970s to core recovery in 1997, which they also related to** 

**c hanges in the salinity field. Prior to 1950, declines in**  **ostracode abundance and diversity were followed by rapid recovery. Following the crash in the late 1970s,**  **the population has not recovered. The ostracode and foraminiferal faunas in the period from the late 1970s**  **on are dominated by individual species ( P**  **eratocytheridea setipunctata**  **and Ammonia parkinsoniana typica**  **), inter preted as showing survivor-type dominance.**  **P erato** 

**c ytheridea setipunctata**  **is known to tolerate extreme salinity fluctuations from less than 5 practical salinity**  **units (psu) to 42 psu (Alvarez Zarikian et al.,**  **2001: 140). Brewster-Wingard**  **et al. (2001) and Trappe and**  Ecosystem HistoryHunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 19 **Brewster-Wingard (2001) noted similar patterns in the molluscan assemblages from cores in eastern and cen**  **tral Florida Bay. In every core examined, Brachidontes**  **exustus, a mollusk known to tolerate large salinity vari**  **ations (10–44 psu measured in the field) and reduced**

**w ater quality, became the dominant species in the**  **upper portions of the cores from approximately 1980 on. The exception was in Whipray Key, where**  **Brachi dontes**  **reached its peak in the late 1970s and then de clined. In almost every core, with the exception of the**  **Ta**

**ylor Creek core, increases in the relative abundance of**  **Brachidontes corresponded to declines in molluscan**  **diversity. Brewster-Wingard et al.**  **(2001) interpreted this as opportunistic dominance.** 



### Status of Research

A

CCOMPLISHMENTS AND QUESTIONS RESOLVED **• M ost researchers have reached the consensus that** 

**rainfall and climatic patterns are the strongest dri ving factor in determining Florida Bay salinity pat**  **terns. Anthropogenic influences play a secondary role.** 

**• An indication of an increasingly stressed system is** 

**the dominance of species that tolerate extreme fluc tuations in salinity.This pattern of dominance is un**  **precedented in cores prior to the latter quarter of the 20th century.** 

**• Careful comparison of faunal data and biochemical** 

**data to instrumental salinity records for the past 50**
**y ears has demonstrated the validity of using pale**  **oecologic techniques to interpret downcore salinity patterns that extend beyond instrumental data**  **records.**

**• Increasing the coverage of Florida Bay by adding new** 

**cores will elucidate bay-wide trends.**

**• Increased refinement of proxy data has allowed** 

**more accurate interpretation of downcore results.**

RECENT ACCOMPLISHMENTS

**• Ground-truthing of ostracode Mg:Ca-ratio-based** 

**paleosalinity reconstruction with instrumental salin ity records (1950–present) confirms that the Mg:Ca** **method yields salinity values within 1–4 psu of salin ity maxima and minima over the past 50 years.**  **• A method of reducing molluscan-assemblage data** 

**to a single salinity value has been developed. • T** **he hypothesis that decadal patterns of salinity are**

**driven by climatological factors, including rainfall,**

**w as supported by analyses of the sediment-core pa**  **leosalinity record from Rankin Lake. The Rankin Lake paleosalinity record matches records obtained**  **in earlier studies of Russell Key and Bob Allen Key. • T** **he Rankin Lake core indicates the strong influ ence of freshwater at the site near the bottom of the** 

**core.**

**Cronin and Dwyer (Cronin et al.,**  **2003) have tested the accuracy of their downcore salinity estimates based**  **on a comparison of the Mg:Ca ratios in ostracode shells to historical instrumental salinity records from the**  **Russell Bank. These historical records date back to** Figure 3.2 **Comparison between instrumental salinity (black line) and salinity calculated from Mg/Ca ratios of ostracodes in Rus**  **sell Bank core 19B (dashed gray line). Instrumental data from Robblee**  **et al. (2000, 2001). The measured instrumental salinity**  **curve was constructed by computing monthly mean values for Whipray, Rankin, and Bob Allen Basins and then obtaining a**  **grand mean for the central region.** Ecosystem HistoryFlorida Bay Synthesis Hunt and Nuttle

20 FWRI Technical Report TR-11 **1947 and have been compiled by Robblee et al.**  **(2000, 2001). Figure 3.2 compares the Mg:Ca paleosalinity**  **curve against the instrumental record of salinity for the past 50 years. Both the instrumental records and the** **paleosalinity curve show large decadal swings in salin ity in central Florida Bay from salinities exceeding 50** **psu to those in the low 20s. For salinity maxima dur ing the early 1990s, late 1970s, and mid-1960s, the dif**  **ference between paleosalinity and instrumental salinity**

**w as approximately –1.1., 0.9, and 3 psu, respectively.The**  **differences in the four periods of Florida Bay salinity mimima (1993–1995, the 1980s, the late 1960s to early**  **1970s, and near 1960) were 0.3 psu, 3.6 psu, 1.9 psu, and 0.8 psu, respectively. Given the temporal gaps in the**  **instrumental record, the error on the sediment core age estimates, and the spatial and temporal averaging** **used for both records, these comparisons provide a re markable confirmation that the Mg:Ca-based shell** 

**c hemistry method yields accurate estimates of past**  **salinity to within less than 1–4 psu. W**  **ingard (unpublished report) has developed a method to reduce the core samples to a single averaged**  **salinity value for molluscan faunal assemblage data. Presence and absence data for live mollusks and for nu** **merous environmental parameters, including salin ity, have been recorded in Florida Bay since 1995**  **(http://sofia.usgs.gov/exchange/flaecohist/). These salinity data have been compiled and examined sta**  **tistically to determine the mean, median, minimum, maximum, standard deviation, and confidence inter** 

**va l for each mollusk species observed live. Any species** **with a confidence level above 5 or number of obser**

**v ations less than 15 were deleted from the modern**  **database. The modern salinity information was then combined with data from a core sample. It was then** 

**w eighted based on the percent abundance of each**  **species present in the sample core assemblage, and a cumulative average salinity value was produced for the**  **entire sample. This method has allowed the average salinity value to be directly compared to instrumental**  **records of salinity and can be used by modelers. A preliminary comparison (Wingard, unpublished**  **report) of the cumulative, weighted-average salinity data from three cores and the instrumental records of**  **salinity compiled by Robblee et al.**  **(2000, 2001) has been completed. It is important to note that this method**  **is only as good as the modern data upon which it is based. During the period of observations between**  **1995 and 2000, salinity values in excess of 48 psu were never recorded, and only four site surveys were con**  **ducted in water exceeding 40 psu during the course of the study (Brewster-Wingard**  **et al., 2001, and unpub**  **lished data). This lack of high-salinity observations means that the modern database is skewed toward**  **lower salinities. Despite this problem, the cumulative**

**w eighted averages show downcore trends and can be**  **compared with the instrumental records because they give a precise numerical value, unlike standard analy**  **ses of assemblage data.**

ONGOING RESEARCH

**• Dwyer and Cronin are continuing to examine the** 

**ecology of the ostracode Loxoconcha matagordensis**  **in order to refine their understanding of the role of temperature versus salinity in the Mg:Ca ratios in the** **shells.They also plan to examine the different mag nesium ionic concentrations of fresh versus marine** 

**w aters.These studies may provide another way to de**  **termine past freshwater influx into Florida Bay. • W**  **ingard, Stamm, and Murray are conducting growth experiments and calibrating water chemistry to shell** 

**c hemistry for the molluscan species**  **Chione cancel lata.**  **T hese experiments should allow them to be**  **able to extract salinity data from the metal:Ca ratios and stable isotopic ratios (**  **18 O and**  δ **13 C) in the indi**  **vidual growth increments of the shell. • W**  **ingard, Cronin, Dwyer, Orem, Holmes, and others are completing analyses on cores from Rankin Lake.**  **Results will help determine whether hypersalinity bull’s-eyes noted in this area over the past 15 years**  **are a recent phenomenon or if they existed under natural flow conditions.**  **• W ingard, Stamm, and Murray are conducting salin**  **ity-stress tests on common molluscan species found within modern Florida Bay. They are also testing** **sediment cores in order to refine the average salin ity values for each molluscan species used in the cu**  **mulative, weighted-sample, average-salinity method discussed above.** 

UNRESOLVED QUESTIONS AND NEEDED RESEARCH **• H ow**  **did salinity change in Florida Bay on a seasonal**

**basis prior to significant alteration of freshwater flow into the bay? What were the extremes in sea**  **sonal change?**



## ° **W ingard and others are researching the bio** 

**c hemistry of individual molluscan growth incre**  **ments to address this question.**

**• Did hypersalinity zones form in Florida Bay prior to** 

**instrumental data recordings in the past two decades? If so, how often, what was the duration, and** 

**w ere these linked to natural climatic patterns or to**  **anthropogenic change?**



## ° **Examination of Rankin Core by USGS groups is**

**beginning to address these questions.**

**• Additional cores are needed from critical areas** 

**within the bay, such as from transects along the** Ecosystem HistoryHunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 21 **margins of northern and eastern Florida Bay and the Cape Sable–Ten Thousand Islands area, where short**  **term salinity oscillations are large. • A** **ttempts should be made to locate areas with records**

**extending back into the early 1800s in order to ex amine 50–100 years of salinity patterns prior to any**  **alteration of the environment. • A**  **better understanding of the controls on shell bio**

**c hemistry should be developed, especially in coastal**  **areas where fresh and marine waters mix.This effort should include refining our understanding of the**  **salinity and temperature effects on shell chemistry by**  **integrating trace elemental (principally Mg-Ca, but also strontium [Sr] and barium [Ba]) analyses**  **with stable isotopic analyses.**



## ° **Zarikian and Swart plan to continue their stable**

**isotopic studies of water, ostracodes, and corals.**



## ° **Dwyer and Cronin are continuing their studies of**

**Mg-Ca in water and ostracodes.**



## ° **Swart, Zarikian, Dwyer, and Cronin hope to work**

**together on the same cores, examining both iso topic and trace elements in ostracode and**  **foraminifer shells.**

**• Knowledge of modern ecology of organisms being** 

**used in downcore studies should be refined.**



## ° **W ingard and others are continuing tests**  **in situ and** **in the laboratory on mollusks to determine toler ance to salinity extremes.** 

**• Examine modern data (Montague and Ley, 1993.** 

**See discussion in Nelsen et al.**  **(2002) to determine whether mean salinity or standard deviation in salin**  **ity exerts more control over benthic fauna and flora. • A**  **carbon budget for Florida Bay should be developed**

**in order to contribute to a better understanding of the carbon isotope record of the cores and provide** **a better means for interpreting historical freshwa ter influx into the bay (Halley and Roulier, 1999).**  **• W e need to perform additional “groundtruthing”of** **paleosalinity methods (Mg:Ca in ostracodes; cu mulative, weighted-sample average of mollusks) by**  **comparing the results of these methods on new, short sediment cores from key sites with the fairly**  **continuous instrumental salinity record available since 1985.** 

**• Calibrate Mg:Ca ratios in other ostracode species and** 

**apply them to new areas of study within the bay.**

**• Measured and reconstructed salinity and forcing** 

**factors (rainfall, evaporation, groundwater, and dis**

**c harge from sloughs) should undergo more rigorous**  **statistical analyses. • A** **pply paleosalinity data to Natural System Model**

**simulations to test the model’s accuracy in predict ing the trends determined from the paleorecord.**  **Begin with paleosalinity data that has been “groundtruthed”by comparison with instrumental**  **records of Robblee et al.**  **(2000, 2001).**



## Nutrient Patterns and Trends

**Restoration efforts to reestablish natural rates of fresh**

**w ater discharge into Florida Bay potentially could**  **cause additional harm to the bay if the quality of the**

**w ater entering the system is not considered. It is es** **sential to understand the prealteration patterns of nu trient influx into the bay and nutrient cycling within**  **the bay in order to provide the baseline information for nutrient modeling.** 



### Methods

**Sediments have been geochemically analyzed by both research groups (University of Miami/NOAA and**  **USGS) to extract information from sediment cores dated using**  **210 Pb and other methods of dating (Table**  **3.1). Orem et al.**  **(1999a) typically analyzed the sediments for organic carbon, total nitrogen, and total phospho**  **rus. Nelsen et al.**  **(2002) analyzed organic carbon, total aluminum, and lead. Swart**  **et al. (1999) discussed the** **possible use of trace elements in calcareous organ isms as a proxy for nutrients.** 


### Findings

LOWER TAYLOR SLOUGH AND MANGROVE FRINGE **• U ranium isotope studies indicate that phosphorus** 

**contamination at the northern end of Taylor Slough appears to be fertilizer-derived. However, phos**  **phorus contamination in Taylor Slough diminishes to background by mid slough; therefore, Taylor**  **Slough does not appear to be a source of nutrients to eastern Florida Bay.** 

**• Eastern Florida Bay does appear to be a source of nu** 

**trients to the mangrove zone at the southern end of Ta** **ylor Slough.**

**Orem et al.**  **(1997, 1999a), Orem (1998), and Gough et al.**  **(2000) conducted detailed surveys of nutrients, metals, and major ion geochemistries in Taylor Slough** **and in eastern and central Florida Bay from 1996 to pre sent. The study involved analyses of surface water,**  **sediment porewater, and solid phase sediments from cores (Table 3.1, Figure 3.1; Taylor Slough cores are not**  **included because they are not within Florida Bay). Cores were dated using**  **210 Pb,**  **137 Cs, and**  **14 C. Results**  **from Taylor Slough showed that there is some degree of nutrient contamination (phosphorus) at the head of**  **the slough. Uranium isotope studies indicated that this phosphorus contamination appeared to be fertil**  Ecosystem HistoryFlorida Bay Synthesis Hunt and Nuttle

22 FWRI Technical Report TR-11 **izer-derived.The phosphorus contamination in Taylor Slough diminished to background levels by mid**  **slough, so Taylor Slough does not appear to be a source of nutrients to eastern Florida Bay. Rather, Florida Bay**  **appears to be a source of nutrients to the mangrove zone at the southern end of Taylor Slough.** 

EASTERN AND CENTRAL FLORIDA BAY

**• Beginning in the mid 1980s, nutrification (increases** 

**in nitrogen and phosphorus) has occurred in portions of eastern and central Florida Bay as indicated by**  **abrupt shifts in organic carbon, total nitrogen, and total phosphorus. Pass Key, located closest to ter**  **restrial influx, showed the most pronounced shifts, and Bob Allen Key, the most southerly site, showed**  **the least pronounced shifts. • A**  **large multidecadal-productivity event in the mid**

**1700s, which was characterized by greatly elevated levels of organic carbon and nitrogen, was observed**  **in two cores from Whipray Basin.**

**Orem et al.**  **(1999a) conducted analyses on organic carbon, total nitrogen, and total phosphorus from five**  **sites in eastern Florida Bay (Table 3. 1, Figure 3.1).They found “sudden and dramatic shifts”indicating increased**  **nutrification that could not be explained by diagenetic processes. The sediments at Pass Key showed two**  **episodes of increased nutrification in the mid-1970s and after 1985. Nutrification at Bob Allen and Russell**  **banks began in the early 1980s. The shifts in nitrogen and phosphorus occurred just prior to the reported**  **microalgal blooms and seagrass die-off events in 1987. Tw**  **o cores from Whipray Basin, which preserve a long record dating back into the 1700s, were analyzed**  **by Orem**  **et al. (1999a). Downcore profiles at these sites**  **illustrated a large productivity event that occurred in the mid-1700s.This event was multidecadal and char**  **acterized by greatly elevated levels of organic carbon and nitrogen, probably representing a period of ex**  **tensive algal blooms. Interestingly, total phosphorus**

**w as not elevated during this time span. This produc**  **tivity event occurred during the Little Ice Age and may correspond to a period of higher rainfall in the**  **Everglades. Higher rainfall would contribute to more extensive land runoff into Florida Bay, which may have**  **triggered the productivity event.**

WESTERN FLORIDA BAY–WHITEWATER BAY AREA

**• Organic carbon records from Jimmy Key indicate that** 

**hurricanes help to flush organic carbon out of the bay.**

**Nelsen et al.**  **(2002) analyzed and contrasted organic carbon content in Oyster Bay, Jimmy Key, and Coot Bay** **cores (Table 3.1; Figure 3.1).They found that organic car bon decreased by a factor of two from Oyster Bay to**  **Coot Bay and by a factor of four from Oyster Bay to Jimmy Key. Aluminum was closely correlated to organic**  **carbon at Oyster Bay and Coot Bay because of erosion and mixing of the mangrove peats, which contribute**  **the organic carbon and the associated clay and quartz, which in turn contributes the aluminum. Storm de**  **posits and subsequent dissolution then concentrate the aluminum and organic carbon. Large organic carbon**  **excursions at Oyster Bay correspond to hurricane**

**ev ents because of an increase in organic detritus.The** **trend in organic carbon at Oyster Bay is towards a de cline from the first to the second half of the 20th cen**  **tury. At Coot Bay, organic carbon increases upcore, but at Jimmy Key it is segmented. The periods of or**  **ganic carbon increase at Jimmy Key (1900 to mid 1930s and after mid-1970) correspond to periods of decreased** **hurricane activity, whereas the period of declining or ganic carbon (mid-1930s to mid-1970s) took place dur**  **ing a period of increased hurricane activity.These data support the hypothesis that hurricanes contribute to**  **flushing of organic carbon from the bay (Nelsen et al.,**  **2002: 424, 442).**

TRACE–ELEMENT ANALYSES OF CORAL **Swart et al.**  **(1999) tested the use of barium (Ba) as a proxy for nutrient enrichment.They found that Ba in**  **creased when salinity decreased, but they concluded that the controls on barium were “enigmatic”and that** **more research was necessary to understand the dis tribution of barium within the bay.** 



### Status of Research

A

CCOMPLISHMENTS AND QUESTIONS RESOLVED

**• Multidecadal shifts in nitrogen and phosphorus** 

**have been documented in sediments deposited prior to anthropogenic change, illustrating that these shifts**  **occur naturally and can be of long duration.**

**• Recent dramatic increases in nitrogen, phosphorus,** 

**and total carbon have occurred in eastern Florida Bay and show decreasing amplitude with increasing dis**  **tance from Taylor Slough.**

ONGOING RESEARCH

**• Orem**  **et al. are currently working on analyses of** 

**carbon, nitrogen, and phosphorus from a Rankin Lake core.** 

UNRESOLVED QUESTIONS AND NEEDED RESEARCH

**• Certain trace elements within calcareous skeletons** 

**(cadmium [Cd], barium, and manganese [Mn]) may be proxies for nutrient enrichment (see Swart**  **et** Ecosystem HistoryHunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 23

**al., 1999, for discussion of previous research on this**  **method).This method could be tested and used on downcore specimens.**  **• T he use of**  δ **13 C as a proxy for nutrient fluxes, in** 

**combination with other analyses, should be ex plored.** 

**• Additional analyses from critical areas within the bay** 

**should be conducted in order to increase our un derstanding of past changes in nutrients.** 



## Occurrence and Pattern of Algal Blooms

**Only minimal ecosystem-history research has been done to contribute information on past algal blooms,** **and little of this work provides direct evidence. How**

**ev er, this is an area where there is the potential to ob**  **tain significant new information.**



### Methods

**Huvane and Cooper (2001) have conducted assem blage analyses of diatoms, microscopic “algae”whose** **siliceous shell, or frustule, is well preserved in the sed iments (Table 3. 1, Figure 3.1). Diatoms can be plank**  **tonic or epiphytic and can be indicative of many environmental factors. Edwards (Wingard**  **et al., 1995;**  **Ishman et al.,**  **1996; Brewster-Wingard et al.,**  **1997, 1998b) examined dinoflagellate cysts, a stage in the life cycle**  **of dinoflagellates, preserved in the sediments (Table 3.1, Figure 3.1).**  **Orem et al.**  **(1999a) inferred bloom conditions based on analyses of organic carbon, total nitrogen, and total**  **phosphorus. Swart et al.**  **(1999) inferred bloom condi tions based on a shift in**  δ **13 C in small**  **Siderastrea radi**

**ans corals collected throughout Florida Bay.** 


### Findings

**• Surface sediments from eastern Florida Bay show in** 

**dications of nutrient (C, N, and P) enrichment from 1980 to the present, which could be related to known**  **microalgal blooms within Florida Bay. • T** **he multidecadal-productivity event noted in sed**

**iment geochemistry from Whipray Basin cores may represent a period of extensive algal blooms.** 

**Orem et al.**  **(1997) analyzed surface sediments from eastern Florida Bay, including sites near Pass Key and**  **Russell Key banks.These analyses show indications of nutrient (C, N, and P) enrichment over the past two**  **decades.This nutrient enrichment could be related to recent microalgal blooms and/or seagrass die-off within**  **Florida Bay. The analyses of two cores from Whipray basin (Orem**  **et al., 1999a) may highlight a period of ex**  **tensive, multidecadal bloom conditions during the mid-1700s.**  **• Do wncore changes in abundance and assemblages** 

**of dinoflagellates and diatoms have been examined at some sites in Florida Bay. Additional studies of the**  **ecology of dinoflagellates and diatoms are needed to interpret the findings in terms of bloom conditions.** 

**T he findings on diatoms (Huvane and Cooper,**  **2001) and on dinoflagellate cysts (Wingard et al.**  **, 1995; Ishman**  **et al., 1996; Brewster-Wingard**  **et al., 1997, 1998b)**  **have been inconclusive to date. Additionally, detailed studies of the biology and ecology of diatoms and di**  **noflagellate cysts are needed to accurately interpret the findings. In addition, because these phytoplankton** **are found in the less than 63-μm fraction of the sedi ments, they are more susceptible than the benthic** **microfauna (greater than 63 μm) to transport, rede position, and reworking processes.** 

**• Increases in heavy excursions of**  δ **13 C may indicate** 

**the occurrence of algal blooms.**

**Swart et al.**  **(1999) analyzed** δ **13 C in small**  **Sideras trea radians**  **corals collected throughout Florida Bay (Table 3.1, Figure 3.1).They separated the corals into two**  **groups—those with** δ **13 C enrichment from approxi**  **mately 1989 to 1993 and those with** δ **13 C depletion over**  **the same time period. Corals showing the maximum** δ **13 C depletion, including the coral with the long record** **from Lignumvitae Key, occurred around 1984.Two pos sible causes for**  δ **13 C increases seen in the first group**  **of corals: (1) either a relative decrease in the influence of carbon derived from marine sources or (2) an in**  **crease in photosynthesis, which may indicate algal blooms.They discussed the contradictory evidence of**  **the** δ **13 C patterns seen in the two groups of corals.They**  **concluded that “the most probable cause is increased oxidation of organic material in the northeastern por**  **tion of Florida Bay and an increase in algal blooms in the western part of the bay.”** 



### Status of Research

ONGOING RESEARCH

**• No known research on downcore phytoplankton re** 

**mains is currently being conducted. • C**  **ontinued analyses of** δ **13 C in ostracodes,** 

**foraminifera, mollusks, and corals are part of several ongoing studies, but the primary intent of these**  **analyses is to address Question 1.**

UNRESOLVED QUESTIONS AND NEEDED RESEARCH **T he potential exists to extract information from sedi**  **ment cores about phytoplankton blooms via analyses of the remains in the core and through inferences**  Ecosystem HistoryFlorida Bay Synthesis Hunt and Nuttle

24 FWRI Technical Report TR-11 **based on changes in sediment geochemistry, carbon isotopes, and faunal assemblages. However, a great deal**  **of work needs to be done to understand the ecology of the living phytoplankton and to understand the sig**  **nature left in sediments following a bloom. In addition, the relationship between**  δ **13 C and blooms needs to**  **be tested and calibrated in the modern environment before information can be accurately applied to pale** **oanalyses. The questions that could be addressed in clude the following:** 

**• Prior to human alteration of flow and circulation in** 

**Florida Bay, did planktonic blooms occur? If yes, what was their timing and duration? What natural** 

**ev ents may have triggered blooms?**  **• D id the frequency and duration of blooms change** 

**after the construction of the Flagler Railroad or after the alteration of freshwater flow into Florida Bay?** 

**• Can algal blooms be recognized in the sedimentary** 

**record? If so, can they be characterized and quanti fied?**  

## Seagrass Trends and Patterns

**A significant amount of ecosystem history research has addressed changes in seagrasses specifically and**  **subaquatic vegetation (SAV) in general over time and the effects of changes in environmental components**  **(salinity, nutrients, water quality) on the vegetation. T** **hese questions are critical to restoration.The massive die-off in 1987–1988 focused public attention on the** **plight of Florida Bay and the changes that were oc curring in the ecosystem. It is important to place these** 

**c hanges in historical context over decadal and even cen** **tennial time scales to determine if die-offs and fluc tuations in seagrass abundance are natural, cyclical** 

**ev ents. In addition, ecosystem history data from sed** **iment cores can provide insights into long-term se quences of change preceding die-offs.** 



### Methods
**Basic assemblage analyses and geochemical analyses have been used to detect downcore trends and patterns**  **in subaquatic vegetation (SAV) from sediment cores dated using**  **210 Pb and other methods of dating (Table**  **3.1). Cronin (Cronin e t al.,**  **2001) and Wingard (Brew ster-Wingard**  **et al., 1998a, 2001; Brewster-Wingard and**  **Ishman, 1999) have used ostracodes and mollusks in their downcore analyses of SAV trends by applying data** **gathered in Florida Bay. Modern studies have estab lished that some ostracode and mollusk species pre**  **fer living as epiphytes on T**  **halassia or**  **Halodule (two**  **common true seagrasses in Florida Bay), some prefer macrobenthic algae (such as**  **Chondria or**  **Laurencia ),**  **and some are SAV generalists that do not have a pref erence for a particular species of grass or algae. The** **modern data were gathered through field observa tions and samples collected from 1995 to the present** **(field data available via http://sofia.usgs.gov/flaeco hist/). (See Salinity Trends and Patterns methods sec**  **tion for a discussion of taphonomic and sediment transport considerations in assemblage analyses.)** **Geochemical analyses of sediments can provide in formation on the presence and distribution of sea**  **grasses (Orem et al.,**  **1999b).The concentration of lignin phenols in sediments is a potential marker for histor**  **ical seagrass abundance in Florida Bay. Seagrasses in Florida Bay, although angiosperms, have a lignin phe**  **nol distribution similar to that of gymnosperms ( i.e.,**  **little or no syringyl phenols present). Apparently the syringyl phenol content of the lignin in the seagrasses**  **has been lost evolutionarily in the transition of these angiosperms back to the aquatic realm. This charac**  **teristic allows seagrass lignin (syringyl-phenol poor) to be differentiated from the other dominant lignin**  **source in Florida Bay (mangroves; syringyl-phenol rich). Analyses of organic carbon and total nitrogen**  **(Orem et al.,**  **1999a) may also provide information about seagrass die-offs, especially when combined with fau**  **nal assemblage and/or lignin phenol data.**


### Findings

**• F requent changes have occurred in the relative abun** 

**dance of epiphytal species of ostracodes and mol lusks over the past century.** 

**• Prior to the mid-20th century, epiphytal ostracodes** 

**w ere relatively rare at sites in central and eastern**  **Florida Bay, suggesting a greater abundance and/or density of SAV over the past 50 years than in the first**  **half of the century. Epiphytal mollusks, although not rare, increased significantly in relative abun**  **dance from approximately 1940 to the 1970s at most sites.These data raise the possibility that dense and**  **abundant seagrass beds may not be natural; if this finding is true, it will have great implications for**  **restoration. • A**  **decline in SAV-dwelling ostracodes and mollusks**

**occurred in cores from Whipray, Russell, Bob Allen, and Pass keys during the 1970s and 1980s.** 

**• Relative abundances of mollusks with a strong pref** 

**erence for T**  **halassia have declined since approximately**  **1970 in eastern Florida Bay and since 1910 at Whipray Ke** **y, whereas SAV generalists have increased. These** **findings may indicate that the amount of macroben thic algae has increased more than**  **T halassia**  **has. Cronin**  **et al. (2001) found that ostracode assem**  **blages during 1900–1940 at Whipray Basin, Bob Allen** Ecosystem HistoryHunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 25 **Ke y mudbank, Russell Key Bank, and Park Key were** 

**c haracterized by moderate to large proportions of**  **Per atocytheridea,**  **which is typically found associated with mud and**  **Halodule substrates. Ostracode species as**  **sociated with T**  **halassia and macroalgae were less com**  **mon during this period. From approximately 1930 to 1950,**  **P eratocytheridea**  **declined significantly, whereas Loxoconcha**  **(a T**  **halassia indicator) and**  **Xestoleberis (an**  **SAV generalist) increased (Figure 3.3).This pattern of long-term decline in**  **P eratocytheridea,**  **coincident with an increase in species associated with**  **T halassia**  **and macrobenthic algae, was seen in cores from central,**  **eastern, and northern Florida Bay. This shift suggests greater abundance and/or density of SAV in central**  **Florida Bay during the past 50 years than in the first half of the century. A second shift occurred in the**  **1970s and 1980s, when a decline in T**  **halassia - and algal**  **dwelling species occurred in most cores. Cronin et al.** **(2001: 176) stated that “although the strength of the de cline varied by species and by site, the stark contrast**  **between the abundance of epiphytal species during the 1950s and 1960s and the very low abundance at times**  **during the following two decades suggests a broad regional shift occurred at this time.” These shifts in** **the 1970s and 1980s may be related to large-scale sea grass die-offs (principally**  **T halassia**  **). Brewster-Wingard**  **et al. (1998a), Brewster-Wingard**  **and Ishman (1999), and Trappe and Brewster-Wingard (2001) noted frequent and relatively dramatic shifts** **in the populations of the epiphytal species of mol lusks. Cores from Whipray Key, Russell Key Bank, and**  **Ta ylor Creek all show increases in epiphytal mollusks**  **beginning around 1940, so the molluscan data agree with the ostracode data (Figure 3.3).There was a gen**  **eral increase in epiphytal organisms during the latter half of the 20th century, indicating a greater SAV cov** **erage during this period than in the first half of the cen tury. The molluscan epiphytal species were split into**  Figure 3.3 **P ercentage of abundance of select mollusk and ostracode species that are indicators of sub-aquatic vegetation, plotted against**  **estimated age for Russell Bank core 19B. Light gray are species indicative of any type of sub-aquatic vegetation (generalists). Black are species primarily indicative of**  **T halassia**  **(specialists). Note different percent abundance scales.** Ecosystem HistoryFlorida Bay Synthesis Hunt and Nuttle

26 FWRI Technical Report TR-11**two groups based on modern field observations (Fig ure 3.3): (1) species that have a strong preference for**  **T**

**halassia and (2) nonspecific SAV dwellers that may be**  **found on either T**  **halassia or macrobenthic algae.These** **data illustrate an interesting trend—the relative abun dance of**  **T halassia**  **dwellers has declined since ap proximately 1970 at Bob Allen and Russell keys and**  **since 1910 at Whipray Key, whereas the nonspecific SAV dwellers have increased. The ostracode**  **Xestoleberis is** **a nonspecific SAV dweller, and its trends in abun dance agree with the molluscan data.**  **• Do wncore profiles of lignin phenols from a Pass Key** 

**core show large variations in lignin-phenol distrib utions over short time intervals, therefore reflecting**  **the proximity of this site to the mangrove zone along the coast and to the outlet of Taylor Creek and thus**  **to the influence of decaying mangrove and terrestrial plant detritus.** 

**• At Bob Allen Keys, the lignin-phenol distributions** 

**show downcore variations in the abundance of sea grass over time. Seagrass abundance appears to**  **have been increasing since a recent minimum around 1960.** 

**Downcore profiles of lignin phenols were ana l** **yzed from Pass Key and Bob Allen Keys (Orem et al.,**  **1999b). The Pass Key core shows large variations in lignin phenol distributions over short time intervals.**  **T hese variations are consistent with the proximity of**  **this site to the mangrove zone along the coast and to the outlet of Taylor Creek and the influence of decay**  **ing mangrove vegetation and influx of terrestrial plant detritus. At Bob Allen Keys, the lignin distributions**  **show downcore variations in the abundance of seagrass**

**ov er time. At Bob Allen, seagrass abundance appears**  **to have been increasing since a recent minimum around 1960.** 

**• Surface sediments from eastern Florida Bay show in** 

**dications of nutrient (C, N, and P) enrichment from 1980 to the present; which could be related to recent**  **seagrass die-off within Florida Bay.**

**T**

**he analyses conducted by Orem et al.**  **(1999a) (dis cussed under Question 3 above) at sites near Pass Key**  **and Russell Key banks indicated that nutrient (C, N, and P) enrichment from 1980 to the present could be related**  **to recent seagrass die-off within Florida Bay.**



### Status of Research

A

CCOMPLISHMENTS AND QUESTIONS RESOLVED

**• Common trends in mollusk and ostracode epiphy** 

**tal species across basins and regions of Florida Bay indicate that while substrate and seagrass coverage**  **may be patchy, it appears that there are bay-wide forcing factors affecting the abundance and distri**  **bution of the beds. • F**  **requent and relatively rapid changes occur in the**

**epiphytal indicator species, implying that the SAV itself goes through frequent and significant changes.**  **• T here is evidence of increasing macrobenthic algae** 

**abundance in Florida Bay. • T** **rends in SAV distribution throughout the 20th cen tury imply that dense and abundant seagrass beds**  **occurred in an already altered system. This finding has important implications for restoration.** 

ONGOING RESEARCH

**• Current USGS work is focused on completing analy** 

**ses of a core from Rankin Lake. This core was from an area of documented seagrass die-off (P. Carlson,** **personal communication) and was collected to ex amine the long-term (decadal-scale) sequences of** 

**c hange in a number of variables prior to the die-off** 

**ev ent in 1987–1988. Ostracode and molluscan as**  **semblages, ostracode geochemistry (Mg:Ca ratio), sediment geochemistry, and lignin phenols are being**  **analyzed downcore.**

**• An additional core from the site of seagrass die-off** 

**at Barnes Sound is currently being processed and will be analyzed by the USGS group for faunal assem**  **blage data and Mg:Ca ratios. A core from Whipray Basin will be analyzed for lignin phenols.** 

**• Samples have been collected and processed to begin** 

**to quantify the relationships between molluscan species and SAV species.** 

UNRESOLVED QUESTIONS AND NEEDED RESEARCH **• T he causes of seagrass die-off are still poorly un** 

**derstood. Detailed studies of sediment cores from sites of known die-off should help researchers ex**  **amine the decadal-scale sequences of change that have led to the recent die-off events. Multiple forc** **ing factors are undoubtedly at play in massive die off events, and long-term data may allow researchers**  **to better understand the interaction of these factors prior to die-offs.**  **• T he potential influence of climate variability and its** 

**role in factors that directly affect sea-grasses, such as light attenuation, disease, and salinity fluctua**  **tions, need additional study. • A**  **quantitative analysis of modern vegetation and epi**

**phytic species would allow more refined interpre tations of the downcore assemblages.**  Ecosystem HistoryHunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 27 

## Higher-Trophic-Level Species

**Ecosystem history research and analyses of sediment cores have contributed very little to Question 5, in**  **large part because Question 5 has been focused on the higher-trophic-level species, which are generally ab** **sent or not well represented in the cores.The only ex ception is the molluscan fauna. As Brewster-Wingard**  **et al. (2001) pointed out, mollusks are well preserved**  **in the cores, and they represent a number of trophic categories (filter feeding, grazing, scavenging, and car** **nivory). Simple measures of molluscan faunal diver sity in cores from eastern and central Florida Bay have** **illustrated patterns of change over time (Brewster W**  **ingard et al.,**  **2001; Trappe and Brewster-Wingard, 2001), but these measures have not been rigorously**  **tested. An apparent trend toward decreasing diversity has been observed in the upper portions of most of the**  **cores beginning between 1960 and 1980. If Question 5 were to expand and examine the** **lower invertebrates, paleoecologic data could con tribute more valuable data from the benthic micro**  **fauna. Some of these trends are discussed under Question 1 and Question 4 above.** 



### Status of Research

ONGOING RESEARCH

**• No active research on higher trophic levels, other** 

**than molluscan faunal assemblage analyses, is cur rently being done. The current focus of the mollus**  **can studies is to address Question 1 and Question 4, but molluscan faunal changes in response to salin** **ity and benthic habitat will provide secondary in formation to address Question 5.** 

**• Benthic microfaunal assemblage analyses are also** 

**contributing data about changes in the Florida Bay benthic habitat over time.** 

UNRESOLVED QUESTIONS AND NEEDED RESEARCH **• T here are significant questions about changes in** 

**benthic habitat that could be addressed (and in part are being addressed) by expanding Question 5 to**  **include lower invertebrates.These organisms form the bottom of the food chain and are therefore essential**  **to the survival of the higher-trophic-level organisms. Because the lower invertebrates are more readily** **preserved in sediment cores, decadal- to centennial scale analyses of environmental change and its effect**  **on animals in Florida Bay would be possible.**

**• More rigorous analyses of the molluscan faunal di** 

**v ersity data should be conducted.**  **• T he use of mollusks as proxies for higher-trophic**  **level diversity should be explored.**



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**v egetation and associated fauna in northeastern Florida**  **Bay. Estuaries 16: 703.**
**NELSEN,T., G. GARTE, C. FEATHERSTONE, H.WAN LESS, J. TREFRY, W.–J. KANG, S. METZ, C. AL**  **V**

**AREZ–ZARIKIAN,T. HOOD, P. SWART, G. ELLIS, P. BLACKWELDER, L. TEDESCO, C. SLOUCH, J.**  **PA CHUT, and M. O’NEAL. 2002. Linkages between** **the South Florida peninsula and coastal zone: a sedi ment-based history of natural and anthropogenic in**  **fluences. Pp. 415–449 in**  **J.W. Porter and K. G. Porter, eds. T** **he Everglades, Florida Bay, and Coral Reefs of the Florida Keys: An Ecosystem Sourcebook. CRC Press,**  **Boca Raton, Florida. OREM, W. H. 1998.Taylor Slough and eastern Florida**  **Bay: geochemical studies in support of ecosystem restoration in south Florida. United States Geological**  **Survey Information Sheet.**
**OREM, W. H., C. W. HOLMES, C. KENDALL, H. E. LERCH, A. L. BATES, S. R. SILVA, A. BOYLAN, M.**  **CORUM, and C. HEDGMAN. 1999a. Geochemistry of Florida Bay sediments: nutrient history at five sites in** **eastern and central Florida Bay. Journal of Coastal Re search 15: 1055–1071.** 
**OREM, W. H., H. E. LERCH, A. L. BATES, C. W. HOLMES, and M. MAROT. 1999b. Lignin phenols in**  **sediments from Florida Bay as indicators of seagrass history [extended abstract]. Pp. 191–193**  **in 1999 Florida**  Ecosystem HistoryHunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 29**Bay and Adjacent Marine Systems Science Confer ence, Key Largo, Florida, November 1999, Program**  **and Abstracts.**
**OREM,W. H., H. E. LERCH, and P. RAWLIK. 1997. De scriptive geochemistry of surface and pore water from** **USGS 1994 and 1995 coring sites in south Florida wet lands. USGS Open-File Report 97-454.** 
**ROBBLEE, M., G. CLEMENT, D. SMITH, L. BOCHIC CHIO, and R. HALLEY. 2000. Design and Develop**  **ment of the Florida Bay Salinity Database. Poster presented December 2000 at the Greater Everglades**  **Ecosystem Restoration Conference. Available online at http://sofia.usgs.gov/geer/2000/posters/fbsalinitydb/**  **index.html.**
**ROBBLEE, M., G. CLEMENT, D. SMITH, and R. HAL LEY. 2001. Salinity pattern in Florida Bay: A synthesis**  **(1900–2000). Pp. 34–36 in**  **Programs and Abstracts–2001 Florida Bay Science Conference.** 
**SMITH, III,T. J., A. M. FOSTER, P. R. BRIERE, A.W. COF FIN, J. W. JONES, C. R.VAN ARSDALL, and L. J. FRYE.**  **2002a. Historical aerial photography for the Greater Everglades of south Florida: The 1940, 1:40,000 photo**  **set. U.S. Geological Survey Open File Report 02-327.**
**SMITH, T. J., III, A. M. FOSTER, P. R. BRIERE, J. W. JONES, and C. R.VAN ARSDALL. 2002b. Conversion**  **of historical topographic sheets (T-sheets) to digital form: Florida Everglades and vicinity. United States Ge**  **ological Survey, Open-File Report 02-204. [CD–ROM]**
**SMITH, T. J., III, H. HUDSON, M. B. ROBBLEE, G. V. N. POWELL, and P. J. ISDALE. 1989. Freshwater flow** **from the Everglades to Florida Bay: a historical re construction based on fluorescent banding in the coral**  **Soleastrea bournoni. Bulletin of Marine Science 44:**  **274–282.**
**SWART, P. K., G. F. HEALY, R. E. DODGE, P. KRAMER, J. H. HUDSON, R. B. HALLEY, and M. B. ROBBLEE.**  **1996. The stable oxygen and carbon isotopic record from a coral growing in Florida Bay: a 160-year record** **of climatic and anthropogenic influence. Palaeogeog raphy, Palaeoclimatology, Palaeoecology 123: 219–237.** 
**SWART, P. K., G. F. HEALY, L. GREER, M. LUTZ, A. SAIED, D. ANDEREGG, R. E. DODGE, and D. RUD**  **NICK. 1999.The use of proxy chemical records in coral skeletons to ascertain past environmental conditions**  **in Florida Bay. Estuaries 22: 384–397.**

**T**

**AFT, W. H., and J. W. HARBAUGH. 1964. Modern carbonate sediments of southern Florida, Bahamas,** **and Espiritu Santo Island, Baja, California and com parison of their mineralogy and chemistry. Publications**  **in Geological Science. Stanford University, Berkeley, California.** 
**TRAPPE, C. A., and G. L. BREWSTER–WINGARD. 2001. Molluscan fauna from Core 25B, Whipray Basin,**  **Central Florida Bay, Everglades National Park. U.S. Geological Survey Open File Report 01-143.** 
**TURNEY,W. J., and B. F. PERKINS. 1972. Molluscan dis tribution in Florida Bay. Sedimenta III. University of**  **Miami, Rosenstiel School of Marine and Atmospheric Sciences, Miami, Florida.** 

**W**

**ANLESS, H. R., and M. G. TAGETT. 1989. Origin, growth and evolution of carbonate mudbanks in Florida**  **Bay. Bulletin of Marine Science 44: 454–489.**
**WILLARD, D. A., G. L. BREWSTER–WINGARD, C. FELLMAN, and S. E. ISHMAN. 1997. Paleontological**  **Data from Mud Creek Core 1, Southern Florida. U.S. Geological Survey Open File Report 97-736. 14 p.** 
**WINGARD, G. L., S. E. ISHMAN,T. M.CRONIN, L. E. EDWARDS, D. A. WILLARD, and R. B. HALLEY. 1995.**  **Preliminary analysis of down-core biotic assemblages: Bob Allen Keys, Everglades National Park, Florida Bay.**  **U .S. Geological Survey Open-File Report. 95-628.**  Ecosystem History

## Introduction

Question 1 **—How and at what rates do storms, changing freshwater flows, sea level rise, and local evaporation**  **precipitation patterns influence circulation and salinity patterns within Florida Bay and exchanges between the**  **bay and adjacent waters?**

**Th e research conducted addressing Question 1 was in** **tended to produce quantitative predictions of circu lation and salinity responses within Florida Bay.** **Exchange between the bay and the Gulf of Mexico, ex**

**c hange between the bay and the coastal zone of the** **Florida Keys, and oceanographic, climatic, and hy drological driving processes were also areas that were** **to be addressed.Table 4.1 includes relevant represen tative references to research addressing driving forces,** **system characteristics, and their intersection.The Re search Summary highlights major findings to date.** 



### Background

**T he south Florida coastal system surrounding and in**  **teracting with the interior waters of Florida Bay (made up of the gulf and Atlantic waters of the Florida Keys,**  **the Dry Tortugas, and the southwestern Florida shelf) is highly coupled by the combined influence of coastal**  **and oceanic currents (Lee et al.,**  **2002).The bay itself is a lagoonal system; a complex network of shallow, often**  **intertidal, banks isolate the interior portions of Florida Bay from the direct influence of regional or larger**  **scale oceanographic processes (Figure 4.1). As a result, local and direct climatic processes, such as the inflows**  **of surface and groundwater, rainfall, evaporation, and wind-driven flow, greatly affect salinity, circulation,**  **and exchange processes. T** **he climate of south Florida is subtropical, with a comparatively small annual temperature range but** **distinct wet (summer-fall) and dry (winter-spring) sea sons. During the wet season, showers associated with** **the afternoon sea breeze occur almost daily, and trop ical storms are transient occurrences. During the dry** **season, cold fronts pass through the region on an ap proximately weekly basis, accompanied by increased**  **wind speeds and clockwise-rotating wind directions. Spatially, the bay can be thought of as four distinct** **regions subject to different geophysical forcings, topo graphic constraints, and freshwater inputs.The north**  **eastern region of Florida Bay is not significantly affected by**  **tides or directly influenced by the surrounding ma rine waters of the Atlantic and Gulf of Mexico.This re**  **gion is the direct recipient of freshwater flows from Ta** **ylor Slough and the C-111 canal system. Upstream**

**w ater-management practices influence the quantity,** **timing, and distribution of fresh water entering this re gion. Runoff varies spatially across the northern bound**  **ary, with the greatest flow through Trout Creek. Wind**

**ev ents often determine the timing of freshwater dis** 

**c harges on hourly to daily time scales, and regional**  **rainfall cycles ( e.g.,**  **seasonal and El Niño/La Niña driven) influence discharges on annual to multiyear**  **time scales. Salinity along the northern boundary of the bay responds very rapidly to rainfall and/or discharge** 

**ev ents. High flow causes dramatic freshening in the**  **small bays along the northern boundary. Subsequently, fresh water slowly mixes with the more saline Florida**  **Bay waters to the south and southwest over a period of weeks to months (Johns**  **et al., 2001a).**  **T he central region of Florida Bay receives less di**  **rect freshwater inflow, but fresh water can move into central Florida Bay through McCormick Creek into**  **T**

**errapin Bay, through Alligator Creek into Garfield Bight, as well as over the Buttonwood Embankment.**  **Groundwater inputs have also been hypothesized. Under historically higher water levels, these surface** **and groundwater inputs were presumably more sig nificant throughout the southern Everglades. During**  **times of reduced precipitation and high evaporation, this central area can become hypersaline, with salin** 

30 FWRI Technical Report TR-11 

# Chapter 4 Physical Processes

Lead Authors Dr. Thomas Lee (University of Miami), Dr. Elizabeth Johns (NOAA/AOML), and Dr. Peter Ortner (NOAA/AOML) Contributors Joseph Boyer, Jeff Chanton, Shuyi Chen, John Hammrick, Clinton Hittle, Villy Kourafalou , Chris Langevin, Victor Levesque, Frank Marshall , Zaki Moustafa, William Nuttle, Eduardo Patino, Joseph Pica, Rene Price, Michael Robblee, David Rudnick, Ray Schaffranek, DeWitt Smith, Ned Smith, Eric Swain, Peter Swart, Zafer Top, Paul Trimble, Sandra Vargo, John Wang, Paul WillisHunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 31 **ity often exceeding 40 practical salinity units (psu) and historically as high as 70 psu (Boyer and Jones, 2001;**  **Robblee et al.,**  **2001). High salinity persists over peri ods of weeks to months, indicating that like waters of**  **the northeastern region, those of the central region have a relatively long residence time.**  **T he western region of Florida Bay is the least topo**  **graphically isolated, sharing an open boundary with the Gulf of Mexico and exchanging water with the**  **central region of Florida Bay through the main Flamingo channel and with the Atlantic Ocean through**  **passages in the middle Keys.This western region is also subject to robust tidal mixing. Therefore, residence** **times in the western region are shorter than in the cen tral and northeastern regions, and salinity can show a**  **relatively rapid response to meteorological events such as tropical storms and cold fronts. Oceanographically,** **the entire coastal region of south Florida is one inte grated system (Figure 4.2). Florida Bay is connected to**  **the southwestern Florida shelf and, on occasion, to** T able 4.1 **Research categories defined by Question 1 and representative references to relevant research.**

System Characteristics Driving Exchange with Process Salinity Patterns Circulation Patterns Adjacent Waters

General Characteristics **Robblee et al.**  **(2001), Boyer et al.**  **Lee and Williams (1999), Lee N. Smith (2002), Smith and Pitts (1997), Boyer and Jones (2001),**  **et al. (1999), Lee**  **et al. (2002), Lee and Smith (2002),**  **Lee et al.**  **(2002), Johns et al.**  **(2002), D. Smith (2001) Yang (1999), Lee and Williams**  **(2001a), D. Smith (2001) (1999), Lee**  **et al. (1999, 2002)** 

W

inds and Storms **J ohns**  **et al. (2001b), D. Smith Lee and Williams (1999), Lee Lee and Smith (2002), Smith and**  **Goldenberg et al.**  **(2001), (2001), R. Smith et al.**  **(2001) et al.**  **(2002), Smith and Pitts Pitts (2002), N. Smith (2001), Johns et**  **Albrecht et al.**  **(2003) (2002), Wang et al.**  **(1994), al.**  **(2001b) N. Smith (2001)** 
Precipitation **Swart and Price (2001), Nuttle et**  **No observed effect of No observed effect of precipitation**  **W**

**illis (1999),Trimble et al. al.**  **(2000, 2001) Johns et al.**  **precipitation on circulation on exchanges with adjacent waters (2001), Mattocks (pers. com.), (2001a)**  **has been reported. has been reported.**  **Pielke et al.**  **(1999)**
Evaporation **Swart and Price (2001), Nuttle et**  **No observed effect of No observed effect of**  **Pratt and Smith (1999), al.**  **(2000, 2001) evaporation on circulation has evaporation on exchanges**  **N. Smith (2000), Price et al.**  **been reported. with adjacent waters has been**  **(2001), Mattocks (pers. com.) reported.** 

Surface Water **Lee et al.**  **(2002) Ortner et al.**  **Lee et al.**  **(2002), Langevin et**  **No observed effect of surface Hittle**  **et al. (2001),**  **(1995), Nuttle et al.**  **(2000, 2001), al.**  **(2002a) water on exchanges with**  **V**

**osburg et al.**  **(2001), Swart and Price (2001), Johns**  **et adjacent waters has been**  **Cable et al.**  **(2001) Swart and al.**  **(2001a), Langevin et al.**  **(2002a), Price (2001), Levesque and Schaffranek**  **et al. (2002), Hurricane**  **P**

**atino (2001),Trimble et al.**  **(2001) Georges Workshop** 

Groundwater **Fitterman et al.**  **(1999), Fitterman Langevin et al.**  **(2002a) No observed effect of**  **Price and Swart (2001), and Deszcz-Pan (2001), groundwater on exchanges**  **Fitterman and Deszcz-Pan Langevin et al.**  **(2002a) with adjacent waters has been**  **(2000, 2002),Vosburg et al.**  **reported (2001),Top and Brand (2001)** 

Sea Level and Tides **Lee et al.**  **(2001, 2002), Johns Lee and Smith (2002), Smith N. Smith (1998), Smith and Maul and Martin (1993),**  **et al. (2001a)**  **(1998), Wang et al.**  **(1994) Lee (2003), Lee and Smith Smith (1997), Frederick**  **et al. (2002), Smith and Pitts**  **(1994) (2002), N. Smith (2001)** 
Boundary Currents **Ortner et al.**  **(1995), Lee et al.**  **Lee et al.**  **(2002),Yang et al.**  **Lee et al.**  **(2001, 2002), Lee and Williams (1999), (2001, 2002)**  **(1999) Yang**  **et al. (1999)**  **Lee and Smith (2002)**

Prediction **Nuttle et al.**  **(2000, 2001), Cosby Wang et al.**  **(1994), Kim et al.**  **HYCOM model group et al.**  **(1999), Wang et al.**  **(1994), (1999) Marshall (2001), Walker (1998),**  **Kim et al.**  **(1999)** Physical Processes**more remote regions of the Gulf of Mexico. As a result,**

**w estern Florida Bay can be influenced by the delivery**  **of fresh water from rivers discharging into the Ten T** **housand Islands region and along the west coast of Florida (the Shark, Broad, Harney, and Lostmans rivers).**  **T hese river waters are carried southward along the**  **southwestern Florida coastline and around Cape Sable in a general pattern of outflow through the Keys to the**  **reef tract (Lee et al.,**  **2001, 2002). Freshwater inflow from remote gulf regions is more likely during sum**  **mer and fall and has been shown to include that from Mississippi River floods (Ortner**  **et al., 1995). Subsequent**  **transport of this water to Florida Bay and the Keys is aided by the Loop Current and the Florida Current.**  **Finally, the southern region of Florida Bay differs from the central region because it has an open con**  **nection through the middle Keys passages and at times can receive an influx of Atlantic Ocean water. The**  **southern region may also be a source of bay waters to the coral reef areas of the Florida Keys National Ma**  **rine Sanctuary (FKNMS). Circulation of water in western Florida Bay and ad**  **jacent coastal regions on subtidal time scales is strongly influenced by local wind forcing that results in seasonal**  **flow patterns: southward toward the Keys in winter and spring, northwestward into the gulf in summer, and**  **southwestward toward the Tortugas in the fall. Episodic transport processes can deliver warm, salty water to the**  **reef tract from Florida Bay in the spring and early summer. During the winter, cold, turbid water intru**  **sions from Florida Bay can occur.**


### Research Summary

**To date, researchers have documented regional oceano** **graphic and hydrological driving processes. Circula tion in the outer portion of Florida Bay, the adjacent**  **southwestern Florida shelf, and Florida Keys; exchange between Florida Bay and the Keys coastal zone; the po**  **tential pathway for exchange across the western boundary; and the patterns of salinity variation**  **throughout the bay and adjacent marine systems are among those processes. These results were derived**  **from several extensive observational programs that have now collected almost 10 years of data on regional** 

**w ater properties, meteorology, and flow.**  **By comparison, major uncertainties remain about circulation within the interior basins, interbasin ex**  **ch ange, flow across the bank tops, the effect of evap**  **orative processes upon bank-top waters, groundwater** Florida Bay Synthesis Hunt and Nuttle

32 FWRI Technical Report TR-11 Figure 4.1 **LANDSAT–7 extended thematic mapper image of Florida Bay, showing its shallow bank bathymetry and four principal subregions.** Physical Processes**entering the bay across its northern boundary, and the quantitative details of exchange across the bay’s ex** **tensive and complex western boundary. The hydro logical model of surface waters entering northeastern**  **Florida Bay has been improved over the past few years, and progress has been made on expanding the model** **to the entire northern boundary and the lower south**

**w estern shelf including the Shark River slough. How** 

**ev er, we still do not have an adequate hydrodynamic**  **model of the interior of Florida Bay. As a result, our ability to rigorously forecast** 

**c hanges in salinity within the bay resulting from** **planned modifications in upstream water manage ment is inadequate. Nonetheless, a water budget has**  **been developed for Florida Bay based upon long-term (31 years) salinity data.The budget takes into account**  **seasonal and interannual variations in the supply of fresh water (Nuttle**  **et al., 2000). A depiction of the cli** **matic cycle of surface runoff, evaporation, and pre cipitation over the 31-year period is shown in Figure** **4.3. Across the whole bay, discharge from the estuar ine creeks amounts to about 2 cm/year, or about 20%**  **of the annual rainfall. In the northeast region, where the majority (98%) of the creek discharge enters the bay,**  **creek discharges amount to about 67% of the annual rainfall. Similar to the 31-year average, the majority of** **the freshwater inflow is now concentrated in the north eastern part of the bay and has a major influence on** **salinity variations therein, effectively inhibiting hy persalinity. Conversely, the lack of freshwater flow to**  **the central bay exacerbates hypersalinity. Higher discharges through the Shark River slough**  **and higher water levels in the southern Everglades could redistribute freshwater input to the bay and**  **could provide greater input to the central basins in particular. Integrated hydrological/hydrodynamic mod**  **els incorporating the most recent observational data and process-study results linked to appropriate re** **gional/boundary hydrodynamic and atmospheric mod els are required to rigorously address the most central**  **management concern: what salinity distributions will result from various upstream water-management al**  **ternatives.This has become a principal objective of the Florida Bay and Florida Keys Feasibility Study (FBFKFS).**  **Th e principal findings are summarized below and**  **relevant citations are enumerated in Table 4.1.** Hunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 33 Figure 4.2 **Schematic representation of the average flow patterns in the interconnected south Florida coastal circulation system.The single arrows represent mean current directions, whereas the double arrows represent the Loop Current and the Florida Current.**  Physical ProcessesSALINITY

**• Historical salinity data and salinity proxy data show** 

**that large salinity changes are not yet understood. T** 

**hose changes have commonly taken place in Florida Bay seasonally, interannually (the El Niño/Southern**  **Oscillation, ENSO), decadally (the North Atlantic Oscillation, NAO), and for even longer periods.**  **• H istorical data from the salinity synthesis database** 

**(Robblee et al.,**  **2001) show that Florida Bay has be haved as a marine lagoon for the past several**  **decades. Salinities have reached as high as 70 psu in the central bay on a few occasions and typically ex**  **ceeded 40 psu during drought years such as 1989–1990. For example, following the wet period of**  **1994–1995, salinity increased until tropical storms in 1999 induced a decrease, which was followed by an**  **other increase during the drought years of 2000 and 2001. Recent data from 2000–2002 indicate that Florida**  **Bay salinity may again be on the rise. • V**  **ariability of Florida Bay average salinity is directly related to the net flux of fresh water from the com**  **bined influence of evaporation, precipitation, and runoff. For the bay as a whole on seasonal or annual**  **time scales, evaporation is approximately equal to precipitation, while runoff is roughly 20% of either.** 

**• Recent studies have narrowed the range of evapo** 

**ration to around 75–180 cm/year.**

**• Shallow banks, which restrict water exchange, tend** 

**to separate the bay’s interior into three regions with distinct salinity variations. The northeastern basin** **is the most isolated from oceanic influences, re ceives most of the surface runoff, and has the largest**  **seasonal cycle of salinity.The central basin receives little runoff and has the highest salinity. The west**  **ern basins have the greatest oceanic exchange and the smallest seasonal change in salinity.** 

**• Continuous surveys of the bay’s salinity patterns** 

**show large spatial gradients coinciding with the wide, shallow banks that tend to inhibit interbasin**  **exchanges.**

FRESHWATER INPUT

**• Stable isotopic markers indicate that the dominant** 

**source of fresh water for northeastern Florida Bay is Everglades runoff, whereas for the western region,**  **precipitation has a stronger influence. In the central region, a mixture of runoff and precipitation provides**  **the fresh water.**

**• Measurements and modeling (both hydraulic and re** 

**gression) of surface inflows to the bay from the Ever glades continue to improve. These analyses show**  **that there have been increasing inflows to Taylor Slough and the C-111 canal since 1985 as a result of**  **management activity. • T**  **rout Creek contributes the largest volume of fresh**

**w ater to northeastern Florida Bay, varying from –6**  **to 32 m 3**  **/s. By contrast, the flow from each of the other eight creeks ranges from –1.4 to 6 m**  **3 /s. Negative**  **flows can occur during the dry season and storm**

**ev ents.**  **• F or the Ten Thousand Island region of the western** 

**Everglades, the mean annual river discharge is es timated at 13.3 m**  **3 /s for Harney River, 11.0 m**  **3 /s for**  **Broad River, and 12.4 m 3**  **/s for Shark River.**

**• Shark River’s low-salinity plume waters are com** 

**monly advected southward around Cape Sable to**

**w estern Florida Bay and the Keys reef tract by wind**  **driven coastal flows.**

**• Groundwater inflows are believed to be most influ** 

**ential along the northern boundary of the bay; how**

**ev er, estimates of the volume of this flow range over**  **four orders of magnitude. New measurements and h** 

**ydraulic modeling should help to put bounds on the inflow estimates.** 

CIRCULATION AND EXCHANGE **• T he entire south Florida coastal system, consisting** 

**of the southwestern Florida shelf, the Florida Keys reef tract, and western Florida Bay, is highly con** **nected by local and oceanic circulation patterns re sponding to wind and boundary-current forcing.**  **• L arge-volume, wind-forced flows through the Keys** 

**passages provide linkage for gulf-to-Atlantic exchange through the open western region of Florida Bay.**  **• M easurement of sea level slopes across the Florida** 

**Ke ys provides a tool for monitoring gulf-to-Atlantic** **transports of heat, salt, nutrients, and toxic algae to ward** **the reef tract.** Florida Bay Synthesis Hunt and Nuttle

34 FWRI Technical Report TR-11 Figure 4.3 **A verage seasonal rainfall, runoff, evaporation, and net** **freshwater gain/loss in Florida Bay (Nuttle, personal communi cation).**  Physical Processes**• Seasonal cycles in local wind forcing produce sea**  **sonal patterns in circulation pathways, connecting south Florida coastal waters through western Florida**  **Bay and transporting Everglades freshwater discharges. Southward flows through the Keys pas** **sages predominate in winter and spring, north northwestward flows in summer, and southwestward**  **flows toward the Tortugas in the fall.**

**• Seasonal cycles in south Florida coastal current sys** 

**tems provide seasonal pathways for local larval re cruitment and opportunities for recruitment from** 
**remote sources. • T**  **he south Florida coastal region is surrounded by an intense, large-scale oceanic boundary current (the** **Loop Current–Florida Current system) and its evolv ing eddies that link local coastal waters to remote up**  **stream river sources in the Gulf of Mexico.**

PREDICTION **Steady progress has been made toward developing a predictive capability for salinity and circulation changes**  **in Florida Bay and connecting coastal waters. • Tw** **o-dimensional hydrodynamic models with coarse**

**grids have been developed for Florida Bay as pilot projects by J.Wang (finite element) and J. Hammerick** **(finite difference). The results are encouraging be cause the model outputs of salinity fields are simi**  **lar to observed salinity patterns.**

**• Better estimates of surface and groundwater inflows** 

**are available from recent measurements and hy draulic-model results of the United States Geolog**  **ical Survey (USGS) and the South Florida Water Management District (SFWMD).** 

**• Improved estimates of evaporation are available** 

**from recent studies by R. Price, P. Swart, W. Nuttle, and N. Smith.**  **• I mproved estimates of precipitation patterns and** 

**quantities are available from calibrated Next Gen eration Radar (NEXRAD) measurements (P. Willis).**  **• M easurements of interior-basin circulation and ex** 

**c hange processes are available to improve under**  **standing of bay dynamics, quantify residence times, and help to validate and improve hydrodynamic**  **models (T. Lee, E. Johns,V. Kourafalou, and N. Smith). • M**  **odeling Terms of Reference (MTR) were estab**

**lished by the Physical Science Team (PST) and ap proved by the Program Management Committee**  **(PMC). • A**  **Standard Data Set has been established for model**

**use (J. Pica).**

**• An interagency, nested-model program has been** 

**formulated using regional hydrodynamic and hy drological models to provide boundary conditions**  **for the Florida Bay model (SFWMD, USGS, and the National Oceanic and Atmospheric Administration**  **[NOAA]).**


## Driving Processes

Wi nds and Storms

**W inds in south Florida, including Florida Bay, follow**  **a regular seasonal pattern: weak southeasterly winds and daily sea breezes in summer, persistent north**  **easterly winds in fall, and the regular passage of cold fronts causing moderate increases in wind speed and** **a clockwise rotation of wind direction during the win ter. During hurricane season (summer–early fall), the**  **persistent southeasterly tradewind and sea breeze pattern can be interrupted by the passage of tropical**  **storms, often resulting in substantial increases in wind speed, precipitation, and runoff, which can flow di** **rectly into the central basin. Due to the absence of sig nificant topography in south Florida, winds overall**  **are highly coherent across the bay, with the exception of locally intense convective events. Low-frequency**  **wind stress varies seasonally (Smith, 2002). Because low-frequency scatter about the monthly mean is an** **important measure of wind forcing, this seasonal vari ability is significant.** **Recent measurements indicate that there is a sig nificant response of the salinity patterns, sea level,**  **currents, and turbidity of Florida Bay and adjacent coastal waters to wind forcing associated with the pas**  **sage of even relatively weak tropical cyclones (Johns et**  **al., 2001b; Hurricane Georges Workshop report,**  **http://www.aoml.noaa.gov/flbay/hurgeocoverpage. html).**  **Based on results from several research efforts at different locations, the effect of storms on water**  **levels in the Everglades and in Florida Bay and the freshwater flow response after storms pass has been** 

**c haracterized (D. Smith, 2001; Johns**  **et al., 2001b; Smith**  **et al., 2001).**  **Mattocks (personal communication) used a version of the Advanced Regional Prediction System (ARPS)** **mesoscale atmospheric weather prediction model re configured to match South Florida Water Management** **District (SFWMD) models at a 3.2-km resolution and in cluded land use and soil types. His model shows** **mesoscale structures in wind, evaporation, and precip itation fields that are associated with land use and land**  **sea interactions, including the sea breeze. Strong, divergent downdraft outflows that occur beneath thun**  **derstorms and over the Florida Keys appear to produce their own sea-breeze convergence fronts.The different** **soil types and land uses, together with the spatial pat** Hunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 35 Physical Processes**terns in the wind fields, determine spatial patterns in the**

**ev aporation and precipitation fields over south Florida**  **and the surrounding waters, including Florida Bay. Indications are that we are entering a period of en**  **hanced Atlantic hurricane activity (Goldenberg et al.,**  **2001) and that the prior two or three decades represented a period of diminished activity.The difference apparently** **reflects a multidecadal climatic oscillation. If the as sumption is made that the probability of a tropical storm** **affecting south Florida is directly related to overall ac tivity, then Florida Bay is more likely to be affected by**  **a storm than it has been for several previous decades. Goldenberg**  **et al. (2001) suggested that this pattern is**  **likely to continue for an additional 10 to 40 years.**


### Precipitation

**South Florida in general, including Florida Bay, has pro nounced dry (winter-spring) and wet (summer-fall)**  **seasons. Nuttle et al.**  **(2000) used 31 years of historical data to show that the seasonal rainfall pattern for the** **bay as a whole is nearly balanced by bay-wide evap oration. The distribution of rainfall is highly hetero**  **geneous due to the dominance of local convective**

**ev ents, sea-breeze convergence, and to variations** **caused by urban development effects known as “de sertification”(Pielke**  **et al., 1999). However, significant** **climatic variability is possible and has been docu mented within the period of record of the ongoing**  **monitoring. T** 

**rimble et al.**  **(2001) indicated that low-frequency meteorological modes associated with ENSO and the**  **P**

**acific Decadal Oscillation can also have significant ef fects on south Florida rainfall and freshwater supply** 

**v ariability. For example, Johns**  **et al. (2001a) have shown**  **that the El Niño of 1998 reversed the seasonal rainfall pattern over south Florida, causing a winter-spring** 

**w et season and a summer-fall dry season.**  **T**

**here is excellent agreement between independent data set tests that used NEXRAD radar and rain gauges**  **(Willis, 1999). Cumulative rainfall distributions are nearly identical except for the highest rainfall rates.**  **Radar-estimated rainfall distributions provide the high resolution needed to resolve spatial patterns over** **south Florida and Florida Bay. This NEXRAD precip itation product, done on a research basis for two years,**  **has now been mapped to the SFWMD grid and is archived at SFWMD.These efforts have paved the way**  **for an operational rainfall-distribution product that can be input to atmospheric models.** 


### Evaporation

**Evaporation in marine systems is a function of air and wa**  **ter temperature differences, specific humidity, and wind speed. Although winds are highly coherent across** **the bay, ongoing studies suggest that there are signif icant spatial differences in evaporation minus precip**  **itation (E – P) (Price et al.,**  **2001). Recent estimates of**

**ev aporation in Florida Bay were derived using a vari**  **ety of independent methods and the comparison of those results is encouraging.**  **Nuttle et al.**  **(2000, 2001) estimated that bay-wide an nual evaporation, based on calibration of steady-state**  **box models that used historical salinity data for each of four regions in the bay, was 110 cm. Pratt and Smith**  **(1999) estimated annual evaporation to be 73 cm by using a Dalton Law formula. Subsequent to this study,**  **Smith (2000) refined the application of the Dalton Law approach by including the effect of increasing estimated**  **annual evaporation. On the other hand, estimates based on surrogate data differ by up to a factor of**  **three. Evaporation-pan data are available for several**
**y ears from Flamingo, a site located on the northern**  **shore of the bay. The average of these data is 210 cm/year (National Climatic Data Center, http://www.**  **ncdc.noaa.gov), which appears to be too high to accept directly as an estimate of evaporation in the bay.** **A distinct seasonal cycle underlies the mean an nual water loss, with a maximum in late summer and**  **a minimum in mid winter. Calculations using the Long Ke** **y C-MAN data in bulk aerodynamic formulas indi cate average evaporative water losses of approximately** **0.7 cm/day in September and October and approxi mately 0.3 cm/day in December and January. Unpub**  **lished data from this 15-month study (N. Smith, personal communication) indicate a mean daily evap**  **orative water loss of 0.5 cm and a total annual water loss of approximately 180 cm.Therefore, reliable evapora**  **tion estimates appear to be converging upon the 75–180 cm/year range, but more research is required to con**  **firm this amount.**


### Surface-Water Input

**A significant amount of surface water enters Florida Bay directly only along its northern boundary with the**  **southern Everglades and is concentrated at present in the northeastern region. Fresh water occasionally en**  **ters the central bay directly if there is enough rain. For example, during and after Hurricane Irene, fresh water** **from the Everglades was able to flow over the Button**

**w ood Embankment (Johns**  **et al., 2001a).**  **F reshwater runoff enters principally through nat** **ural channels cut through the mangrove and button**

**w ood-confining berms (Hittle, 2001; Hittle**  **et al., 2001).** **USGS measurements indicate that Trout Creek con tributes the largest annual discharge of fresh water into**  Florida Bay Synthesis Hunt and Nuttle

36 FWRI Technical Report TR-11 Physical Processes**northeastern Florida Bay, varying from about 110,000 to 190,000 acre-ft/yr (4.3 m**  **3 /s to 7.4 m**  **3 /s). By contrast,**  **the annual discharge from each of the other eight creeks varies between 10,000 and 45,000 acre-ft/yr (0.4** 

**m 3**  **/s to 1.8 m 3**  **/s). Negative flows over the mangrove em bankments can be caused by storm events, and net neg**  **ative monthly average flow, which usually lasts for several months, occurs in all creeks during every dry**  **season represented by the data. Cable**  **et al. (2001) reported on the relationship be** **tween precipitation and inflow into Florida Bay, find ing that fall and winter storms cause pulses of** **freshwater inflow, with the flow in Taylor Creek show ing a marked response to the storms. Typically, water**  **levels in the Everglades were found to be highest in early fall and lowest in the winter. Tropical storms**  **cause the water levels in the Everglades and Taylor Slough to rise relatively rapidly and then recede slowly**  **after the storms pass. The water level’s rise is on the order of hours, whereas the fall is on the order of** 

**w eeks. During the winter, northeasterly winds drive** 

**w ater out of Taylor Creek into Florida Bay.** **Stable isotopic markers have identified the prin cipal sources of fresh water in various regions of the** **bay (Swart and Price, 2001). Freshwater inputs to north eastern Florida Bay are dominated by contributions**  **from Everglades runoff. Rainfall has a strong signal in the west, and both rainfall and runoff provide fresh** 

**w ater to the central portion of the bay.**  **Surface freshwater inputs from the rivers of the southwestern coast of Florida (primarily the Broad,**  **Harney, and Shark rivers) may also be significant to Florida Bay, particularly in its western region. Levesque**  **and Patino (2001) reported measurements of water level, velocity, specific conductance, and temperature**  **in each of these three rivers during the calendar year 1999. Discharges from the three rivers are influenced**  **by the semidiurnal tides, wind, and freshwater flows**  **from the watershed. All three rivers are well mixed, with**

**v ery little vertical gradient except near the coastal**  **front.The only evidence of stratified, bidirectional flow is around the time of slack tide. Instantaneous dis** 

**c harges ranged from –2,400 to +3,500 cfs (–68 to +99** 

**m 3**  **/s) in the Broad River, –15,600 to +12,900 cfs (–442 to +365 m**  **3 /s) in the Harney River, and –10,100 to +10,500**  **(–286 to +247 m 3**  **/s) in the Shark River. When tidal ef fects have been filtered from the data, the residual**  **flows ranged from –900 to +2,500 cfs (–25 to +71 m 3**  **/s), –3,600 to +5,700 cfs (–102 to 161 m**  **3 /s), and –2,300 to**  **+4,400 cfs (–65 to +124 m 3**  **/s) for the Broad, Harney, and Shark rivers, respectively. Mean annual residual**  **discharge values have been reported to be 400 cfs (11**

**m 3**  **/s or 284,000 acre ft/year) for Broad River, 440 cfs (12.4**

**m 3**  **/s or 320,000 acre ft/year) for Shark River, and 470 cfs (13.3 m**  **3 /s or 343,000 acre ft/year) for Harney River**  **(Levesque and Patino, 2001).**


### Groundwater Input

**Anecdotal or historical information suggests that prior to water management, groundwater inputs to south**  **Florida estuaries like Biscayne Bay and Florida Bay**

**w ere significant. At present, because of lowered water**  **tables and the intrusion of seawater into the coastal aquifer, fresh groundwater may be prevented from** **discharging directly into Florida Bay. However, ground**

**w ater may be passing from the Floridan aquifer into**  **the surficial aquifer and then into Florida Bay. Because the Floridan aquifer is saline, the discharging ground** 

**w ater would be saline, not fresh. This hypothesis is** **supported by geophysical measurements in the south ern portions of Everglades National Park (ENP) be**  **tween Flamingo and U.S. 1 that indicate that the aquifer is saltwater-saturated from the surface to a depth of at**  **least 15 m (Fitterman et al.,**  **1999; Fitterman and Deszcz P** 

**an, 2000, 2002). Results from the integrated surface groundwater model of the southern Everglades suggest**  **that groundwater seepage beneath the Buttonwood Embankment may be allowing brackish water from the**  **Everglades to discharge into northeastern Florida Bay (Langevin**  **et al., 2002). Model results suggest that sur**  **face water can be impounded on the north side of the embankment, creating a hydraulic drive for ground** 

**wa ter discharge into Florida Bay. However, data are**  **lacking to support these model results. V** 

**osburg et al.**  **(2001) reported on surface water and groundwater measurements taken at two locations in**  **the dwarf mangrove wetlands along Taylor Creek near its mouth at Florida Bay. The water level of surface** 

**w ater and groundwater were measured at both sites.**  **Surface-water levels demonstrated a relatively rapid response to rainfall, runoff, tide, and wind, whereas the**  **groundwater response was less rapid. However, groundwater response times were different at each** **site, which was attributed by the authors to the differ ences in sediment type.** **Price and Swart (2001) provided recent additional in formation about the role of groundwater in the hydro**  **logic regime of Florida Bay and the adjacent areas of the Everglades. The extent of saltwater intrusion into the**  **surficial aquifer increases from east to west, extending about 6 km inland along the C-111 canal basin to about**  **20–28 km inland at Shark River Slough (Fitterman and Deszcz-Pan,2000,2001).Groundwater may be discharged**  **into the overlying surface waters of the Everglades within this strip, which more or less parallels the coastline. An**  **empirical calculation of groundwater discharge yields**

**v alues of about 0.04–0.175 cm** **3 /day.**  Hunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 37 Physical Processes**T op and Brand (2001) also recently studied ground** 

**w ater in Florida Bay. They used anomalies in the dis**  **solved helium concentrations in groundwater to estimate groundwater inputs to Florida Bay.These au**  **thors used a box model to estimate that the input of groundwater to Florida Bay was 2.5–4.0 cm/day in the**  **summer and 10–16 cm/day in the winter. Radon-data estimates yielded a groundwater flux of 0.8–1.7 cm/day.**  **According to Top and Brand (2001), saline water from the Florida aquifer is under artesian pressure and is ris**  **ing through breaks in the confining layer, where it mixes with the shallow aquifer before entering Florida** **Bay.This two-layer structure of the aquifer system ex plains the difference between the helium and radon**  **flux estimates. Note that the radio-isotope values convert to hy**  **pothesized groundwater inflows of 575 to 3,680 m 3**  **/s. Based on these results, if true, groundwater would ap**  **pear to be a significant source of saline water to Florida Bay. However, these estimates have large differences** **and appear to conflict with mass-balance water-bud get estimates and the observed large seasonal salinity** 

**va riations.** 



### Sea Level and Tides

**Sea level variability in Florida Bay is controlled by wind and tidal forcing, strongly modified by topogra**  **phy and coastline (Wang et al.,**  **1994). Regional sea level is thought to have risen rapidly in the last century**  **(Maul and Martin, 1993; see also the Key West sea level record from 1913 to present, available from the Na** **tional Climatic Data Center [NCDC]), but the impli cations of that observation are not addressed here.**  **Differences in sea level between basins and across tidal passages can be a dominant factor controlling**  **flow and renewal of bay waters.The diurnal tide of the Gulf of Mexico combined with the semidiurnal tide of**  **the Atlantic results in a mixed tide.This results in the largest tidal ranges south of Savannah, Georgia, for the**  **region near the mouth of the Shark River (>2 m at spring tide). Measurements at East Cape indicate a**  **mean tidal range of only 75 cm. The mean range is half that at the southern end of the western boundary,**  **just north of Marathon. However, the tide entering the interior part of the bay is strongly damped by the**  **shoals and mud flats, decreasing the range to just a few cm in the northeast (Smith, 1997).**  **Smith (1997) also reported upon spatial patterns of tidal water-level fluctuations in the interior portion of**  **Florida Bay and the seasonal pattern of water-level fluctuations at subtidal frequencies. Wind set-ups of** **10–30 cm are observed inside the bay, but the basin-to basin variations in wind forcing are not well understood**  **at present. An annual change in sea level of about 30 cm is widespread over the western North Atlantic and**  **extends into the interior of the bay as well.**


### Boundary Currents

**T he Loop Current in the Gulf of Mexico and its exten**  **sion, the Florida Current in the Atlantic, surround the south Florida coastal waters and the Keys. Both are part**  **of the Gulf Stream system, which is one of the strongest and best-studied western boundary currents. Both cur** **rents are complex and can generate eddies and mean ders that can affect how the currents interact with Florida** **Bay.Together these oceanic currents cause sea level dif ferences across the Keys that can drive flows through** 

**w estern Florida Bay. Lee and Smith (2002) recently**  **showed that changes in sea-level slopes across the Keys are a direct response to tide and wind forcing. They** **have suggested a longer period response to Loop Cur rent extensions into the Gulf of Mexico. Wind forcing**  **affects sea level differently on the Atlantic and gulf sides of the Keys, causing sea-level slopes that can en** **hance the exchanges of bay waters with the surround ing regions. The boundary currents and their induced** **flows along western Florida Bay can transport river wa ters and/or algal blooms from remote regions to inter**  **act with the bay (Lee et al.,**  **2001, 2002).** 

## Influence of Driving Processes
Salinity

**Florida Bay ’s**  **salinity varies with time on a wide range of scales. Bay salinity normally reflects the annual wet**  **and dry seasons driven by regional precipitation and temperature patterns but also responds to episodic**  **meteorological events such as tropical storms and cold fronts. In addition, Florida Bay salinities are influenced**  **by interannual El Niño/La Niña cycles and by decadal** 

**v ariability in precipitation driven by Atlantic Ocean**  **multidecadal forcing. Variability on all of these time scales (and even longer scales, the causes of which are** **completely unknown) can be seen in historical salin ity and “salinity proxy”(**  **i.e., paleoecological) data.**  **A preliminary analysis of historical data from the Salinity Synthesis database (Robblee**  **et al., 2001) shows**  **that for the past few decades, the bay has behaved as a marine lagoon, with salinities as high as 70 psu re** **ported on a few occasions in central Florida Bay. Dur ing drought years, salinity typically exceeds 40 psu** 

**ov er most of the bay. Estuarine (**  **i.e., mesohaline) con**  **ditions are rare in recent history and are associated with episodic events such as hurricanes and tropical storms**  **or with other periods of above-average rainfall ( e.g.,**  Florida Bay Synthesis Hunt and Nuttle

38 FWRI Technical Report TR-11 Physical Processes**1994–1995). Increased water releases from the C-111 canal can also lower salinities across the bay during rel**  **atively dry years ( e.g.,**  **1983–1985). Salinity variability is greatest in the northeast and**  **decreases to the west. Boyer et al.**  **(1997) and Boyer and Jones (2001) have described a decadal trend in** **monthly salinity values collected by Florida Interna tional University’s (FIU) Southeast Environmental Re**  **search Center (SERC) in Florida Bay from 1989 to 1999. During that decade, salinity in the eastern, central,**  **and western regions declined by 13.6, 11.6, and 5.6 psu, respectively.This “trend”was due largely to very**  **high salinities during the 1989–1990 drought and is not descriptive of the substantial interannual vari**  **ability of salinities in the bay. For example, following the wet period of 1994–1995, salinity increased until**  **tropical storms in 1999 induced a decrease, and data from the drought years of 2000 and 2001 indicated that**  **salinities increased again. More recent data from 2002 and early 2003 indicate another general freshening**  **trend (see South Florida Program (SFP) Web site at www.aoml.noaa.gov/SFP for monthly survey maps of**  **salinity posted by NOAA’s Atlantic Oceanographic and Meteorological Laboratory [AOML] and the Uni** 

**v ersity of Miami’s [UM] Rosenstiel School of Marine**  **and Atmospheric Science [RSMAS]).**

WINDS AND STORMS**In combination with upstream water-management re leases (that are due to flood-control restrictions), storms** **can affect salinity by causing pulsed freshwater in flows even in the “dry” season. Tropical storms can**  **cause Everglades water levels to rise rapidly and then recede slowly as fresh water seeps down into north**  **eastern Florida Bay. Northeasterly winds drive fresh**

**w ater out of the Everglades into Florida Bay. Biogeo** 

**c hemical materials in these freshwater flows follow**  **similar input patterns (Cable et al.,**  **2001). Higher-salin ity water moves from Florida Bay into the mangrove**  **fringe area for several months during the dry season in typical years.**  **Along the southwestern coast of the Everglades, river discharge is affected by tidal forces, but tidal-forc**  **ing effects can be masked by storm events (Levesque and Patino, 2001).Wind-driven flows can redirect low** **salinity plumes from discharges in the western Ever glades into western Florida Bay and the Keys.**  **Wi nd-driven currents tend to advect water masses**  **and realign salinity patterns in the direction of the flow, causing low-salinity bands of river discharge and**  **subsequent transport to connecting regions (Johns et**  **al., 2001b). At present, the extent to which these plumes**  **exchange with the interior waters of Florida Bay is unclear.**  **During the past several years, a number of tropi cal cyclones have influenced the south Florida region**  **through intense wind forcing, rainfall, or both. Johns et al.**  **(2001b), D. Smith (2001), and R. Smith et al.**  **(2001) recently showed that, although not as intense as in** **past periods of cyclone activity, these events caused sig nificant and long-lasting (~months) changes in salin**  **ity patterns and turbidity in Florida Bay.**

PRECIPITATION AND EVAPORATION **Florida Bay salinity patterns are a function of spatial and temporal patterns in precipitation, evaporation,** **runoff, and exchange with the gulf and Atlantic. Evap oration and precipitation are the two largest compo**  **nents of the Florida Bay water budget, but we lack good spatial resolution for them.Their respective pos**  **itive and negative effects upon salinity are addressed under Driving Processes, above. Interannual varia**  **tions in salinity appeared to be affected primarily by fluctuations in rainfall, which not only falls directly into**  **the bay but also results in variations in the volume of surface water discharged into Florida Bay from the**  **southern Everglades. An annual water budget for Florida Bay has been**  **constructed using 31 years of salinity, hydrological, and climate data (Nuttle**  **et al., 2000, 2001). A simula**  **tion using a calibrated box model in which runoff was doubled decreased salinity in the eastern bay, in** **creased variability in the southern bay, but had no ef fect in the central or western regions of the bay. During**  **1965–1995, annual runoff from the Everglades was one fifth of the annual direct rainfall into the bay, and an**  **nual evaporation slightly exceeded annual rainfall. On a seasonal basis, rainfall, evaporation, and runoff** 

**we re not in phase, leading to a strong seasonal pattern**  **of salinity in the bay.**

SURFACE–WATER INPUTS **Surface discharges from Trout Creek and Taylor Slough significantly affect salinity patterns and variability in** **northeastern Florida Bay, where minimum salinity oc curs near river mouths and strong gradients occur in**  **the basin. In the fall, when sea level is relatively high, interbasin exchange is enhanced, resulting in more**  **surface fresh water reaching the central basin. The same can occur directly during tropical storms if the** 

**w ater table is sufficiently high (see Hurricane Georges**  **W orkshop report available at http://www.aoml.** **noaa.gov/flbay/hurgeocoverpage.html). Enhanced ex**

**c hange and tropical storms help reduce hypersalinity**  **in the bay’s interior. River discharges, from sources both remote from and local to Florida Bay can be trans**  **ported by coastal and boundary currents to different parts of the south Florida ecosystem for mixing and ex**  Hunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 39 Physical Processes**c hange. Under appropriate wind conditions, flow from**  **rivers along the southwestern Florida coastline can reduce salinities along the perimeter of the interior bay** **and perhaps into its westernmost basins. Clear exam ples are the transport of the Shark River plume to** 

**w estern Florida Bay to help buffer salinity in that re**  **gion (Lee et al.,**  **2001, 2002) and the transport of Mis sissippi River waters to the Florida Keys (Ortner**  **et al., 1995). Exchange of surface water discharged into the** 

**w estern bay with adjacent interior basins is not well** **understood at present, and new observations are un derway to better resolve these processes.** 

GROUNDWATER INPUTS **No large-scale effects of groundwater on salinity have been observed. Observing this input is made more**  **difficult by the fact that the primary groundwater input is thought to be saline. However, anecdotal evidence**  **indicates the existence of local springs, and scientists in nearby Biscayne Bay have observed similar springs,**  **at least within a few hundred meters of the shoreline (J. Proni, personal communication).** 

SEA LEVEL AND TIDES **At times of high sea level in the fall, especially during and after tropical storms, overland flow can occur di** **rectly into the central basin, thereby reducing hyper salinity (see above). On the other hand, low sea level** **can restrict exchange between adjacent basins by min imizing overbank exchange. Runoff to central Florida**  **Bay is probably more common in the fall tropical storm season, when annual water levels are relatively high,**  **but could occur at any time of the year. Higher water levels may facilitate movement of this fresh water**  **across banks to the south and west. However, seasonal or wind-induced high water along the northern bound** **ary may also hinder freshwater flow to the bay by re ducing the head gradient.** 

BOUNDARY CURRENTS **Ortner et al.**  **(1995) and Lee et al.**  **(2001, 2002) have clearly shown that fresh water from remote sources in**  **the eastern Gulf of Mexico, transported by boundary currents, can have a significant effect on the salinity pat**  **terns in south Florida coastal waters, including the**

**w esternmost regions of Florida Bay. Boundary cur**  **rents surrounding south Florida coastal waters can also change sea-level slopes and gulf-Atlantic flows**  **through western Florida Bay that enhance bay-water exchange with adjacent waters.** 



### Circulation

**T he interior portion of Florida Bay is made up of a**  **complex maze of shallow basins separated by mud banks and mangrove islands. The bay is openly con**  **nected to the southwestern Florida shelf along its wide**

**w estern boundary, but exchange with the Atlantic**  **coastal zone of the Keys is restricted to a few narrow tidal channels through the Keys island chain. The** **northern boundary is mangrove fringed, with fresh**

**w ater input in the northeastern region through Taylor**  **Slough and Trout River.The rapid fall-off of tidal range with distance from the western boundary and the dra**  **matic increases in salinities observed in the interior basins indicate poor water exchange between the** **northeastern and central portions of the bay with ad jacent subregions.**  **T he entire south Florida coastal ecosystem, except**  **for the interior of Florida Bay, is highly connected by a regional recirculation system.This regional circula** **tion is driven by the combined forcing of winds, sea level slopes, oceanic currents such as the Florida**  **Current and Loop Current, and eddies at the offshore boundaries (Lee and Williams, 1999; Lee**  **et al., 1999,** **2002). Seasonal patterns in wind forcing result in sea sonal shifts in the regional circulation system and pre**  **ferred pathways of exchange between waters of the southwestern Florida shelf (including the nearshore** 

**w aters of the southwestern Everglades and western**  **Florida Bay) and the waters of the Keys Atlantic coastal zone. Everglades discharges are typically advected**  **southeastward along the western boundary of Florida Bay’s interior and through the channels of the middle**  **Ke ys to the reef tract in the winter and spring. They** **move toward the Dry Tortugas in the fall and north**

**w estward to the west Florida shelf in the summer, fol**  **lowed by entrainment by the Loop Current and return to the Keys coastal zone (Lee**  **et al., 2002). Advective time**  **scales to reach the Keys Atlantic coastal waters range from one to two months in winter, spring, and fall to**  **as much as six months in the summer.**

WINDS AND STORMS **Coherent mesoscale and synoptic-scale wind forcing causes alongshore barotropic currents, which are** **geostrophically balanced by coastal sea level on ei ther side of the Keys, and cross-Key sea-level slopes that**  **drive exchange of Atlantic water with Florida Bay water on daily to weekly time scales. A strong alongshore-cur**  **rent response to alongshore wind forcing was found for the Keys Atlantic coastal zone (Lee and Williams,**  **1999) and for the southwestern Florida shelf (Lee et al.,**  **2002) for synoptic-scale and seasonal-scale winds.The seasonal pattern of the wind forcing results in sea**  **sonal circulation patterns that link the south Florida coastal waters along the western boundary of interior**  **Florida Bay (Lee et al.,**  **2002): southward gulf-to-At** Florida Bay Synthesis Hunt and Nuttle

40 FWRI Technical Report TR-11 Physical Processes**lantic flows in winter and spring, northwestward flows to the gulf in summer, and southwestward flows toward** **the Dry Tortugas in fall.This pattern is clearly demon strated in the trajectory pathways of Lagrangian drifters**  **that have been regularly released over the past few**
**y ears (Figure 4.4).**  **Mean cross-shelf flows on the southwestern shelf and along the western boundary of interior Florida** **Bay indicate an estuarine-like circulation. Estuarine like circulation has offshore flow in the upper layer and**  **onshore flow in the lower layer, suggesting a response to prevailing eastward winds and buoyancy-forcing** **from freshwater discharges through the western Ever glades.**  **T he transient effect that storms have on circulation**  **depends upon wind strength, direction, and duration. Large increases in current speeds have been observed**  **in western Florida Bay and along the southwestern Florida shelf and the Keys coastal zone with the pas**  **sage of tropical storms (Johns et al.,**  **2001b).**

PRECIPITATION **Precipitation has not been observed to have any direct effects upon circulation.** 

EVAPORATION**Evaporation has also not been observed to have any di rect effects upon circulation. However, some anti-es**  **tuarine flow (flow toward areas with high rates of**

**ev aporation) presumably results from net evapora**  **tion during the dry season.**

SURFACE–WATER INPUTS **Surface-water inputs through the small rivers of the** Hunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 41 Figure 4.4 **Representative seasonal trajectories of satellite-tracked surface drifters (Lee et al.,**  **2002).** Physical Processes**w estern Everglades tend to form a low-salinity band in** **the nearshore waters that is entrained by coastal cur rents and transported to western Florida Bay and the**  **Ke ys (Johns**  **et al., 2001a). This is a passive response to**  **existing circulation. The amount of buoyancy-forcing from these small rivers (5–30 m**  **3 /s) appears to be in**  **sufficient to produce a dynamic coastal current within the low-salinity plume. Salinity observations do indi**  **cate that freshwater discharges to the northeastern bay tend to move slowly to the south and west and can**  **serve as a passive tracer of the bay’s interior circulation.**

GROUNDWATER INPUTS **Isotope-derived estimates of groundwater inputs to Florida Bay vary by several orders of magnitude (see**  **above under Driving Processes). Efforts are underway by** **USGS and SFWMD to resolve this discrepancy by applying improved hydrological models. Ground** 

**w ater-forcing is not included in present bay hydro**  **d**

**ynamic or water-budget models. It does not appear necessary for conservation of mass or for simulation**  **of large seasonal salinity cycles. The between-basin flows that would result from the higher estimates are** **also inconsistent with available intrabasin flow ob servations.** 

SEA LEVEL AND TIDES **W ater movements occur on time scales ranging from** **minutes to seasons to years. Tidal currents often ac count for a large part of the variation in coastal currents**  **and are important for local mixing and dispersion of materials. However, because of the regular reversal** **of tidal currents, they are not efficient transport mech anisms over distances larger than a few kilometers. In**  **the interior of the bay, cross-bank sea-level slopes are believed to have an important influence on driving**  **flows between basins and ultimately on residence times. Subtidal or low-frequency currents, driven by**  **sea-level slopes caused by wind or offshore boundary currents, are principally responsible for linking adja** **cent as well as remote regions to south Florida ecosys tems. Cross-Key sea-level slopes drive flows through** **the Keys tidal passages at tidal and subtidal frequen cies that couple the gulf and Atlantic coastal regions**  **of south Florida (Lee and Smith, 2002).**

BOUNDARY CURRENTS**Although boundary currents are the dominant fea ture of the regional circulation, their effect is indirect** **within Florida Bay. Long-term moored current obser**

**v ations indicate a mean southward flow on the south** 

**w estern Florida shelf that can transport eastern gulf** 

**w aters, including river discharges from the west Florida**  **shelf and Mississippi River to the Dry Tortugas and through western Florida Bay to the Keys coastal zone**  **(Lee et al.,**  **2002).The origin of the mean flow is not clear, but the position of the Loop Current appears to influ**  **ence mean flow magnitude and may be the driving force.To more fully understand the relevant processes**  **will depend upon rigorous, calibrated regional model simulations incorporating field observations and satel**  **lite data.**


### Exchanges with Adjacent Waters

**Exchanges with adjacent waters are related to three of the driving forces that have been discussed above,**  **specifically winds and storms, sea level, and boundary currents. Waters of the interior portion of Florida Bay** **interact with waters from two very different conti nental shelves: the wide, north-south-oriented south** 

**w estern Florida shelf to the west and the narrow,**  **curving Keys coastal zone and its shallow, reef-tract topography to the east and south.These two shelf re**  **gions exchange waters with each other through the tidal**

**c hannels between the Keys and with the strong oceanic**  **currents at their outer edges: the Loop Current in the Gulf of Mexico and the Florida Current on the At**  **lantic side of the Keys.There is strong interaction with the Florida Current by way of eddy processes through**  **out the Keys shelf domain. It is apparent by looking at satellite imagery, water-property distributions, and**  **model results that a similar process occurs along the outer edge of the southwestern Florida shelf. Recent**  **drifter trajectories (Yang, 1999) indicate that there is a discontinuity between midshelf waters in the region** **offshore of Tampa Bay that is possibly related to the am plitude of river discharge.** **Current measurements by N. Smith (2002) in sev eral channels connecting interior subbasins of Florida**  **Bay, suggest a generally southward motion of waters from the north-central region of the bay that seem to** **diverge toward the Atlantic and gulf in the southeast ern region of the bay. Exchange between basins appears**  **to be strongly influenced by wind direction as well as magnitude. Little is known about the physical processes**  **that regulate water renewal in the bay’s interior or about the preferred pathways of circulation.** **Mean flows through the western boundary of in terior Florida Bay (between East Cape and Marathon)**  **have been roughly estimated from long-term current observations to indicate an inflow (eastward) of about**  **1,300 m 3**  **/s in the northern portion and an outflow (westward) of about 300 m**  **3 /s in the southern region,**  **giving a net inflow across the section of about 1,000 m 3**  **/s (Smith and Pitts, 2002; N. Smith, 2002). Because 400–500** 

**m 3**  **/s of this inflow exits southward through the mid dle Keys passages, approximately 500–600 m**  **3 /s are**  Florida Bay Synthesis Hunt and Nuttle

42 FWRI Technical Report TR-11 Physical Processes**av ailable for transport into interior regions of Florida**  **Bay. Tidal, subtidal, and long-term transports into Florida Bay are neither well resolved nor understood.**  **It is also unclear what portion of the net inflows to the Florida Bay interior are used to balance mean sea level**  **rise, account for evaporative water losses, or drive residual circulation. Observations have also quantified** **tidal-period transports (N. Smith, 2002). To some de gree, mixing during tidal exchanges must import gulf**  **and Atlantic water into Florida Bay and export bay**

**w ater to the gulf and to Hawk Channel. Further ob**  **servations and calibrated model simulations are needed before the net exchange resulting from this**  **process can be quantified.**

WINDS AND STORMS **W ind forcing was found to set up cross-Key sea-level**  **slopes that can drive large flows into or out of western Florida Bay (Lee and Smith, 2002). Strong easterly and**  **northeasterly winds during the fall cause a positive cross-Key slope and consequently inflow to the bay**  **from the Atlantic. Gulf-to-Atlantic outflows from the bay are associated with negative cross-Key sea-level**  **slopes from southeasterly (summer), westerly (winter), and northerly (spring) winds.Wind-driven exchanges**  **through the middle Keys can produce net flows of 1,000–2,000 m**  **3 /s over the duration of the event (typi** **cally 1–10 days) for Long Key Channel alone and pos sibly two to four times this amount of net flow for all**  **of the middle Keys channels. Recent current measurements in the main shipping** 

**c hannel at Key West indicate a net northward flow** **into the gulf that appears to be related to the prevail ing westward winds and suggests an Ekman response**  **in the Keys coastal zone (Smith and Pitts, 2002). The magnitude of this flow has not yet been determined.**  **However, when combined with the gulf-to-Atlantic flows in the middle Keys, this information provides an**  **indication of a possible clockwise recirculation around the lower Keys.**  **Subtidal transports through passages in the upper Ke** **ys are much weaker than the middle Keys and ap pear to be highly influenced by onshore or offshore**  **winds that may cause a set-down or set-up of water level in northeastern Florida Bay (N. Smith, 2001).** 

SEA LEVEL AND TIDES **It is clear that the volume transports through the Keys passages are produced by cross-Key sea-level slopes** **and that low-frequency changes are strongly depen dent on wind forcing over the dynamically different**  **shelf regimes on either side of the Keys.The strongest flows occur in the middle Keys channels, where the**  **combined subtidal outflows toward the reef tract can be as high as 7,000 m**  **3 /s during winter cold-front pas**  **sages, and inflows to western Florida Bay can reach 2,800 m**  **3 /s during fall northeast-wind events.The mag**  **nitude of these flows is 100–200 times larger than the total freshwater inflows to Florida Bay.The mean flow**  **through the middle Keys passages is estimated to be approximately 800 ± 100 m**  **3 /s toward the reef tract**  **(Figure 4.5).The cause of the mean flow is uncertain but appears to be related to the mean sea level difference**  **between the gulf and Atlantic and may be influenced by**  **the Loop Current position. A series of investigations by**  **N. Smith (1998), Smith and Lee (2003), Lee and Smith (2002), Smith and Pitts (2002), and N. Smith**  **(2001) have quantified the magnitudes and variability of the inflows and outflows of Florida Bay through the**  **Ke ys tidal passes and across the western boundary in**  **the gulf transition region.**

BOUNDARY CURRENTS **Boundary currents provide the coupling of the gulf and Atlantic through western Florida Bay via sea level dif**  **ferences and along the seaward edges of the gulf and Atlantic shelves through eddy and wind-driven ex** 

**c hanges (Lee**  **et al., 2001, 2002). Boundary currents can**  **transport remote waters, including river discharges, to near the bay. Eddies shed by these currents and related**  **d**

**ynamic mesoscale features can enhance exchange between the currents and adjacent shelf regions. Con** **tinued monitoring and modeling of boundary cur rents and their relationship to local circulation and**  **exchange processes is essential.**



## Prediction

**Observational data alone are not sufficient to predict salinity patterns, circulation, freshwater input, and ex**  **ch anges with adjacent waters under different restora**  **tion and climatic scenarios. Because of the physical complexities of the bay, these data need to be com**  **plemented by calibrated models, a number of which are listed below.** 



### Fresh Water Inflow

**To predict salinity, hydrological models that can pro**  **vide estimated runoff at the hydrodynamic model’s terrestrial boundary are essential.The freshwater-dis** 

**c harge model must also be able to estimate runoff** **under various Comprehensive Everglades Restora tion Plan (CERP) alternatives.The USGS has developed**  **a hydrodynamic transport model to simulate water flow and salt fluxes through connected surface and** **groundwater systems. An algorithm has been devel oped that synchronizes surface-water tidal-compati**  Hunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 43 Physical Processes**ble time steps with groundwater stress periods and that assures mass conservation of simulated flux quantities** **across the surface-groundwater interface and land surface boundary in the coupled model (Swain and**  **Langevin, 2001; Swain et al.,**  **2002). Hydraulic expres sions derived from studies of hydrologic processes in** **the Everglades have been formulated to link flow re sistance, wind stress, and evapotranspiration processes**  **to the vegetation properties and shallow flows typical of these low-gradient wetlands. Two applications of**  **the coupled model have been made that are largely within the confines of ENP (Figure 4.6).The Southern** **Inland and Coastal Systems (SICS) model encom passes the Taylor Slough wetlands, part of the C-111**  **drainage basin, and subtidal embayments along the northern coastline of Florida Bay.The Tides and Inflows**  **in the Mangrove Ecotone (TIME) model encompasses the SICS model domain, Shark River Slough, other** 

**w estern sloughs, and subtidal embayments and tidal**  **creeks along the southwestern gulf coast. Measured surface-water discharges, water levels, and salt con**  **centrations in tidal creeks; wetland water levels and flow velocities; groundwater heads and salinities sup** **plemented by subsurface salinity maps; and soil prop erties are used for model calibration and verification.**  **T**

**ide levels and salt concentrations along the coast and discharges and water levels at hydraulic control struc**  **tures, bridges, and culverts are used to drive the SICS and TIME simulations. The models simulate flow ex** 

**c hanges and saltwater fluxes between the surface and**  **groundwater systems in response to these multiple driving forces, which could be altered based on pro** **posed changes to the system. Insight into flow pat terns and salt fluxes, which can be obtained only**  **through hydrodynamic transport models, is needed to fully evaluate the potential effect of restoration deci** **sions for the greater Everglades on ecologically sensi tive, land-margin ecosystems bordering the northern**  **coastline of Florida Bay and the southwestern gulf coast of Everglades National Park.**  Florida Bay Synthesis Hunt and Nuttle

44 FWRI Technical Report TR-11 Figure 4.5 **A verage sub-tidal flow through the middle Keys passages (Lee and Smith, 2002).**  Physical Processes

### Exchanges with Adjacent Waters

**T**

**he predictions needed from Florida Bay numerical cir culation models can be carried out only with suitable** **inputs along their boundaries. These inputs are nec essary to introduce the complex interactions that dom**  **inate circulation and water exchange between the shallow bay interior and the adjacent shelf and oceanic**  **flows.The boundary conditions must cover a range of time scales to accommodate different types of simu**  **lations planned by the inner Florida Bay modeling teams (interannual, seasonal, and event-oriented sim**  **ulations). Existing global models are not suitable for this task because of their coarse resolution and the lack of** **flexibility in performing simulations that match cur rently planned and future Florida Bay modeling ac**  **tivities. Therefore, it is necessary to develop a regional-scale model that will perform simulations** **that are closely linked to interior Florida Bay model ing needs.The regional model must be dedicated to the** **computation of the required hydrodynamic fields sur rounding the Florida Bay model domain and to the cal**  **ibration of these fields with observational data. Such a model, currently under development, applies the** **three-dimensional, finite-difference community hy drodynamic model HYCOM (Hybrid Coordinate**  Hunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 45 Figure 4.6 **South Florida satellite image showing SICS and TIME model domains (USGS).** Physical Processes**Ocean Model, http://oceanmodeling.rsmas.miami.edu/ h** 

**ycom/) to the coastal waters adjacent to Florida Bay and the Florida Keys, including the Florida Straits, the** 

**w estern Gulf of Mexico and the southwestern Florida**  **Shelf (Figure 4.7).This model is being coupled with an existing large-scale, coarse-resolution application of**  **HYCOM that includes the North Atlantic, the Gulf of Mexico, and the Caribbean.This nested approach en**  **sures the interaction of Florida Bay models with the Loop Current, Florida Current and related eddies, and**  **remote sources of river-induced low salinity.** 

### Circulation Models

**To understand circulation and exchange within the**  **interior of Florida Bay, a fully calibrated and verified circulation model is needed.The growing database of**  **salinity, currents, volume transports, surface and groundwater inputs, and atmospheric forcing is rapidly** **becoming sufficient to provide comprehensive evalu ation and validation of circulation models.To this end,**  **a Standard Data Set has been agreed upon and is under development (J. Pica, personal communication).**  Florida Bay Synthesis Hunt and Nuttle

46 FWRI Technical Report TR-11 Figure 4.7 **A nested-model approach. Planned regional south Florida model area (thick solid line). Thick dashed line marks the Florida Bay and Florida Keys model area.The oceanic waters surrounding the regional model domain are included within the University of**  **Miami’s large-scale North Atlantic, Caribbean, and Gulf of Mexico model (HYCOM).**  Physical Processes**Indeed, the complexities of Florida Bay demand a suit able modeling approach to properly evaluate possible**  **future water delivery schemes to the bay. Expertise and modeling resources are available that can be ap** **plied to this problem in a reasonable time frame. How**

**ev er, two particular problems need to be addressed**  **urgently: (1) the bathymetry, which is not currently**

**av ailable at the detail needed by the models; and (2)**  **the appropriate inputs at the boundaries of Florida Bay models need to incorporate the complex interac**  **tions between the shallow coastal areas within Florida Bay and the adjacent oceanic flows.**  **Both the bathymetry and the boundary conditions must be part of an integrated modeling approach that**  **includes parallel, coupled numerical simulations in Florida Bay and the adjacent seas.This comprehensive**  **modeling tool must get underway soon to correspond with the observational programs and to advise man**  **agement in a timely manner.**


### Salinity Models

**To understand and predict salinity variability in Florida** **Bay, three types of models have been applied: statis tical (regression analyses), mass-balance, and mecha**  **nistic, the last of which will be discussed below under Unresolved Questions and Ongoing Research, Hy**  **drodynamic Models.**

STATISTICAL MODELS **T he PST subgroup evaluating salinity performance**  **measures recommended a two-phase plan to develop updated salinity performance measures to predict** **freshwater runoff. First, a multivariable linear regres sion model that uses lagged terms should be con**  **structed. Second, a time-series model relating the freshwater flows from the operation of the C-111 canal**  **to the salinity of the nearshore embayments should be prepared for use in management decisions. A follow**  **up meeting of the group recommended that the use of Seasonal, Autoregressive, Integrated Moving Average** **(SARIMA) models be explored. A preliminary evalu ation of current salinity performance measures relat**  **ing water levels in the Everglades to the salinity in northeastern Florida Bay has been reported on (Mar**  **shall, 2001). Problems with the use of linear regression models for this data set were identified, particularly sea** **sonality, cross correlation, and autocorrelation of hy drologic parameters. At that time, models and modeling**  **techniques were not capable of adequately simulating the effect of changes in operations of the C-111 canal.**  **A subsequent project for Everglades National Park**

**ev aluated the use of SARIMA models to simulate salin**  **ity in the nearshore embayments of Florida Bay using the Park’s Physical Monitoring Network daily data set**  **(Marshall et al.,**  **2003).The purpose of the evaluation was to determine the appropriate statistical models that**  **could be coupled with the SFWMD South Florida W**  **ater Management Model, also known as the 2x2 (“2 by**  **2”) model. It was found that multivariable linear re gression models were much easier than SARIMA mod**  **els for coupling with the 2x2 model output. Statistical models have been developed that were capable of rea**  **sonably simulating salinity in the nearshore areas. Simulated salinities were functions of water levels in**  **the Everglades and other areas upstream of Florida Bay, Ta** **ylor Slough, and C-111 canal flows; wind; tide; and rainfall. Improvements to the models are currently**  **being incorporated, including the potential inclusion of a term in the model to simulate evaporation.** 

MASS–BALANCE MODELS **Box models by Walker (1998), Nuttle et al.**  **(2000, 2001), Cosby**  **et al. (1999), and Twilley (http://www.ucs.** **louisiana.edu/~rrt4630/mangrove-restudy.htm) ap plied mass-balance calculations to the analyses of wet**  **land hydrology, Florida Bay salinity, and the salinity of Shark River. In each case, these models incorporated** **simplified representations of water flow that are pa rameterized by matching model prediction to observed**  **h**

**ydrology and salinity. W** 

**alker (1998) implemented a set of watershed hy drology models in Everglades National Park. These** 

**w ere used to estimate water and nutrient fluxes into**  **the coastal mangroves. The models constructed monthly water budgets for several wetland basins**  **based on data provided by the 2x2 hydrology model. T** **he aggregated discharge from each basin was related to mean water depth by a generalized power law.The**  **parameters of this power law were estimated by fitting simulated water depths to observations. Over the long** **term, the mean outflow from the basins must be cor rect if the data on other terms in the water balance are**  **accurate. The parameters of the flow model control the variation of estimated flows around the long-term**  **mean value. Walker (1998) lacked the outflow data necessary to validate his watershed models but did find**  **that predicted outflows were correlated with salinity in the coastal bays in the Taylor Slough–C111 area.**  **Nuttle et al.**  **(2001) implemented a mass-balance model for estimating evaporation in Florida Bay.This**  **model calculates salinity, using monthly time steps, from variation in the net supply of fresh water to and** 

**w ater exchange between each of four regions in the bay,** **and water exchange with the Gulf of Mexico. The re gions used in this model correspond to the regions de**  **fined from similarities in water quality (Boyer et al.,**  **1997) and other attributes of the Florida Bay ecosystem.** Hunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 47 Physical Processes**Rainfall and salinity data used to drive the model were measured in the bay. Freshwater runoff was estimated**  **from measured flows in Taylor Slough and the C111 canal that discharge into the mangrove wetlands north**  **of Florida Bay. The four-box model by Nuttle et al.**  **(2001) has been calibrated against salinity data for the period 1993 through 1995 and validated by comparison**  **with salinity data for the period 1996 through 1998.The standard error of prediction is about 2 psu across all** **four regions. Calibration of the model produces esti mates for the unknown seasonal evaporation rates**  **and the exchange rates between basins and with the Gulf of Mexico. These exchange rates can be used to**  **investigate residence times in the bay, information that is needed to understand the processes that con**  **trol nutrient concentrations and plankton blooms. Nuttle**  **et al. (2000) employed two different box mod**  **els. One was essentially the annual averaged version of the four-box model described above, which they used**  **to estimate mean annual evaporation from Florida Bay. T** 

**he other, FATHOM (Cosby et al.,**  **1999), divided the bay into approximately 40 basins, based on morphology,** **and estimated exchanges between basins based on tide driven hydraulic calculations. FATHOM has been used**  **to analyze the influence of changing runoff into Florida Bay (Nuttle**  **et al., 2000), but the calculated exchange** **rates and resulting residence times have yet to be val idated by comparison with observation.**  **T**

**willey (http://www.ucs.louisiana.edu/~rrt4630/ mangrove-restudy.htm) modeled salinity in the Shark**  **River by using boxes representing upper and lower reaches along the channel. The model included the**  **effects of advection, estimated from long-term records of freshwater flow and dispersion, determined by cal** **ibration.This is one of a set of models under develop ment as part of a study of mangrove-forest dynamics.** 



## Unresolved Questions and Ongoing Research

Driving Processes

WINDS AND STORMS **Although the synoptic-scale and seasonal winds over south Florida coastal waters appear to be highly co**  **herent over the whole region, there is now evidence from high-resolution numerical atmospheric models**  **(Mattocks, personal communication; Albrecht et al.,**  **2003) that indicates considerable spatial variability as a result of mesoscale activity associated with convec**  **tive systems and sea breeze development. A number of questions remain: What are the long-term effects of**  **the daily development of convergent wind patterns ove**  **r the bay? What are the magnitudes, spatial, and temporal scales of this mesoscale wind forcing? How**  **does it influence the south Florida seascape in terms of water levels, evaporation and precipitation patterns,**  **circulation and exchange between water bodies, and surface and groundwater inflows to the bay? What is**  **the effect of winds on residence times of the interior**

**wa ters of the bay? It is not clear what changes may**  **occur from intense cyclones, nor how long these**

**c hanges may persist. Predictive modeling of different**  **classes of tropical cyclones is needed to anticipate these impacts.** 

PRECIPITATION **Considerable progress has been made with regard to the process of making precipitation observations into**  **an operational product. Applicable NEXRAD data fields have been mapped onto the SFWMD hydrolog** **ical (2x2) grid and are now archived at the SFWMD. Lo cally generated statistical functions relating radar**  **reflectance to tropical convective rainfall are now being used (Willis, 1999). As a result, we are now ready to ad**  **dress a number of unresolved questions in regard to precipitation such as: Do the spatial patterns of bay sur**  **face salinities measurably change as a result of the heterogeneity of precipitation? To what degree has**  **precipitation over the bay been changing because of land-use changes on the peninsula?** 

EVAPORATION **Price et al.**  **(2001) described an investigation that is de signed to provide mean rates of evaporation and its** 

**v ariation both spatially and temporally in Florida Bay.**  **T his investigation will be the first systematic attempt**  **at determining evaporation in Florida Bay and tying mean estimates of evaporation to longer-term moni** **toring efforts ongoing in the bay. Questions to be an swered by this project include these: What is the mean**  **rate of evaporation in Florida Bay? What is the spatial and temporal variation of evaporation? How reliable** **are long-term estimates of evaporation? How much ad ditional precision can be gained by refinement of sta**  **ble isotope methods? Other questions regarding evaporation include**  **• T o what degree does the seasonality of evaporation**  **need to be considered in evaluating the effect that different salinity patterns have upon water-man**  **agement scenarios? • W** **hat is the effect of the bay’s bank-and-basin topog raphy upon evaporation?** 

**T he rate of evaporation over the extensive, shallow**  **banks may be different from the average estimates used to date. Neither instrumented-platform meteo**  **rological data nor synoptic radiation surveys have** Florida Bay Synthesis Hunt and Nuttle

48 FWRI Technical Report TR-11 Physical Processes**c haracterized conditions over shallow, seasonally ex**  **posed banks. Although the radiation-forcing over the banks will be the same as elsewhere, the different** 

**c haracteristics of the water column (shallow) and bot** **tom (dense sea grass) are expected to affect how out going heat flux is partitioned, which in turn could**  **significantly change local evaporation rates.**

SURFACE-WATER INPUTS **Simulation models under construction by USGS and SFWMD in conjunction with their ongoing measure**  **ment programs are expected to resolve any remaining uncertainty concerning surface-water discharges into**  **Florida Bay. Hydrodynamic transport models have been developed that are capable of being linked to**  **upland-management models to address the effect of freshwater inflows on tempering salinities and con** 

**ve ying nutrients and contaminants to Florida Bay and**  **southwest coastal estuaries. Langevin et al.**  **(2002) of USGS have developed a coupled surface-groundwa**  **ter model of the southern Everglades that is capable of simulating flow and salinity patterns in coastal em** **bayments of northern Florida Bay in response to nat urally occurring hydrologic events in the wetlands and** **the effects of upland-management practices on fresh**

**wa ter releases.The model provides the ability to eval**  **uate the complex exchange and interaction of water and dissolved salt between the Everglades wetlands, the**  **Florida Bay estuaries, and the underlying Biscayne Aquifer. Further enhancements of the model are on**  **going, and its computational domain is being extended to include Shark River, Lostmans River, and other** 

**w estern sloughs within Everglades National Park south**  **of Tamiami Trail (Schaffranek et al.,**  **2002). Both mod els are being developed at temporal and spatial reso**  **lutions that are facilitating the formulation of new estuarine species models (Cline and Swain, 2002) in the**  **Across Trophic Level Simulation System (ATLSS). T** **hese models will allow researchers and managers to assess the ecological health of the total ecosystem and**  **to develop and evaluate performance measures within CERP (DeAngelis**  **et al., 2002).** 

GROUNDWATER INPUTS **T he discrepancy between isotope-derived estimates**  **and the more traditional hydrological approaches (well heads and models) has been discussed above, as has** **the discrepancy between mass-balance and flow ob servations and isotope estimates. Clearly, many unre**  **solved questions remain concerning not only the absolute amount of groundwater input to Florida Bay**  **but also its temporal and spatial variability and the resulting salt and nutrient fluxes. The consensus at** **present is that the water-quality implications of ground w** **ater input from either the southern Everglades or Florida Keys may be more significant than its physical**  **consequences unless the larger estimates prove to be**
**correct.**

SEA LEVEL AND TIDES **No major unresolved issues remain concerning tides. Studies are underway concerning the effects of sea**  **level differences on interbasin exchange and upon flow through the passages between the Florida Keys.**  **It is also not clear how long-term sea level differences between the gulf and Atlantic affect the observed mean**  **southeastward flow that transports water to the Florida Ke** **ys reef tract. However, Frederick**  **et al. (1994) and others have**  **noted an acceleration in local sea level rise over the past century. The extent of this is not entirely clear nor is**  **there yet an adequate geophysical explanation. Such a sea level rise would certainly have implications con**  **cerning bay restoration targets. A SFWMD study has concluded, however, that the currently projected sea**  **level rise does not substantially affect CERP project**

**w ater deliveries.While not precisely a “research issue,”**  **additional tide gauge benchmarks are needed near each water-level recorder in Florida Bay and all the gulf** **coast stations to obtain absolute sea level measure ments. Multiple stations are in place, but many others**  **remain to be installed.The USGS mapping division and the USGS St. Petersburg laboratory are currently work** **ing to establish elevations at many gulf-coast plat forms.** 

BOUNDARY CURRENTS**Questions concerning the effects of boundary cur rents are given below under System Characteristics.**  **Modeling and observational studies are continuing to address how boundary currents are influencing the** 

**v ariability of flow through Florida Bay and the ex** 

**c hanges that take place between boundary currents and**  **adjacent shelf waters.**


### System Characteristics

SALINITY**Although the spatial and temporal variability of salin ity in Florida Bay is well documented and continues to** **be monitored both with field surveys and fixed in struments, a number of unresolved questions remain,**  **including the following: • H**  **ow is the salinity of Florida Bay influenced by** 

**atmospheric forcing on time scales from daily to in terdecadal, including significant transient meteoro**  **logical events such as hurricanes and tropical storms? • H**  **ow do the spatial patterns of evaporation, precip**  Hunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 49 Physical ProcessesFlorida Bay Synthesis Hunt and Nuttle

50 FWRI Technical Report TR-11 **itation, and basin residence time affect bay salinity distributions?**  **• F or example, does hypersalinity occur where it does** 

**because evaporation is greater over broad shallow banks than in the rest of the bay or because ex** 

**c hange with lower-salinity water is restricted?**  **• H ow**  **do the salinity records inferred from paleoe**

**cological data compare with salinity values mea sured over the past 45 years?** 

**• Is there a statistical transfer function sufficient to ad** 

**equately describe the effect of freshwater flows on salinity for the purposes of predicting the effect of**  **restoration scenarios upon bay salinities?**

**• If so, over what spatial domain does it apply?** 

CIRCULATION **Circulation and exchange between isolated basins in the interior of the bay is the subject of several ongo**  **ing field research projects and will be a focus of the forthcoming interior Florida Bay model. Scientists**  **from RSMAS, AOML, Harbor Branch Oceanographic Institute, ENP, and USGS have at various times been**  **maintaining arrays of current, temperature, salinity, and**

**w ater-level recorders within basins and channels dur** **ing wet and dry seasons. Additional observations in clude shipboard Acoustic Doppler Current Profiler**  **(ADCP) observations, salinity surveys, and surface drifter trajectories.These data will be used to directly**  **compute salt transports, water exchange, and interior circulation. In contrast, the exchange between the Gulf**  **of Mexico and western areas of the bay has yet to be quantified and is one of the principal unresolved ques**  **tions concerning circulation. A better understanding of flow across banks, and**  **bank characteristics in general ( e.g.,**  **cover, elevation, salinity, and temperature), will be necessary for suc**  **cessful hydrodynamic and ecological modeling of the bay’s interior.The bathymetry of Florida Bay, particu**  **larly with respect to the shallow banks, needs to be more adequately described for use by modelers. It is**  **not clear to what degree remote sensing ( e.g.,**  **LIDAR) can be used to address this deficiency, given the den**  **sity of seagrass. The depth over many of the banks is approximately equal to or less than the range of sea** **sonal fluctuations in mean sea level. What conse quences might this have for rates and patterns of**  **interbasin water exchange in the interior portion of the bay? What are the rates and pathways of exchange**  **between the interior basins and across the banks in the**

**w estern, central, and eastern regions of Florida Bay and**  **with the southwestern Florida shelf? On a regional scale, very little is known about the** **cause of the net southward flow that couples the east ern gulf and Atlantic coastal region of the Keys and its**  **long-period variations.This flow transports low-salin ity discharges from rivers emptying into the south**  **eastern gulf around Cape Sable to western Florida Bay, where they can interact with interior waters of the**  **bay as well as with the Atlantic coastal waters of the Ke** **ys. It is essential to better describe and understand this flow in order to aid future model development and**  **facilitate informed management decisions. What is the influence of the Loop Current or synoptic winds** 

**ov er the west Florida shelf on driving this flow? Are**  **topographic constraints on the southwestern Florida shelf important? How is the flow related to observed**  **southward flows farther north on the west Florida shelf that appear to diverge from the coast before**  **reaching the southwest shelf (Yang et al.,**  **1999)?**

EXCHANGES WITH ADJACENT WATERS**During the dry season, high-salinity waters from west ern Florida Bay and the gulf transition region are trans**  **ported southward toward the Florida Keys National Marine Sanctuary. There is evidence from the large** **scale hydrographic surveys that at times these high salinity waters can form a near-bottom, salty layer in**  **the Hawk Channel region. However, very little is known about this process. How are the salty bottom layers**  **formed? What are their spatial extent and transport pathways? What are their durations?**  **Analysis of current records taken in different years suggest that up to 500–600 m**  **3 /s could be available for**  **exchange with the interior of Florida Bay. Transports across the western boundary are very uncertain at this** **time; however, field research is planned to improve un derstanding of transport processes and help quantify**  **this exchange. There are also unresolved questions regarding the bank “overtopping”process and whether**  **this could explain the observed net outflow from the central part of the bay.**  **Mean gulf-to-Atlantic flows through western Florida Bay to the Keys coastal zone and reef tract** **have been estimated from observations and are be lieved to be connected to the boundary currents (Loop**  **Current and Florida Current) surrounding south Florida (Lee and Smith, 2002). More effort is needed to** **quantify and monitor this mean flow to better under stand the physical processes involved. Is it related to**  **the position and configuration of the Loop Current as gulf models and satellite observations suggest? Cou**  **pling of a large-scale model that includes the gulf and Straits of Florida to a finer-scale Florida Bay model is**  **needed to address this issue.**


### Hydrodynamic Models

**Researchers developing and applying mechanistic** Physical ProcessesHunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 51**models have pursued two radically different ap proaches: the aggregated representation of hydrology**  **and salinity in mass-balance models, described above, and the detailed representation of tide and wind-dri** 

**v en water movements in wetland hydraulic and estu**  **arine hydrodynamic models, for example, the RMA-10 model (Kim**  **et al., 1999). The PST reviewed the RMA**  **10 some time ago, but little work has proceeded on it since that time. The review raised fundamental con**  **cerns both in regard to the degree to which the model**

**w as calibrated and verified and also in regard to more**  **basic issues such as boundary conditions and transport processes within the bay’s interior (http://www.aoml.**  **noaa.gov/flbay/pmcphysci.html). J. Wang (personal communication) recently applied the finite-element**  **model CAFE3D in 2-D mode with realistic winds and tides to estimate salinity fields in Florida Bay resulting** **from a “climatological” run-off hydrography. Multi**
**y ear simulations have been made and show patterns**  **similar to observations (http://anole.rsmas.miami.edu/ people/jwang/Florida_Bay_Model.html).**  **T he FBFKFS of CERP convened a Hydrodynamic**  **Model Review Workshop in June 2002, and a Review P** 

**anel was assigned to assess prospects for the suc cessful modeling of Florida Bay hydrodynamics to be**  **used as a management tool.This panel provided strong support for the development of a numerical hydrody** **namic model because of the need to support water quality and seagrass modeling of the bay.The panel also** **firmly recommended not combining different nu merical modeling frameworks (specifically, hybrid mix**  **ing of finite-element and finite-difference numerical grid solutions for hydrodynamic and water-quality** **modeling). The panel’s recommendations were gen erally consistent with the Physical Sciences Team’s**  **previously issued Modeling Terms of Reference. During this workshop, the SFWMD described their**  **exploratory analysis for determining the feasibility and applicability of a finite-difference model based**  **on the Environmental Fluid Dynamic Code for Florida Bay. SFWMD’s Phase I of model evaluation was com**  **pleted in 2002 and was intended to help provide a basis for further development and application of a hy**  **drodynamic model for the FBFKFS and other projects. Phase I was done under contract by J. Hammrick, of**  **T**

**etra Tech, Inc. Numerical-model grids were generated, a five-year calibration data set was synthesized (and in**  **corporated into the Physical Sciences Team’s Standard Data Set), and the performance of the model was eval** **uated. Simulations of water-surface elevation, cur rents, and temperature were judged to be more than**  **adequate for confidence in long-term prediction of these quantities. Using the observationally defined**  **inflows and their associated observed salinities, the model tended to overpredict salinity, particularly in the** **northeastern portion of Florida Bay. This overpredic tion seemed likely to be due to uncertainties in esti**  **mates of freshwater discharge, evaporation, or other boundary exchanges.**  **Th e Phase I final report is currently under review**  **at the SFWMD. Based on past comments from the Physical Science Team, the Florida Bay Science Program** **Science Oversight Panel, the Feasibility Study’s work shop Review Panel, and information gained from Phase**  **I, a detailed work plan for Phase II is being written.This phase will consist of the completion of a validated cir**  **culation model for the interior bay that will enable the SFWMD, the United States Army Corps of Engi** **neers (USACE), and other partner agencies to evalu ate potential restoration alternatives as part of the**  **FBFKFS. The success of this model development and application will be highly dependent upon inputs from** **boundary models, including a regional, oceanic hy drodynamic model for the Gulf of Mexico and Atlantic**  **boundaries and a regional hydrologic model at the Everglades boundary.** 



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**w est Florida coastline and its effect on adjacent marine**  **environments. Bulletin of Marine Science 54(3): 1074–1075.** 
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**w ater flow from estuarine creeks into northeastern**  **Florida Bay.Water-Resources Investigations Reports 01- 4164, U.S. Geological Survey,Tallahassee, Florida.** 
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**ve ys. Pp. 16–17**  **in 2001 Florida Bay Science Confer**  **ence. (Abstract)**
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**w ater/groundwater flow and solute transport in the** **southern Everglades, Florida, Second Federal Intera gency Hydrologic Modeling Conference, July 28–Au**  **gust 1, 2002. 12 p. LEE,T. N., E. JOHNS, D.WILSON, and E. WILLIAMS.** **1999. Site characterization for the Tortugas region: Phys ical oceanography and recruitment.Tortugas 2000: Re**  **port by the Florida Keys National Marine Sanctuary.**
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**v al recruitment. Bulletin of Marine Science 64: 35–56.** **LEVESQUE, V. A., and E. PATINO. 2001. Hydrody namic characteristics of estuarine rivers along the**  **southwestern coast of Everglades National Park. Pp. 23–25**  **in 2001 Florida Bay Science Conference. (Ab**  **stract) MARSHALL, F. E., III. 2001. Florida Bay salinity trans**  **fer function analysis. Pp. 20–22 in**  **2001 Florida Bay Sci ence Conference. (Abstract)** 
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**NUTTLE, W. K., J. W. FOURQUREAN, B. J. COSBY, J. C. ZIEMAN, and M. B. ROBBLEE. 2000. Influence of net** **fresh water supply on salinity in Florida Bay.Water Re sources Research 36: 1805–1822.** 
**NUTTLE, W. K., R. PRICE, and P. K. SWART. 2001. Es timating evaporation from Florida Bay. P. 102**  **in initial**  **Conference Abstracts, 16th Biennial Conference of the Estuarine Research Federation, November 2001, St.**  **P**

**ete Beach, Florida.**
**ORTNER, P. B., T. N. LEE, P. J. MILNE, R. G. ZIKA, E. CLARKE, G. PODESTA, P. K. SWART, P. A.TESTER, L.**  **P. A TKINSON, and W. R. JOHNSON. 1995. Mississippi** **River flood waters that reached the Gulf Stream. Jour nal of Geophysical Research 100: 13595–13601.** 
**PIELKE, R. A., R. L. WALKO, L. STEYART, P. L.VIDAL, G.**  **E. LISTON, W. A. LYONS, and T. N. CHASE. 1999. T** 

**he influence of landscape change on weather in South Florida. Monthly Weather Review 127: 1663–1673.**  **PRATT,T. C., and N. P. SMITH. 1999. Florida Bay Field Data Report.Technical Report CHL-99-11, Waterways**  **Experiment Station, U.S. Army Corps of Engineers, Vic**  **ksburg, Mississippi.**
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**ROBBLEE, M. B., G. CLEMENT, D. SMITH, and R. HALLEY. 2001. Salinity pattern in Florida Bay: A syn**  **thesis (1900–2000). Pp. 34–36 in**  **2001 Florida Bay Science Conference. (Abstract).** 
**SCHAFFRANEK, R. W., H. L. JENTER, and A. L. RISCASSI. 2002. Overview of the “Tides and Inflows in**  **the Mangroves of the Everglades”(TIME) project of the U**  **.S. Geological Survey’s South Florida Ecosystem Pro gram, Second Federal Interagency Hydrologic Mod**  **eling Conference, July 28–August 1, 2002. SMITH, D. 2001. Marine physical conditions: Ever**  **glades National Park October 1998 through December 1999. South Florida Natural Resources Center, Ever**  **glades National Park, Homestead, Florida.**
**SMITH, N. P. 1997. An introduction to the tides of Florida Bay. Florida Scientist 60: 53–67.**  **SMITH, N. P. 1998. Tidal and long-term exchanges through channels in the middle and upper Florida**  **Ke ys. Bulletin of Marine Science 62: 199–211.** **SMITH, N. P. 2000. Evaporation and the precipitation**

**ev aporation balance in Florida Bay. Florida Scientist 63:**  **72–83. SMITH, N. P. 2001. Wind-forced interbasin exchanges**  **in Florida Bay. Pp. 40–41 in**  **2001 Florida Bay Science Conference. (Abstract)**  **SMITH, N. P. 2002.Tidal, low-frequency and long-term mean transport through two channels in the Florida**  **Ke ys. Continental Shelf Research 22: 1643–1650.**  **SMITH, N. P., and T. N. LEE. 2003. Volume transport through tidal channels in the middle Florida Keys.**  **J ournal of Coastal Research 19(2): 254–260.**  **SMITH, N. P., and P. A. PITTS. 2002. Regional-scale and long-term transport patterns in the Florida Keys.**  **Pp. 343–360 in**  **J. W. Porter and K. G. Porter, eds. The Everglades, Florida Bay, and Coral Reefs of the Florida**  **Ke ys: An Ecosystem Sourcebook. CRC Press, Boca**  **Raton, Florida.**
**SMITH, R. H., E. JOHNS, D. WILSON, T. N. LEE, and E. WILLIAMS. 2001. Moored observations of salinity** 

**v ariability in Florida Bay and South Florida coastal** 

**w aters on daily to interannual time scales. Pp. 42–43**  **in 2001 Florida Bay Science Conference. (Abstract)** **SWAIN, E. D., and C. LANGEVIN. 2001. Developing in sight into coastal wetland hydrology through numer**  **ical modeling. Pp. 44–46 in**  **2001 Florida Bay Science Conference. (Abstract)** 
**SWAIN, E. D., C. D. LANGEVIN, and M. A.WOLFERT. 2002. Cooperative linkage of numerical models for**  **coastal wetlands planning. Pp. 375–380 in**  **A WRA Spring**  **Specialty Conference, 13–15 May 2002. SWART, P. K., and R. M. PRICE. 2001. Insights into the**  **origin of salinity variations in Florida Bay over short and long time periods. Pp. 47–48**  **in 2001 Florida Bay Science**  **Conference. (Abstract)**

**TO P,**  **Z., and L. E. BRAND. 2001. Helium as tracer of groundwater input into Florida Bay. Pp. 49–50**  **in 2001**  **Florida Bay Science Conference. (Abstract)**
**TRIMBLE, P. J., E. R. SANTEE, III, R.VAN ZEE, L. G. CA DA** **VID, J. T. B. OBEYSEKERA, and A. ALI. 2001. Sim ulation of the influence of climatic variability on fresh** 

**wa ter inflow to Florida Bay during the 20th Century.**  **Pp. 50–51 in**  **2001 Florida Bay Science Conference. (Ab stract)**  **TWILLEY, R. Evaluating the response of mangrove** Hunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 53 Physical Processes**w etlands to alterations of freshwater flow in Ever**  **glades National Park. http://www.ucs.louisiana.edu/ ~rrt4630/mangrove-restudy.htm.** 

**V**

**OSBURG, B. M., J. E. CABLE, J. P. BRADDY, E. REYES, D.**  **L. CHILDERS, and S. E. DAVIS. 2001. Wetland hy drogeologic responses along the Taylor Creek system,**  **southeastern Everglades, Florida (USA). Pp. 52–53 in**  **2001 Florida Bay Science Conference. (Abstract)**

**W**

**ALKER, W. W. 1998. Estimation of inputs to Florida Bay. Report prepared for U.S. Army Corps of Engi**  **neers & U.S. Department of the Interior. http:// wwwalker.net/flabay/.**  **W ANG, J., J.VAN DE KREEKE, N. KRISHNAN, and D.**  **SMITH. 1994. Wind and tide response in Florida Bay. Bulletin of Marine Science 54: 579–601.** 
**WILLIS, P. 1999. An evaluation of NEXRAD (WSR88D) data as a measure of fresh water flux into the Florida**  **Bay/Everglades System. P. 153 in**  **1999 Florida Bay Sci ence Conference. (Abstract)** 

**Y**

**ANG, H., R. H. WEISBER, G. P. P. NIILER, W. STURGES, and W. JOHNSON. 1999. Lagrangian cir**  **culation and forbidden zone on the West Florida shelf. Continental Shelf Research 19: 1221–1245.**  Florida Bay Synthesis Hunt and Nuttle

54 FWRI Technical Report TR-11 Physical Processes

## Introduction

Question 2 **—What is the relative importance of the influx of external nutrients and of internal nutrient cycling in** **determining the nutrient budget of Florida Bay? What mech anisms control the sources and sinks of the bay’s nutrients?** 
**Ecological changes within Florida Bay, including Tha**  **lassia testudinum mass mortality and algal blooms,**  **which have been evident during the past two decades, have commonly been attributed to many of the same**  **human activities that have changed the Everglades.The diversion of freshwater to the Atlantic coast by canals** **has increased the salinity of the bay. Freshwater dis**

**c harges from canals to the Atlantic Ocean were roughly**  **four times larger than discharges to sloughs that flowed toward Florida Bay during the 1980s. Additionally, an**  **thropogenic nutrient inputs from the Florida Keys, Gulf of Mexico, the atmosphere, and the Everglades**  **may have increased. Inputs from the gulf may include phosphorus, which is transported by longshore currents**  **from the central Florida coast, and nitrogen (N), which originates in the Everglades and flows into the gulf**  **through Shark River Slough. Th**  **e main informational needs relative to nutrient**

**c ycles in Florida Bay is an understanding of the factors** **that triggered and maintain the mass mortality of sea grasses and the episodic phytoplankton blooms. Also** **critical is sufficient understanding to enable us to as sess the effects of various environmental management** **strategies being considered for bay restoration. In par ticular, we need to accurately predict the sensitivity of**  **the bay’s nutrient cycles to changing freshwater flow into the bay and to the resultant change in the bay’s** **salinity regime. For much of the bay, any factor that in creases phosphorus (P) availability either by increas**  **ing input or decreasing removal is likely to exacerbate the current problems of the bay. Recent evidence also**  **indicates that algal blooms in the central and western bay are sometimes stimulated by nitrogen (N) enrich**  **ment.Thus we need a thorough understanding of the bay’s nutrient cycles. Questions that the current mon**  **itoring and research program must address in order to meet these needs follow.**  **T he water column in Florida Bay is generally olig**  **otrophic, and phytoplankton biomass has historically been quite low throughout the system. Although phy**  **toplankton in Florida Bay are generally phosphorous limited (Fourqurean**  **et al., 1993; Phlips and Badylak,**  **1996; Lavrentyev et al.,**  **1998), other resources ( e.g.,**  **light, nitrogen, silicon) may also be important in control** **ling plankton biomass in some areas of the bay (Lavren tyev**  **et al., 1998). Dissolved inorganic phosphorous**  **(DIP) concentrations are near detection limits (20 nmol), but concentrations of dissolved inorganic ni**  **trogen (DIN) can be relatively high (median value 3.3 μmol, but concentrations >10 μmol are not uncom**  **mon) and dominated by ammonium (Fourqurean et al.,**  **1993; Boyer et al.,**  **1997; as summarized in Fourqurean and Robblee [1999]).** **A spatial analysis of data from the monitoring pro gram conducted by Boyer**  **et al. (1997) resulted in the** **delineation of three groups of stations (eastern, cen tral, and western) that have robust similarities in water** **quality (Figure 5.1). We deem these spatially contigu ous groups of stations to be the result of similar hy**  **drodynamic forcing and processing of materials; hence,**

**we call them “zones of similar influence.”The eastern**  **bay zone acts most like a ‘conventional’estuary in that it has a quasi-longitudinal salinity gradient caused by** **the mixing of freshwater runoff with seawater. In con trast, the central bay zone is a hydrographically isolated**  **area with low and infrequent terrestrial freshwater input, a long water residence time, and high evapora** 

FWRI Technical Report TR-11 55 

# Chapter 5 Nutrient Dynamics

T eam Leaders Joseph N. Boyer (Florida International University),

Brian Keller (Florida Keys National Marine Sanctuary, PMC) Contributors Joe Boyer, Larry Brand, Bill Burnett, Jaye Cable, Paul Carlson, Carl Cerco, Randy Chambers,

Jeff Chanton, Dan Childers, Reide Corbett, Jeff Cornwell, Susan Dailey, Cynthia Heil, Gary Hitchcock, John Hunt, Ron Jones, Jennifer Jurado, Chris Kelble, Brian Keller, Steve Kelly, Mike Kemp, Gary Kleppel, Margurite Koch-Rose, Bill Kruczynski, Brian Lapointe, Chris Madden, Bill Mcpherson, Frank Millero, Bill Nuttle, William Orem, Ed Phlips, Rene Price, Enrique Reyes, Dave Rudnick, Eugene Shinn, Fred Sklar, DeWitt Smith, Richard Stumpf, Peter Swart, Zafer Top, Gabe Vargo, Cecilia Weaver, Laura Yarbro, Jia-Zhong Zhang**tive potential.The western bay zone is the most influ enced by the Gulf of Mexico tides and is also isolated**  **from direct overland freshwater sources.** 

### Summary of Knowledge

**Research on nutrient dynamics in Florida Bay focuses on the exchange of nutrients with adjacent regions**  **(“external”dynamics), the cycling of nutrients within Florida Bay (“internal”dynamics), and the influence of**  **these processes on ecosystem structure and function, i.e.,**  **on spatial and temporal variation (Table 5.1). A continuing program of monitoring and research, in**  **cluding computer modeling, addresses the question of how human activity is affecting the nutrient dynam**  **ics of Florida Bay and how future restoration actions will alter these dynamics.**  **• W hat do we know about status and trends in water**  **quality over space and time?**



## ° **Objective analysis shows that there are three zones**

**(eastern, central, and western) in the bay that ex hibit significant differences in water-quality char**  **acteristics due to nutrient inputs, tidal advection, and water residence time.** 



## ° **In general, DIP concentrations increase and DIN**

**decreases from east to west, resulting in a shift from P limitation to N limitation.** 



## ° **Central bay waters have high ammonium con**

**centrations, which may indicate a bottleneck in the process of nitrification.** 



## ° **T emporal trends over a 13-year period of record**  **show bay-wide declines in total phosphorus (TP), total nitrogen (TN), and chlorophyll**  **a and an over**  **all increase in turbidity (cloudiness of the water). • W** **hat do we know about sources and amounts of ex ternal nutrient loading to Florida Bay?** 



## ° **T errestrial nutrient loading fluctuates with fresh**  **w ater flow, but flow-weighted concentrations de**  **crease with increasing flow.**



## ° **Phosphorus loading from the Everglades is a small**

**proportion of the Florida Bay nutrient budget. Most phosphorus (P) appears to be derived from**  **the Gulf of Mexico.**



## ° **Nitrogen output from the southern Everglades**

**(including Shark River Slough) is a significant proportion of the Florida Bay nutrient budget**  **(similar in magnitude to atmospheric loading). Most nitrogen flowing from the wetlands is in the**  **form of dissolved organic compounds. Studies on the bioavailability of dissolved organic nitrogen**  **(DON) are currently underway.**



## ° **T he atmospheric input of nutrients is large, and** 

**most atmospheric nitrogen is inorganic.**



## ° **Knowledge of the bay’s nutrient budget is coarse**

**ov er time and space (annual averaging for entire** **bay). Large uncertainty exists regarding the mag nitude of nutrient exchange at the Gulf of Mexico**  **boundary and regarding saline groundwater**

**sources.**



## ° **T here is a measurable effect of water manage** 

**ment on the quantity and distribution of water and nutrients through the length of the Taylor**  **Slough–C-111 basin system, influencing inputs to Florida Bay.** 



## ° **A serious disconnect exists between upland/canal**

**loading estimates and actual input to the bay be cause of unmeasured nutrient processing in the in**  **tervening wetland/mangrove areas. • W**  **hat do we know about internal nutrient-cycling processes?** 



## ° **Benthic denitrification is higher than expected**

**based on denitrification: N-loading relationships in other estuaries.** 



## ° **T he balance of N** **2 fixation and denitrification in the**  **bay is highly variable, but there appears to be a net loss of N in the overall system.** 



## ° **Sediment regeneration of ammonium under dark**

**conditions is low relative to benthic dissolved oxy gen demand.** 



## ° **Sediment regeneration of ammonium decreases**

**with increases in sediment chlorophyll a**  **concen tration, indicating that the microphytobenthos is** **important in regulating water column N concen trations.** 



## ° **T here is very little, if any, P flux out of the sedi** 

**ments, with the exception of the western bay-shelf**

**area.**



## ° **High rates of organic carbon (C) and N fluxes**

**occur, both into and out of sediments over diel cy cles (particularly in the central and western bay).** 



## ° **Phosphorus sorption-desorption varies strongly as** Florida Bay Synthesis Hunt and Nuttle

56 FWRI Technical Report TR-11 Figure 5.1 **Zones of similar water quality in Florida Bay.** Nutrient Dynamics**a function of temperature and salinity.**



## ° **T he decreasing bayward gradient in iron content** 

**of sediments has implications in P availability, sulfide toxicity, and primary production in the**  **benthos.**



## ° **T he seagrass community is a major sink for nu** 

**trients from either the water column or sediment pore waters in the bay.**  

## Patterns and Trends in W ater Quality
**A network of water-quality monitoring stations was es tablished in 1989 (and funded by SFWMD in 1991) to**  **investigate both spatial patterns and temporal trends in water quality in an effort to elucidate mechanisms**  **behind the recent ecological change. One of the primary** Hunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 57 T able 5.1 **Research topics defined by Question 2 (cells in the matrix) and key references to the associated research.**

Research Topics Spatial Variation Temporal Variation

W ater-Quality Patterns and Trends **F ourqurean**  **et al., 1993; Boyer**  **et al., 1999;**  **Boyer et al.,**  **1997; Burd and Jackson, 2002**  **Burd and Jackson 2002** Overall Nutrient Budget **Boyer and Jones, 1999; Boyer and Jones** 
**, 1999;**  **Rudnick et al.,**  **1999; Rudnick**  **et al., 1999;**  **Cerco et al.,**  **2000 Cerco**  **et al., 2000**  **External Nutrient Loading**

**T**

**errestrial Inputs Everglades**  **Walker, 1998; Rudnick Walker, 1998; Rudnick**  **et al., 1999**  **et al., 1999**  **Mangroves Childers**  **et al., 1999a,b; Da** **vis Childers et al.,**  **1999a,b; Davis et al.,**  **2001; Sutula et al.,**  **2001, et al.,**  **2001a,b; Cable et al.,**  **2003 2001; Sutula**  **et al., 2001, 2003**  **Ke ys**  **Kruczynski and McManus, 2002 Atmospheric Inputs**  **Nuttle et al.,**  **2000 Groundwater Inputs**  **Shinn et al.,**  **1994; Corbett et al.,**  **1999, 2000a,b; Price and Swart 2001**  **Gulf of Mexico Rudnick**  **et al., 1999**  **Atlantic Ocean Szmant and Forrester, 1996**  **Internal Nutrient Cycling**

**N 2**  **Fixation Cornwell, 2001; Owens and Cornwell, 2001**  **Benthic Flux Rudnick, 1999; Carlson and**  **Y**

**arbro, 1999; Yarbro and Carlson, 1999; Chambers**  **et al.,**  **2001; Yarbro and Carlson, unpublished**  **Nitrification/Denitrification Kemp and Cornwell, 2001**  **Kemp and Cornwell, 2001 Microbial Loop**  **Cotner et al.,**  **2000; Boyer**  **et al., 2006**  **Boyer et al.,**  **2006 DOM Remineralization**  **Boyer et al.,**  **2006 Boyer**  **et al., 2006**  Seagrass Effects on Water Quality **Madden and McDonald, 2006; Madden and McDonald,2006;**  **Madden et al.,**  **2003; Madden**  **et al., 2003;**  **McDonald et al.,**  **2003; McDonald**  **et al., 2003;**  **Gras et al.,**  **2003; Gras**  **et al., 2003;**  **Nielson et al.,**  **2006 Nielson**  **et al., 2006**  Higher-Trophic-Level Effects on W ater Quality Wa ter Quality Modeling **Cerco et al.,**  **2000** Nutrient Dynamics**purposes for conducting long-term monitoring projects is to be able to detect trends in the measured variables** 

**ov er time.These programs are usually initiated as a re** **sponse to public perception (and possibly some sci entific data) that ‘the river-bay-prairie-forest-etc. is**  **d**

**ying.’ In the case of Florida Bay, during 1987, the im petus was the combination of a seagrass die-off, in**  **creased phytoplankton abundance, sponge mortality, and a perceived decline in fisheries.** 


### Period of Study

**Climactic changes occurring over the data-collection period of record had major effects on the health of the**  **bay. Precipitation rebounded from the drought during the late 1980s and has been greater than the long-term** 

**av erage (9.2 cm mo**  **–1 ) for 9 of the past 12 years (Figure**  **5.2). Early in the record, salinity and total phosphorus (TP) concentrations declined baywide, while turbidity**  **increased dramatically.The salinity decline in eastern and central Florida Bay was dramatic early on but has**  **since stabilized into a regular seasonal cycle (Figure 5.3). Some of the decrease in the eastern bay could be ac**  **counted for by increased freshwater flows from the Everglades, but declines in other areas point to the cli**  **mactic effect of increased rainfall during this period. Th**  **e central bay continues to experience hypersaline conditions (greater than 35 practical salinity units**  **[psu]) during the summer, but the extent and duration of the events are much smaller.**  **Chlorophyll a**  **concentrations (CHLA), a proxy for phytoplankton biomass, were particularly dynamic**  **and spatially heterogeneous (Figure 5.4). The eastern bay generally has the lowest CHLA, and the central bay**  **has the highest. In the eastern bay, which makes up roughly half of the surface area of Florida Bay, CHLA**  **have declined by 0.9 μg l –1**  **or 63%. Most of this decline occurred over a few months in the spring-summer of**  **1994 and has remained relatively stable. The isolated central bay zone underwent a fivefold increase in**  **CHLA from 1989 to 1994, and then rapidly declined to previous levels by 1996. In western Florida Bay, there** 

**w as a significant increase in CHLA, but median con**  **centrations remained modest (2 μg l –1**  **) by most estu arine standards.There were significant blooms in the** **central and western bay immediately following Hur ricane Georges (November 1998), but it was Hurri**  **cane Irene’s large rainfall input (October 1999) that induced a large bloom throughout the bay. It is im** **portant to note that these changes in CHLA (and tur bidity) happened years after the poorly understood**  **seagrass die-off in 1987. It is possible that the death and decomposition of large amounts of seagrass biomass**  **might partially explain some of the changes in water quality of Florida Bay, but the connections are tempo**  **rally disjunct and the processes are indirect and not**

**w ell understood.**  **As mentioned previously,TP concentrations have declined baywide over the 12-year study period (Fig**  **ure 5.5). As with salinity, most of these declines occurred during the early part of the study. Unlike most other**  **estuaries, increased terrestrial runoff may have been partially responsible for the decrease in TP concen** **trations in the eastern bay because the TP concentra tions of the runoff were at or below ambient levels in**  **the bay.The elevated TP in the central bay was mostly due to high evaporation. It is important to understand**  **that almost all the phosphorus measured as TP is in the form of organic matter, which is less accessible to**  **plants and algae than inorganic phosphate. T** 

**he DIN pool is made up of three components: am monium (NH**  **4 +**  **), nitrate (NO 3**  **– ), and nitrate (NO**  **2 –**  **).The**

**w estern bay is lowest in DIN; phytoplankton in this re**  **gion may be limited by N availability on a regular basis (Figure 5.6). DIN in the eastern bay is a little**  **higher and is mostly in the form of NO 3**  **– ,**  **and highest levels are found in the central bay as NH**  **4 +** 

**. T** 

**urbidities in the central and western bay have increased tremendously since 1991 (Figure 5.7). Tur**  **bidity in the eastern bay increased twofold from 1991 to 1993, whereas those in the central and western bays** **increased by factors of 20 and 4, respectively. Gener ally, the eastern bay has the clearest water, which is due**  **to a combination of factors such as high seagrass cover, more protected basins, low tidal energy, and shallow**  **sediments. We are unsure what caused it, but the loss of seagrass coverage may have destabilized the bottom**  **so that it is more easily disturbed by winds. An extensive set of contour maps of water-quality**  **parameters for Florida Bay is available at http://serc. fiu.edu/wqmnetwork/.** 



### Recent Conditions

**Most water-quality variables during 2001 generally followed typical annual trends, with one prominent ex** **ception. All regions of the bay experienced a pro** Florida Bay Synthesis Hunt and Nuttle

58 FWRI Technical Report TR-11 Figure 5.2 **Monthly average rainfall in the Florida Bay area, 1991–2005.**  Nutrient Dynamics**longed period of hypersalinity during the summer months. Most of this was due to the previous dry year,**  **which set up the system for this occurrence.The annual pattern in CHLA was unremarkable—no blooms re**  **ported. Total phosphorus values declined from very high levels in the fall of 2000 to normal levels in 2001.**  **T he western bay showed elevated DIN during the**  **early part of 2001 but was not excessive compared with other years.Turbidity continued to fluctuate above** **post-1993 levels. Note that the high turbidities ob served in the western bay during the winter also cor**  **related with elevated TP. NOAA/AOML also has a water-quality monitor**  **ing program in Florida Bay. Its primary purpose is to measure physical aspects of the system (see Question**  **1), but there is also a nutrient component to the sampling. An example of this is the analysis of phos** **phorus (Figure 5.8) using long-path-length liquid wave guide technology from Zhang and Chi (2002).**  

## Exogenous Sources of Nutrients

**A budget of Florida Bay’s exogenous nutrient sources, which was estimated for the 2001 Florida Bay Confer**  Hunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 59 Figure 5.3 **Monthly median salinity in the three Florida Bay zones.** Nutrient Dynamics**ence, included inputs from the Everglades, wastewater and storm water from the Florida Keys, saline ground** 

**w ater, the Gulf of Mexico, the Atlantic Ocean, and the**  **atmosphere. Results from this exercise, with revision of the estimated saline groundwater source, are pre**  **sented in Figures 5.9–5.11.**



### Nutrient Inputs from the Everglades: T aylor Slough–C-111 and Shark River

**Nutrient outputs from the Everglades in this budget have been estimated from inputs to Everglades Na**  **tional Park wetlands from canals as reported by Rud nick**  **et al. (1999).This approach can only be considered** **a rough estimate because of nutrient-processing dur ing transport through the southern Everglades. How** 

**ev er, these estimates are more likely to be correct than** **estimates of most other components of the bay’s nu trient budget.The accuracy of estimates for the south**  **eastern Everglades nutrient outputs is indicated by results of Sutula**  **et al. (2003).This study found that TN**  **and TP inputs from the mouths of mangrove creeks into Florida Bay in 1997 were similar to estimated inputs to**  **the wetland that year (TN loads differed by 7%, and TP loads differed by one metric ton per year).**  Florida Bay Synthesis Hunt and Nuttle

60 FWRI Technical Report TR-11 Figure 5.4 **Monthly median chlorophyll a**  **in the three Florida Bay zones.** Nutrient Dynamics**Studies of nutrient export from Taylor River,Trout Creek, and McCormick Creek (Sutula**  **et al., 2003; Davis**  **et al., 2003) have provided insights into the relationship**  **between patterns of freshwater discharge and those of nutrient dynamics and output into Florida Bay. Nutri**  **ent outputs have been found to increase with increasing**

**w ater discharge. As observed for inflows to Everglades**  **National Park wetlands from canals, this increase is not linear; flow-weighted mean nutrient concentrations**  **decrease with increasing discharge (Rudnick et al.,**  **1999; Figure 5.12). Output of phosphorus to Florida Bay is mostly as dissolved organic phosphorus, but it**  **is very low in magnitude. During the dry season, both suspended solids and phosphorus are imported into**  **the mangrove ecotone from the northeastern region of the bay. Output of nitrogen is also largely as dissolved**  **organic nitrogen, but this quantity is high, resulting in a very high TN:TP ratio in creek outputs (molar ratio** 

**av erage near 200).**  **During the next year, RECOVER (the monitoring and assessment program of the Comprehensive Ever** **glades Restoration Plan [CERP]) will expand the net**

**w ork of creek discharge and nutrient-sampling stations**  **to include new sites along Florida Bay’s coastline and the western Everglades rivers. A total of eight paired** **(upstream-downstream) stations are planned, includ** Hunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 61 Figure 5.5 **Monthly median total phosphorus in the three Florida Bay zones.** Nutrient Dynamics**ing four creeks entering Florida Bay and four rivers en tering the Gulf of Mexico. It should also be noted that**  **the Florida Coastal Everglades Long Term Ecological Research (LTER) is providing information on nutrient**  **processing in the southern Everglades and mangrove zone, with particular emphasis on the formation, trans**  **port, and decomposition of dissolved organic matter.**



### Ground Water

**T he input of nutrients to Florida Bay via ground water** **remains highly uncertain. No new estimates of ground**

**w ater flux have been made since the 2001 conference.**  **At that time, it was evident that subsurface freshwa ter inputs are negligible. Ground water beneath Florida**  **Bay and its mangrove ecotone along the Everglades coast is saline (Reich**  **et al., 2002; Price, 2001; C. Reich**  **and E. Shinn, personal communication). Thus, fresh ground water beneath the Everglades that flows toward**  **Florida Bay appears to rise toward the surface, over denser saline water, to the north of the bay boundary**  **(Price, 2001). In contrast to fresh ground water, significant ad** 

**v ection of saline ground water into the bay may occur** **from beneath the bay itself. Based on groundwater tracer (radon, methane) concentrations, Corbett**  **et al.** Florida Bay Synthesis Hunt and Nuttle

62 FWRI Technical Report TR-11 Figure 5.6 **Monthly median dissolved inorganic nitrogen in the three Florida Bay zones.** Nutrient Dynamics**(1999, 2000a) have estimated a bay-wide vertical groundwater flow of about 1 cm/d or higher (Top**  **et al., 2001).The nutrient budget presented at the 2001 Florida**  **Bay Conference used this value along with nutrient concentrations of 0.1 μmol TP, 1 μmol DIN, and 10**  **μmol TN. These concentrations are typical of wells at pristine sites in the Florida Keys (E. Shinn, personal** **communication). However, C. Reich and E. Shinn (per sonal communication) now report that these concen**  **trations are considerably lower than those found in**

**w ells throughout Florida Bay. Over a four-year period,**  **concentrations averaged approximately 1.5 μmol TP, 80 μmol TN, and 44 μmol NH**  **4 .**  **Still assuming a 1-cm/d groundwater flow, these higher concentrations would**  **result in a groundwater nutrient input of 38 MT/y for TP, 8,800 MT/y for TN, and 5,000 MT/y for DIN. Com** **pared to nutrient inputs from the Everglades, these es timated groundwater inputs are about 10 times higher**  **for TP, about 6 times higher for TN, and more than 100 times higher for DIN. Some caution may be advised be**  **fore applying these well-water concentrations because they may be affected by biogeochemical processes**  **such as adsorption or denitrification prior to discharge, thus lowering their input into surface waters.**  **However, if this groundwater-input estimate of DIN is accurate, it would represent about 75% of all in**  Hunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 63 Figure 5.7 **Monthly median turbidity in the three Florida Bay zones.** Nutrient Dynamics**organic nitrogen inputs to the bay. Furthermore, at such a high concentration, this inorganic nitrogen** 

**w ould be readily available for algal and submerged**  **aquatic vegetation (SAV) productivity (in contrast to the low-concentration input from the Gulf of Mexico). It**  **should be noted that this estimated groundwater DIN input is equivalent to 18 μmol m**  **–2 h**  **–1**
**, or roughly half** **of the median nocturnal nutrient flux across the sed iment–water interface, as measured along the north**  **ern Florida Bay coast. It is also roughly equal to the median nocturnal benthic input found in the interior** **bay (P. Carlson, personal communication). The sur prisingly high magnitude of the groundwater DIN**  **input estimate, combined with the fact that ground**

**w ater is usually hypersaline, is grounds for skepticism**  **regarding the estimated 1 cm/d groundwater input as a rate that occurs commonly throughout the bay.This**  **does not, however, preclude the possibility that large inputs of ground water occur at some locations in the**  **bay, particularly near the Keys (see below). An additional source of uncertainty in groundwa**  **ter input is the depth from which the ground water is advected. For example, advective flow through surfi** **cial sediments can be caused by current-induced gra dients over topographic expressions such as sand**  **ripples (Huettel and Gust, 1992). Presumably, flow over** Florida Bay Synthesis Hunt and Nuttle

64 FWRI Technical Report TR-11 Figure 5.8 **W ater column phosphate concentration in Florida**  **Bay.**

Figure 5.9 **Estimates of the annual exchange of total phosphorus at Florida Bay’s boundaries. Everglades estimates are annual me**  **dian inputs to wetlands from canals (since 1979 for Shark Slough and since 1984 for Taylor Slough and the C-111 basin).**  Figure 5.10 **Estimates of the annual exchange of TN at Florida Bay’s boundaries. Everglades estimates are annual median inputs**  **to wetlands from canals (since 1979 for Shark Slough and since 1984 for Taylor Slough and the C-111 basin). Note that flow** **weighted mean TN concentrations have been consistently de creasing since 1985 in both systems and that medians provided here**  **may be higher than those of recent years.**

Figure 5.11 **Estimates of the annual exchange of inorganic nitrogen at Florida Bay’s boundaries. Everglades estimates are annual me**  **dian inputs to wetlands from canals (since 1979 for Shark Slough and since 1984 for Taylor Slough and the C-111 basin).**  Nutrient Dynamics**banks, corals, or a host of other features could set up such shallow, subsurface flows. Flow through the**  **seafloor caused by currents flowing over topography or waves may be responsible for the elevated tracer con** **centrations in the water column.The nutrient concen trations of these advected waters are probably lower**  **than those sampled in wells and thus would lower the estimates of nutrient flux from groundwater flow.** **An additional mechanism that can drive ground**

**w ater flow is the difference in tidal elevations across**  **narrow reefs or barrier islands (Bokuniewicz and Pavlik, 1990; Reich**  **et al., 2002; Chanton**  **et al., 2003). Observa**  **tions of seepage in the Upper Keys are consistent with this hypothesized mechanism (Chanton**  **et al., 2003). On**  **an annual average basis, the water level in Florida Bay is several cm higher than the water level in the Atlantic**  **(Reich et al.,**  **2002). However, the Atlantic has a daily tidal range of roughly half a meter, whereas daily water**  **levels in Florida Bay are relatively constant.Therefore, during a high Atlantic tide, the ocean level is higher** **than the bay’s water surface, creating a pressure dif ferential pushing water from the Atlantic toward**  **Florida Bay. In contrast, when the Atlantic tide is low, the situation is reversed, and there is a pressure dif**  **ferential pushing ground water from Florida Bay toward the Atlantic (Reich**  **et al., 2002).**  **T he porous nature of the Key Largo Limestone**  **that underlies the Upper Keys is consistent with this delivery of ground water to Florida Bay by this tidal**  **pumping mechanism. Studies employing viral and**

**c hemical tracers have documented horizontal and ver**  **tical transport rates of meters per day for water flow in the subsurface (Dillon**  **et al., 1999, 2000, 2003; Paul**  **et al.,**  **1995, 1997, 2000; Lapointe et al.,**  **1990; Reich et al.,** **2002). Hydraulic conductivity in the Key Largo Lime stone ranges between 1,400 and 38,000 meters per day**  **(Dillon et al.,**  **1999; Vacher et al.,**  **1992). Dillon et al.**  **(1999) followed water-table height as a function of Atlantic tide**  **in an onshore well on Key Largo. In this well, the groundwater table oscillated with Atlantic tide with**  **only a 1.4-hour lag between Atlantic high tide and the highest water level in the well (Dillon**  **et al., 1999).**  **T here was only a 60% dampening of the tidal ampli** **tude as the pressure wave moved through the car bonate rock.The extremely transmissive nature of the**  **Ke ys aquifer system, in conjunction with the varying** **head differentials, promotes the interaction of sub surface waters with surface waters.**  **Ground waters in the shallow subsurface of the Ke** **ys contain dissolved nutrients from organic mate rials disseminated within the matrix (Sansone**  **et al., 1990) and are further contaminated from on-site**  **sewage-disposal systems. Sewage in the Florida Keys is discharged into more than 600 disposal wells that**  **penetrate the permeable Key Largo Limestone to depths of 10–30 m. Additionally there are an estimated**  **24,000 septic tanks and 5,000 cesspits on the islands (Kruczynski and McManus, 2002). Recent research has**  **demonstrated a direct interaction between waste water delivered to the subsurface via injection wells and sur**  **face waters (Corbett et al.,**  **2000b; Dillon et al.,**  **1999, 2000, 2003). Natural tracers, including**  **15 N of seagrass**  Hunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 65 Figure 5.12 **Relationship between TN and TP concentrations (annual flow-weighted mean) in waters flowing into Shark River Slough and annual water discharge into the slough.**  Nutrient Dynamics**tissue, have indicated that the greatest impact of groundwater discharge is along the shore of the Florida**  **Bay side of the Upper Keys (Corbett et al.,**  **1999). Nu trient inputs from Keys ground water may be domi**  **nated by wastewater inputs and so are considered in the next section.The associated nutrient load to coastal** 

**wa ters would be substantial without significant sub**  **surface biogeochemical alteration.This is particularly true with respect to phosphate delivery, which has**  **been shown to be the limiting nutrient in eastern Florida Bay. Studies of the fate of nutrients injected into**  **Class 5 wells in the Keys suggest phosphate removal with moderate nitrate attenuation (Corbett**  **et al., 2000b;**  **Dillon et al.,**  **2003). Although it is understood that phos phate may be removed during transport, it is not clear**  **whether this removal will be sustained. One question of particular importance is whether the phosphate** **may be released at some point to the phosphorus-lim ited waters surrounding the Keys, thus creating a sig**  **nificant water-quality problem for the marine environment. If phosphate uptake is ephemeral, then**  **long-term transport of phosphorus to coastal waters may occur through the limestone aquifers. There is**  **some evidence that the limestone surrounding Class 5 injection wells may saturate with phosphorus (Dil**  **lon et al.,**  **2003).**


### Atmospheric, Keys Waste Water, Keys Storm Water, and the Gulf of Mexico Nutrient Inputs

**T he remaining components of the Florida Bay nutri**  **ent budget (atmospheric, Keys wastewater and storm**

**w ater, and the Gulf of Mexico) have not been revised**  **since the 2001 conference. Atmospheric deposition is certainly an important nutrient source, particularly** **with regard to the relatively high input of inorganic ni trogen. The estimates in Figures 5.9–5.11 are derived**  **from a study by T. Meyers in 1999 and 2000 on Long Key (T. Meyers, personal communication). Although bulk** **deposition of nitrogen can be estimated from a long term National Atmospheric Deposition Program**  **(NADP) site in Everglades National Park, few data are**

**av ailable to estimate dry deposition of nitrogen or**  **phosphorus. Furthermore, phosphorus estimates in south Florida are often suspect because of the conta**  **mination of low ambient concentrations (Redfield, 2000). Estimates of the Florida Keys and Gulf of Mex** **ico contributions are based on methods and data de scribed in Rudnick**  **et al. (1999). The Keys estimate**  **entails far less uncertainty than the gulf estimate. It should be noted that the gulf contribution provided**  **here (Figures 5.9–5.11) probably overestimates inputs to interior Florida Bay because the flow meters that pro**  **duced the data used in the calculation were west of Florida Bay’s mud banks. A large proportion of water**  **flow measured by these flow meters never entered the bay. It should also be noted that a large discrepancy be**  **tween the estimates of Rudnick et al.**  **(1999) and Cerco et al.**  **(2000) exists.The latter estimate was based on flow fields derived from a hydrodynamic model (Table 5.2).** 


### Summary

**T he major source of TP and TN was the Gulf of Mex**  **ico (Figures 5.9, 5.10) and the major source of DIN was ground water (Figure 5.11). The smallest source of TP** 

**wa s Taylor Slough–C-111 (Figure 5.9). The smallest**  **input of TN was from the Keys (Figure 5.10), whereas the smallest inputs of DIN were from Shark River and**  **Ta ylor Sough–C-111 (Figure 5.11).**  

## Internal Nutrient Cycling

Benthic Nutrient Fluxes

**In situ benthic metabolism and nutrient regeneration** 

**w ere measured seasonally for 3 years (1997 through**  **2000) at five sites near the northern Florida Bay coast (Rudnick**  **et al., 2001) and for 1.5 years (1997–1998) at six**  **bay sites away from the northern coast (Carlson and Y** 

**arbro, 1999). Additional flux measurements have been made more recently in sediment cores (Cornwell and** **Owens, 2003).The most notable results of these stud ies have been that phosphorus fluxes are very low**  **(typically not significantly different from zero) and that inorganic nitrogen fluxes from sediment to water**  **are surprisingly low. Sediments consistently removed nitrates and nitrites from the water column under dark** **and light conditions. Compared to rates of sedimen tary oxygen uptake in the dark, rates of ammonium re**  **lease have been found to be very low. Median O:N (oxygen:nitrogen) molar ratios in dark chambers at**  **northern coastal sites greatly exceeded that expected from the mineralization of algal or seagrass detritus,**  **ranging from 51 to 124 (O uptake:N release) (Rudnick et al.,**  **2001). Given the high organic matter concentra tions of central Florida Bay, the finding of consistently**  **low (<50 μmol m –2**  **h –1**  **) ammonium fluxes from Rankin Lake sediments (Carlson and Yarbro, 1999; Kemp and**  **Cornwell, 2001) is surprising. Studies by Cornwell**  **et al. (2000) and Kemp and**  **Cornwell (2001) provide insights of mechanisms that explain the observed low rates of ammonium regen**  **eration. They found that ammonium fluxes were negatively correlated with benthic chlorophyll**  **a con**  **centrations (Figure 5.13), perhaps because benthic algae stimulate coupled nitrification-denitrification.**  Florida Bay Synthesis Hunt and Nuttle

66 FWRI Technical Report TR-11 Nutrient Dynamics**T hese studies found that net N**  **2 fluxes were typically** **from sediment to water (dentrification exceeding ni trogen fixation). Denitrification rates (dark N**  **2 fluxes)**  **at six sites averaged 127 ± 87 μmol m –2**  **h –1**  **in August and 65 ± 82 μmol m**  **–2 h**  **–1 in March.These fluxes greatly ex** **ceeded ammonium fluxes. Further support for the in ference that low inorganic nitrogen regeneration is**  **attributable to coupled nitrification-denitrification was provided by**  **in situ h**  **ypoxia experiments (Rudnick et al.,**  **2001). Dissolved oxygen and nutrients were followed in a time series over 28 hours in dark benthic cham**  **bers. When dissolved oxygen in the water column dropped below 0.2 mg/L, ammonium fluxes increased**  **five fold. Y** 

**arbro and Carlson (unpublished) measured ben thic fluxes of filterable reactive phosphorus (FRP),**  **NH 4**  **+ , s**  **ilicate, TP, TN, dissolved organic phosphorus (DOP), and DON in seagrass beds in the eastern bay**  **(Sunset Cove and Swash keys), central bay (Rankin Lake and Calusa Key), and western bay (Johnson and**  **Rabbit Key basins). FRP fluxes ranged from uptakes of 3 μmol m**  **–2 h**  **–1 in Johnson Key Basin in the western bay**  **to releases of 1–2 μmol m –2**  **h –1**  **in the eastern bay. Dis solved organic phosphorus (DOP) fluxes (2–4 μmol** 

**m –2**  **h –1**  **) were considerably higher than FRP fluxes and**

**w ere more often released from the benthos, especially**  **at central and western bay sites. These small fluxes are in sharp contrast to the large phosphorus pool in**  **surficial sediments (1–12 μmol gDW –1**  **). Additionally, the sharp increase in sediment phos**  **phorus from east to west in the bay was not reflected in benthic fluxes. Keeping in mind that these fluxes rep**  **resent net flux to or from the seagrass community, we estimate that ammonium and the sum of FRP and**  **DOP fluxes can meet 20%–50% of the phytoplankton demand in the eastern and western regions of Florida**  **Bay but only 5%–10% of the phytoplankton demand in the highly productive,**  **Synechococcus -dominated north**  **central bay.** 

### Internal Nutrient Cycling: Carbonate-Phosphorus-Iron Relations

**A study by Chambers et al.**  **(2001) documented the spatial variation in sediment phosphorus, iron, and** **sulfur.Total sediment phosphorus decreases on a west east gradient across Florida Bay, similar to the pattern** **in which surface-water quality decreases. Mineral sul fides and extractable iron in Florida Bay sediments**  **decrease on a north-south gradient. Most inorganic phosphorus in the sediment is associated with abun**  **dant calcium carbonate minerals and not with reactive iron oxides that occur in very low concentrations. Iron** 

**av ailability limits mineral sulfide formation, but dis**  **solved sulfide concentrations in Florida Bay sediments are high. Experimental addition of reactive iron to sea** **grass plots in Florida Bay stimulated phosphorus re tention in the sediment and buffered plants from toxic** **sulfide accumulation. Phosphorus availability to sea grass still appears to limit production in carbonate** **sediments more than sulfide toxicity. Generation of in organic phosphorus in seagrass sediments may occur** **directly via mineralization of organic matter and in directly via concomitant carbonate mineral dissolution**  **(Ku et al.,**  **1999).**


### Role of Sediment Resuspension in Phosphorus Cycling

**Phosphorus is retained on the surface of calcium car bonate sediments (Zhang and Fischer, 2001). Within a**  **few minutes of sediment resuspension, phosphate that is weakly bound to particle surfaces is released to the** 

**w ater column, where it may be used by phytoplankton.**  **Coprecipitation of calcium phosphate with calcium carbonate may scavenge dissolved phosphate out of the** 

**w ater column.**  **T**

**otal sedimentary phosphorus (TSP) was frac tionated into five chemically defined pools (Zhang and**  Hunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 67 T able 5.2 **Comparing Florida Bay nutrient budgets (positive into system) (from Cerco et al.,**  **2000).**

Rudnick et al. Model Dry Season Model Wet Season
To tal P Total N Total P Total N Total P Total N System (kg/day) (kg/day) (kg/day) (kg/day) (kg/day) ( kg/day)
**Everglades 7.1 685**  **3.0 679 9.1 1,753**  **Atmosphere 104.1 1,945**  **127.0 2,393 127.0 2,393** 
**Ke ys Loads**  **115.1 466 54.9 238**  **54.9 238**
**W estern Boundary**  **1,112.3 21,918 192.7 3,105**  **-589.6 –6,217 Ke** **ys Passes –493.2 –32,877**  **101.8 2,068 158.4 4,154** 
Net 845.5 –7,863 479.4 8,483 –240.2 2,321 Nutrient Dynamics**Fischer, 2001): (1) adsorbed (readily exchangeable) in organic and organic phosphorus, (2) Fe-bound inor**  **ganic phosphorus, (3) autogenic apatite calcium carbonate-bound inorganic and organic phosphorus,** **(4) detrital apatite phosphorus, and (5) refractory or ganic phosphorus. This study observed a strong gra**  **dient of decreasing TSP from the west (14.6 μmol g –1**  **) to the east (1.2 μmol g** **–1 ) across central Florida Bay**  **(Zhang et al.,**  **2004). Among the five pools, autogenic apatite calcium**  **carbonate-bound phosphorus accounted for the largest fraction of phosphorus (45% of TSP; Zhang**  **et al., 2004);**  **inorganic phosphorus dominated this pool (70%–90%). T** **he refractory organic phosphorus (24% of TSP) and iron-bound inorganic phosphorus (19% of TSP) were** **the second largest pools. Adsorbed phosphorus ac counted for 8% of TSP (60% organic phosphorus), and**  **detrital apatite phosphorus composed the smallest fraction (5% of TSP). Overall, organic phosphorus ac**  **counted for 38% of TSP.**



### Nutrient Flux at the Sediment–Water Interface

**Y**

**arbro and Carlson (1999) measured silicate fluxes that ranged from –337 μmol m**  **–2 h**  **–1 at Rankin Lake,**  **(September 1997) to 766 μmol m –2**  **h –1**  **(August 1998). Ammonium fluxes ranged from –8.3 μmol m**  **–2 h**  **–1 at**  **Rankin Lake (November 1998) to 156 μmol m –2**  **h –1**  **at Sunset Cove in November 1998.Total dissolved nitro**  **gen fluxes were highly variable between sites and sampling dates, ranging from –340 μmol m**  **–2 h**  **–1 at**  **Rabbit Key Basin in August 1998 to 193 μmol m –2**  **h –1**  **at Sunset Cove in November 1998. Dissolved organic ni**  **trogen (DON) also varied between sites and sampling dates, ranging from 5.7 μmol m**  **–2 h**  **–1 at Swash (May**  **1998) to 250 μmol m –2**  **h –1**  **at Rabbit Key Basin (August 1998). Net DON flux was always from the sediment to**  **the water column. Because filterable reactive phosphorus (FRP) con**  **centrations generally were very low, flux estimates**

**w ere highly variable (Yarbro and Carlson, 1999).Total**  **dissolved phosphorus and FRP fluxes ranged from net uptakes of –6.23 to –0.02 μmol m**  **–2 h**  **–1 and sediment**  **releases of 0.02 to 11.57 μmol m –2**  **h –1**  **. M ost fluxes were**  **less than 1 μmol m –2**  **h –1** 

**.** 

### Seagrass Modeling

**An ecological model of the Florida Bay seagrass com munity, funded by USGS through the Critical Ecosys**  **tems Initiative, was conceived as a means of enhancing the ability of managers to improve health of the Florida**  **Bay ecosystem, seagrass habitat in particular (Madden** Florida Bay Synthesis Hunt and Nuttle

68 FWRI Technical Report TR-11 Figure 5.13 **Results from denitrification study conducted by Cornwell (2001). This figure indicates the importance of benthic**  **microalgae in the nitrogen cycle. Ammonium uptake from the**

**w ater column is associated with high chlorophyll concentrations.**  Nutrient Dynamics**et al., 2003, McDonald and Madden, 2003; Figures 5.14,** **5.15). This model is a dynamic, mechanistic simula tion of seagrasses, emphasizing nutrient cycling and**  **nutrient demand related to seagrasses. It is being used as a tool for determining the causes of seagrass mor** **tality due to environmental stress and to calculate nu trient-sink characteristics of the seagrass community.**  **In scenario analyses, this model was used to test the effects of individual and simultaneous multiple**  **stressors, at levels measured to occur in situ**  **on primary productivity. Application of multiple stressors involv**  **ing elevated nutrients, salinities, and elevated sulfide concentrations produced dramatic results in the**  **Tha lassia**  **growth profile. Biomass declined continuously from the point of application of simultaneous stressors**  **in January throughout the growing season as T** **halas sia**  **rapidly died off. Examination of processes under ly** **ing this model behavior revealed that photosynthesis, though operational, was impaired and functioning at** **such a low level that the net daily production was neg ative throughout the growing season.** **Interaction of the above- and below-ground com partments played a strong role in the trajectory of the** **seasonal biomass curve in the model. Exchanges of or ganic carbon and nutrients between leaf and root com**  **partments are seasonally variable and critical for survival of submerged plants.The modeled plants can** **mobilize below-ground resources to supplement car bon input to the above-ground compartment should**  **autotrophic assimilation become deficient.The amount of carbon in the root/rhizome material available for**  **growth supplementation can control the outcome of plants subjected to stress conditions. Therefore, the** **status of the below-ground compartment can deter mine the survival of the entire plant. Conversely, when** **conditions are unfavorable to growth and below ground resources are depleted, the existence of above**  **ground plant material can mask a plant community in fragile condition. We believe that this model’s con** **ceptualization is realistic and is likely close to the phys iological and community reactions that occur in the real**  **system, emphasizing the importance of thresholds and nonlinear reactions, which can be tracked and re** 

**v ealed by model analysis.** **A series of model runs were made to determine nu trient demand under a range of C:N ratios (15–36) and**  **C:P (400–1800) ratios typical of the bay. On an annual basis, P supplied to sediment pore waters via organic**  **remineralization and rock dissolution each averaged about 1–1.5 mg P m**  **–2 d**  **–1**
**, whereas P exported from the**  **Everglades averaged 0.05 mg P d –1**  **to overlying waters in Little Madeira Bay (Rudnick**  **et al., 1999). Depending**  **on tissue ratios of nutrients applied to the model, these rates supply from >1,000% to only 30% of P demand by**  **T halassia.**  **Significantly, the C:P ratio estimated by in**

**v erse modeling required to use 100% of the available**  **sediment P regenerated daily (2.3 mg –2**  **d –1**  **) is 500:1, which approaches the average C:P ratio of 800:1 that**  **has been measured empirically in Little Madeira Bay and northeastern Florida Bay.**  

## Influence of Florida Bay Water Quality on the Reef Tract

Nutrient Export Through Keys Passes

**T he rate of outflow was estimated by Lee and Smith**  **(2002) from measurements made in Channel 5 and Channel 2 near Long Key in 1997 and 1998. The long**  **term mean was 370 m 3**  **/s (11.7** × **109 m 3**  **/y).The estimated exports (MT/y) were TP = 180; TN = 4,600; DIN = 200** **(Figures 5.9–5.11). Nutrient concentrations were mea sured as part of FIU’s monitoring (Jones and Boyer,** **2002), and the flux calculation assumed median con centrations.**  **Based on these estimates, Florida Bay is a sink for approximately half of the inputs of TP and TN and**  **more than 80% of the inputs of DIN. Additional export of N and P from Florida Bay may occur in the form of** **drift seagrasses and algae but no quantitative esti mates have been made of these exports.** 



## W ater-Quality Modeling

**T he water-quality model (Cerco**  **et al., 2000) linked** **modules including water-column eutrophication, sea grass dynamics, sediment diagenesis, solids and nu**  **trient resuspensions, and benthic algal production.To our knowledge, this is a first for Florida Bay. In fact, we** **know of few systems that currently have a model ap plication to rival the current effort in Florida Bay. How** 

**ev er, the model requires substantial upgrading to fully**  **represent processes in the bay. Nutrient loads from various sources to the bay**  **and surrounding waters were calculated for the model study. Estimates indicated that the atmosphere is the**  **largest loading source to the bay. Runoff from the mainland is the smallest source of phosphorus and sec**  **ond smallest source of nitrogen. Paradoxically, runoff appears to be the most intensely studied loading**  **source.There are large degrees of uncertainty as to what the greatest loads are. Attention should be devoted to**  **accurately quantifying atmospheric and phosphorus loads from the Keys.**  **No in situ**  **measures of nitrogen fixation were avail able to us. Rates associated with seagrass beds, mea**  **sured in other systems, were adapted for the model.** Hunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 69 Nutrient Dynamics**Estimated nitrogen fixation associated with seagrass leaves equals the estimated atmospheric nitrogen load.**  **T**

**he sum of nitrogen fixed in the leaves and roots makes nitrogen fixation the largest single source to the system.** **Measures of nitrogen fixation are currently being con ducted and these measures should be swiftly incorpo**  **rated into the model and into system nutrient budgets. Measures of denitrification within benthic sedi**  **ments were also unavailable. Rates of denitrification**

**w ere calculated by the sediment diagenesis model,**  **with values adapted from Chesapeake Bay. Calculated denitrification roughly equals total nitrogen fixation.**  **Denitrification rates should be measured and used to**

**v erify the computations provided by the model.**  **T**

**he model underestimates the amount of nitrogen in both the sediments and water column. Sensitivity** **analysis indicates that the shortfall is unlikely to origi nate from the loading estimates. Either a source of**  **nitrogen has been omitted or the estimated loads are greatly in error.Potential sources of omission or error in**  **clude groundwater,nitrogen fixation,and denitrification. T** 

**he model does not indicate that material does not concentrate in the central basins.This behavior may be** **attributed to several factors. First, the underlying hy drodynamic calculations may not concentrate mater**  **ial. Second, the linkage method may introduce errors in the computed hydrodynamic field.Third, the water**  **quality grid and numerics may introduce artificial dispersion. Dye-tracer tests indicated that the water** **quality model qualitatively tracks transport in the hy drodynamic model in Florida Bay. (Transport is not** **equivalent on the western shelf because of artificial dis persion and boundary-condition specification.) The** **tracer tests led us to the conclusion that the underly ing hydrodynamics prevent computation of hyper**  **salinity and concurrent concentration of nitrogen and other materials.**  **Interpretation of results from the water-quality** Florida Bay Synthesis Hunt and Nuttle

70 FWRI Technical Report TR-11 Figure 5.14 **Ecosystem process model of south Florida estuarine systems. Conceptual diagram of Florida Bay seagrass model emphasiz ing major nutrient cycles. (Madden**  **et al., 2003).**  Nutrient Dynamics**model was severely compromised by the lack of a ver ified hydrodynamic model operable on the same time**  **scale as the water-quality model. Successful simulation of a ten-year sequence of** 

**w ater quality was virtually impossible without corre**  **sponding hydrodynamics.The highest priority should be given to applying a detailed, volume-conservative**  **h**

**ydrodynamic model to the bay and adjoining wa ters.The model should simulate at least a ten-year pe**  **riod and provide good agreement to salinities observed within that period.**  **T he major uncertainty in the system’s nutrient**  **budget is transport across the western boundary and through the Keys passes.This transport cannot be ob**  **served on a long-term basis. Computation via a model is the only alternative for long-term budget estimates.**  **High priority should be given to estimating flow across system boundaries once a verified hydrodynamic**  **model is available. Sensitivity analysis indicated that model compu**  **tations are very sensitive to the biological activity at the sediment–water interface. In the present model, this ac**  **tivity is represented by the benthic algal component, and as formulated, the model cannot represent all ob**  **served fluxes, especially those of dissolved organic matter. Attention should be devoted to quantifying**  **sediment–water fluxes, to investigating the nature of the benthic community, and to process-based model**  **ing of this community. A great number of observations have been col**  **lected in the bay since this study commenced, and considerably more is known about the bay than was**  **known a few years ago. Once suitable hydrodynamics are available, the water-quality model should be reap**  **plied on a ten-year time scale and validated with the latest observations of conditions and processes in the** **bay. Concurrent with the reapplication, first-order im provements (**  **e.g., division of dissolved organic matter** **into labile and refractory components) can be incor porated into the water-quality model.** **As part of the Florida Bay and Florida Keys Feasi bility Study of the CERP, a new attempt is currently**  **being made to develop, calibrate, validate, and apply a Florida Bay water-quality model.**  

## Current and Ongoing Research

Unresolved Questions

**P**

**ast informational needs relative to nutrient cycling in Florida Bay have been coupled to understanding the**  **factors that triggered the mass mortality of seagrass and what initiated and maintained the phytoplankton**  **blooms. Current needs have become more focused around assessing the effects of various environmental**  **management strategies being considered for bay restoration. In particular, we need to accurately predict**  **the sensitivity of the bay’s nutrient cycles to changing freshwater flow to the bay and the resultant change in** **the bay’s salinity regime. For much of the bay, any fac tor that increases phosphorus availability, either by**  **increasing sources or decreasing removal, is likely to exacerbate the current problems of the bay. Recent** 

**e vidence also indicates that algal blooms in the cen**  **tral and western bay are also stimulated by nitrogen enrichment.Thus we need a thorough understanding**  **of the bay’s nutrient cycles, particularly with regard to the fate and effects of dissolved organic nitrogen in** **puts from the Everglades. Understanding the mecha nisms that have triggered and are sustaining algal** **blooms in the bay is fundamental to restoration deci sion-making. This understanding entails quantifying** **the nutrient demands of these algae and how these nu trients are supplied. Questions that the future pro**  **gram should address in order to meet these needs are as follows:** 

**• W hat are the sources of nutrients that sustain algal**  **blooms?**

**Understanding the mechanisms that have trig gered and are sustaining algal blooms in the bay is fun**  **damental to restoration decision-making. This understanding entails quantifying the nutrient de**  **mands of these algae and how these nutrients are supplied.** 

**• H ow**  **will changing freshwater flow directly and in**

**directly alter the supply and availability of nutri ents in the bay? What effect does changing salinity**  **have on nutrient availability in the bay?**



## ° **How will the quality and quantity of nutrient out** Hunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 71 Figure 5.15 **T heoretical phosphorus demand by**  **T halassia**  **in mg per m**  **2 per day as calculated by the seagrass model to satisfy**  **seagrass primary productivity rates in northeast Florida Bay.** Nutrient Dynamics**puts from the Everglades change with restoration?**



## ° **W hat is the fate and effect of dissolved organic**  **matter from the Everglades and how will this**

**c hange with restoration?** 



## ° **W hat effect does changing salinity have on nutri**  **ent cycling and availability in the bay? W**  **ith increased freshwater flow expected from restoration of the Everglades and Florida Bay, nutrient** **loading from the Everglades watershed will also prob ably increase. For nitrogen, most of this loading will be**  **in the form of dissolved organic compounds. The sources, fate, and effects of DON from the Everglades** 

**w atershed are unknown, and predictions of how chang** **ing freshwater flow will influence these DON dynam ics are highly uncertain. Measurements of the**  **composition and bioavailability of Everglades DON to Florida Bay’s microbial communities (pelagic, epi**  **phytic, and benthic) are essential in order to assess the functional relationship of Florida Bay and its watershed.**  **Although the magnitude of this expected increase is unknown, this direct input may be less important than**  **the indirect effect of an altered salinity regime caused by**  **increased freshwater influx. Altered salinity can af fect internal nutrient cycling by (1) altering community** **structure (such as changing seagrass-species domi nance, thus changing nutrient storage and cycling),** **and (2) modifying specific processes, such as phos phorus surface reactions and sulfate reduction. A** 

**c hange in freshwater flow and salinity could also alter**  **nutrient processing in the mangrove zone and thus alter nutrient exchange along the bay’s northern bound**  **ary, the Gulf of Mexico boundary with the Everglades, and near mangrove islands in the bay.**  **Th e factors that influence the loading of nutrients**  **into Florida Bay and the availability of nutrients within the bay are not well understood. In particular, we need** **to understand the effect that potential environmental management actions, such as increasing freshwater**  **flow and decreasing salinity, will have on the bay’s nutrient transformations and fluxes. Information on**  **suspended sediment particles and on factors that may influence the mobilization and immobilization of phos**  **phorus in carbonate sediments is critical. Results of past experiments (Zhang**  **et al., 1999) need to be evaluated**  **in the context of the development of a water-quality model to assess the sufficiency of current data for es**  **timating salinity effects. Given the unusually high ammonium concentra** **tions of the bay and the potential for nitrogen limita tion in the western bay, experiments on factors that may** **influence key nitrogen transformations, such as nitri fication and denitrification, are also needed. Experi**  **ments that explore how nutrient cycling is altered by**

**c hanges in seagrass community structure and physi**  **ological condition (particularly below-ground nutrient**

**c hanges) are also important but have yet to be done.** 

**• W hat effect does a change in seagrass community**  **structure have on nutrient availability in the bay? Has seagrass mortality only increased nutrient avail**  **ability by releasing nutrients from this detrital source or has seagrass mortality also caused other less di**  **rect changes, such as a decrease in the capacity of the sediments to sequester nutrients?** 

**T he lag of several years between the onset of sea**  **grass mass mortality and the occurrence of algal blooms in the bay argues against the hypothesis that only nu**  **trients released from dead seagrass tissue fuel the blooms. However, the increase in nutrients from this** **detrital source, combined with a net decreased up take capacity associated with seagrass mortality, may**  **explain the bloom’s temporal patterns.Thus, we need estimates of net benthic nutrient uptake or release**  **rates over a range of seagrass growth rates, mortality rates, and detrital decomposition rates for different**  **seagrass species. The accuracy of such estimates may depend largely upon understanding sedimentary nu** **trient transformations, including how seagrass roots af fect nutrient mobility and how such processes change**  **with seagrass mortality. Seagrass mortality may have indirectly affected nutrient cycles in the bay. For ex** **ample, sediment resuspension increases with de creasing seagrass density, and phosphorus associated**  **with this suspended sediment may be available to phytoplankton. Finally, changing seagrass cover also in**  **fluences the biomass and activity of benthic algal mats. T** **his change in microbial mats in turn affects nitrogen**

**av ailability by altering patterns of nitrification, deni**  **trification, and nitrogen fixation. Measurements of the quantitative relationships of these processes within**  **the algal and SAV community structures are needed. Given the shallow depth and restricted circula**  **tion of Florida Bay, internal cycling and transformations of nutrients probably have a strong influence on the**  **structure and productivity of bay communities.These nutrient pathways and transformations have not been** 

**w ell studied. Essential measurements include nutrient**  **uptake by primary producers (especially seagrass and phytoplankton), the exchange of nutrients between**  **the sediments and the water column, the diagenesis of nutrients within the sediments (especially phospho**  **rus–carbonate reactions and nitrogen transformations), and microbial and inorganic reactions within the water**  **column (such as nitrification and phosphorus sorption to and removal from suspended sediment).** 

**• H ow**  **do we deal with the spatial heterogeneity of in**

**ternal nutrient cycling in the bay?** Florida Bay Synthesis Hunt and Nuttle

72 FWRI Technical Report TR-11 Nutrient Dynamics**T here is no unified field theory for ecology—**  **process rates from one area may not be applicable to another. What other factors are important in driving**  **these processes?**

**• W hat is the quantitative role of microphytobenthos**  **in nutrient cycling and how is this likely to change with Everglades restoration?** 

**T he microphytobenthos has been shown to be in**  **fluential in regulating benthic flux rates. Fluxes in the form of drift seagrasses and algae have not been de**  **termined.**

**• T o what extent is atmospheric deposition of nutrients**  **contributing to ecological changes in Florida Bay? W**  **hat is temporal variability (including long-term trend) of this nutrient source?** 

**Atmospheric inputs have been shown to be a sig nificant component of external nutrient loading, es**  **pecially of nitrogen.There are no estimates of long-term trends in atmospheric nutrient-loading at present.** 

**• Is ground water an important nutrient source in** 

**Florida Bay? If so, what is the spatial and temporal pattern of this input?** 

**Given the high nutrient content of the groundwa ter beneath most of the bay, any groundwater flux ap**  **proaching recently published rates (about 1 cm d –1**  **)**

**w ould result in a very high nutrient flux.The accuracy** **of these estimates should be checked—sites with sig nificant upward groundwater advection should be**  **identified; if found, nutrient concentrations at these sites should be measured.**  

### Summary of Ongoing Research

**• Continued monitoring of ambient water quality in** 

**Florida Bay. • C**  **ontinued monitoring of freshwater inflows and**

**loads with expansion of network along Florida Bay and southwest Florida gulf coast beginning.**  **• C ontinued monitoring of coastal circulation and bi** 

**ological and chemical parameters, with interpreta tion of transport and exchange of south Florida**  **coastal waters.**

**• Expanded research into nutrient cycling in wet** 

**land/mangrove areas and seagrasses/epiphytes.**

**• Study of carbonate system–phosphorus–iron rela** 

**tions.**

**• Characterization of chemical structure of organic** 

**carbon and nitrogen from wetland/mangrove areas.**

**• Assessment of microbial bioavailability of organic** 

**carbon and nitrogen from wetland/mangrove areas.**

**• Expanded measurements of benthic nitrogen fixa**  **tion, nitrification, and denitrification rates.**

**• Measurements of phytoplankton nitrogen uptake** 

**rates.**

**• Quantification of microbial loop parameters: het** 

**erotrophic bacterial numbers, bacterial production, nanoflagellate/protist grazing rates, and phyto**  **plankton primary production. • E**  **ffects of variability in regional climate, freshwater**

**inputs, disturbance, and perturbations on the coastal Everglades ecosystem.**  **• D ev**  **elopment of nitrogen and phosphorus mass**

**balance models and measurements of nutrient cy cling rates in Florida Bay.** 

**• Assessment and monitoring of dissolved nitrogen in** 

**Florida Bay.**

**• Measurement of nutrient fluxes through Florida** 

**Ke ys passes.** 

**• Monitoring of salinity and estimates of fluxes of** 

**w ater and total nitrogen and phosphorus across the**  **southern Everglades mangrove zone. • D**  **ev elopment of an integrated hydrodynamic and** 

**w ater-quality model to evaluate relationships with**  **freshwater flow and oceanic/gulf hydrodynamics and exchange is in a planning phase.** 

**• Seagrass uptake kinetics of phosphorus.** 

**• Influence of dissolved organic matter on seagrass,** 

**epiphyte, and phytoplankton productivity. • S**  **eagrass survival and productivity under single and**

**multiple stresses.**

**• Dynamic simulation model analysis of spatial pat** 

**terns of seagrass productivity, community structure, and nutrient demand.** 



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**JONES, R. D., and J. N. BOYER. 2002. FY2001 Annual Report of the South Florida Estuarine Water Quality**  **Monitoring Network. SFWMD/SERC Cooperative Agreement #C-10244. SERC Technical Report T-177.**  **http://serc.fiu.edu/wqmnetwork/SFWMD–CD/Data/ 2001EWQS.pdf** 
**KEMP, W. M., and J. CORNWELL. 2001. Role of ben thic communities in the cycling and balance of nitro**  **gen in Florida Bay. Final report to EPA Region 4.**
**KRUCZYNSKI, W. L., and F. McMANUS. 2002. Water quality concerns in the Florida Keys: sources, effects,**  **and solutions. Pp. 827–881 in**  **J. W. Porter and K. G. P** 

**orter, eds. The Everglades, Florida Bay, and Coral Reefs of the Florida Keys: An Ecosystem Sourcebook.**  **CRC Press, Boca Raton, Florida.**
**KU, T. C. W., L. M. WALTER, M. L. COLEMAN, R. E. BLAKE, and A. M. MARTIN. 1999. Coupling between** **sulfur recycling and syndepositional carbonate disso lution: Evidence from oxygen and sulfur isotope com**  **positions of pore water sulfate, South Florida platform. Geochimica Cosmochimica Acta 63: 2529–2546.** 
**LAPOINTE, B. E., J. D. O’CONNELL, and G. S. GAR RETT. 1990. Nutrient couplings between on-site sewage**  **disposal systems, groundwaters, and nearshore surface**

**w aters of the Florida Keys. Biogeochemistry 10: 289–307.** 
**LAVRENTYEV, P. J., H. A. BOOTSMA, T. H. JOHEN GEN, J. F. CAVALETTO, and W. S. GARDNER. 1998. Mi** **crobial plankton response to resource limitation: in sights from the community structure and seston**  **stoichiometry in Florida Bay, USA. Marine Ecology Progress Series 165: 45–57.** **LEE,T. N., and N. P. SMITH. 2002.Volume transport vari ability through the Florida Keys Tidal Channels. Jour**  **nal of Continental Shelf Research 22:1361-1377.**
**MADDEN, C. J., and A. McDONALD. 2006. An Eco logical Model of the Florida Bay Seagrass Commu**  **nity. Model Documentation Version II. South Florida W**  **ater Management District. MADDEN, C. J., A. McDONALD, S. KELLY, and M.**  **K OCH. 2003. Use of a dynamic, mechanistic simulation**  **model to assess ecology and restoration of the Florida Bay seagrass community. P. 148**  **in 2003 Florida Bay**  **Science Conference, 13–18 April 2003,Palm Harbor, Florida. (Abstracts)** 
**McDONALD, A., and C. J. MADDEN. 2003. A model of seagrass dynamics in Florida Bay: Evaluation and ap**  **plication. P. 180 in**  **2003 Florida Bay Science Conference, 13–18 April 2003,Palm Harbor, Florida. (Abstracts)** 
**NIELSON, O., M. S. KOCH, H. S. JENSEN, AND C. J. MADDEN. 2006.**  **T halassia testudinum**  **phosphate uptake kinetics at low**  **in situ concentrations using a**  **33 P radio**  **isotope technique. Limnology and Oceanography 51: 208–217.** 
**NUTTLE, W. K., J. W. FOURQUREAN, B. J. COSBY, J. C. ZIEMAN and M. B. ROBBLEE. 2000. Influence of net** **fresh water supply on salinity in Florida Bay.Water Re sources Research 36:1805-1822.** 

**O WENS, M., J. C. CORNWELL. 2001. Nitrogen cycling** **in Florida Bay mangrove environments: sediment**

**w ater exchange and denitrification. P. 90**  **in 2001 Florida**  **Bay Science Conference. (Abstract)**

**PA UL, J. H., M. R. McLAUGHLIN, D. W. GRIFFIN, E.** **K. LIPP, R. STOKES, and J. B. ROSE. 2000. Rapid move ment of wastewater from on-site disposal systems into**  **surface waters in the Lower Florida Keys. Estuaries 23: 662–668.** 

**PA UL, J. H., J. B. ROSE, J. BROWN, E. A. SHINN, S.**  **MILLER, and S. FARRAH. 1995. Viral tracer studies indicate contamination of marine waters by sewage dis** **posal practices in Key Largo, Florida. Applied and En vironmental Microbiology 61: 2230–2234.** 

**PA UL, J. H., J. B. ROSE, and S. C. JIANG. 1997. Evidence** **for groundwater and surface marine water contami nation by waste disposal wells in the Florida Keys.**  **Wa ter Research 31: 1448–1455.**  Hunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 75 Nutrient Dynamics**PHLIPS, E. J., and S. BADYLAK. 1996. Spatial variabil ity in phytoplankton standing crop and compostion in**  **a shallow inner-shelf lagoon, Florida Bay. Bulletin of Marine Science. 58: 203-216.**  **PRICE, R. 2001.The hydrology of the Everglades. Ph.D. Dissertation. University of Miami, Florida.** 
**PRICE, R. M., and P. K. SWART. 2001. Seawater intru sion: A mechanism for groundwater flow into Florida**  **Bay. Pp. 31–33 in**  **2001 Florida Bay Science Conference. (Abstract)**  **REDFIELD, G.W. 2000. Ecological research for aquatic science and environmental restoration in South Florida.**  **Ecological Applications 10: 990–1005.**
**REICH, C. D., E. A. SHINN,T. D. HICKEY, and A. B.TI HANSKY. 2002.Tidal and meteorological influences on**  **shallow marine groundwater flow in the upper Florida Ke** **ys. Pp. 659–676 in**  **J. W. Porter and K. G. Porter, eds. T** **he Everglades, Florida Bay, and Coral Reefs of the Florida Keys: An Ecosystem Sourcebook. CRC Press,**  **Boca Raton, Florida.**
**RUDNICK, D.T. 1999. Benthic nutrient fluxes near the**

**w etland ecotone of Florida Bay. 15th International**  **Conference of Estuarine Research Federation, New Orleans, Louisiana, USA. 25–30 September 1999.** 
**RUDNICK, D., Z. CHEN, D. CHILDERS,T. FONTAINE, and J. N. BOYER. 1999. Phosphorus and nitrogen inputs** **to Florida Bay: the importance of the Everglades wa tershed. Estuaries 22: 398–416.** 
**RUDNICK, D., S. KELLY, C. DONOVAN, J. CORN WELL, and M. OWENS. 2001. Patterns of inorganic**  **nitrogen flux from northern Florida Bay sediments. Pp. 96–97**  **in 2001 Florida Bay Science Conference. (Ab**  **stract)**
**SANSONE, F. J., G. W. TRIBBLE, C. C. ANDREWS, and J. P. CHANTON. 1990. Anaerobic diagensis within**  **Recent, Pleistocene, and Eocene marine carbonate frameworks. Sedimentology 37: 997–1009.** 
**SHINN, E. A., R. S. REESE, and C. D. REICH. 1994. F**  **ate and pathways of injection-well effluent in the Florida Keys. U. S. Geological Survey Open-File Report**  **94–276. SUTULA, M., J. DAY, J. CABLE, and D. RUDNICK.**  **2001. Hydrological and nutrient budgets of freshwater and estuarine wetlands of Taylor Slough in southern**  **Everglades, Florida, USA. Biogeochemistry 56: 287–310. SUTULA, M., B. PEREZ, E. REYES, D. CHILDERS, S.**  **DA VIS, J. DAY, D. RUDNICK, and F. SKLAR. 2003. Fac** **tors affecting spatial and temporal variability in ma terial exchange between the Southeastern Everglades** 

**w etlands and Florida Bay, USA. Estuarine and Coastal**  **Shelf Science 57: 757–781.**
**SZMANT, A. M., and A. FORRESTER. 1996.Water col umn and sediment nitrogen and phosphorus distrib**  **ution patterns in the Florida Keys, USA. Coral Reefs 15: 21-41.** 

**TO P,**  **Z., L. E. BRAND, R. D. CORBETT, W. BURNETT, and J. CHANTON. 2001. Helium and radon as tracers**  **of groundwater input into Florida Bay. Journal of Coastal Research 17: 859–868.** 

**VA CHER, L. H., J. J.WRIGHTMAN, and M.T. STEWAR.** **1992. Hydrology of meteoric diagenesis: effect of Pleis tocene stratigraphy on freshwater lenses of Big Pine**  **Ke y,**  **Florida. Pp. 213–219 in**  **C. W. Fletcher and J. F. W** 

**ehmiller, eds. Quaternary Coasts of the United States, Marine and Lacustrine Systems. SEMP Special Publi**  **cation, No. 48.**

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**Y**

**ARBRO, L. A., and P. R. CARLSON. 1999. Nutrient flux at the sediment–water interface in Florida Bay. Pp.**  **106–108 in**  **1999 Florida Bay and Adjacent Marine Sys tems Science Conference. (Abstract)**  **ZHANG, J.–Z., and J. CHI. 2002. Automated analysis of nanomolar concentrations of phosphate in natural wa**  **ters with liquid waveguide. Environmental Science and Technology 36: 1048–1053.** 
**ZHANG, J.–Z., and C. FISCHER. 2001.The role of sed iments resuspension in phosphorus cycle in Florida**  **Bay. Pp. 98–99 in**  **2001 Florida Bay Science Conference. (Abstract)** 
**ZHANG, J.–Z., C. FISCHER, C. KELBLE, and F. MILLERO, 1999. Phosphate distribution coefficients**  **for suspended sediments in Florida Bay. P. 77 in**  **1999 Florida Bay and Adjacent Marine Ecosystems Science**  **Conference. (Abstract)**
**ZHANG, J.–Z., C. J. FISCHER, and P. B. ORTNER. 2004. Po**  **tential availability of sedimentary phosphorus to sediment resuspension in Florida Bay. Global Biogeo** 

**c hemical Cycles 18: 4008–4022.**  Florida Bay Synthesis Hunt and Nuttle

76 FWRI Technical Report TR-11 Nutrient DynamicsFWRI Technical Report TR-11 77 

## Introduction

Question 3**—What regulates the onset, persistence, and fate of planktonic algal blooms in Florida Bay?** 

**F rom the 1950s to the mid 1980s, Florida Bay was char** **acterized by expansive seagrass beds, mangrove is lands, and crystal-clear water. In the past 16 years,**  **there have been some dramatic changes in the ecology of Florida Bay; examples are the die-off of large areas**  **of seagrass and the appearance of intense blooms of planktonic algae. There is a general consensus in the** **scientific community that these phenomena are in dicative of changes in key environmental conditions**  **within the bay.The shift in primary producers and the alteration of the photic environment in Florida Bay**  **have been hypothesized to have major effects on the flora and fauna of the bay (**  **e.g., Boesch**  **et al., 1993).**  **F ourqurean and Robblee (1999) have recently reviewed** **many of the changes. In this paper, we examine the cur rent state of knowledge about the character and causes**  **of planktonic algal blooms in the bay. In reviewing the scope of our knowledge on algal**  **blooms in Florida Bay, it is important to keep in mind that detailed monitoring of water quality in the bay has** **been underway for just over a decade.This is a some what surprising fact considering the importance of**  **this aquatic resource to Florida and the surrounding**

**w aters of the Atlantic Ocean and Gulf of Mexico. One**  **of the factors that triggered the initiation of extensive multidisciplinary research in the bay was the on set of**  **massive cyanobacterial blooms over large areas of the bay in the early 1990s.**  **T**

**he first quantitative indications of major increases in phytoplankton densities in the interior regions of**  **Florida Bay came from chlorophyll a**  **data collected by Florida International University (FIU) (Boyer**  **et al., 1997, 1999). Boyer**  **et al. ’s**  **(1999) research, which began in 1988, indicated a significant step increase in chloro** **phyll levels in 1991–1992. The increase in algal bio mass within the bay was corroborated by incidental**  **observations by individuals frequenting the bay for other research and recreation activities. In 1993, a sep**  **arate research group from the University of Florida joined FIU in monitoring efforts that revealed high**  **concentrations of cyanobacteria in the central portion of Florida Bay (Figure 6.1; Phlips and Badylak, 1996;**  **Phlips et al.,**  **1999). In 1994, the phytoplankton research efforts were expanded further to include the Florida**  **Marine Research Institute [now the Fish and Wildlife Research Institute]. All three research teams observed**  **large cyanobacterial blooms in the central regions of the bay, particularly during the summer and fall (Phlips**  **et al., 1999; Steidinger**  **et al., 2001).**  **During the same period, algal blooms were also recorded in the western region of the bay (Figure 6.1).** **However, these blooms were typically dominated by di atoms, not by cyanobacteria. (Phlips and Badylak, 1996;**  **Phlips et al.,**  **1999; Steidinger et al.,**  **2001) Recent efforts by** **researchers from the University of Miami focusing on the western bay have provided further support for**  **the importance of diatom blooms in the western region. Analysis of sediment cores from the western side of** **Florida Bay indicate that diatom blooms along the west ern margin were a well-established feature by 1970,**  **significantly prior to the increases in cyanobacteria blooms within the bay’s interior (Jurado, 2003). Most re**  **cently, chemotaxonomic studies of phytoplankton in the bay have been initiated using full-spectrum photodi** **ode array detectors and high-performance liquid chro matography analysis (Louda, 2001).** 


### Regional Differences

**T he observed disparity in the quantity and quality**  **( i.e.,**  **composition) of phytoplankton biomass in dif ferent parts of the bay manifests the need to view phy**  **toplankton dynamics by ecological zones. In contrast to the numerous phytoplankton blooms encountered** **in the western and central regions of Florida Bay, al most no blooms are located in the eastern portion of**  **the bay (Figure 6.1).There have been several efforts to divide Florida Bay into ecologically distinct zones.**  **T hese zonal breakdowns have been based on a vari**  **ety of parameters, including geology (Prager et al.,**  **1996), distributions of benthic plants (Zieman et al.,**  

# Chapter 6
Plankton Blooms

T eam Leaders Gary Hitchcock (University of Miami), Ed Phlips (University of Florida), Larry Brand (University of Miami), Douglas Morrison (ENP, PMC)Florida Bay Synthesis Hunt and Nuttle

78 FWRI Technical Report TR-11 **1989), faunal distributions (Thayer and Chester, 1989; Holmquist**  **et al., 1989), and water-quality characteris**  **tics (Phlips et al.,**  **1995, Boyer et al.,**  **1997, 1999; Burd and Jac**  **kson, 2001).These efforts have yielded from 3 to 20 zones with different boundary designations.The lack**  **of consensus on the specific boundaries and number of zones is largely attributable to differences in the** 

**c hoice of parameters used in the discrimination of the**  **regions. If the focus is limited to the frequency of phyto**  **plankton blooms and the general composition of the blooms, it is possible to define three general regions**  **that roughly follow longitudinal lines of demarcation (Figure 6.2): (1) The eastern region of the bay, east of** **80°39 ́W and west of the Florida Keys, where major phy toplankton blooms are seldom observed; (2) the cen**  **tral region of the bay, between 80°39 ́W and 80°49 ́W, where bloom concentrations of cyanobacteria (**  **i.e., greater than 1 million cells per ml) are regularly en**  **countered; and (3) the western region of the bay, west of 80°49 ́W, which experiences periodic blooms of di**  **atoms.These regions provide a useful context for dis cussing both the character of blooms in the bay and the**  **factors that control them. In the most general terms, phytoplankton standing**  **crops are dictated by factors that control gains and losses of algal biomass (Figure 6.3). From a gain per**  **spective, the most obvious contributor to the increase in phytoplankton biomass is cell growth. Net growth**  **rates are under the control of resource availability, such as nutrient and light, and of factors that affect the rates** **of photosynthetic and respiratory activity, such as tem perature, salinity, and oxygen level. Algal biomass can**  **also increase as a consequence of inputs to the water column from the benthos through resuspension or in**  **flows of water from adjacent environments. In terms of loss functions, one of the most impor**  **tant overriding considerations is water residence time. In many coastal ecosystems, phytoplankton biomass is** **limited by the flushing-rate of water that has lower phy toplankton content. Flushing rates are generally related**  **to a combination of rainfall inputs, tidal mixing, and** Figure 6.1 **Biovolume of Synechococcus elongatus**  **(Large Syn.), other cyanobacteria, dinoflagellates, diatoms and other phytoplank ton at four sampling sites representative of different regions of Florida Bay (Phlips**  **et al., 1999).**  Plankton BloomsHunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 79 **wind-driven circulation. Many environments with long residence times tend to have higher phytoplankton**  **crops than do environments with short residence times, assuming that nutrient and light availability are sim**  **ilar (Monbet, 1992).There are also biological processes that contribute to the loss of biomass in many aquatic** **ecosystems, such as grazing by benthic and plank tonic filter-feeding organisms. The rates of loss are**  **closely tied to the structure and abundance of the grazer community and to environmental factors that** **affect the rate of activity, such as salinity, tempera ture, and phytoplankton composition (**  **e.g., presence of**  **toxic species).**


### Summary of Research

**Research to date indicates that there are three eco logically distinct regions within the bay from the stand**  **point of algal blooms: the northeastern, central, and**

**w estern regions.The nature and causes of blooms can** **be most appropriately summarized within the con text of these three regions (Table 6.1).**  NORTHEASTERN REGION

**• Algal blooms are largely absent from the north** 

**eastern region of Florida Bay. The phytoplankton community of the northeastern region is a diverse**  **mixture of cyanobacteria, dinoflagellates, diatoms, and microflagellates, none of which form blooms.**  **• T he lack of algal blooms in the northeastern region** 

**of Florida Bay is largely attributable to the severe phosphorus limitation characteristic of the region.**  **Despite significant water inflows to the region from the Everglades, the very low phosphorus levels in**  **these inputs combined with the calcium-carbonate rich waters of the region, result in nutrient-limited**  **conditions.**

CENTRAL REGION

**• Large algal blooms have been a common feature of** 

**the central region since 1992. The focal point for blooms in the central region is in the north-central**  **region from Rankin Basin extending into Whipray Basin.The greatest bloom activity is generally in the**  **summer and early fall, although blooms have been** Figure 6.2 **Florida Bay basin configurations.** Plankton BloomsFlorida Bay Synthesis Hunt and Nuttle

80 FWRI Technical Report TR-11

**observed in other seasons. In the fall and early sum mer, blooms originating in the northern central re**  **gion are pushed southward by prevailing wind-driven circulation into the southern central region, where**  **they can spread out into the Atlantic reef tract through cuts in the Florida Keys.The dominant bloom-form**  **ing alga in the central region is the picoplanktonic**
**cy anobacterium**  **Synechococcus cf.**  **elongatus, though** **several species of diatoms and dinoflagellates occa sionally occur in bloom proportions.**  **• N utrient limitation of phytoplankton growth in the**  **central region appears to switch back and forth from phosphorus to nitrogen.The nature of the sources of**  **nutrients for blooms in the central region has been a subject of considerable debate, yielding several**  **h**

**ypotheses: (1) a significant supply of nutrients for algal production is available from the flocculent** **muddy sediments within the region; (2) a ground**

**w ater source of phosphorus is present within the re**  **gion that, in combination with nitrogen from the northeastern region, feeds algal blooms; (3) nutrients**  **from the shelf region west of the bay are available to blooms in the central region via tidal exchange;**  **and (4) atmospheric deposition is a significant source of nutrients (particularly N) for algal primary pro** **duction. These hypotheses are not mutually exclu sive, and several mechanisms may be operational at**  **the same time. • T** **he domination of blooms in the central region by**

**Synechococcus cf.**  **elongatus is attributable to the unique**  **ecophysiological characteristics of this species of**
**cya nobacterium. These characteristics include (1)** **wide tolerance to salinity, (2) superior ability to com pete for phosphorus at low concentrations, (3) abil**  **ity to regulate buoyancy and thereby take advantage of nutrients available in the sediments, and (4) lower**  **susceptibility to grazing losses.**

WESTERN REGION **• A lgal blooms are also a common feature of the west** 

**ern region of Florida Bay. In contrast to the cyanobac** Figure 6.3 **Gain versus loss-functions for phytoplankton stand ing crops.** 

T able 6.1 **Summary of research on plankton blooms by region.**

W

est Central East

**General Phlips and Badylak, 1996 Phlips and Badylak, 1996 Phlips and Badylak, 1996**  **Characteristics Boyer et al.,**  **1997, 1999 Boyer et al.,**  **1997, 1999 Boyer et al.,**  **1997, 1999 Phlips**  **et al., 1999**  **Phlips et al.,**  **1999, 2002 Phlips et al.,**  **1999 Steidinger**  **et al., 2001 Steidinger**  **et al., 2001 Steidinger**  **et al., 2001**  **J urado, 2003** 

**Nutrients Lapointe**  **et al., 1990, 1994**  **Robblee et al.,**  **1991 Carlson**  **et al., 1994**  **Durako, 1994 Zieman**  **et al., 1994**  **P**

**aul et al.,**  **1995a,b T** 

**omas et al.,**  **1999 Lapointe**  **et al., 2002**  **Composition and Tomas et al.,**  **1999 Richardson**  **et al., 2001**  **Growth Rates Jurado, 2003 Grazing and**  **Lynch and Phlips, 2000 Flushing**  **Brenner et al.,**  **2001** Plankton BloomsHunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 81

**terial blooms in the north-central region, these blooms are dominated by diatoms.The diatom-dom** **inated blooms in the western region are mainly com posed of**  **Rhizosolenia spp., although**  **Chaetoceros spp.**  **and pennates are major genera in terms of cellular biomass. Diatom blooms in the western region begin**  **in late summer and are advected into the bay from shallow coastal waters off Cape Sable.**  **• T he diatom-dominated blooms in western Florida** 

**Bay are mainly limited in their growth by nitrogen, either singly or in combination with phosphorus**  **and/or silicon supply. Temperature, salinity, and light do not appear to be important factors in the ini**  **tiation or maintenance of diatom blooms. Maximum growth rates of the diatom community during bloom**  **initiation in the western region range from 1 to 2 day –1** **(first-order rate constant) based on increases in net plankton (greater than 5 μm size fraction), chlorophyll** 

**a ,**  **or biogenic silica.The onset of diatom blooms on the western Florida Shelf appears to be associated**  **with enhanced riverine outflow, predominantly from the Shark River.The onset of increased diatom bio**  **mass occurs within the riverine, low-salinity plume near Cape Sable.** 


## Eastern Florida Bay

**Phytoplankton abundance is lower in the eastern part of the bay than it is in the other two zones within the**  **bay (Figure 6.1). Chlorophyll a**  **concentrations in the eastern bay are typically less than 2 mg m**  **–3 through**  **out the year. Phlips et al.**  **(1999) reported that the max imum chlorophyll**  **a concentrations in this region were**  **less than 5 mg m –3**  **between August 1993 and October 1997, with most values less than 1 mg m**  **–3 (Figure 6.4).**  **Similarly, Boyer et al.**  **(1997, 1999) observed low chloro phyll**  **a concentrations in eastern Florida Bay for the pe**  **riod between 1989 and 1997 (mean = 0.85 mg m –3**  **). T** **he phytoplankton communities in the eastern bay are principally composed of centric diatoms (**  **e.g., T** 

**halassiosira sp.), dinoflagellates (**  **e.g., Protoperidium**
**spp., Ceratium**  **sp., Prorocentrum micans**  **), and small**
**cy anobacteria that constitute the major fraction of cel**  **lular biovolume (Phlips and Badylak, 1996). Steidinger** Figure 6.4 **Chlorophyll a**  **concentrations and salinities at sampling sites representative of different regions in Florida Bay (Phlips et al.,**  **1999).** Plankton Blooms**et al. (2001) reported that the dominant phytoplankton**  **taxa in the region from fall 1994 to early summer 1995**

**w ere dinoflagellates, whereas cyanobacteria were the** **most abundant taxa from late 1996 to spring 1997. Cel lular biovolume serves as a useful index to phyto**  **plankton biomass that is independent of physiologically induced changes in pigment concentrations such as**  **those that occur in chlorophyll a** 

**. In eastern Florida Bay,**  **total phytoplankton biovolume is less than 1 μm 3**  **ml –1** 
**, a value much less than that in the western and central**  **bay (Figure 6.1) (Phlips et al.,**  **1999). Tw**  **o factors result in strong phosphorus limita tion of primary production in the region, helping to ex**  **plain the low phytoplankton concentrations that typify this region of the bay.The eastern region of Florida Bay**  **receives significant freshwater inputs from Taylor Slough and the C-111 canal system. Salinity values in** **the eastern basins are on average lower than in the cen tral and western bay, with typical values from 20 prac**  **tical salinity units (psu) to 30 psu (Figure 6.4) (Phlips et al.,**  **1999).The external surface-water inputs to east ern Florida Bay are very low in phosphorus (Boyer**  **et al.,**  **1999). In addition, the high concentrations of cal cium in the region tend to bind free phosphate.**  

## Central Florida Bay

**Over the past twelve years, the central region of Florida Bay has been the site of intense and prolonged algal**  **blooms. In the eastern region of the bay, biovolumes of phytoplankton seldom exceeded 1 million μm**  **–1 /ml;**  **however, in the central bay phytoplankton biovolumes have regularly exceeded 10 million μm**  **–1 /ml (Phlips**  **et al.,**  **1999). The intensity of blooms in the central bay is somewhat masked by the fact that the chlorophyll con**  **tent of phytoplankton in the central region is relatively low when compared to the chlorophyll content in the** 

**w estern bay and some other coastal ecosystems in**  **Florida (Phlips et al.,**  **1999, 2002). It has been hypothe sized that this is partially attributable to the very shal**  **low depth of the central region of the bay (generally less than 2 m), resulting in high light availability and sun**  **adaptation by algal cells (Phlips et al.,**  **1999). It is also pos sible that the domination of the plankton community**  **by the cyanobacterium**  **Synechococcus cf.**  **elongatus and** **the nutrient limitation contribute to the low ratio. Ir respective of the causes for the low ratios, it is impor**  **tant to consider the ratio when evaluating the intensity of blooms in the bay. For example, peak chlorophyll con**  **centrations in the St. Johns River in northeast Florida are three to four times those in central Florida Bay, but** **the peak biovolumes of phytoplankton are very simi lar (Phlips**  **et al., 2000). These considerations manifest**  **the fact that the 20–40 mg m –3**  **c hlorophyll levels com** **monly encountered in central Florida Bay are repre sentative of serious bloom conditions, whereas similar** 

**c hlorophyll levels in other ecosystems might be viewed**  **as moderate bloom levels. Over the twelve years since the initiation of major**  **phytoplankton blooms in central Florida Bay, the most intense blooms have occurred during the summer and** **early fall, except during 1993 and 1994, when high phy toplankton standing crops persisted throughout the** 
**y ear.Three of the past ten years (1993, 1994, and 1998)**  **had particularly intense blooms. In central Florida Bay, phytoplankton blooms originate in the northern**  **part of the region. For most of the peak bloom season (May–September), phytoplankton populations in the**  **south-central region are relatively low. However, in the fall and early winter, passing cold fronts, along**  **with the concomitant shift in wind direction to the north, displace phytoplankton-rich water southward.**  **T his recurring pattern is apparent in the appearance**  **of bloom concentrations of phytoplankton as far south as the Florida Keys reefs.**  

### Cause of Blooms in the Central Region

**T he apparent rise of planktonic algae blooms in the**  **central region of Florida Bay in the early 1990s raises two fundamental questions: (1) What changes occurred**  **in the region that facilitated the onset of the blooms, and (2) What are the nutrient sources that have sus**  **tained blooms since that time? In relation to the first question, the onset of blooms indicates one of two**  **possibilities: (1) more nutrients were made available for phytoplankton production either through redirec**  **tion of internal reserves and/or increases in external loading, and/or (2) biomass loss terms were dramati**  **cally reduced.The presence of a thick, organic sediment layer in the north-central region of Florida Bay indicates** **that this region of the bay has historically been pro ductive. Prior to the 1990s, seagrasses were most likely**  **the dominant primary producers in the central bay. Even after 1990, seagrasses were still present in the re**  **gion, although were not as prominently as in previous**
**y ears.**  **One of the principal hypotheses about the cause of phytoplankton blooms in the central bay focuses on**  **the role of seagrass die-off in making internal nutrient reserves available for planktonic production (Robblee**  **et al., 1991; Carlson**  **et al., 1994; Durako, 1994; Zieman**  **et al., 1994). There are a number of ways that the re** **duction of seagrass populations could enhance nutri ent availability for planktonic production, including (1)**  **through the addition of recyclable nutrients from dead seagrass, (2) by increasing access to sediment-bound**  Florida Bay Synthesis Hunt and Nuttle

82 FWRI Technical Report TR-11 Plankton BloomsHunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 83 **nutrients via increased resuspension and diffusion, and (3) by reducing competition for nutrients between**  **phytoplankton and epiphytic or benthic algae living in seagrass communities. In addition to increasing nu** **trient availability, the reduction in seagrass commu nities can affect phytoplankton loss processes. The**  **populations of filter-feeding organisms associated with seagrasses can influence phytoplankton densities, par**  **ticularly in very shallow environments like Florida Bay.The physical presence of dense seagrass beds also**  **increases the sedimentation of algae by reducing the potential for resuspension of algae and sediments.**  **T he importance of seagrass die-off in the stimu**  **lation of phytoplankton blooms is not a universally accepted concept. Some researchers have suggested** **that this line of reasoning is backwards and that in creases in planktonic production have actually led to**  **the demise of seagrasses (Lapointe et al.,**  **2002).The au thors of this hypothesis cited observations by local**  **users of the bay of increases in turbidity prior to the seagrass die-off in the late 1980s as evidence (DeMaria,** **1996). However, these observations were principally re stricted to the western region of the bay and therefore**  **do not provide substantial insight into what occurred in the central bay during the 1980s.The north-central**  **region of the bay is very shallow (generally less than 2 m deep), and it remains to be demonstrated if blooms** **could cause the demise of seagrass populations as a re sult of decreased light availability. It is possible that such**  **an argument might be more tenable in the western bay and shelf environments, where average depths are**  **greater. Irrespective of which came first, the seagrass die**  **off or the algae bloom, the central questions remain the same: what are the sources of nutrients for phyto** **plankton blooms and has the trophic state of the cen tral bay increased over the past few decades. It is**  **important to consider the possibility that the overall pool of nutrients may have remained stable but that the**  **distribution has changed, along with changes in loss terms. This argument falls within the concept of “al** **ternative stable states.”Under this scenario a major en vironmental disruption that resulted in seagrass die-off** **could have ushered in environmental conditions con ducive to the persistence of phytoplankton blooms.** **Such disruptive events could include major storms, pro longed drought or flood periods, or a major shift in nu**  **trient loading. T** **he first step in addressing these questions is to identify what nutrients actually limit the production po** **tential of phytoplankton in the central bay.There is lit tle doubt that primary production in the eastern region**  **of the bay is strongly phosphorus-limited (Lavrentyev et al.,**  **1998; Tomas et al.,**  **1999).There is also significant e**  **vidence indicating that the western region of the bay and adjacent shelf environment are commonly limited**  **by nitrogen or nitrogen-phosphorus co-limitation.This**  **information suggests that there is an excess supply of phosphorus to this region.The nutrient limitation sta**  **tus of the central bay is more ambiguous. A number of biogeochemical indicators, such as the ratios of total**  **nitrogen (TN): total phosphorus (TP) and inorganic N:inorganic P, indicate that phosphorus should be the**  **most limiting nutrient (Fourqurean et al.,**  **1993; Boyer et al.**  **1997, 1999). However, it is well known that many organic N molecules are not readily available to phy**  **toplankton, whereas many organic P molecules are bioavailable due to the activity of phosphatase en**  **zymes (Vitousek and Howarth, 1991). The results of nutrient-enrichment bioassays in the central region of**  **the bay suggest that the limiting status can alternate between phosphorus and nitrogen (Tomas**  **et al., 1999).**  **T**

**his observation implies that at different times, changes in the loading rate of either nutrient could stimulate**  **increases in phytoplankton production. A number of h** 

**ypotheses have been forwarded regarding potential sources of phosphorus and nitrogen for phytoplank**  **ton blooms in the central region of Florida Bay. Many of these hypotheses deal specifically with the north-cen** **tral region of the bay, where blooms appear to origi nate. It is important to recognize that these hypotheses**  **are not mutually exclusive. It is likely that various pathways of nutrient supply operate simultaneously,** 

**ev en though the relative importance of each varies** 

**ov er time and space.** 

HYPOTHESIS 1—INTERNAL SUPPLY OF NUTRIENTS **T here are a number of potential internal sources of ni**  **trogen and phosphorus for phytoplankton production (Rudnick**  **et al., 1999). The thick layer of flocculent or**  **ganic sediments found in the north-central region of the bay represents a potential pool of bioavailable ni** **trogen and phosphorus. The recent die-off of sea grasses in the region has made this pool more**  **accessible via enhanced diffusion and resuspension processes.There has been considerable debate within**  **the scientific community about whether the size of this pool and the rate of supply from the sediments are**  **sufficient to sustain the blooms observed over the past decade. The size and availability of the sediment nu**  **trient pool is certainly an issue that warrants further attention.The current information available is insuffi**  **cient to either accept or reject this hypothesis. T** **here are a number of biological processes that affect the internal supply rate of bioavailable nutri**  **ents. For example, nitrogen fixation by autotrophic and heterotrophic bacteria and cyanobacteria is a potential**  Plankton Blooms**source of nitrogen. In some aquatic ecosystems, nitro gen fixation can represent a major source of nitrogen**  **(Phlips et al.,**  **1986). Conversely, denitrification processes can result in a loss of bioavailable nitrogen. The rela**  **tive roles of nitrogen fixation and denitrification are the subject of ongoing research (Cornwell, 2001).** **Other key elements of internal supply of nutri ents for phytoplankton production are the rates of re** 

**c ycling of nutrients within the north-central region**  **and of export of nutrients from the region. Due to the severe restriction of tidal exchange of water between**  **the north-central region and the waters of the Gulf of Mexico and the Atlantic Ocean, water residence times**  **are long.The restriction should provide more time for recycling and less opportunity for nutrient washout. Ini**  **tial modeling efforts indicate that residence times in the north-central region are on the order of months**  **(Jackson and Burd, 1999; Top et al.**  **2001) and could be extended during drought periods.Very little is known** **about the actual rate constants for recycling, sedi mentation, or export of nutrients.** 

HYPOTHESIS 2—GROUNDWATER SOURCES OF PHOSPHOROUS **Phosphorite deposits were created during the Miocene in northeastern Florida and subsequently transported**  **into south Florida by Appalachian erosion, resulting in high phosphorus levels observed in geological for**  **mations in certain areas of south Florida (Brand, 1996). Groundwater outflows from these formations can con** **tain high phosphorus levels (Brand, 2002). The distri bution of water-column phosphorus correlates well**  **with the phosphorite deposits (Brand, 2002).There has been an effort, though unsuccessful to date, to dis**  **cover direct phosphorus-rich groundwater inputs within the north-central region of Florida Bay. In a**  **less direct manner, phosphate mining in central Florida may have increased the input of phosphorus into the**  **southwestern coast of Florida. It has been hypothesized that the phosphorite deposits are a persistent source**  **of phosphorus that has not changed significantly over the past few thousand years (Brand, 2002). Although** **phosphate mining over the past century may have in creased the input of phosphorus into coastal waters,**  **the extent to which P from this source was transported to Florida Bay and how this has changed over the past**  **century is unknown. The timing of phytoplankton blooms (in the 1990s) does not seem to support a hy** **pothesis that this P source has been an important fac tor driving changes in Florida Bay phytoplankton.**  **T**

**here is little evidence that phosphorus input to Florida Bay has increased substantially in the past two decades.**  **Overall, many questions remain about the importance of groundwater inputs of nutrients to algal blooms in**  **Florida Bay, but there is an active research effort un derway (Corbett**  **et al., 2000).** 

HYPOTHESIS 3—EXTERNAL LOADING OF NUTRIENTS**Current information on geographical gradients of crit ical nutrient elements in and around Florida Bay sug**  **gests that two of the major external surface-water sources of bioavailable nitrogen for the north-central** **region are the eastern half of the bay and the Ever glades boundary. Conversely, phosphorus gradients in**  **the region indicate that the most likely source of bioavailable phosphorus is from the western portion**  **of the bay. These nutrient gradients suggest that the blooms in the north-central part of the bay could be fed**  **by nitrogen inputs from the east and by phosphorus**  **inputs from the west. It has been hypothesized that phytoplankton** **blooms in north-central Florida Bay are a result of in creases in nitrogen loading related to recent changes** **(since 1980) in water-management practices in south east Florida (Brand, 2002).The following scenario is en**  **visioned for explaining the increase in N load to Florida Bay. In the early 1980s, agricultural runoff from the**  **Everglades Agricultural Area (EAA) was diverted south via the South Dade Conveyance System (Light and** **Dineen, 1994; South Florida Water Management Dis trict, 1992).Walker (1991) observed significant increases**  **in nitrate in water flowing south through the C-111 canal toward Florida Bay and through the S12A station** **where water flows into the Shark River system. Un fortunately, there is little nitrogen concentration data** **for Florida Bay before the beginning of the large re gional monitoring program in 1989.Therefore, it is dif**  **ficult to determine the degree to which nitrogen levels in the north-central region of Florida Bay were af**  **fected by the later alterations in flow. This scenario also depends on several assumptions for which the ev**  **idence is currently lacking or insufficient.The primary assumption is that there is sufficient water exchange** **between the western shelf, the putative source of phos phorus, and the north-central bay to sustain blooms.** **Current hydrodynamic data are insufficient to estab lish this rate of exchange.There is also a need to more** **carefully examine the nutrient-limitation status of phy toplankton in the central bay. As mentioned above,** 

**c hemical data indicate that the north-central region** **should be phosphorus-limited, but bioassay data in dicate a mixed limitation status.** 

HYPOTHESIS 4—SEWAGE AS A SOURCE OF NUTRIENTS **Another potential source of nutrients is sewage and other nutrient-rich freshwater runoff from land in**  Florida Bay Synthesis Hunt and Nuttle

84 FWRI Technical Report TR-11 Plankton BloomsHunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 85 **nearby areas of high human activity. In the case of Florida Bay, this would primarily be the heavily popu**  **lated Florida Keys. Human activities in the Florida Keys generate considerable amounts of N and P (U.S. EPA,**  **1992), and a fraction of this is clearly entering the local**

**w aters (Lapointe**  **et al., 1990, 1994; Shinn**  **et al., 1994;**  **P**

**aul et al.,**  **1995a,b). The problem with this hypothesis is that the source of nutrients is downstream of the**  **algal blooms, not upstream. Sewage may be causing local eutrophication and leading to algal overgrowth of**  **the coral reefs downstream but cannot be the source of the nutrients generating the algal blooms upstream to**  **the northwest. Concentrations of nitrogen, phosphorus, and chlorophyll all decrease, not increase, along tran**  **sects from northern Florida Bay to the Florida Keys.The algal blooms in Florida Bay are, in fact, the farthest**  **from the Florida Keys and the human population.**

HYPOTHESIS 5—ATMOSPHERIC INPUTS**Until recently, the potential role of atmospheric de position of bioavailable nutrients in supporting algal**  **blooms in Florida Bay was largely discounted. However, recent information indicates that such inputs may in**  **deed be an important element to the broader nutrient budget of the bay (Rudnick**  **et al., 1999).** 


### Domination by Cyanobacteria

**One outstanding feature of algal blooms in the central region of Florida Bay is the domination of the cyanobac**  **terium Synechococcus**  **cf. elongatus.**  **A study of algal blooms in the region from 1993–1997 showed that**  **S. cf.**  **elongatus represented over 90% of total phytoplankton** **biovolume in most instances when total phytoplank ton biovolume exceeded 5 million μm**  **3 /ml (Phlips**  **et al., 1999). Although cyanobacteria are the most abundant**  **phytoplankton in central Florida Bay, other taxonomic groups can play important roles (Phlips**  **et al., 1999;**  **Steidinger et al.,**  **2001). For example, between May 1994 and April 1995, the diatoms**  **Cyclotella choctawatcheeana and**  **Chaetoceros cf.**  **salsugineus we**  **re frequently impor tant elements of phytoplankton biomass (Steidinger**  **et al.,**  **2001). Again, in July 1995, March 1996, and January 1997, diatoms were numerous.** **Based on empirical observations and experimen tal studies, a number of hypotheses have been for** 

**war ded to explain the domination of**  **Synechococcus cf.**  **elongatus in the central region of Florida Bay. Several**  **of these hypotheses are based on some of the unique ecophysiological characteristics of this cyanobacterium.**  **Several research groups have demonstrated the broad range of salinities over which**  **S. cf.**  **elongatus can sus**  **tain high growth rates (5–50 psu; Phlips and Badylak, 1996; Richardson, 2001). Because of the isolation of**  **central Florida Bay from tidal mixing and the proxim ity of the north-central bay to the adjoining Everglades,** **this region is subject to wide swings in salinity. For ex ample, salinities exceeded 40 psu during the drought**  **period of 1992–1994 but dropped to as low as 11 psu during subsequent flood periods, such as 1995 and**  **1997 (Figure 6.4) (Phlips et al.,**  **1999; Boyer et al.,**  **1999). T** **he euryhaline tolerances of S.**  **cf. elongatus**  **probably provide the cyanobacterium with an advantage in**  **terms of long-term prominence. However, it does not fully explain the fact that intense blooms of**  **S. cf.**  **elon gatus**  **have been observed during times when salinities have remained in a moderate range (25–35 psu.)**  **Another factor that may contribute to the success of**  **S. cf.**  **elongatus is its ability to compete for nutrients** **at low concentrations (Richardson, 2001). As a pi coplanktonic species, one might expect**  **S. cf.**  **elongatus to have low half-saturation constants for nutrient up** **take, strictly because of surface area to biovolume con siderations. Experimental studies have provided**  **support for this hypothesis. A study of the kinetics of phosphorus (PO**  **4 -P)-dependent growth compared four**  **important phytoplankton species found in the bay: the cyanobacterium**  **Synechococcus cf.**  **elongatus, an**  **unidentified spherical picoplanktonic cyanobacterium, and the diatoms**  **Chaetoceros cf.**  **salsugineus and**  **Cy clotella choctawhatcheeana**  **(Richardson et al.,**  **2001).The results of growth tests revealed maximal growth rates**  **for S.**  **cf. elongatus,**  **the spherical cyanobacterium, C.**  **cf. salsugineus,**  **and C. c** **hoctawhatcheeana of 1.38, 1.37, 2.48,**  **and 3.37 divisions day –1** 
**, respectively.The half-satura**  **tion constant for growth, K u**  **, w as determined to be**  **0.005–0.05 μmol liter –1**  **for the latter three species.The K** **u for**  **S. elongatus could not be determined because the** **growth rate was still maximal at the lowest test con centration of phosphate. A test of phytoplankton re**  **source-based competition using Equilibrium Resource Competition theory predicts that**  **S. cf.**  **elongatus is the**  **superior competitor under phosphorus-limitation over the range of salinities examined (15–50 psu). The su**  **perior competitive ranking of S.**  **cf. elongatus**  **can be at tributed to the exceptionally low K** **u v** **alues.The model ranked the spherical cyanobacterium second in terms**  **of phosphate competition, with the diatoms last. In competition experiments under steady and varying**  **P-limitation, S.**  **cf. elongatus**  **also dominated in terms of biovolume at the end of all experiments at all salini**  **ties.Thus, with sufficient time, S. elongatus**  **should com petitively displace all the other species under** **phosphorus-limited conditions. Competition experi ments further revealed that under nitrogen-limiting** **conditions, the two species of cyanobacteria usually co dominated in terms of biovolume under steady- and**  **non-steady-state conditions. In summary, under both** Plankton Blooms**steady-state and non-steady-state conditions, the**
**cy anobacterium**  **S. cf.**  **elongatus is the superior com** **petitor for orthophosphate and can frequently out compete diatoms under N-limiting conditions.**  **Related to the question of nutrient competition is the ability of**  **S. cf.**  **elongatus to regulate its buoyancy by** **altering the presence of gas vesicles (Phlips and Bled soe, unpublished data). Under phosphorus-limited**  **conditions, the presence of gas vesicles diminishes and**  **S. cf.**  **elongatus cells lose buoyancy. It has been** **suggested that with the loss in buoyancy, nutrient-de pleted cells sink to the sediment–water interface, where** **they can take advantage of higher nutrient availabil ity (Phlips**  **et al., 1999).**  **Besides the characteristics that may enhance the competitive advantage of**  **S. cf.**  **elongatus in acquiring**  **resources for growth, there may also be ways this species is favored by lower magnitudes of certain loss**  **terms. Butler et al.**  **(1995) proposed that S.**  **cf. elongatus** 

**w as responsible for the observed demise of sponges in** **Florida Bay because of its adverse effect on the filtra tion apparatus of sponges. Although there is evidence**  **that sponges can effectively filter out S.**  **cf. elongatus**  **from the water column (Lynch and Phlips, 2000), the long**  **term effects of filtering the mucilage-producing**
**cy anobacterium are not known. Irrespective of the di**  **rect effects of S.**  **cf. elongatus**  **on sponge health, it is clear that the diminishing sponge populations in the bay re**  **sult in reduced grazing pressure on phytoplankton and thereby increase the potential for blooms (Lynch**  **and Phlips, 2000). As in the case of sponges, the relationship be** 
**tween S.**  **cf. elongatus**  **and other grazers, both benthic (**  **e.g., bivalves) and planktonic (**  **e.g., zooplankton), are**  **not well defined. There is evidence that zooplankton grazing rates are periodically high enough to affect phy**  **toplankton population dynamics (Brenner et al.,**  **2001). In grazing experiments, daily metabolic carbon de**  **mand of the net zooplankton community ranged from less than 2% to greater than 100% of the phytoplank**  **ton carbon stock. Microphytoplankton growth rates ranged from 0.08 to 2.33 divisions d** **–1 at 50% available**  **light. Diatoms, dinoflagellates, and the cyanobacterium Synechococcus**  **typically dominated the microphyto plankton community, although chlorophytes and**  **prasinophytes were occasionally major constituents. Microzooplankton grazing rates ranged from 0.00 to**  **5.28 d –1** 
**, and their average ingestion rates ranged from**  **0.67 to 3.42 mg C m –3**  **d –1**  **. T hese ingestion rates corre**  **spond to a daily ingestion demand ranging from less than 1% to greater than 300% of the initially available**  **carbon, indicating that microzooplankton are capable of exerting a controlling influence on the phytoplank**  **ton community. Despite the observed grazing rates, the frequency of cyanobacterial blooms in the north-cen**  **tral region of the bay demonstrates that grazing activity is frequently not sufficient to prevent blooms, although**  **it may play a role in their ultimate demise.There is no information on whether the domination of**  **S. cf.**  **elon gatus**  **in the north-central region is in any way related to selective avoidance by grazers, either benthic or**  **planktonic.**



## W estern Florida Bay

**T he highest phytoplankton biovolume in western**  **Florida Bay generally occurs in the late summer to winter, when the annual diatom bloom reaches its sea**  **sonal peak. Phytoplankton composition in the western bay is distinct from composition in the central bay be**  **cause a higher proportion of total biovolume occurs in diatoms. Phlips and Badylak (1996) were the first to**  **identify the species composition of bloom components in western Florida Bay. They found that centric (pre**  **dominantly Rhizosolenia**  **) and pennate ( Cocconeis, Nav**  **icula, Surirella ) diatoms were dominant species in terms**  **of cell abundance in December 1993. Steidinger et al.** **(2001) subsequently reported that other taxa, espe cially cyanobacteria, may also account for a large frac**  **tion of total biovolume in western Florida Bay and could equal the biovolume attributed to diatoms. In** **2000 and 2001, Jurado (2003) conducted a study of net phytoplankton (diatom) silica demand at Carl Ross**  **Ke y in western Florida Bay. She found that centric di**  **atoms (predominantly Rhizosolenia**  **spp., Chaetoceros**  **spp., and T**  **halassiosira nitzschiodes ) and pennate di**  **atoms ( Nistchia, Navicula, Gyrosigma**  **spp.) dominated the netphytoplankton fractions (greater than 5 μm).**  **T hese observations are in general agreement with**  **Phlips and Badylak’s (1996) results. Peak concentrations of chlorophyll**  **a (2–9 mg m**  **–3 ) were higher than values** **observed in the eastern bay but less than concentra tions in the north-central basins. Netplankton chloro**  **phyll a**  **accounted for more than 50% of total pigment biomass.**  **Although relatively few, if any, observations of phytoplankton-community species composition in** 

**w estern Florida Bay exist prior to 1990, biogenic silica**  **in the sedimentary record from Carl Ross Key suggest that an increase in the abundance of diatoms has oc** **curred since 1960 (Figure 6.5). Biogenic silica is a dis tinct marker for the presence of diatoms. Although** **only two values exist from the sedimentary record be fore 1960, the vertical profile suggests that biogenic sil**  **ica concentrations increased from less than 1 mg silicon (Si) to greater than 1 mg Si (g sediment)**  **–1 sometime**  Florida Bay Synthesis Hunt and Nuttle

86 FWRI Technical Report TR-11 Plankton BloomsHunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 87 **after 1950, although values in the last decade have been highly variable.This trend suggests that enhanced**  **diatom biomass in western Florida Bay has developed within the past four or five decades.**  **Cellular division rates determine the success of a species in the natural environment. Net growth rates**  **equal the difference between the cellular division rate and the sum of all processes that represent losses, in**  **cluding grazing, sinking, advection, and death. Net increases in phytoplankton communities of as little as**  **0.1 day –1**  **result in an increase of less than 1 to greater than 20 mg m**  **–3 c**  **hlorophyll a**  **in less than a month. Al though we have no direct measures of netphyto**  **plankton growth rates in western Florida Bay, community growth rates for netplankton have been es**  **timated from increases in chlorophyll a**  **and biogenic silica in dilution gradient experiments. This method,**  **principally developed by Landry and Hassett (1982) and their colleagues, provides a measure of maximum** **growth. In March 2001, when phytoplankton abun dance was low, netplankton chlorophyll**  **a exhibited**  **growth rates of 1.5 day –1** 
**, increasing to 2.9 day** **–1 in May,**  **Ju ly,**  **and September, as netplankton biomass increased. By November 2001, netplankton biomass had reached**  **a stationary phase, and maximum growth rates were again ca. 1 day** **–1**

**. Grazing losses ranged from 0.6 to**  **1.75 day –1**  **in these experiments, yielding net growth rates of 0.5 (November) to greater than 1.3 day** **–1 in** **May and September. Although these experiments rep resent only the potential for diatom growth**  **in situ, they suggest that conditions in summer-fall provide di**  **atoms with a setting for growth rates that exceed the sum of losses.**  **Exchange of surface waters in western Florida Bay with the West Florida Shelf is evident in the nature of** **the phytoplankton community and property distribu tions. Salinity values in western Florida Bay show less**  **temporal variability than in the central or eastern basins. On average, basins in the western bay have a** **higher average salinity (mean = 35.2 psu) and lower av erage TN (30.5 μmol kg** **–1 ) and dissolved inorganic ni**  **trogen (DIN) (<2 μmol kg –1**  **) than do those in the eastern or central bay (Boyer**  **et al., 1999). Chlorophyll**  **a con** **centrations from the long-term FIU monitoring pro gram averaged 1.9 mg m**  **–3**
**, which, as suggested by**  **Phlips et al.**  **(2000), is less than the average values in the central bay but higher than in the eastern bay.** **Ratios of TN:TP (x = 55.6) and DIN:SRP (soluble re active phosphorus) (x = 51.8) in the western bay are** **higher than Redfield values but lower than those in ei ther the eastern or central basins.These characteristics**  **suggest that the western bay is strongly influenced by the surface waters of the West Florida Shelf that ex** 

**c hange along the boundary of Everglades National**  **P**

**ark. The influence of coastal processes is evident in tidal exchange, which is much greater in the western**  **bay than in the interior or eastern basins because the amplitude of the tides is damped from west-to-east**  **across the bay (Wang et al.,**  **1994). Bioassays at two locations along the western mar** **gin of Florida Bay (Sprigger Bank and Sandy Key) in dicate that nitrogen is a primary nutrient that limits**  **phytoplankton growth (Tomas et al.,**  **1999). In more than 70% of the bioassays between March 1994 and May**  **1997, Tomas found that nitrogen in combination with silica stimulated growth more than did individual ad** **ditions of phosphorus or silica. When individual nu trients were excluded from otherwise complete**  **enrichments (all nutrients – N, or all nutrients – P), the lack of nitrogen yielded a final biomass that was sim** **ilar to controls. Phosphorus limitation of phytoplank ton growth rates was detected in about 20% of all** **experiments, and iron was even less frequently iden tified as a nutrient potentially limiting growth.**  **T he responses to N and Si enrichments are con** **sistent with the marine waters that flow into the west ern margin of Florida Bay and the fact that diatoms**  **frequently dominate these waters.The observations of** Figure 6.5 **V ertical profile of biogenic silica in a sediment core from**  **Carl Ross Key.The sediment samples with corresponding dates were kindly provided by Dr. J. Trefrey, Florida Institute of Technology**  **(Jurado, 2003).** Plankton BloomsFlorida Bay Synthesis Hunt and Nuttle

88 FWRI Technical Report TR-11 **T**

**omas et al.**  **(1999) were confirmed by Jurado (2003), who found that nitrogen was the principal nutrient limit** **ing both total phytoplankton and netplankton (di atom) growth in western Florida Bay during the**  **2000–2001 diatom bloom (Figure 6.6). Bioassays were made in September and November 2000, as diatom**  **abundance increased, and in January and March 2001, when diatom biomass declined. The results consis**  **tently showed that enrichments with nitrogen, and secondarily silica or phosphorus, stimulated growth of**  **natural populations incubated under simulated in situ conditions. An assessment of temperature and irradi**  **ance during the course of the year suggests that these two parameters did not effectively limit the growth of**  **diatoms in western Florida Bay. Thus nutrient supply may be the main factor that accounts for the enhanced**  **growth of diatoms in summer and fall in western Florida Bay.** **Seasonal distributions of salinity, nutrients, chloro phyll**  **a ,**  **and biogenic silica on the West Florida inner shelf, south from the Ten Thousand Islands to the west**  **ern boundary of Everglades National Park, indicate that diatom blooms observed in western Florida Bay**  **originate in coastal waters off the southwestern Florida Shelf.These features develop in the shallow coastal wa** **ters west of Cape Sable and are associated with the low salinity plume emanating from the Shark River and**  **other riverine sources along the southwestern Florida coast. A chlorophyll**  **a “plume” spreads south from** **Cape Sable to the western margin of Florida Bay dur ing the fall (Figure 6.7). Bimonthly cruises of the NOAA**  **SFERPM Program between 1998 and 2003 have mapped surface-water properties (salinity, nutrients, chloro**  **phyll a** **, and particulate matter) in this region. Spatial**  **distributions of these properties indicate that the Shark River is a major source of nutrients, especially silicate,**  **supporting the diatom bloom. Concentrations of dis solved inorganic nutrients in the Shark River plume at** **bimonthly intervals indicate that the average concen trations of silicon, inorganic nitrogen, and phosphorus**  **in the plume of the Shark River indicate excess silicate relative to inorganic nitrogen and phosphorus. Little**  **seasonal variation exists in nutrient concentrations, so the volume of freshwater flow appears to be the pri**  **mary determinant of nutrient flux to the inner shelf. On the southwestern Florida Shelf, exogenous nu**  **trients that support diatom growth are derived from the Shark River plume and along-shore flow. Increased**  **freshwater flow from rivers often occurs in June at the onset of the rainy season and provides silicates to the** **inner shelf that contribute to development of the di atom bloom. Between 1998 and 2000, the diatom-dom**  **inated bloom on the inner shelf began between August and October. Estimates of the fluxes of nitrate, phos**  **phate, and silicate from along-shore advection (based on bimonthly nutrient measurements and alongshore** **currents from ADCP currents made by T. Lee and col leagues) and that from the Shark River (derived from**  **river discharge and bimonthly nutrient measurements)**

**w ere for the period of bloom inception in 1999 (Jurado,**  Figure 6.6 **Bioassay results from September 2000 at Carl Ross Key (Jurado, 2003). Values correspond to increases in chlorophyll**  **a biomass relative to a control in an incubation of 24 hours.The total**  **phytoplankton community was filtered on Whatman GF/F filter, and the netplankton fraction on a 5-μm Nuclepore filter.The com**  **bination of nitrogen plus phosphorus or silicon typically results in the greatest stimulation of phytoplankton growth.** 

Figure 6.7 **Contours of total chlorophyll a**  **concentrations (top) and surface salinity (bottom) in October 2000 during the peak of**  **the annual diatom bloom. Maximum chlorophyll a**  **concentration was 17 mg l** **–1 off middle Cape Sable (Jurado, 2003).**  Plankton Blooms**2003).This is the latest year in which Shark River flow data were available at the time the estimates were**  **made.The resulting flux estimates suggest that during bloom inception, exogenous nutrient sources that sup**  **port diatom bloom development are largely met by the southerly flow along the southwestern Florida Shelf**  **(Figure 6.8). When the bloom is at its maximum, after the onset of the rainy season, Shark River is a major** **source of nitrate, nitrite, and phosphate. Alongshore ad**

**v ection of silicate appears to be the primary source of**  **this essential nutrient for diatoms, at least in that year. In summary, diatom blooms in the western basins**  **of Florida Bay are a seasonal extension of blooms that initiate on the southwestern Florida Shelf. Various**  **species of Rhizosolenia**  **and Chaetoceros**  **are the domi nant members of this assemblage, in combination with** **pennates that are likely resuspended from the bot tom. Diatoms begin net growth (**  **i.e., growth rates ex**  **ceed losses) with the onset of the rainy season. Bioassays suggest that nitrogen, often in combination**  **with phosphorus and/or silica, potentially “limit” growth. Nutrients that support diatom growth are de**  **rived from riverine sources, principally Shark River, and along-shelf (southerly) advection.The relative contri**  **bution of inorganic nitrogen, phosphorus, and silicon**

**v aries with the stage of the bloom, and likely varies** 
**ye arly with variations of river discharge and alongshore**  **flow.**



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FWRI Technical Report TR-11 91 Plankton Blooms92 FWRI Technical Report TR-11 

## Introduction

Question 4 **—What are the causes and mechanisms for the observed changes in the seagrass community of Florida** **Bay? What is the effect of changing salinity, light, and nu trient regimes on these communities?** 

**Seagrass beds are an important component in many coastal marine environments; however, there are few** **locations in the world where seagrasses are as domi nant in the hydroscape as they are in south Florida**  **(Fourqurean et al.,**  **2002). Seagrasses are the dominant biological community in Florida Bay, historically cov** **ering more than 90% of the 180,000 ha of subtidal mud banks and basins within the bay (Zieman**  **et al., 1989).**  **By comparison, mangrove islands cover only about 7% of Florida Bay. Because of the shallow nature of Florida**  **Bay (mean depth less than 2 m; Schomer and Drew, 1982), seagrasses are also the dominant physical feature**  **of the bay, and their presence greatly affects physical,**

**c hemical, geological, and biological processes in this sys** **tem (Zieman, 1982). Seagrass communities are also im portant to the economy of south Florida because they** **provide food and shelter to numerous fish and inver tebrate species, many of which are commercially im**  **portant to the region (Powell et al.,**  **1989; Thayer and Chester, 1989; Tilmant, 1989; Chester and Thayer, 1990).**  **In addition, the waters of western Florida Bay form a hydrodynamic link between the Everglades and the**  **coastal waters of the southwestern Florida peninsula and eastern Gulf of Mexico to the north and the Florida**  **Ke ys reef tract and the Atlantic Ocean to the south**  **(Schomer and Drew, 1982).The seagrass communities of this region form an important buffer by intercept** **ing the flow of water and reducing nutrient and par ticulate loads in the waters reaching the reef tract**  **(Kenworthy et al.,**  **1998). Continued loss of seagrasses along this margin and proposed increases in water**  **flow from the Everglades could result in greater exports of nutrients and particulates out of Florida Bay and onto**  **the reef tract (Kenworthy et al.,**  **1998). Resource man agers will need to consider actions that might aid in the** **reestablishment of continuous seagrass cover in west ern Florida Bay.This would be an important step in re**  **ducing sediment-resuspension-induced turbidity along this boundary that could reverse the cascading de**  **clines that characterize the present system. Seagrasses act as integrators of**  **net c**  **hanges in**

**w ater-quality variables, which tend to show rapid and**  **wide fluctuations when measured directly.The shallow distribution of seagrasses places them in close prox**  **imity to the land–sea interface, a region experiencing a rapid growth of human populations.This coastal dis**  **tribution also places seagrass communities at the end of the watershed pipe, so the health of these commu**  **nities reflects not only direct coastal influences but larger-scale, landscape-to-regional influences as well.**  **Because most seagrasses are benthic-perennial plants, they are continuously subjected to stresses and dis**  **turbances that are associated with changes in water quality along the land–sea interface.To a large extent,** **seagrass abundance determines public perception re garding the “health”of the coastal waters of Florida (Go**  **erte, 1994; Boesch et al.,**  **1993, 1995). Thus, the recent**

**c hanges in the distribution and abundance of sea**  **grasses within Florida Bay have been perceived as a**

**c hange in the health of the bay. For these reasons, sea**  **grasses may be the best indicators of changes in the Florida Bay ecosystem (Fourqurean**  **et al., 1992).** **Although the initial die-off originated in the inte rior basins of the bay (Robblee**  **et al., 1991), the great**  **est changes in seagrass abundance in the present system are occurring far from the Everglades-Florida**  **Bay land–sea interface (Durako et al.,**  **2002).The spatial patterns of changes in abundance from 1995 to 2000**  **suggest that the most perturbed environment in Florida Bay with respect to seagrasses is currently along the** 

**w estern and southern margins of the bay. Much of the**  **focus of management and restoration efforts in south Florida have been directed toward landscape-scale**  **modifications and an extensive flood-control system to increase the quantity of freshwater delivered to north**  **eastern Florida Bay and, more recently, to Shark River slough.**  

### Seagrass Communities in Florida Bay

**Seagrasses continue to be the dominant biological** 

# Chapter 7 Seagrass Ecology

T eam Leaders Michael Durako (University of North Carolina at Wilmington), Joseph Zieman (University of Virginia), Michael Robblee (USGS, PMC)Hunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 93 **community in Florida Bay. Of the more than 14,000 Braun-Blanquet samples (each 0.25 m** **2 ) taken in the bay**  **from 1995 to 2000 by the Fisheries Habitat Assessment Program (FHAP; Durako**  **et al., 2002), approximately**  **97% contained seagrass. In northeastern Florida Bay, T** 

**halassia w** **as present at 75.9% and Halodule**  **w as pre**  **sent at 69.0% of the 762 randomly selected stations sampled from May 1999 to May 2000 (Bacon**  **et al., 2001).The entire south Florida coastal zone, including**  **the areas west of Florida Bay and within the Florida Ke** **ys National Marine Sanctuary (FKNMS), is domi nated by seagrass habitats. Fourqurean**  **et al., (2002) as**  **sessed seagrass species composition and density at 1,207 sites distributed across 19,402 km**  **2 of nearshore**  **marine and estuarine environments in south Florida. At these sites, a total of 8,434 quadrats (each 0.25 m** **2 total**  **area = 2,108.5 m 2**  **) were sampled from 1996 to 1998. At least one species of seagrass was observed at 1,056 of**  **the 1,207 sites, or 87.5% of all sampling sites. T**  **halassia testudinum**  **(turtlegrass) was the most commonly en countered species, being found at 898 sites.**  **Halodule wrightii**  **(shoalgrass) was the second most commonly encountered species, occurring at 459 sites, followed**  **by Syringodium filiforme**  **(manateegrass, 239 sites), Halophila decipiens**  **(paddlegrass, 96 sites), Ruppia mar**  **itima (widgeongrass, 41 sites) and**  **Halophila engelman nii**  **(stargrass, 28 sites).** 

### Recent and Historical Changes

**A widespread die-off of seagrasses within Florida Bay began in 1987 (Robblee**  **et al., 1991; Table 7.1; http://peo**  **ple.uncw.edu/durakom/seagrass/seagrass.htm). This**

**ev ent was first observed by backcountry fishing guides** **who reported the occurrence of “potholes”in the sea grass beds in the bights along the north-central part**  **of Florida Bay. Extensive areas of T**  **halassia began dying**  **rapidly in central and western basins, and by 1990, 4,000 ha were completely lost and 24,000 ha were af**  **fected by the die-off (Robblee et al.,**  **1991). T** **he patterns of changes in seagrass abundance in Florida Bay have recently undergone four phases: 1) pri**  **mary die-off; 2) secondary mortality, with mortality primarily due to light attenuation; 3) seagrass recov** **ery associated with improving water clarity; and 4) re newed primary die-off in areas where die-off has not**  **been previously observed.The initial phase of primary seagrass die-off occurred only in Florida Bay, which is** **the most continentally influenced and least oceani cally flushed of all of the extensive south Florida sea**  **grass beds, and it occurred only in the most densely developed beds within the bay. To this day, no occur** **rence of primary seagrass die-off has been found out side of the densest seagrass beds within Florida Bay,**  **and no primary seagrass die-off has occurred in sparse or medium-density beds within the bay.** 

PRIMARY SEAGRASS DIE–OFF **T he first phase of primary seagrass die-off occurred**  **during the relatively dry and clear period of 1987 to early 1991. During this period, density, standing crop,**  **and productivity of T**  **halassia w**  **ere high but then de clined as the die-off progressed (Durako, 1995; Zieman**  **et al., 1999). Some stations had shown large increases** **in seagrass standing crop in the period prior to the die off (Zieman**  **et al., 1999). In addition,**  **Batophora oerstedi and**  **Halodule spread rapidly into die-off patches (Thayer**  **et al., 1994). At this time, Florida Bay waters as a whole**  **remained as clear as they had been in the years just prior to the die-off, with limited turbidity from sus**  **pended sediments in the immediate vicinity of the denuded die-off patches.** 

SECONDARY MORTALITY **Several years after the initiation of the seagrass die-off, Florida Bay began exhibiting widespread and chronic**  **turbidity with a concomitant decline in T**  **halassia and**  **Halodule in Johnson Key Basin and Rankin Lake**  **(Stumpf et al.,**  **1999). The increase in turbidity, which began during the fall of 1991, was principally due to** 
**cy anobacteria-dominated microalgal blooms and re**  **suspended sediments, which were associated with the loss of seagrasses on the western banks and was most**  **severe in the western and central bay (Phlips and Badylak, 1996).These blooms may have been initiated**  **by the nutrients liberated by the die-off of seagrasses**  **(Butler et al.,**  **1995). Loss of seagrass cover was the major factor of the increases in sediment resuspension**  **in the bay (Prager, 1998). This resulted in a negative feedback loop in which loss of seagrass cover from**  **die-off led to exposed, easily resuspended sediments and more widespread losses of seagrasses due to tur**  **bidity. Sponge mortality, changes in juvenile lobster population dynamics (Butler**  **et al., 1995), and indica** **tions of cascading effects on plant and animal com munities in adjacent systems (**  **e.g., sea urchin**  **population explosions and unbalanced growth of Sy**  **ringodium filiforme in the waters of the Florida Keys Na**  **tional Marine Sanctuary southwest of Florida Bay; K** **enworthy et al.,**  **1998; Rose et al.,**  **1999) were also ob served. From 1992 to 1995, salinities showed a pro**  **gressive decline throughout the bay (Boyer et al.,**  **1999). During this time, there was speculation regarding**  **how much seagrass had been lost, with as much as 100,000 acres (40,000 ha) estimated with no supporting** **data. With the decline in water clarity, aerial photog raphy became useless in determining seagrass distri**  **bution over much of Florida Bay. Because of the** Seagrass EcologyFlorida Bay Synthesis Hunt and Nuttle

94 FWRI Technical Report TR-11 T able 7.1 **Florida Bay seagrass die-off milestones.**

Event or Observation Date Significant Publication/Research Initiated
**SPOT image shows no die-off patch in Rabbit Feb 2, Ke** **y Basin, Johnson Key Basin, or Rankin Lake. 1987**
**“Potholes”seen in T**  **halassia beds in Rankin Lake Summer FIU/SERP water-quality monitoring initiated.**  **and Cross Bank by back-country fishing guides. 1987 Heat stress kills tagged conch in Hawk Channel Jul 1987**  **(Berg); coral bleaching at Looe Key (Causey); fish dying on Cross Bank (Holmquist, Robblee).**  **Robblee observes die-off patches Late Fall**  **along north shore of Johnson Key. 1987**  **Guides contact Susan Bell about dying seagrasses. Mar 1988 Guides meet Mike Robblee and Jim Tilmant at Apr 1988 Robblee and Zieman visit Rankin Lake and**  **Little Rabbit Key and observe extensive die-off. Johnson Key Basin.**  **ENP consults Jay Zieman. May 1988 Zieman provides ENP a trip report on die-off,**  **indicating its uniqueness and stressing need to monitor and conduct research. Carlson-Durako**  **survey Johnson Key Basin. Zieman observes lesions were not apparent. Spring–**  **Robblee and Holmquist observe phytoplankton Summer bloom NE of Long Key.**  **1988 SPOT imagery shows large die-off patch in Jun 1988**  **Rabbit Key Basin. Sep 1988 Robblee provides memo on seagrass die-off to**  **Superintendent Finley. Finley provides funds for researchers to evaluate die-off.**  **Nov 1988 ENP-sponsored field trip: Robblee, Carlson, Durako,Fourqurean, Muehlstein, Porter, and**  **Zieman visit die-off areas. Labyrinthula**  **detected. Apr 1989 Durako in**  **itiates studies on morphometric changes, Braun-Blanquet abundance, and demography.**  **Carlson begins studies on hypoxia/sulfide-ADH, ethylene, H**  **2 S, conducts bucket experiments.**  **May 1989 Robblee initiates studies of seagrass associated animal responses to die-off in Rankin Lake,**  **J ohnson and Rabbit Key basins. Monitoring of**  **plant community response to T**  **halassia die-off**  **initiated. J**  **un 1989 Zieman completes version 1 of his conceptual model of seagrass die-off.**  **Zieman initiates long-term T**  **halassia productivity**  **measurements near four core die-off areas. Jul 1990 Thayer**  **et al. investigate plant community response**  **to die-off in Johnson and Rabbit Key basins.**
**Halodule begins to colonize die-off patches. 1990–1991**  Seagrass EcologyHunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 95 **Earliest observation of persistent turbidity Apr 1991 Robblee et al.,**  **1991: Marine Ecology caused by tidally resuspended sediments**  **Progress Series 71: 297–299. First published observed in Johnson Key Basin. Kuss,**  **observations of the die-off: clear, warm, DiDomenico, Robblee observers.**  **hypersaline conditions. Early conceptual models of die-off**  **Fall 1991 Durako-Kuss: Labyrinthula**  **effects on T**  **halassia developed: Zieman, Carlson-Durako.**  **photosynthesis. Cyanobacteria bloom begins in Rabbit Key basin. Nov 1991**  **Hurricane Andrew passes over south Florida; Aug 24, has little direct impact on Florida Bay.**  **1992 High rainfall occurring the week after Andrew Approx.** 

**w ashes mangrove “rot”into Florida Bay.**  **Sep 1, Zieman observes that this event began the 1992**  **severe turbidity events in the bay. Major turbidity plume from western**  **Dec 22, Florida Bay reaches Big Pine Key.**  **1992**
**A pr 1993 Zieman**  **et al. look at light-reduction effect on**  **T**

**halassia in Rabbit Key basin and Sunset Cove.**  **Oct 1993 Hefty et al.:**  **DERM initiates seagrass monitoring of northeastern basins.**  **J un 1994 Hall-Durako: 107 stations previously sampled**  **in 1983–84 are resampled for decadal comparison of seagrass abundance.** 
**Oct 1994 Series of faunal studies conducted in mid-1980s are repeated as a part of the decadal comparison**  **program: Thayer, Matheson and Camp, Robblee. Nov Durako-Hall: Preliminary test of EMAP-based**  **1994 Braun-Blanquet sampling.**
**V**

**ery wet spring and summer; true estuarine Spring Durako-Hall: Fish Habitat Assessment conditions exist throughout Florida Bay.**  **1995 Program (FHAP) initiated. Landsberg-Blakesley:**  **Labyrinthula spatial and**  **temporal dynamics. Oct Montague initiates field studies in northern**  **1995 Florida Bay; starts construction of a mesocosm system to look at effects of salinity fluctuations.**  **Halophila engelmannii first observed in Johnson Oct 1996**  **Ke y basin, suggests a shade-adapted community.** 

**A ug 1997 Stumpf examines satellite imagery to detect** 

**c hanges in seagrass abundance from 1986–1997.**  **Rudnick: Florida Bay ecosystem conceptual model. 1997 Oct 1997 Carlson-Blakesley initiate banktop die-off**  **studies. Nov 1997 Fourqurean**  **et al. sample two areas in Rabbit Key**  **Basin to examine scale-based variability in potential**  **T halassia**  **ecoindicators. Flowering of**  **T halassia**  **and Halodule**  **widespread. May 1998** T able 7.1 **Florida Bay seagrass die-off milestones. (continued)**

Event or Observation Date Significant Publication/Research Initiated Seagrass EcologyFlorida Bay Synthesis Hunt and Nuttle

96 FWRI Technical Report TR-11 **continuing concern regarding the extent of seagrass**

**c hanges within Florida Bay and the need to monitor the** **effects on seagrass communities of proposed water management alterations for the restoration of the Ever**  **glades-Florida Bay ecosystem, the FHAP was initiated during spring 1995. The turbid conditions in western** **Florida Bay from 1995 to 1997 made measuring and in terpreting seagrass losses and changes in species dis**  **tributions more complicated because of the primary die-off versus secondary effects attributable to light lim**  **itation. Early FHAP data (1995–1997) indicated that seagrass decline in the western basins was primarily**  **due to degraded water quality because mortality was signified by a general thinning of shoots, rather than**  **the occurrence of distinct die-off patches surrounded by**  **dense beds. A comparison of seagrass distributions in Florida Bay between 1984 and 1994 (Hall**  **et al., 1999a)**  **and between 1995 and 1998 (Durako et al.,**  **2002) also in dicated that the chronically turbid regions had exhib**  **ited the most significant losses of T.**  **testudinum.**

STABILIZATION AND RECOVERY **F ollowing the initial die-off and period of widespread**  **turbidity, seagrass abundance has shown three distinct phases (Zieman**  **et al., 1989**  **, 1999): at stations associated**  **with primary seagrass die-off, standing crop declined from 1989 to 1995; standing crop remained stable from**  **1995 through 1997; and standing crop has increased during the past several years (1998–2001).**  **T halassia**  **has shown little net change in abundance (±8% of the mean) at the bay scale from 1995 to 2001 (Figure 7.1),**  **although at the basin-scale, abundance has varied by an average of ±30% (losses then gains in the west, con** **trasted with stability or gains in the middle and east ern basins). Most of the increase in seagrass abundance**  **has resulted from expanding coverage by Halodule**  **(Figure 7.2; + 200% baywide, + 450% in Johnson Key and Rabbit Key Basins; Durako and Hall, 2000). Thus, the**  **dominance of T**  **halassia is declining, and mixed turtle**  **grass and shoalgrass beds are becoming more common. In the past five years, relative**  **T halassia**  **abundance has dropped from being more than five times that of**  **Halo dule**  **to being less than three times more abundant; in spring 1997,**  **Halodule replaced**  **T halassia**  **as the most abundant seagrass in Johnson Key Basin (Durako**  **et al., 2002). During fall 1996, the small-bodied, low-light**  **adapted seagrass Halophila engelmannii**  **w as observed**  **at one station in Johnson Key Basin. By spring 1998, this species was present at 15 of the 32 stations in this**  **basin. T** **he passage of Hurricane Georges west of the bay in the fall of 1998 uprooted much of the**  **Halophila in**  **J ohnson Key Basin (it was observed only at five stations**  **nine days after the storm); reduced the cover of Tha**  **lassia (especially in areas where it had been sparse); and** **removed much of the litter layer on the bottom. How**

**ev er, by spring 1999,**  **Halophila cover increased in John**  **son Key Basin, and this species was observed in Rankin Lake, Whipray Basin, and Twin Key Basin. This rapid**  **increase in spatial distribution suggests the hurricane may have played a role in distributing**  **Halophila propagules (Durako**  **et al., 2002). Longer internodes**  **and deep apical meristems on short shoots of T** **halas sia**  **at Barnes Key were observed shortly after Hurricane Hurricane Georges passes west of Florida Bay. Sep 1998**  **“Classic”die-off patches present on bank edge Oct 1998 east of Big Rabbit Key.**  **Barnes Key eastern bank and basin dense T** 

**halassia, crystal-clear water.** 
**Fa ll 1998 Koch: Sulfide phytotoxicity studies on**  **T halassia** 

**. New “classic”die-off observed in Barnes Key Jan 1999 Hall-Blakesley monitor changes in**  **T halassia**  **area and in Sunset Cove. characteristics and**  **Labyrinthula abundance.**  **Die-off patches present on bank to east of Apr 1999 Barnes Key and in basin north of key.**  **Flowering of T**  **halassia and**  **Halodule again May 1999**  **observed in core samples from several stations. Hurricane Irene passes west of Florida Bay. Oct 1999**  **Flowering of T**  **halassia observed in field,**  **May 2000 recruiting seedlings observed in cores.**  T able 7.1 **Florida Bay seagrass die-off milestones. (continued)**

Event or Observation Date Significant Publication/Research Initiated Seagrass EcologyHunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 97**Georges, suggesting the hurricane resuspended sed iments in Florida Bay. Hurricane Irene also reduced sea**  **grass cover in areas of sparse T**  **halassia and reduced**  **Halophila distribution as determined by before-and**  **after sampling by FHAP. Another recent dramatic change in the ecology of** **seagrasses in Florida Bay is the widespread occur rence of flowering in both**  **T halassia**  **and Halodule.**  **In spring 1999, reproductive short-shoots of**  **T halassia** 

**w ere present at 19 sites in 7 basins across the bay; re**  **productive short-shoots of Halodule**  **w ere present at 24**  **sites in 4 basins in the western part of the bay (Durako et al.,**  **2002). In spring 2000, flowering T**  **halassia was ob**  **served at 19 sites in 6 basins. The recent increases in seagrass cover and the dramatic increase in flowering**  **may reflect improvements in water quality, although shifts from turtlegrass to shoalgrass and the appear**  **ance and spread of Halophila engelmannii**  **are often as sociated with declining light availability.**  **Since 1998, there has been an upturn in abundance,**

Figure 7.2 **Changes in relative abundance, as determined by Braun-Blanquet sampling, of Halodule**  **from spring 1995 to spring 2001.** Seagrass Ecology

Figure 7.1 **Changes in relative abundance, as determined by Braun-Blanquet sampling, of T** **halassia from spring 1995 to spring 2001.** Florida Bay Synthesis Hunt and Nuttle

98 FWRI Technical Report TR-11 **productivity, standing crop, and flowering of T**  **halassia and**  **Halodule that seems to be associated with improv**  **ing water clarity (Zieman et al.,**  **1999; Durako et al.,**  **2002). Some of this improvement in water clarity may be due**  **to a decrease in unvegetated bottom (Durako et al.,** **2002). However, as recovery begins to occur at the orig inal die-off sites, a new instance of primary seagrass die**  **off that began in January 1999 has been observed north of Barnes Key.This new primary die-off is occurring in**  **an area where die-off has not been previously observed, but it has some characteristics very similar to those ob**  **served during the initial seagrass die-off in 1987.The area has excessively dense beds of**  **T. testudinum,**  **with die-off patches interspersed among the dense beds, and the**  **same unusual seagrass morphologies (“twinning”) have been observed in surviving shoots (Zieman**  **et al., 1999).**  **Seagrasses affected by the new die-off have symptoms like those of the 1987 event;**  **i.e., the short-shoot meris**  **tem tissue appeared to be the tissue most immediately affected. Meristems seemed mushy and smelled like**  **“mustard,”whereas the rest of the blade looked green and healthy (Carlson**  **et al., 1990).** 

P

ALEOECOLOGICAL INVESTIGATIONS **Although not part of the seagrass research program, paleoecological investigations add relevant information**  **for understanding how recent seagrass changes fit into the matrix of historical expansion and contractions**  **of seagrass cover. At present, it appears that seagrass coverage, as estimated both by the abundance of sea** **grass-associated microfossils and by chemical signa tures in the sediments, has shown repeated cycles of**  **presence and absence at the core sites.Thus, the recent**

**c hanges in seagrass cover are apparently not un**  **precedented. However, the paleoecological data come from only a few selected locations, limiting the confi** **dence that can be placed in their general applicabil ity. Therefore, it would be extremely valuable to have**  **additional paleoecological information from more sites throughout the bay.**  

### Conceptual Models for Seagrass Die-Off

**Early in the die-off studies, conceptual models were de**

**v eloped of hypothesized die-off mechanisms and the**  **conditions and processes leading up to the die-off. Initially, the model developed by Zieman**  **et al. w** **as a mostly process-oriented model and placed strong em** **phasis on the historic conditions leading up to the die off. The other model was developed by Carlson and**  **Durako and was a more mechanistic model with more emphasis on the die-off process. These conceptual**  **models are shown in the accompanying figures. T** **he Zieman et al.**  **(1999) model (Figure 7.3), has three major phases: A**  **Developmental Phase (A–C), in**  **which a combination of natural and anthropogenic processes contributed to an extensively developed**  **(overdeveloped, actually) T**  **halassia ecosystem; an**  **Ini tiation Phase**  **(D–G), in which the heavily developed system interacted with a suite of environmental stresses**  **to produce the initial die-off episodes; and a Mainte**  **nance Phase (G–L–G and repeat), in which the process**  **became self-sustaining. In this model, the interactions of the dense**  **T halassia**  **and the environmental stresses formed the primary trigger to the initial die-off**  **episodes. T** **he Carlson and Durako model (Figure 7.4) in cluded over-developed**  **T halassia**  **as a component but focused more on the role of physiological stress, es**  **pecially hypoxia and sulfide toxicity, as major drivers. In addition, this model gives a much larger role to the**  **effects of a slime mold, Labyrinthula,**  **as a causative el ement. Although both of these models have matured**  **as research has progressed, the process has been one of small refinements, and both have changed little in**  **the past decade. As research progressed and the conceptual mod**  **els matured, seagrass researchers found much common** Figure 7.3 **Zieman et al.**  **model for seagrass die-off.** Seagrass EcologyHunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 99 **ground on which to agree. Among these points of agreement are the following:** 

**• Primary seagrass die-off is species-specific, restricted** 

**to T**  **halassia testudinum.**

**• Primary die-off occurs only in very dense beds;** 

**sparse and medium-density beds have never been shown to have primary die-off.** 

**• Primary die-off has occurred in Florida Bay only. It has** 

**occurred in continentally influenced regions of the bay with reduced circulation and reduced flushing.** 

**• Primary die-off occurs principally during late sum** 

**mer–fall or fall–early winter. Both the Sunset Cove and Barnes Key die-off events were first observed** **during January–February. Most significantly, pri mary die-off does not occur in the hottest months of** 

**summer.**

**• Researchers with experience in Florida Bay prior to** 

**the initial primary die-off found the waters to be clear and the seagrasses mostly free from epiphytes** **during 1987–1989. Reduced water clarity and epi phytic growth followed seagrass die-off by several** 
**y ears.** 

**F actors such as high water temperature, prolonged**  **h**

**ypersalinity, and excessive seagrass biomass (due to lack of recent disturbances, including hurricanes and**  **reduced salinities), which lead to increased respiratory demands, hypoxia, and sulfide toxicity are some of the**  **physiological stressors thought to have contributed to T** 

**halassia die-off (Robblee**  **et al., 1991; Carlson**  **et al., 1994). Observations indicated that the waters of Florida**  **Bay were generally clear, warm, and hypersaline in most areas exhibiting die-off. High water-column light**  **attenuation from suspended sediments or eutrophic phytoplankton growth was not present at the initiation**  **of the die-off or for the first several years (Boyer et al.,**  **1999). Lesions were frequently observed on blades of**  **T**

**halassia in areas affected by die-off, but they were not** **universally present during the earliest phases. An un described species of marine slime mold in the genus**  **Labyrinthula w**  **as the most common microorganism isolated from short-shoots affected by die-off (Porter** **and Muehlstein, 1989). Physiological stress and a neg ative carbon balance are associated with infection of**  **T**

**halassia by**  **Labyrinthula (Durako and Kuss, 1994).**  **Based on these early observations and data, the two conceptual models were formulated (the Zieman**  **et al. model and the Carlson and Durako model) incorpo**  **rating distal and proximal elements thought to have contributed to die-off.These models also included pre**  **dictions of negative cascades following die-off. Establishing the relative contribution of (primary)**  **die-off versus mortality induced by light stress to the recent losses of**  **T halassia**  **in western Florida Bay is problematic. There is a high spatial coincidence be**  **tween the distribution patterns of seagrass loss, Labyrinthula**  **abundance (Landsberg et al.,**  **1996; Blakesley**  **et al., 1998), high sediment-sulfide levels**  **(Carlson et al.,**  **1994), and turbidity (Phlips et al.,**  **1995; Stumpf**  **et al., 1999). Increases in**  **Halodule in the bay may**  **reflect its lower light requirements (Williams and McRoy, 1982; Dunton and Tomasko, 1994), ability to**  **rapidly spread into areas where the T**  **halassia canopy**  **has been removed (Thayer et al.,**  **1994), or resistance to disease. There has been little change in**  **T halassia**  **and Halodule**  **abundances in basins that are periodically sub jected to low salinities. This may reflect the effects of**  **intermediate disturbance ( sensu**  **Connell’s Intermedi ate Disturbance Hypothesis) in maintaining a mixed**  **species sub-climax (See fig. 13 in Zieman, 1982) as well as offering a low-salinity refugium from disease—**  **Labyrinthula has never been found in Florida Bay at**  **salinities below 15 practical salinity units (psu) (Blakesley**  **et al., 1998).** 


### Summary of Research

**Research on seagrass dynamics has focused on the** Figure 7.4 **Carlson and Durako model for seagrass die-off.** Seagrass EcologyFlorida Bay Synthesis Hunt and Nuttle

100 FWRI Technical Report TR-11 **influence of internal conditions in the ecosystem and external driving factors on plant growth and metabo** **lism. It has also emphasized documentation of the se quence and pattern of seagrass die-off and recovery in**  **Florida Bay (Table 7.2). The principal findings of this**

**w ork are as follows:** 

**• Primary die-off is associated with high-density**  **T ha**  **lassia beds. High-density beds result in conditions**  **that increase stress on Th**  **alassia: high sediment**  **sulfide levels (greater than 2–4 mmol); self-shading of shoots; nighttime/early morning anoxia/hypoxia** **in meristems; and increased susceptibility to leaf to-leaf transmission of**  **Labyrinthula. Recent die-off**  **in the Barnes Key area occurred where T**  **halassia densities and standing crop are among the highest**  **in Florida Bay.**

**• Geographic variation in patterns of seagrass loss** 

**suggests multiple causes and a distinction between primary die-off and secondary mortality.There is a**  **high spatial coincidence between the distribution of T** 

**halassia loss,**  **Labyrinthula abundance, high sedi**  **ment-sulfide levels, and turbidity, but determining the relative contributions of these factors to die-off**  **v ersus secondary mortality has been difficult.** 

**• Recent bay-scale changes in seagrass distribution and** 

**abundance following the region-scale primary sea grass die-off (1987–1991) are largely due to secondary**  **mortality of T**  **halassia associated with areas of chronic**  **turbidity (since 1994) in western Florida Bay. These**

**c hanges are most likely due to light limitation as**  **indicated by stand-thinning in T**  **halassia beds with**  **concommitant increases in low-light-adapted species such as**  **Halodule wrightii and**  **Halophila engelmanii. T** **here has also been a loss of T**  **halassia in northern**  **Little Madeira Bay, near the mouth of the Taylor River, followed by colonization by**  **Halodule and**  **Rup pia.**  **T he cause of this loss is unknown. Primary acute**  **die-off (rapidly developing dead patches within dense beds) is known to be currently occurring (ini**  **tiated in 1999) only in the high-density T**  **halassia beds of the Barnes Key area. A chronic die-off is oc**  **curring in dense beds in Sunset Cove. However, the etiologies of these two sites are different.**  **• T he boom-and-bust pattern of**  **Halodule and**  **Ruppia**

**ch aracteristic of the Joe Bay and Highway Creek**  **areas of northeastern Florida Bay prior to 1991 has** T able 7.2 **Research topics defined by Question 4 (cells in the matrix) and key references to the associated research.**

Plant Growth and Seagrass Die-off and Research Topic Metabolism Recovery

**General Characteristics Robblee**  **et al., 1991; Fourqurean**  **et al., 1992;**  **Thay er**  **et al., 1994; Hall**  **et al., 1999a,b;**  **Stumpf et al.,**  **1999; Zieman et al.,**  **1999; Durako and Hall, 2000; Bacon**  **et al., 2001;**  **Durako et al.,**  **2002**
**Te mperature and Salinity Chesnes**  **et al., 1999**  **Blakesley et al.,**  **1998; Boyer et al.,**  **1999; F**  **ourqurean et al.,**  **2003 Light Attenuation**  **Williams and McRoy, 1982; Prager, 1998; Stumpf et al.,**  **1999; Dunton and Tomasko, 1994; Fourqurean**  **et al., 2003**  **Thay er**  **et al., 1994; Frankovich**  **and Zieman, 2001; Holmquist et al.,**  **1989**
**Nutrients Fourqurean**  **et al., 1992, 2003 Butler**  **et al., 1995; Fourqurean**  **et al., 2003** 
**Anoxia and Sulfide Erskine and Koch, 2000**  **Barber and Carlson, 1993; Carlson**  **et al., 1994; Erskine and Koch, 2000** 
**Disease Durako and Kuss, 1994;**  **Porter and Muehlstein, 1989; Durako and Kunzelman, 2002 Muehlstein, 1992;**  **Blakesley et al.,**  **1998, 1999a,b**
**Dense Grass Beds Durako, 1995; Hall**  **et al., 1999a Durako, 1994, 1995; Durako**  **et al., 2001** 
**Sediment Characteristics Carlson**  **et al., 1994** 
**Climate**

**F reshwater Inflow Fourqurean**  **et al., 2003**  Seagrass EcologyHunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 101

**stabilized with the occurrence of relatively constant estuarine/marine salinities and the lack of periodic**  **intense hypersaline conditions. • T** **here has been little net change in seagrass distrib**

**ution and abundance since 1995 in central basins that are periodically subjected to low salinities or**  **have shallow sediments and lower overall densities of**  **T halassia.**  **T hese conditions may reduce density-re** **lated stresses and allow robust species communi ties to develop; low salinity may also provide refugia**  **from disease because Labyrinthula**  **has never been ob served in Florida Bay in salinities below 15 psu.**  **• T he variable abundances of seagrass-associated mi** 

**crofossils in cores suggest repeated cycles of seagrass presence and absence at core locations over the past** **200 years.Thus, the recent changes in seagrass abun dance may not be unprecedented.**  **• A statistical, discriminant-function model of sea** 

**grass species occurrence has been developed. The model predicts that an increase in freshwater delivery**  **to Florida Bay will result in an expansion of Ruppia**  **maritima and**  **Halodule wrightii distribution into the**  **northeastern bay with a concomitant loss of T** **halas sia**  **in this region.**

WHY DID SEAGRASS DIE–OFF OCCUR ONLY IN FLORIDA BAY? **Unique characteristics of the Florida Bay ecosystem make it susceptible to conditions that contribute to**  **primary die-off. Other marine areas with high T** **halas sia**  **densities and carbonate sediments, such as the Lakes Region of the lower Keys, did not experience ex**  **tensive die-off in the late 1980s. Relative to these other areas, the central basins in Florida Bay are isolated**  **from tidal influences and are subject to relatively high continental influence.** 



## Effect of Ecosystem Characteristics on Growth and Survival

**“Physiological stressors such as elevated water tem perature, prolonged hypersalinity, excessive seagrass**  **biomass leading to increased respiratory demands, h** 

**ypoxia and sulfide toxicity, and disease are some of the factors thought to have contributed to**  **T halassia**  **die-off. However, the causative mechanisms responsible for ini** **tiating the die-off remain incompletely understood (Rob blee**  **et al., 1991; Carlson**  **et al., 1994; Durako, 1994; Durako**  **and Kuss, 1994; Durako et al.,**  **2002).” —Durako**  **et al., 2002**  **Changes in plant morphology and metabolism measured in the field provide indicators of response**  **of seagrasses to environmental stressors in advance of die-off. Zieman**  **et al. (1999) reported results of long**  **term monitoring at sites of pre-existing die-off and at sites not yet affected by die-off:** 

**“Measurements were made of short-shoot density, stand ing crop, leaf morphology and productivity of**  **T halassia**  **testudinum. Seagrass beds in Florida Bay have continued**  **to decline in density and biomass since the die-off event began in 1987. In contrast to the loss of seagrass density** **and standing crop, we found that mass-specific pro ductivity increased markedly from 1989 to 1995 at the die**  **off sites. The increases in mass-specific productivity of seagrasses in Florida Bay occurred at the same time**  **that transmission of light to the bottom was decreasing dramatically. Despite increasing productivity on a mass**  **specific basis over the period 1989–1995, area productivity of**  **T halassia testudinum**  **decreased at three of the five die-off sites.This can be explained by a change in shoot**  **density and size.”**

**Seagrasses in Florida Bay are meristem-depen dent and depend on rhizome growth and branching to**  **maintain or increase their populations. Excess carbon from photosynthesis is needed for production and**  **growth of apical meristems to allow lateral growth and spread of populations. Core samples (15-cm di**  **ameter) obtained during the springs of 1998 and 1999 FHAP sampling indicated that the mean branching**  **frequency was 0.24 during this period, or one rhizome apical branch produced for every four short-shoots**  **(Paxson and Durako, 2001). This is very similar to the branch frequency of 0.28 observed during the early die**  **off from 1989 to 1990 (Durako, 1994). The relationship between rhizome branching in 1998 and shoot density** 

**c hanges from 1998 to 1999 was significant (**  **P < 0.0001);**  **however, the r**  **2 v** **alue of 0.12 was low. Carlson**  **et al. (1994) have reported that alcohol de**  **h**

**ydrogenase (ADH) increases in T**  **halassia exposed to**  **h**

**ypoxic conditions, exacerbating the carbon drain on below-ground tissues. Apical meristem density and**  **branch frequency (rhizome apical density normalized to short-shoot density) may act as “ecoindicators”of the**  **potential for increase or decrease of seagrass density.**



### T emperature

**T he large-scale distribution of marine plants is largely**  **controlled by temperature.The effects of temperature on seagrasses have been extensively investigated and**  **are well known. The range of thermal tolerance in tropical species is about half that of temperate species;**  **upper thermal limits are similar for both groups, but tropical species are less tolerant of low temperatures**  **(Zieman et al.,**  **1989). Because tropical species are grow ing near the upper temperature limits, thermal effects**  **of discharges from electrical power plants can result in mortality during the warm summer months, al**  **though the productivity of these species may have been enhanced during the winter (Barber and Behrens,**  Seagrass EcologyFlorida Bay Synthesis Hunt and Nuttle

102 FWRI Technical Report TR-11 **1985). T**  **halassia may show defoliation or reductions in** **leaf length when temperatures fall below 15°C or ex ceed 30°C (Phillips, 1960; Zimmerman and Living**  **stone, 1976; Durako and Moffler, 1985). Temperatures below or above these extremes have been observed on**  **bank tops in Florida Bay. Syringodium**  **seems to be more tolerant of low temperatures than**  **T halassia**  **(no defo liation at temperatures just below 15°C);**  **Syringodium has maximal growth between 23°C and 29°C, whereas**  **for T**  **halassia maximal growth occurs between 23°C** **and 31°C (Zimmerman and Livingstone, 1976). In shal low bays with widely fluctuating temperatures,**  **Tha lassia, Syringodium,**  **and Halodule**  **have narrower leaf widths, suggesting increased stress (McMillan, 1978).**  **Ruppia has a wide tolerance to temperatures (7°–35°C)**  **and has highest growth rates during the cooler spring months (Phillips, 1960; Pulich, 1985). Water tempera**  **tures are not expected to be significantly affected by altered water management.** 


### Salinity

**Salinity plays a very important role in controlling ben thic plant communities in the upper estuaries of Florida**  **Bay. Areas of high variability in salinity have a low biomass of submerged plants (Montague and Ley,**  **1993). Mesocosm studies (Chesnes et al.,**  **1999) have pro duced data on how fluctuating salinities may affect** **turtlegrass, shoalgrass, and widgeon grass. Unfortu nately, operational difficulties plagued the mesocosm** **facility, which slowed progress and resulted in prob lems with maintaining proper controls.**  **T he role of hypersalinity in seagrass die-off still re**  **mains unclear. Salinities during the initial die-off episodes in 1987–1989 were accompanied by hyper**  **salinities ranging from 45 psu to 70 psu.The Barnes Key die-off clearly did not correlate with this level of salin** **ity but showed many of the other stresses that ac companied the primary die-off. Although the role of**  **h**

**ypersalinity may vary relative to other stresses, low salinity provides refugia from**  **Labyrinthula, because in**  **fection by that organism does not occur at <15 psu (Blakesley**  **et al., 1999b).** 


### Light

**Light penetration to the leaf blades, which sets the limits for seagrass photosynthesis, varies as a function**  **of depth, turbidity, and epiphyte cover.**

TURBIDITY **To assess the relationship between water clarity and**  **seagrass recovery in Florida Bay, Carlson et al.**  **(2001) have continuously measured subsurface and bottom**  **photosynthetically active radiation (PAR) at seven sta tions in Florida Bay since the fall of 1998. In addition**  **to continuous light data, discrete water samples for analysis of turbidity, color, chlorophyll, and total sus**  **pended solids and plant samples for epiphyte light attenuation measurements have been collected** **monthly. Diffuse attenuation coefficients vary sea sonally and between basins within Florida Bay: atten**  **uation is higher in winter than in summer and is generally higher in the basins that lost large amounts**  **of seagrass in die-off episodes between 1987 and 1991. P** 

**ersistent phytoplankton blooms in the north-central region of the bay are associated with high (greater**  **than 3) Kd values, but water clarity at most sites was higher in 2000 than in 1999.** 

EPIPHYTES **T here are spatial and temporal gradients in species**  **composition of epiphytes, with coralline red algae being more dominant in western high-flow areas of the** **bay (Frankovich and Fourqurean, 1997). Fleshy epi phytes have restricted distributions, occurring only** **near bird islands and near the Keys. The cyanobac terium**  **L yngbya**  **is very common in the Syringodium fil**  **iforme beds in the west (Frankovich and Zieman, 2001).**  **Epiphyte attenuation is higher in winter and spring (30%–50%) than in summer and fall (15%–30%), and** 

**v alues are higher in the eastern region of the bay**  **(greater than 40%) than in the western region (ca. 20%). Calcium carbonate derived from calcareous algae**  **and resuspended sediment composes more than half of the epiphyte load.** **Epiphytic light attenuation has also been mea sured using Mylar strips and a light-attenuation mea**  **surement apparatus that has been successfully employed by investigators in Australia and Chesa**  **peake Bay (Frankovich and Zieman, 2001). The Mylar strips have been set out within various seagrass mead** 

**o ws across the bay for a sufficient time period to allow**  **for the accumulation of epiphytic organisms. Distinct epiphytic communities consisting of benthic diatoms,**  **coralline red algae ( Melobesia membranacea, Hydrolithon**  **f**

**arinosum ), and filamentous red and brown algae occur**  **seasonally in various regions across Florida Bay.These**

**v arious epiphyte functional forms, and combinations**  **thereof, result in differing levels of light attenuation at the leaf surface relative to the amount of epiphyte**  **loading. Epiphyte loads at Barnes Key are at lower than 5% of bay-wide averages (Frankovich and Zieman,**  **2001). Highest epiphyte loads are in areas of highest seagrass productivity, so epiphytes are not reducing**  **production (Frankovich and Zieman, 2001). Grazers may have an important role in controlling**  **epiphyte abundance. Snails (50/m 2**  **) and hermit crabs are** Seagrass EcologyHunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 103 **conspicuous at Rabbit Key Basin (Frankovich and F** **ourqurean, 1997). In Florida Bay,**  **Bittium occurs at den**  **sities of about 3/m 2** 
**, whereas in the Indian River Lagoon,**  **Bittium occurs at densities of 20/**  **Halodule short-shoot or**  **at 1000s/m 2** 

**. Macroalgae such as**  **Laurencia are patchy in abun** **dance. It is unknown at present whether its abun dance has changed in response to the changes in**  **seagrass abundance (although these data are in the FHAP dataset). Jeff Holmquist found that**  **Laurencia accumulation did not kill underlying**  **T halassia.** 



### Nutrients

**W**

**orldwide, many estuaries have undergone loss of seagrasses as a result of eutrophication.The mechanism**  **for nutrient-enrichment-induced seagrass losses is that increased nutrients lead to increased epiphyte**  **loads and consequent shading and deterioration of the seagrasses (Cambridge**  **et al., 1986). Phytoplankton** **blooms usually follow rather than cause seagrass die offs. As stated above, epiphyte loads on seagrasses are** **relatively low in Florida Bay and do not seem to be re ducing production.** 



### Sulfide

**Carlson et al.**  **(1994) and Erskine and Koch (2000) have explored the potential links between elevated sedi**  **ment-sulfide concentrations and seagrass mortality (a hypothesis long proposed to account for seagrass die** **off). Hydrogen sulfide is a known plant toxin. High sul fide levels in sediments have been observed during and**  **after die-off episodes (Carlson et al.,**  **1994). Sulfide con centrations greater than 2–4 mmol have been mea**  **sured in die-off sites, but it is not known if this is a cause or an effect of die-off. If sulfide concentrations are less**  **than 2 mmol, no die-off has been observed. However, photosynthetic rates in**  **T halassia**  **increase as a function of increasing sulfide up to 6 mmol, and sulfide levels**  **up to 10 mmol have failed to produce visual signs of acute sulfide toxicity, although high sulfide levels have**  **been shown to result in reduced leaf-elongation rates (Erskine and Koch, 2000).**  **A series of field experiments has been undertaken to help us understand how sulfide concentrations may**  **influence seagrass growth and abundance and to clear up uncertainties between the two conflicting sets of re** **sults. A submersible pulse-amplitude-modulated flu orometer (Diving-PAM) was used to investigate**  **photosynthetic yields of T**  **halassia testudinum leaf ma**  **terial in situ**  **within bucket experiments established by Carlson. Photosynthetic yields were significantly lower**  **in buckets with added glucose and acetate (Figure 7.5), although both treatments should have increased sed**  **iment sulfide levels.**


### Labyrinthula Infection

**A theoretical model for die-off as a disease (Blakesley et al.,**  **1999a) has suggested three different roles that Labyrinthula**  **might play in Florida Bay under different environmental conditions. These roles include (1) a**  **nonpathogenic parasite, (2) an opportunistic secondary pathogen, and (3) a primary pathogen. Five different** **factors were discussed as critical elements in deter mining the role(s) of**  **Labyrinthula in seagrass health at**  **a particular site in Florida Bay (Blakesley et al.,**  **1999b). Salinity controls infection (infection does not occur**  **at less than 15 psu). Seagrass density determines the extent to which**  **Labyrinthula infection spreads because**  **the slime mold transmission is thought to depend on blade-to-blade contact (Muehlstein, 1992). Patho**  **genicity of a particular strain of Labyrinthula**  **will de termine severity of infection (Muehlstein**  **et al., 1988).**  **Environmental stressors (abiotic factors), such as low light or high temperatures, may weaken**  **T halassia**  **and, in combination with the infection by pathogenic**  **Labyrinthula, may cause seagrass die-off. Resistance to**  **disease due to genetic factors or production of phenolic compounds may be important in determining the**  **health of T**  **halassia in Florida Bay.**  **Blakesley et al.**  **’s (1999a) model predicted that in** **areas with high seagrass density, high salinity, “sub optimal seagrass conditions (environmental stress),”**  **and presence of pathogenic Labyrinthula,**  **the slime mold could contribute to either chronic or acute die**  **off by acting as an opportunistic secondary pathogen.** Figure 7.5 **Photosynthetic quantum yields of T** **halassia in Carl**  **son buckets exposed to high glucose (HIG), low glucose (LOG), molybdate (MO4), acetate (ACE), shaded (SHD), and shaded**  **with glucose (SHG) relative to controls inside (CON) and outside (OC) plots.**  Seagrass EcologyFlorida Bay Synthesis Hunt and Nuttle

104 FWRI Technical Report TR-11**Under the same conditions but without environmen tal stress, Blakesley**  **et al. (1999b) suggested that**  **Labyrinthula, acting as a primary pathogen, could still**  **cause “thinning”or patchy die-off. Labyrinthula**  **occur rence was found to have significant adverse influences**  **on branching frequency ( P**  **= 0.03), shoot density ( P**  **= 0.004), and apical density (**  **P = 0.033) (Paxson and Du**  **rako, 2001), suggesting that this microorganism may have an adverse influence on seagrass growth and**  **carbon balance ( sensu**  **Durako and Kuss, 1994). T** 

**he occurrence of Labyrinthula**  **has also been shown to affect photosynthetic characteristics of**  **T halassia**  **(Durako and Kuss, 1994). Durako and Kuss (1994) demonstrated that**  **Labyrinthula infection reduces oxy** **gen production and may increase susceptibility to sul fide.These results indicate that reduced photosynthetic**  **capacity may be caused by Labyrinthula**  **-induced lesions or elevated sulfide.This may make**  **T halassia**  **more sus ceptible to sulfide toxicity, hypoxia, or disease by im**  **posing a negative carbon drain on belowground tissues. Photosynthetic yields of**  **T halassia testudinum**  **leaf material measured**  **in situ at Sunset Cove and Cross**  **Bank by using a Di ving-PAM w** **ere signifi cantly lower**  **in regions of T**  **halassia leaves that had visible lesions.**  **T hese patterns agree with those previously reported**  **by Durako and Kuss (1994). However, close-interval**  **Diving-PAM-fl uorescence measurements along an in**  **dividual leaf with several visible lesions indicated the reductions in photosynthesis were restricted to the im**  **mediate area of the lesion.Quantum yields of lesion-free leaf regions of short-shoots also declined along transects**  **from dense, apparently healthy beds to recent die-off patches at both Barnes Key and Cross Bank. The pho**  **tosynthetic characteristics of solitary short-shoots within the die-off patches were significantly lower than those**  **of shoots along the ecotones and shoots only 1 m inside the bed. This indicates that photosynthesis may be** **reduced even in the absence of visible lesions.The Div ing-PAM**  **data also revealed that the severity of stress imposed by the leaf lesions will be a function of the pro**  **portion of total leaf surface that is necrotic,and it remains to be determined what the lethal threshold is for lesion** 
**coverage.**


### Sediment Characteristics

**Carlson (unpublished data) has observed that high porosity sediments correlate with high hydrogen sul**  **fide levels because of the sediments’low permeability. Barnes Key surface sediments have very high poros**  **ity (lots of water and fine sediments) and high levels of hydrogen sulfide.**  **Seagrass die-off has been observed only in biogenic carbonate sediments, which are usually low in iron.**  **However, Florida Bay carbonate sediments have rela tively high iron levels (Carlson**  **et al., 1994). Spatially,**  **iron levels are high near the mainland and toward the**

**w est. The role of atmospheric deposition of iron to**  **Florida Bay remains poorly understood. Addition of iron to sediments decreases the flux of sulfide to**  **Tha lassia**  **(Carlson bucket experiments) and results in a small but significant increase in growth. Iron distrib** **ution may also have a role in controlling phytoplank ton blooms in the bay.**  

## Effect of Ecosystem Characteristics on Community Structure and Distribution

**“The present distribution and species composition of sea grasses in south Florida are a result of the interaction of**  **many factors, the most important being water depth,**

**w ater clarity, and nutrient availability. Changes in the**  **movement and quality of water in the region, whether natural or anthropogenic, are likely to cause changes in**  **the large-scale patterns in abundance and composition of these seagrass beds. It is also likely that the first**  **symptoms of a changing coastal environment will be a**

**c hange in species composition of seagrass beds, not a**  **wholesale loss of seagrass cover ( e.g.,**  **Hall et al.,**  **1999; Du rako**  **et al., 2001 [2002]). For this reason, accurate data on**  **the species composition of the seagrass communities must be collected periodically as a measure of the sta**  **tus of the coastal environment.” —Fourqurean**  **et al., 2002**  

### Correlation with Patterns of Water Quality

**F ourqurean**  **et al. (2003) developed a discriminant func**  **tion model that uses seagrass species occurrence and abundance data from 677 locations and water-quality**  **data from 28 monitoring stations in Florida Bay. This model predicted that the distribution of benthic habi**  **tat types in Florida Bay would likely change if water quality was affected by changes in water delivery to the**  **bay. Specifically, an increase in seasonal delivery of fresh water should cause an expansion of the distrib**  **ution and abundance of Ruppia maritima**  **and Halodule**  **wrightii at the expense of**  **T halassia testudinum**  **along the northeast region of the bay.**  

### Geographic Variation in Seagrass Die-Off

**T he production of distribution and abundance maps**  **of the seagrasses has proven valuable, and these maps provide a quantitative record of distribution and abun** **dance at both basin and bay scales. The changes be tween maps provide clear visualization of where and**  **how much the distribution and abundance changes and** Seagrass EcologyHunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 105**can thus point to “hot spots”that may be related to spe cific forcing events or conditions. The use of seagrass** **cover has become an assessment standard in the re gion (FKNMS, DERM, FHAP). Cover may be a more**  **sensitive performance measure to short-term changes than density because density changes require mortality**  **and recruitment of short-shoots, whereas cover can also**

**v ary in response to changes in the leafiness of short**  **shoots. Short-shoot density may be a better longer-term performance measure and is a quantitative measure** **ment. Density is the net effect of mortality, recruit ment, and life span (demographics).**  **T he recurrence of an acute die-off in Barnes Key** **presented an opportunity to test a portion of the the oretical model by comparing the symptoms and pro**  **gression of an acute event in the Barnes Key mud bank area with the symptoms and progression of what we** **believed to be chronic die-off in Sunset Cove.The hy pothesis was that in Sunset Cove,**  **Labyrinthula acted as**  **a primary pathogen in an environmentally unstressed site, whereas in Barnes Key,**  **Labyrinthula more likely** **played the role of a secondary pathogen in an envi ronmentally stressed site.**  **Comparisons of results for the Sunset Cove and Barnes Key sites revealed that although active die-off** 

**w as occurring in both places, the sites were very dif**  **ferent. At both sites the pattern of die-off was patchy, suggesting disease processes rather than a physical** **process as the primary cause. Both sites had high salin ities (greater than 15 psu) and dense**  **T halassia**  **beds— necessary elements for**  **Labyrinthula infection and** **transmission. However, the data from the two sites re**

**v ealed important differences that are summarized in**  **T**

**able 7.3. T** **hese differences strongly suggest that the mech anisms for the die-offs in Barnes Key and Sunset Cove**  **are not the same. Blakesley et al.**  **(1999b) proposed that the acute die-off in Barnes Key resulted from a series** **of events beginning with heat stress and an initial in fection or disease (not**  **Labyrinthula -induced) that**  **rapidly kills the infected seagrass.The resultant large amount of decaying belowground biomass from the**  **rapidly dying T**  **halassia roots and rhizomes promotes** **microbial activity that in turn elevates the sediment sulfide levels selectively in those vegetative zones**  **where the die-off is occurring or has recently occurred. T** **he high sediment-sulfide levels do not kill seagrass outright but instead further stress the other seagrass**  **in the immediate area. Finally, Labyrinthula,**  **acting as an opportunistic secondary pathogen, infects the al**  **ready weakened remaining seagrass. In contrast, the chronic die-off in Sunset Cove ap**  **pears to be directly caused by Labyrinthula**  **acting as a primary pathogen. Sediment-sulfide levels may re**  **main relatively low in all the vegetative zones tested simply because the slow death of**  **T halassia**  **roots and rhizomes results in a smaller decaying belowground**  **biomass. As a result, the sediment-sulfide levels may remain lower in the vegetative zones than in contrast**  **to the Barnes Key. Such chronic seagrass die-off is still ongoing in many parts of Florida Bay, where the**  **Tha lassia**  **beds are dense enough for transmission of the disease and the salinity is high enough for infection to** 

**occur. Recent high-resolution**  **in situ oxygen measure**  **ments show that the short-shoot meristems of T** **halas sia**  **at the Barnes Key die-off site became anoxic during the night in November and remained anoxic for up to**  **five hours (Borum et al.,**  **2001). In contrast, leaf meris tems at Rabbit Key Basin did not become hypoxic.The**  **Barnes Key samples showed a more rapid decline in oxygen concentration after sunset and slower internal**  **oxygen concentration increases in the morning than did samples from Rabbit Key Basin.**  **T halassia**  **at Barnes Ke**  **y is very dense, with over 1,200–1,500 short shoots/m**  **2 , a v**  **ery high biomass (SC 300 g/m 2**  **), low turnover rate of grass blades (1.2%/day), and very thick**  **litter layer. In Rabbit Key Basin, densities are also high (1,200–1,300 short-shoots/m**  **2 ), but biomass (SC 109**  **g/m 2**  **) and turnover rates (1.7%/day) are more moder ate (Zieman**  **et al., 1999).The long short-shoot stems at**  **Barnes Key lead to increases in diffusion distance for oxygen. Long internodes may be a response to hy**  **poxia or rapid sedimentation.** T able 7.3 **Characteristics of seagrass die-off at two locations in Florida Bay.**

Barnes Key Sunset Cove
**Seagrass loss is rapid. Seagrass loss is slower.**  **Meristem “rots.” Meristem “healthy.”**  **Lesions occur after**  **die-off. Lesions occur**  **before die-off.**  **W ater temps are high in summer.**  **Water temps are “normal.” “High”sediment-sulfide levels (up to**  **“Low”sediment-sulfide levels 7,000 μmol). Levels vary in different zones, but**  **(= 1,600 μmol) in bare, sparse, and highest values are found in active die-off zones.**  **dense seagrass zones.** Seagrass EcologyFlorida Bay Synthesis Hunt and Nuttle

106 FWRI Technical Report TR-11 **Seagrass loss has been recently observed in the northern portion of Little Madeira Bay from the mouth**  **of the Taylor River to the south and west (Bacon et al.,**  **2001), and this area has been recolonized by Halodule**  **and Ruppia.**  **T his new seagrass die-off led to a plan for**  **a series of observations and experiments to test several of the hypotheses that might explain seagrass die-off.**  

## Modeling Change in Benthic Communities

**Statistical modeling was commissioned by the Central and Southern Florida Comprehensive Review Study**  **(Restudy) of the U.S. Corps of Engineers consistent with recommendations from the 1998 Seagrass Modeling**  **W**

**orkshop (Fourqurean et al.,**  **2003). The goal of this**

**w ork is to seek relationships between water-quality** 

**v ariables and seagrass species composition and abun** **dance, which if sufficiently strong, can be used to pre dict the effects of various alterations in Florida Bay**  **salinity regimes.The statistical models developed in this project will be used in conjunction with output from** **other models to predict the effects of Restudy scenar ios on the benthic habitats of Florida Bay. This statis**  **tical model will not address mechanisms or degree of**

**c hange in water quality that result from Restudy sce**  **narios; other models (such as the NSM, FATHOM, and the Florida Bay salinity-transfer-function models**  **currently employed by the Restudy) must simulate**

**w ater-quality changes across Florida Bay that will pro** **vide the input to the new models developed in this pro ject. As a consequence, it is anticipated that the benthic**  **habitat-change predictions of the statistical models will be the most reliable in the regions most closely cou**  **pled with water-management practices ( i.e.,**  **the en closed, mangrove-lined estuaries on the fringe of** **Florida Bay). As the fidelity of the physical water-qual ity models to the behavior of the system declines, the**  **reliability of the benthic changes predicted by our model will also decline. However, because the statis**  **tical relationships will be based on data from a larger number of marine areas and upper estuaries, the basic** **relationships between actual water quality (not mod eled) and benthic habitats will be robust.**  **In addition, other seagrass-modeling efforts have recently been initiated. These include the develop**  **ment of both seagrass unit models for T**  **halassia and**  **Halodule and a landscape model that will take output** **from the unit models. Smith and colleagues are de**

**v eloping a hierarchical approach to modeling the in**  **teraction between plant and physical processes in Florida Bay that involves two distinct spatial scales—**  **the demographic unit (ca. 10 m 2**  **) and the landscape unit (ca. km**  **2 ). A preliminary landscape model of**  **T halassia**  **that explicitly relates patterns of photosynthesis, res piration, and carbon allocation to environmental con**  **ditions that include salinity, temperature, PAR, and nutrient availability has been developed.** **Physical processes such as sedimentation, de composition, and nutrient cycling will be modeled on**  **a spatial scale of the landscape unit. This approach provides a hierarchical framework in which the de**  **mographic units used to simulate plant processes exist in the context of the landscape units, which will define** **the underlying physical environment.The plant char acteristics that are relevant to the feedbacks with the**  **physical environment (such as primary productivity and inputs of dead organic matter) are described sta**  **tistically for the demographic units and used to define the biological environment for each landscape unit. In**  **this manner, the heirarchical framework functions as a dynamic, interactive GIS in which each parameter and**  **process is described and simulated at the appropriate temporal and spatial scales.** 



## Current Research

Field Assessment

**• FHAP is continuing spring and fall sampling and has** 

**incorporated (since spring 2001) measurements of photosynthetic characteristics of**  **T halassia**  **using Div ing-PAM-fluorometry at each station in addition to the**  **Braun-Blanquet and standing-crop measurements.**

**• FWRI (Carlson) is continuously monitoring benthic** 

**light availability at fixed stations in several basins.**

**• Zieman is maintaining the long-term productivity** 

**measurements.**


### Experimental

**• SFWMD is funding a new study entitled “High salin** 

**ity, nutrient and multiple stressor effects on sea grass communities of NE Florida Bay” being**  **conducted by Koch and Durako. The results of this study are intended to help determine the parame**  **ters for the unit model with data from Florida Bay**
**seagrasses.**

**• FWRI (Carlson) bucket experiments have been con** 

**ducted to examine effects of multiple stressors (sul fide, nitrogen, and light) on seagrasses**  **in situ**

**.** 

## Literature Cited

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FWRI Technical Report TR-11 107 **B ARBER, B. J., and P. J. BEHRENS. 1985. Effects of el** 

**ev ated temperature on seasonal**  **in situ leaf productiv**  **ity of T**  **halassia testudinum Banks ex König and**  **Syringodium filiforme, Kützing. Aquatic Botany 22: 61–69.** 

**B ARBER,T. R., and P. R. CARLSON. 1993. Effects of sea** **grass die-off on benthic fluxes and porewater con centrations of CO**  **2 , H**  **2 S and CH**  **4 in Florida Bay**  **sediments. Pp. 530–500 in**  **Biogeochemistry of Global Change: Radiatively Active Trace Gases (R. S. Orem**  **land, ed.). Chapman and Hall, New York.**
**BLAKESLEY, B. A., M. O. HALL, and M. W. WHITE. 1999a. Spatial patterns of**  **T halassia**  **decline and inci dence of**  **Labyrinthula infection in Florida Bay, USA. P.**  **26 in**  **T he American Society of Limnology and Oceanog**  **raphy Conference,“Navigating into the Next Century” Abstracts, 1–5 February, Santa Fe, New Mexico.** 
**BLAKESLEY, B. A., J. H. LANDSBERG, B. B. ACKER MAN, R. O. REESE, J. R. STYER, C. O. OBORDO, and** **S. E. LUCAS–BLACK. 1998. Slime mold, salinity, and sta tistics: implications from laboratory experimentation**  **with turtlegrass facilitate interpretation of field results from Florida Bay. Pp. 164–166**  **in 1998 Florida Bay Sci**  **ence Conference. (Abstract)**
**BLAKESLEY, B. A., J. H. LANDSBERG, M. O. HALL, S. E. LUKAS, B. B. ACKERMAN, M. W. WHITE, J.**  **HYNIOVA, and P. J. REICHERT. 1999b. Seagrass disease and mortality in Florida Bay: understanding the role of**  **Labyrinthula. Pp. 12–14**  **in 1999 Florida Bay and Adjacent**  **Marine Systems Science Conference. (Abstract)**
**BOESCH, D. F., N. E. ARMSTRONG, J. E. CLOERN, L. A. DEEGAN, R. D. PERKINS, and S. L. WILLIAMS.**  **1995. Report of the Florida Bay science review panel on Florida Bay Science conference: A report by principal**  **investigators. Program Management Committee, Florida Bay Research Program, Miami, Florida. 19 p.** 
**BOESCH, D. F., N. E. ARMSTRONG, C. F. D’ELIA, N. G.**  **MAYNARD, H. W. PAERL, and S. L. WILLIAMS. 1993. Deterioration of the Florida Bay ecosystem: An** 

**ev aluation of the scientific evidence. Report to the In**  **teragency Working Group on Florida Bay. National Fish and Wildlife Foundation, Washington, D. C. 27 p.** 
**BORUM, J., O. PEDERSON, T. M. GREVE, J. C. ZIE MAN,T. FRANKOVICH, AND J. FOURQUREAN. 2001.**  **Seagrass dieoff in Florida Bay: meristematic anoxia, a mechanism for the initiation of primary seagrass die**  **off. Pp. 129–130 in**  **2001 Florida Bay Science Conference. (Abstract)** 
**BOYER, J. N., J. W. FOURQUREAN, and R. D. JONES. 1999. Seasonal and long-term trends in the water qual**  **ity of Florida Bay (1989–1997). Estuaries 22: 417–430. BUTLER, M. J., J. H. HUNT, W. F. HERRNKIND, M. J.**  **CHILDRESS, R. BERTELSEN, W. SHARP, T. MATTHEWS, J. M. FIELD, and H. G. MARSHALL.**  **1995. Cascading disturbances in Florida Bay, USA:**
**cy anobacterial blooms, sponge mortality, and impli**  **cations for juvenile spiny lobsters, P**  **anulirus argus. Ma**  **rine Ecology Progress Series 129: 119–125.**

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**C ARLSON, P. R., M. J. DURAKO, T. R. BARBER, L. A.**  **Y**

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**C ARLSON, P. R., L. A. YARBRO, B. J. PETERSON, J.**  **DA VIS, and B. DAVIS. 2001. Recovery potential of sea** **grasses in Florida Bay: The contribution of phyto plankton blooms, sediment resuspension, and**  **epiphytes to light attenuation. Pp. 133 in**  **2001 Florida Bay Science Conference. (Abstract).** 
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**DUNTON, K. H., and D. A.TOMASKO. 1994. In situ**  **pho tosynthesis in the seagrass**  **Halodule wrightii in a hy**  **persaline subtropical lagoon. Marine Ecology Progress Series 107: 281–293.**  **DURAKO, M. J. 1994. Seagrass die-off in Florida Bay (USA): changes in shoot demography and populations**  **d**

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108 FWRI Technical Report TR-11**Changes in Fluxes in Estuaries: Implications for Sci ence to Management (K. R. Dyer and R. J. Orth, eds.).**  **Olsen and Olsen, Fredensborg, Denmark.**
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**orter, eds. The Everglades, Florida Bay, and Coral Reefs of the Florida Keys: An Ecosystem Sourcebook.**  **CRC Press, Boca Raton, Florida.**
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**DURAKO, M. J., and K. M. KUSS. 1994. Effects of Labyrinthula**  **infection on the photosynthetic capacity of**  **T halassia testudinum.**  **Bulletin of Marine Science 54 (3): 727–732.**  **DURAKO, M. J., and M. D. MOFFLER. 1985. Spatial and temporal variation in the growth and proximate com**  **position of T**  **halassia testudinum Banks ex König. Gulf**  **Research Reports 8: 43–49.**

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**on T**  **halassia testudinum carbon balance and adenylate**  **energy charge. Aquatic Botany 67: 275–285.**
**FOURQUREAN, J. W., J. N. BOYER, M. J. DURAKO, L. N. HEFTY, and B. J. PETERSON. 2003. Forecasting the**  **response of seagrass distribution to changing water quality: statistical models from monitoring data. Eco**  **logical Applications 13(2): 474–489.**
**FOURQUREAN, J. W., M. J. DURAKO, M. O. Hall, and L. N. HEFTY. 2002. Seagrass distribution in south** **Florida: a multi-agency coordinated monitoring pro gram. Pp. 497–522**  **in J. W. Porter and K.G. Porter, eds.**  **T he Everglades, Florida Bay, and Coral Reefs of the**  **Florida Keys: An Ecosystem Sourcebook. CRC Press, Boca Raton, Florida.** 
**FOURQUREAN, J. W., J. C. ZIEMAN, and G. V. N. POWELL. 1992. Phosphorus limitation of primary pro**  **duction in Florida Bay: evidence from the C:N:P ratios of the dominant seagrass**  **T halassia testudinum.**  **Lim nology and Oceanography 37(1): 162–171.** 
**FRANKOVICH,T. A., and J. W. FOURQUREAN. 1997. Seagrass epiphyte loads along a nutrient availability**  **gradient, Florida Bay, USA. Mar. Ecol. Prog. Ser. 159: 37–50.** **FRANKOVICH, T. A., and J. C. ZIEMAN. 2001. Epi phytic light attenuation on**  **T halassia testudinum**  **in Florida Bay. P. 143**  **in 2001 Florida Bay Science Confer**  **ence. (Abstract) GOERTE, R. W. 1994. The Florida Bay economy and** 

**c hanging environmental conditions. U.S. Library of**  **Congress, Congressional Research Service Report. No. 94-435 ENR. Washington, D.C. 19 p.** 
**HALL, M. O., M. J. DURAKO, J.W. FOURQUREAN, and J. C. ZIEMAN. 1999a. Decadal-scale changes in seagrass**  **distribution and abundance in Florida Bay. Estuaries 22: 445–459.** 
**HALL, M. O., M. F. MERELLO, B. A. BLAKESLEY, and M. J. DURAKO. 1999b. Interpreting seagrass change in**  **Florida Bay from 1995 to 1998: good news or bad news? P.**  **44 in**  **15th Biennial Conference of the Estuarine Re search Federation Abstracts. New Orleans, Louisiana,**  **25–30 September.**
**HOLMQUIST, J. G., G.V. N. POWELL, and S. M. SOG ARD. 1989. Sediment, water level and water tempera**  **ture characteristics of Florida Bay’s grass-covered mud banks. Bulletin of Marine Science 44: 348–364.** 
**KENWORTHY, W. J., A. C. SWARTZSCHILD, M. S. FONSECA, D.WOODRUFF, M. J. DURAKO, and M. O.**  **HALL. 1998. Ecological and optical characteristics of a large**  **Syringodium filiforme meadow in the southeast**  **ern Gulf of Mexico. Pp. 182–184 in**  **1998 Florida Bay Sci ence Conference. (Abstract)** 
**LANDSBERG, J. H., B. A. BLAKESLEY, A. BAKER, G. McRAE, M. DURAKO, M. O. HALL, R. REESE, and J.**  **STYER. 1996. Examining the correlation between the presence of the slime mold**  **Labyrinthula, and the loss**  **of T**  **halassia testudinum in Florida Bay. Pp. 42–45**  **in 1996**  **Florida Bay Science Conference. (Abstract) McMILLAN, C. 1978. Morphogeographic variation**  **under controlled circumstances in five seagrasses: T** **ha lassia testudinum, Halodule wrightii, Syringodium fili**  **forme, Halophila engelmannii, and**  **Zostera marina. Aquatic**  **Botany 4: 169–189. MONTAGUE, C. L., and J. A. LEY. 1993. A possible ef**  **fect of salinity fluctuation on abundance of benthic**

**v egetation and associated fauna in northeastern Florida**  **Bay. Estuaries 16(4): 703–717. MUEHLSTEIN, L. K. 1992. Host-pathogen interaction**  **in the wasting disease of eelgrass, Zostera marina.**  **Cana dian Journal of Botany 70: 2081–2088.**  Seagrass EcologyHunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 109 **MUEHLSTEIN, L. K., D. PORTER, and F. T. SHORT. 1988.**  **Labyrinthula, a marine slime mold producing**  **symptoms of wasting disease in eelgrass, Zostera ma**  **rina. Marine Biology 99: 465–472.**  **ORTH, R. J., and K. A. MOORE. 1983. Chesapeake Bay: an unprecedented decline in submerged aquatic veg**  **etation. Science 222: 51–53.**

**P**

**AXSON, J. C. and M. J. DURAKO. 2001. Branching fre quency of**  **T halassia testudinum**  **Banks ex König as an in dicator of growth potential within ten basins of Florida**  **Bay. P. 154 in**  **2001 Florida Bay Science Conference. (Abstract)**  **PHILLIPS, R. C. 1960. Observations on the ecology and distribution of the Florida seagrasses. Florida State**  **Board of Conservation Marine Laboratory Professional P** 

**apers Series No. 2. 72 p. PHILLIPS, R. C., and E. G. MEÑEZ. 1988. Seagrasses.**  **Smithsonian Contributions in Marine Science No. 14. 104 p.** **PHLIPS, E. J., and S. BADYLAK. 1996. Spatial variabil ity in phytoplankton standing crop and composition in** **a shallow inner-shelf lagoon, Florida Bay, Florida. Bul letin of Marine Science 58: 203–216.** 
**PHLIPS, E. J., T. C. LYNCH, and S. BADYLAK. 1995. Chlorophyll**  **a ,**  **tripton, color, and light availability in a shallow tropical inner-shelf lagoon, Florida Bay, USA.**  **Marine Ecology Progress Series 127: 223–234. PORTER, D., and L. K. MUEHLSTEIN. 1989. A species**  **of Labyrinthula**  **is the prime suspect as the cause of a massive die off of the seagrass**  **T halassia testudinum**  **in Florida Bay. Mycological Society of America Newslet**  **ter 40: 43.**
**POWELL, A. B., D. E. HOSS, W. F. HETTLER, D. S. PE TERS, and S. WAGNER. 1989. Abundance and distri**  **bution of ichthyoplankton in Florida Bay and adjacent**

**w aters. Bulletin of Marine Science 44: 35–48.**  **PRAGER, E. 1998. Sediment resuspension in Florida Bay. Pp. 59–60**  **in 1998 Florida Bay Science Conference.**  **(Abstract) PULICH,W. M., JR. 1985. Seasonal growth dynamics of**  **Ruppia maritima and**  **Halodule wrightii in southern Texas**  **and evaluation of sediments fertility status. Aquatic Botany 23: 53–66.** 
**ROBBLEE, M. B.,T. R. BARBER, P. R. CARLSON, M. J. DURAKO, J.W. FOURQUREAN, L. K. MUEHLSTEIN,**  **D. PORTER, L. A.YARBRO, R.T. ZIEMAN, and J. C. ZIE**  **MAN. 1991. Mass mortality of the tropical seagrass T**  **halassia testudinum in Florida Bay (USA). Marine Ecol**  **ogy Progress Series 71: 297–299.**
**ROSE, C. D., W. C. SHARP, W. J. KENWORTHY, J. H. HUNT, W. G. LYONS, E. J. PRAGER, J. F.VALENTINE,**  **M. O. HALL, P.WHITFIELD, and J.W. FOURQUREAN. 1999. Overgrazing of a large seagrass bed by the sea**  **urchin L**  **ytechinus variegatus in Outer Florida Bay. Ma**  **rine Ecology Progress Series 190: 211–222. SCHOMER, N. S., and R. D. DREW. 1982. An ecologi**  **cal characterization of the lower Everglades, Florida Bay, and the Florida Keys. U.S. Fish Wildlife, FWS/OBS**  **82/58.1, Washington, D.C. 246 p.**
**STUMPF, R. P., M. L. FRAYER, M. J. DURAKO, and J. C. BROCK. 1999.Variations in water clarity and bottom**  **albedo in Florida Bay from 1985 to 1997. Estuaries 22: 431–444.**  **THAYER, G.W., and A. J. CHESTER. 1989. Distribution and abundance of fishes among basin and channel**  **habitats in Florida Bay. Bulletin of Marine Science 44: 200–219.** 
**THAYER, G. W., P. L. MURPHY, and M. W. LACROIX. 1994. Responses of plant communities in western**  **Florida Bay to the die-off of seagrasses. Bulletin of Marine Science 54: 718–726.** **TILMANT, J.T. 1989. A history and an overview of re cent trends in the fisheries of Florida Bay. Bulletin of**  **Marine Science 44: 3–22. WILLIAMS, S. L., and C. P. McROY. 1982. Seagrass**  **productivity: the effect of light on carbon uptake. Aquatic Botany 12: 321–344.**  **ZIEMAN, J. C. 1982. The ecology of the seagrasses of south Florida: A community profile.U.S.Fish and Wildlife**  **Service, FWS/OBS-82/25, Washington, D.C. 123 p.**
**ZIEMAN, J. C., J. FOURQUREAN, and T. A. FRANKOVICH. 1999. Seagrass dieoff in Florida Bay**  **(USA): Long-term trends in abundance and growth of T** 

**halassia testudinum and the role of hypersalinity and**  **temperature. Estuaries 22: 2B: 460–470. ZIEMAN, J. C., J. W. FOURQUREAN, and R. L. IVER**  **SON. 1989. Distribution, abundance and productivity of seagrasses and macroalgae in Florida Bay. Bulletin**  **of Marine Science 44: 292–311.**
**ZIMMERMAN, M. S., and R. J. LIVINGSTONE. 1976. Seasonality and physico-chemical ranges of benthic**  **macrophytes from a north Florida estuary (Apalachee Bay). Contributions in Marine Science 20: 34–45.**  Seagrass Ecology110 FWRI Technical Report TR-11 

## Introduction

Question 5**—What is the relationship between environ mental and habitat change and the recruitment, growth,**  **and survivorship of animals in Florida Bay?**

**In the context of the Florida Bay Science Program, higher-trophic-level species (HTLS) include zoo** **plankton; benthic invertebrates such as sponges, mol lusks, crustaceans (particularly decapods); fishes;** **marine mammals; marine reptiles; and water birds. Sci entific input about HTLS in the bay is critical to the suc**  **cessful restoration of Florida Bay and associated coastal ecosystems because HTLS are both ecologically and**  **economically important and are viewed as important by**  **the public. Performance measures based on HTLS are essential to protecting and restoring Florida Bay in**  **the Comprehensive Everglades Restoration Plan (CERP) implementation process.**  **HTLS integrate the condition of the ecosystem and reflect it in their responses to environmental** 

**c hange. Question 5 investigates how HTLS respond to** 

**c hanges in the characteristics of the ecosystem, such** **as benthic communities, water quality, and circula tion, and exchange with adjacent ecosystems and the**  **effect of human activities on these characteristics. Question 5 also investigates how HTLS are affected by**  **fishing. Some HTLS play a critical role in regulating ecosystem functions, so changes due to fishing or other** **causes, anthropogenic or natural, can have repercus sions on the entire Florida Bay ecosystem.**  **T**

**he higher-trophic-levels component of the Florida Bay Science Program has approached Question 5 by ad**  **dressing the following questions: • H**  **ow do human activities (**  **e.g., w** **ater management,**

**fishing) and major natural factors influence biolog ical processes affecting growth, survival, and re**  **cruitment of fishery species, protected species, and ke** **ystone species in Florida Bay? • H**  **ow do HTLS community composition and trophic** **structure vary in time and space, what factors are re sponsible, and what processes are affected by the** 

**v ariation?**  **• W hat major processes influence transport of pre**  **settlement stages of fish and invertebrates to and into Florida Bay, what is their schedule, what parts of** **the bay are most affected, and what is their impor tance to recruitment to fisheries inside and outside**  **of the bay? • W**  **hat animals affect major ecological processes in the bay, such as primary productivity and nutrient cy**  **cling, and what is the magnitude of this role?**

**Substantial progress has been made on these top ics but much remains to be done. This chapter syn**  **thesizes recent results, examines historical information relevant to the central question, and identifies needed**  **future work.**



### Description of Higher-Trophic-Level Species in Florida Bay

**T he HTLS component of the Florida Bay Science Pro** **gram encompasses all the animals of the system. Re cent work on higher trophic levels in Florida Bay builds** **on prior research in coastal waters of Everglades Na tional Park (ENP) before or in the 1950s and 1960s,**  **summarized by Tilmant (1989) and Tabb and Roessler (1989); in the 1970s by Schmidt (1979); and in the 1980s**  **by Thay**  **er and Chester (1989), Powell et al.**  **(1989), Sog ard**  **et al. (1989), Holmquist**  **et al. (1989), Robblee**  **et al. (1991), and Ley**  **et al. (1994). More than 250 fish species**  **are known to occur in Everglades National Park coastal**

**w aters (Loftus, 2000), although Schmidt (1979) found** **only 128 fish species in Florida Bay. Tabb (1966) con cluded that individuals of most species left ENP wa**  **ters for unknown seaward spawning areas when they reached sexual maturity.**  **A synthesis of past research for the March 1998** 

# Chapter 8 Higher-Trophic-Level Species

Lead Author Joan A. Browder Contributors Cynthia Yeung, Thomas Schmidt, Mark J. Butler, IV, Maria Criales, Allyn Powell, Don DeAngelis, David Evans, Larry Settle, Bill Sharp, Craig Faunce, Jerald Ault, Anne Marie Eklund, G. Lynn Wingard, Gordon Thayer, Darlene Johnson, David Rumbold, Jeffrey Chanton, C. Chasar, Jerome Lorenz, Ed Matheson, James Colvocoresses, Michael Robblee, Laura Engleby, Chris Koenig, Samantha WhitcraftHunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 111 **HTLS Group Report (Browder et al.,**  **1998) organized the animals of the bay into a generalized food web (Figure** **8.1). The primary producers at the food-web base in clude phytoplankton, epiphytes, benthic algae, sea**  **grass, and mangroves. The Florida Bay fauna is made up of herbivores, detritivores, planktivores, and pisci** 

**vo res at three or four trophic levels.Within the bay, the** **food web has two major branches: pelagic (water-col umn) and benthic (on or near the bottom), which may** **converge at the highest trophic levels. Most of the fol lowing information is summarized from Browder**  **et al. (1998), but new information has been added as cited.** **In the pelagic branch of the food web, filter-feed ing planktonic stages of fishes, crustaceans, mollusks,**  **and other taxa feed on phytoplankton ( e.g.,**  **diatoms, dinoflagellates) in the water column and are preyed** **upon by small, schooling pelagic fish such as bay an cho**  **vies and hardhead silversides.The benthic branch includes filter feeders (**  **e.g., sponges, bivalve mollusks,** **ascidians, polychaetes) and demersal grazers or de tritivores, such as amphipods, harpacticoid copepods,**  **polychaetes, striped mullet, and post-settlement stages of mollusks and other invertebrates.The next level of**  **benthic consumers includes a host of small demersal fish and macroinvertebrates that feed on small inver**  **tebrates. Dominant members of this group include gulf toadfish, goldspotted killifish, rainwater killifish,**  **dwarf seahorse, dusky pipefish, gulf pipefish, spotfin mojarra, silver jenny, white grunt, pigfish, pinfish, and**  **silver perch (Thayer et al.,**  **1999). Pink shrimp and many taxa of small caridean and penaeoidean shrimp also are**  **numerically abundant in the bay (Holmquist et al.,**  **1989; Robblee, personal communication). Juvenile spiny lobsters are abundant in the southwestern portion of**  Figure 8.1 **T rophic levels in Florida Bay.**  Higher-Trophic-Level SpeciesFlorida Bay Synthesis Hunt and Nuttle

112 FWRI Technical Report TR-11 **the bay south of major mud bank barriers (Field and Butler, 1994; Herrnkind**  **et al., 1997). The limited re**  **search in the bay and nearby areas suggests that the demersal fish in the bay are generalists that eat a va**  **riety of benthic invertebrates (Zieman, 1981; Schmidt, 1993a; Ley**  **et al., 1994).**  **Florida Bay supports several highly sought-after game fish, including red drum, spotted seatrout, gray**  **snapper, snook, tarpon, and bonefish (Schmidt et al.,**  **2001, 2002). Sharks are commonly seen during aerial surveys (S. Bass, personal communication) and in**  **clude nurse sharks, bonnethead sharks, and lemon sharks. Rays (**  **e.g., sting rays and manta rays) are com** **monly seen on aerial surveys. Small fish and macroin**

**v ertebrates are the prey of these larger fish.Within the** **Florida Bay area, gray snapper and red drum princi pally eat shrimp and crabs, whereas barracuda,**  **seatrout, and snook eat more fish than crustaceans (Marshall, 1954; Croker, 1960; Yokel, 1966; Fore and**  **Schmidt, 1973; Rutherford et al.,**  **1983; Schmidt, 1986, 1989; Harrigan**  **et al., 1989; Hettler, 1989). Of the abun**  **dant forage fish, those that appear to be important in the diet of some piscivorous fishes are gulf toad fish**  **(lemon sharks, red drum, and bonefish), pinfish (lemon sharks and snook), hardhead silversides (snook),** **goldspotted killifish (barracuda), and rainwater killi fish (barracuda and spotted seatrout) (Schmidt, 1986,**  **1989; Crabtree et al.,**  **1998; Koenig et al.,**  **2001). In south ern Florida Bay, juvenile lobsters constitute a large**  **fraction of the diets of a variety of fish: nurse sharks, bonnethead sharks, southern stingrays, bonefish, per**  **mit, and gulf toadfish (Smith and Herrnkind, 1992). Small mollusks are abundant in Florida Bay and are**  **probably fed on by rays and fish such as sheepshead. T** **he pink shrimp, F**  **arfantepenaeus duorarum, is a key** **component of trophic webs.This species is an impor tant prey of game fish (Croker, 1960; Stewart, 1961,**  **Yok el, 1966; Rutherford**  **et al., 1983; Schmidt, 1986, 1989;**  **Hettler, 1989) and wading birds (Palmer, 1962), linking them to small grazers and detritivores supported by**  **algae and seagrass and mangrove detritus (Fry et al.,**  **1999).The abundant small caridean shrimps in Florida Bay are the principal prey of juvenile pink shrimp**  **(Schwamborn and Criales, 2000). T** **he many piscivorous water birds that live in the bay seasonally or year-round eat small fish and** **macroinvertebrates such as crabs and shrimps, al though this is poorly documented. Piscivorous birds in**  **the bay include double-crested cormorants, brown pelicans, red-breasted mergansers, laughing gulls,**  **ring-billed gulls, royal terns, many wading bird species, and bald eagles and ospreys.The most abundant wad**  **ing bird species in the bay seasonally are white ibis and great egrets (Browder and Bass, unpublished data).**  **T he bay is a major habitat for the great white heron,**  **roseate spoonbill, and reddish egret. All of these species feed in Florida Bay proper or in shallow ponds on the**  **bay’s islands. T** 

**he bottlenose dolphin is another high-level preda tor in Florida Bay and, based on studies elsewhere in**  **south Florida, probably feeds on fish at several trophic levels.The American crocodiles that occur in the north**  **ern bay and the American alligators that penetrate the northern bay during wet years are also predators**  **on the bay’s small-fish populations. Tw**  **o large grazing animals, the West Indian man atee and the adult green sea turtle, may have once**  **been more abundant in Florida Bay than they are today. They also may have influenced the structure** **and productivity of seagrasses as a result of their graz ing. A review by Thayer**  **et al. (1984) described the di**  **etary importance of seagrass to various herbivores and the influence of herbivory on seagrass systems.**  **Green turtles once were the primary consumers of seagrasses in the Caribbean, but they are now few in**  **number everywhere. In a major feeding area in Nicaragua,**  **Th alassia testudinum**  **made up 87% of the diet of green sea turtles, and other seagrasses (**  **Syringodium filiforme**  **and Halodule wrightii**  **) made up another 5%. Grazing by green sea turtles may have profound in**  **fluences on the seagrass community that are different from the effects of grazing by other herbivores. Green**  **sea turtles may feed on T**  **halassia preferentially. They**  **are known to maintain discrete grazing plots in a Tha**  **lassia bed and feed repeatedly on the new growth in** **these plots until food quality deteriorates. It is possi ble that the presence of grazing sea turtles might pre** 

**v ent the type of high-biomass**  **T halassia**  **monoculture that preceded the seagrass die-off in Florida Bay of the**  **late 1980s.The possible impact of loss of sea turtles on Florida Bay was discussed by Jackson**  **et al. (2001). Graz**  **ing by manatees may have a more disruptive effect than that by turtles because the rhizophore is disturbed**  **and might jeopardize recovery (Thayer et al.,**  **1984). T** **he density of large herbivores in Florida Bay today may be too low for them to have much influence on the**  **present ecosystem. Seagrass is the main diet of the caridean seagrass**  **shrimp (Schwamborn and Criales, 2000). Seagrass is also important in the diet of sea urchins and has been**  **reported to be in the diets of some fishes (Thayer et al.,** **1984). Even where grazing animals are more abun dant, it is likely that more energy travels from sea**  **grass to consumers through the detrital than the grazing food web. In Florida Bay today, only the detri**  **tal food web is significant. A conceptual model developed to help guide**  **Florida Bay HTLS research is shown in Figure 8.2.The** Higher-Trophic-Level SpeciesHunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 113 **model incorporates the following major concepts: • C**  **ritical ecosystem characteristics ( i.e.,**  **salinity, water**

**quality, and biological benthic habitat) directly in fluence HTLS at the individual species level. Species**  **and community-level response represents the aggregate influence of these characteristics inte**  **grated over HTLS populations;**

**• Changes in HTLS at the species and community** 

**level occur as the result of driving processes acting on Florida Bay as a whole.These processes influence** **HTLS by their effect on critical ecosystem charac teristics and by controlling the movement of HTLS**  **into and out of Florida Bay;**

**• At the shelf scale, potentially influencing factors in** 

**clude temperatures on spawning grounds, larval transport processes, and fishing;**  **• T he scope of research on HTLS of Florida Bay must** 

**include within-bay, cross-boundary, and greater coastal ecosystem processes, and these processes**  **should be examined at time scales from seasons to decades;** 

**• Higher-trophic-level processes and patterns poten** 

**tially affected by water management occur at the population, community/trophic, and ecosystem level;** 

**• HTLS responses to water management are expected** 

**to occur through water management effects on salin ity, the area of co-occurrence of biologically favorable** **salinity and habitat, the condition of biological habi tat (**  **e.g., seagrass, sponge, coral), animal movements,**  **and loading of nutrients or toxicants;**

**• Intrinsic factors potentially influencing responses** 

**to water management include physiological salinity requirements, dietary and energy requirements,**  **and trophic relationships, all of which may differ by**  **species, life stage, and spawning and migration**

**c haracteristics;** 

**• At the bay scale, other factors with the potential to** 

**influence HTLS include salinity-temperature inter actions, toxicant concentrations in freshwater in**  **flow, and fishing.** 

### Processes Driving Change in the Ecosystem

**Preceding chapters describe some major ecosystem**

**c haracteristics that influence higher-trophic-level** **species in Florida Bay: salinity, water quality, and ben thic habitat. All are subject to change, and an** **understanding of how they might change is being de**

**v eloped in other parts of the Florida Bay program. De**  **termining how their change might affect these species is being determined by HTLS research. Relationships** **between processes driving change, ecosystem charac teristics, and characteristic species and communities of**  **Florida Bay are highly relevant to the CERP, which will influence the change-driving processes. Defining and**  **quantifying these relationships is crucial to preparing performance measures to restore or protect Florida Bay.**  **A ugmenting the descriptions of ecosystem character**  **istics in the preceding chapters are studies on mercury. Th**  **ese studies are defining previously unknown spatial patterns of mercury and methylmercury concentrations**  **in Florida Bay waters, sediments, and biota. T** **he quest for answers to Question 5 must extend beyond Florida Bay to include the greater ecosystem**  **that supports the movements of species into and out of the bay and the processes that affect these move**  **ments. Animal movements, as well as the flow of water, connect Florida Bay not only to the upstream Ever**  **glades and coastal mangrove areas but also to the Florida Keys, the reef tract, the southwestern Florida**  **shelf, and the Dry Tortugas. Many higher-trophic-level species range between the bay and the coastal reefs**  **during their life cycle.The processes driving change in the Florida Bay ecosystem extend beyond the bay both**  **upstream and downstream. T** **he principal anthropogenic processes potentially driving change in the Florida Bay ecosystem are water** **management, contaminant and nutrient inputs, cause**

**wa y and bridge construction in the Florida Keys, and**  Figure 8.2 **Conceptual model of factors affecting higher-trophic level species in Florida Bay.**  Higher-Trophic-Level SpeciesFlorida Bay Synthesis Hunt and Nuttle

114 FWRI Technical Report TR-11 **fishing. Climatic variation and oceanographic processes are other instruments of change in the Florida Bay**  **ecosystem and may cause year-to-year and long-term**

**v ariation.** 

WA TER MANAGEMENT **By affecting freshwater inflow to Florida Bay, water management can affect Florida Bay’s HTLS through the** **effects of freshwater inflow on salinity patterns, nu trients, organic detritus, and contaminant loads. Salin**  **ity directly affects physiological processes that determine growth, survival, and reproductive rates of**  **many higher-trophic-level-species.The area in which a favorable salinity range overlaps with other favorable**  **conditions ( i.e.,**  **shoreline, depth, or bottom habitat) in areas accessible to appropriate life stages determines**  **the productive capacity of the bay for a given species. Salinity gradients may provide orientation cues that**  **promote the successful immigration into the bay of postlarvae spawned offshore that use the bay as a**  **nursery ground. Nutrients and organic detritus may have positive or negative effects depending on con** **centration. In excess, they degrade habitat (via re duced water clarity, low dissolved oxygen, etc.).**  **Effects of water management on salinity patterns, nutrients, and contaminant loads are being studied in**  **other parts of the Florida Bay science program. A major emphasis of the HTLS science plan is determining the**  **possible effect of changes in salinity on animal species and communities. Water management may affect** **higher-trophic-level organisms through effects on im portant living benthic habitat such as seagrass and**  **sponges ( e.g.,**  **through salinity, nutrient, turbidity, or other effects on the organisms that form living benthic** **habitat), and these potential effects are also being eval uated through studies of relationships of HTLS to liv**  **ing benthic habitat.**

FISHING**Many coastal fisheries in south Florida have ecologi cal connections to Florida Bay. Especially notable of**  **these are the commercial fishery for pink shrimp and the commercial and recreational fisheries for gray**  **snapper and spiny lobster. These species and others (sparids, grunts, other snapper, and even groupers)**  **found on the Florida Keys reef tract and in the waters near the Dry Tortugas spend part of their life cycle in**  **Florida Bay. Reef waters near Marathon in the middle Ke** **ys are an important spawning ground for gray snap per (Rutherford, 1989). Shelf waters near the Dry Tor**  **tugas islands are the most important commercial fishing grounds for pink shrimp in Florida, and Florida**  **Bay is the major pink shrimp nursery ground. Florida Bay also contains important spiny lobster nursery**  **habitat, and Everglades National Park is a fishing-free sanctuary for spiny lobster. Nearby areas and parts of**  **Florida Bay outside of ENP support recreational and commercial fishing for Spanish mackerel, spiny lobster,**  **and other species. Recreational fishing is an expanding sport in the**  **Florida Keys, the Tortugas waters, and Florida Bay, both within and outside ENP boundaries.The number of fish**  **ing trips in ENP in 2001 was the highest ever reported (Schmidt**  **et al., 2002). ENP began phasing out com**  **mercial fishing in the bay in the early 1980s, when analyses of recreational and commercial fishery data**  **suggested that overfishing might be occurring. Since then, recreational fishing regulations have been** **strengthened. Later analyses have suggested that en vironmental factors affect abundance (Tilmant**  **et al., 1989; Schmidt**  **et al., 2002).The ratio of kept fish to total**  **fish caught changed dramatically from the 1980s to the 1990s. This may be an artifact of regulatory changes**  **(legal size limits, bag limits, seasonal closures); however, it may be indicative of an increased catch of sizes that** 

**w ere too small to keep (**  **i.e., below legal size limits).**  **Th is issue will be addressed in current and future**  **analyses of size-frequency distributions in the creel census data by ENP and the Fish and Wildlife Research**  **Institute. T** **he growing demand for fish and the popularity of fishing have increased the pressure on fishery pop** **ulations in south Florida. Fishing pressure is espe cially reflected in declining size and density of snappers**  **and groupers and changes in the trophic structure of fish assemblages on reefs (Ault**  **et al., 1998). These** 

**c hanges are apparent even in the Tortugas area and are**  **consistent with similar changes previously detected in the Florida Keys (Ault**  **et al., 1998; Bohnsack**  **et al., 1999;**  **Schmidt et al.,**  **1999).The observed decline in fish abun dance may be due to loss of coral habitat. For example,**  **the total area of Caribbean reef-building corals Acro**  **pora palmata and**  **Acropora cervicornis has declined by**  **93% and 98% respectively since 1983 (Miller et al.,**  **2002).**

OCEANOGRAPHIC PROCESSES **T he Loop Current and Florida Current and their coun**  **tercurrents, the Tortugas Gyre, and coastal eddies are oceanographic features that may influence the migra**  **tion of postlarvae to Florida Bay and to the Florida Ke** **ys reef tract from offshore spawning areas. These processes may affect the timing of abundance peaks**  **and year-class strength in fish and macroinvertebrate populations in the bay and on the reef tract.**  **T he Florida Keys reef tract extends almost without**  **interruption along the entirety of the Florida Keys and is the core component of the Florida Keys National Ma**  Higher-Trophic-Level SpeciesHunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 115 **rine Sanctuary. Florida Bay is connected to the reef tract through interisland channels. Regional-scale and local**  **scale oceanic processes that affect the reef tract likely also affect Florida Bay. Reef tract populations are re**  **plenished not only by their spawning locally but also by**  **their spawning upstream of the reef tract. The up stream distance of sites contributing larvae is princi**  **pally determined by current velocity and larval development rate, which ranges from 2 weeks in some** **invertebrates and fish to up to 12 months in spiny lob ster. Recruitment of some species to the Florida Keys**  **reef tract from as far away as the western Caribbean has been postulated. The argument for multiple up** **stream larval sources for the Florida spiny lobster pop ulation is especially strong, given the wide geographic** **range of the species and its extraordinarily long plank tonic larval life (Lyons, 1980; Yeung**  **et al., 2000; Yeung**  **and Lee, 2002), and is supported by mtDNA analysis (Silberman**  **et al., 1994).** **Having more local sources of larvae may be im portant to most populations. The lower southwest**  **Florida shelf in the vicinity of the Dry Tortugas is one potential source of recruitment to the Florida Keys** **reef tract and Florida Bay. The islands of the Dry Tor tugas and their surrounding shallow waters lie roughly**  **150 km (70 miles) west of Key West and are known for remoteness and relatively unspoiled marine richness**  **(Ault et al.,**  **2002b; Franklin et al.,**  **2003). The coastal shelf in the vicinity of the Dry Tortugas is the major**  **spawning ground for pink shrimp in Florida. Recent research is discovering luxuriant, previously unknown**  **and unmapped coral reefs near the Dry Tortugas and near the Marquesas, which lie between the Dry Tor**  **tugas and Key West (Miller et al.,**  **2001).**

CA USEWAY/BRIDGE CONSTRUCTION **T he flow connecting Florida Bay to the Atlantic Ocean**  **through Lignum Vitae, Indian Key, and Teatable Key**

**c hannels was reduced by the construction of the Fla**  **gler railroad, which became the Overseas Highway.This construction, which occurred in the early 1900s, par** **tially blocked tidal passages and affected bay circula tion and associated water quality (Healy, 1996). By**  **affecting transport between the bay and the Gulf of Mexico and Atlantic Ocean, the construction areas**  **may also have affected the immigration of postlarvae and early juveniles into Florida Bay.The U.S. Corps of**  **Engineers is leading a study to determine whether Ke** **ys passes should be enlarged to restore the health of Florida Bay. The Corps is planning a pilot study of**  **the effect of enlarging passes that have been restricted by**  **the highway. The pilot study will be performed in passes located between Fat Deer (Marathon) and**  **Grassy keys.** 

### Research Approaches

**A major focus of Florida Bay HTLS research has been to characterize the responses of species and species**  **groups to environmental and habitat conditions that**

**va ry in space and time.The topic has been approached**  **via modeling, statistical analyses, experiments, and field measurements. Modeling, supported by labora** **tory experiments, was used to characterize the re sponse of individual organisms and was applied to**  **pink shrimp, spiny lobster, sponges, and spotted seatrout to examine functional responses to salinity and**  **temperature and their consequences for populations. Separately, statistical analyses of historical resource sur** 

**ve y data were used to characterize the response of 11**  **forage species and 9 fishery species to environmental**

**v ariables at the population and community level. Field**  **studies were conducted to characterize the spatial and temporal patterns of immigration of early life stages**  **into Florida Bay from offshore spawning grounds and the density of juveniles on Florida Bay nursery grounds.** **Most work has included an examination of the possi ble effects of salinity because salinity is likely to be af**  **fected by inland water management. A more recent focus of Florida Bay HTLS research**  **has been to examine the effect of HTLS on critical ecosystem characteristics, such as water quality and**  **benthic habitat, that determine habitat quality and define distinct communities. In this regard, sponges are**  **a major interest because of the recent decline in sponge biomass in the bay. Sponges are capable of regulating** 

**w ater clarity through their filter feeding, and the vol**  **ume of water filtered is largely determined by sponge biomass density, which has declined substantially in**  **recent years. Field sampling and comparative analysis of data**  **from fished and unfished areas provided information on the effect of fishing on individual species and species**  **composition. Comparative studies provided evidence that fish**  **ing in ENP affects size distribution within species (gray snapper) and the species composition of communities.**  **Underwater visual resource surveys on the reef tract and near the Dry Tortugas have found signs of over**  **fishing of fish species that occur both on the reef tract and in Florida Bay.**  **One approach to examining the effect of water management on HTLS has been through statistical**  **analyses relating fishery catch or catch per unit effort to indices of freshwater inflow to Florida Bay and**  **nearby southwestern Florida coastal waters. Another approach, already mentioned above, has been to ex**  **amine the effect of salinity on processes that affect the abundance of these species.**  Higher-Trophic-Level SpeciesFlorida Bay Synthesis Hunt and Nuttle

116 FWRI Technical Report TR-11 

### Summary of Recent Results

**T he following summary of recent results, presented as**  **bullets, is organized under specific research questions (subsets of the four topic questions identified above)** **to provide an overview of progress. Table 8.1 orga nizes research activities into specific topics, and these** **topics provide a general framework for a series of sec tions synthesizing recent results and conclusions, by**  **specific research topic.**

**Does salinity affect survival and growth, do salinity pat terns affect faunal abundance and distributions, and** **will changes in salinity patterns affect the bay’s nurs ery function?**  **• F iv**  **e species of sponges found in Florida Bay expe** T able 8.1 **Research topics defined by Question 5 (cells in the matrix) and key references to the associated research.**

Population Level— Individual Level— Research Topic Species Abundance and Community Growth and Survival

**General Read et al.,**  **2001; Limouzy-Paris et al.,**  **1997; Settle et al.,**  **2001; Powell et al.,**  **2004 Characteristics Costello**  **et al., 1986; Robblee**  **et al., 1991;**  **Thay er and Chester, 1989; Powell**  **et al., 1989;**  **Chester and Thayer, 1990; Thayer et al.,**  **1999; P** 

**ow ell, 2002, 2003; Powell**  **et al., 2004;**  **Schwamborn and Criales, 2000; Stevely and Sweat, 2001**  **Salinity Pattern Schmidt et al.,**  **2001; Browder et al.,**  **1999, 2002; Browder et al.,**  **1999, 2001b, 2002; Brewster-Wingard**  **et al., 2001; Camp**  **et al., Butler**  **et al., 2001a; Butler, 1999, 2003;**  **2001; Matheson et al.,**  **2001; Field and Butler, Field and Butler, 1994; Wuenschel, 1994; Lorenz, 2001a**  **2001; Richards and DeAngelis, 2001**
**W ater Quality**  **W ater quality effect on HTLS:**  **Water quality effects on (No results reported)**  **contaminants and humans, piscivorous birds, mammals, and**  **HTLS effect on water quality: reptiles:**  **Evans and Crumley, 2000; Stevely and Sweat, 2001; Peterson and Sepulveda**  **et al., 1998;**  **F ourqurean, 2001**  **Effects on invertebrates: Scott**  **et al., 2002**  **Biological Habitat effect on HTLS:**  **Habitat effect on HTLS: Butler**  **et al., Benthic Habitat Dennis and Sulak, 2001; Robblee**  **et al., 1995; Butler, 2003**  **2001; Matheson et al.,**  **2001; Powell et al.,**  **2001a,b; Ortner et al.,**  **2001; Robblee et al.,**  **2001; Chanton**  **et al., 2001; Herrnkind and Butler,**  **1994; Field and Butler, 1994; Butler et al.,**  **1995; Butler, 2003; Koenig et al.,**  **2001 HTLS effect on habitat:**  **Rose et al.,**  **1999; Peterson and F**  **ourqurean, 2001 Coastal Transport Field and Butler, 1994; Yeung**  **et al., 2001; Settle**  **et al., 2001; Yeung and Lee, 2002;**  **(Larval) Process Yeung and Lee, 2002; Jones et al.,**  **2001; Acosta and Butler, 1997; Criales and Browder**  **et al., 2001a, 2002;**  **Lee, 1995; Criales and McGowan, 1993, Butler**  **et al., 2001b; Criales**  **et al., 2003 1994; Jones**  **et al., 2001; Jones**  **et al., 1970;**  **T**

**abb et al.,**  **1962; Roessler et al.,**  **1969; Smith, 2000; Butler**  **et al., 2001** 
**W ater Management Browder, 1985; Sheridan, 1996**  **Lorenz, 2001a, 2001b and Hydrology Browder, 2000; Johnson**  **et al., 2002a**  **Fishing Faunce**  **et al., 2002; Bohnsack**  **et al., 2001;**  **Schmidt et al.,**  **2001** Higher-Trophic-Level SpeciesHunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 117

**rience high mortality rates at low salinity. None sur vived at 15 practical salinity units (psu) (laboratory**  **experiments).**

**• Pink shrimp from Florida Bay are more sensitive to** 

**low salinity than to high salinity.The salinity of max imum physiological survival varies with temperature.**  **Pink shrimp are more tolerant of high salinity at high temperature and low salinity at low tempera**  **ture. Acclimation improves survival at high salinity (55 psu) but not at low salinity (5–10 psu). Growth of** **pink shrimp is optimal at a salinity of 30 psu (labo ratory).**  **• A salinity optimum of 35 psu has been reported for** 

**postlarval Caribbean spiny lobster. The extreme salinities that sometimes occur in portions of Florida**  **Bay are lethal to lobster postlarvae (laboratory).**

**• Larval and juvenile spottedseatrout survival and** 

**growth are low at salinities over 45 psu (laboratory). • T**  **emperature and salinity have an interactive effect on the metabolic rate of young spotted seatrout.Their**  **metabolic rate in relation to size is biphasic and**

**c hanges isometrically with body mass in early stages,**  **approximating an exponential relationship near unity, but changes isometrically thereafter (laboratory).** 

**• Spotted seatrout catch rates in the recreational fish** 

**ery are negatively related to indices of freshwater in puts to Florida Bay (analyses of creel census data).**  **• W estern Florida Bay is a major nursery ground for**  **spotted seatrout (field study). The high density of planktonic postlarvae suggests that central Florida** **Bay may also be a major nursery ground when con ditions allow. Salinities greater than 45 psu have fre**  **quently occurred in central Florida Bay in the past, which may limit this area’s nursery value.** 

**• Pink shrimp recruitment from Florida Bay could** 

**differ between years, seasons, and regions of the bay due solely to observed salinity and tempera**  **ture variation (simulation model).**

**• Observed salinities during a wet and a dry year** 

**caused a predicted decline in lobster recruitment of approximately 25% in the area of Florida Bay di**  **rectly affected by salinity variation (individual-based model).**  **• H abitat, tidal amplitude, freshwater inflow to Florida** 

**Bay, and salinity were the most widely influential**

**v ariables explaining density in 11 forage species in** **a meta-analysis of data from historical surveys. Sea grass density and tidal amplitude each were signif**  **icant for 10 species, seagrass type and freshwater inflow each were significant for 9 species, and salin**  **ity was significant for 7 species (statistical analyses of combined data sets).** 

**Does water management affect the productive capacity of Florida Bay?**  **• W hen used in alternative testing to select the pre**  **ferred plan for CERP, a statistical model relating an abundance index of pink shrimp in the Tortugas**  **fishery to freshwater inflow to ENP at the Tamiami T** 

**rail during certain months predicted that “natural system”flows (as compared to the 1995-base case or**  **any alternative) consistently produced highest shrimp abundance over a 31-yr period.The selected** **alternative was predicted to lead to abundances in termediate between predictions for the natural sys**  **tem and 1995-base case. • R**  **emnants of molluscan faunas obtained in cores**

**suggest that molluscan faunal diversity and absolute abundance in eastern and central Florida Bay began**  **a decline in the 1960s or earlier and reached a low in the 1970s. The low species diversity and the in**  **creased abundance of Brachidontes exustus**  **are evi dence of a system under stress.** 

**• Fish density in the wet season is positively related** 

**to water depth in coastal marshes and the length of time during which water depths are greater than**  **12.5 cm. Maximum concentration (to roughly twice dry-down density) in low spots (**  **e.g., creeks and shal**  **low pans) occurs when water depths decline below 12.5 cm in adjacent marshes. Successful roseate**  **spoonbill nesting occurred in past years during dry season when mean water depths in the coastal**  **marshes were less than 12.5 cm. Nesting failures in recent years can be explained by out-of-season water**  **releases from the C-111 Canal.**

**W hat affects the balance between benthic and pelagic**  **trophic networks in Florida Bay? • T** **he seagrass die-off was a suspected cause of a shift**

**from benthic to pelagic dominance in the fish com munity, because bay anchovy abundance was much** **greater in 1995 than in 1984–1985. Recent findings dis count this possible cause.The abundance of bay an**  **cho vy in the western bay has fluctuated since it** **reached a maximum in 1995.The diversity and over all abundance of canopy-dwelling fauna have in**  **creased since 1995 without a return to the original T** 

**halassia -dominated seagrass canopy.**  **• B ay**  **anchovy abundance may be related to the pres**

**ence of salinity fronts. Bay anchovy abundance was negatively correlated with salinity and positively** **correlated with salinity standard deviation, chloro phyll, and an index of freshwater inflow in an analy**  **sis of historic data. A study in the Manatee River associated low mean salinity and high salinity stan**  **dard deviation with the presence of fronts and found a relationship between anchovy egg abundance and**  **these indicators of fronts.** Higher-Trophic-Level SpeciesFlorida Bay Synthesis Hunt and Nuttle

118 FWRI Technical Report TR-11 **• Seagrass diversity may determine faunal density. A** 

**principal components analysis suggested that faunal species have affinities to certain seagrass types—**  **T**

**halassia, Halodule, or**  **Syringodium —or with macroal**  **gae. Seagrass type was a significant explaining**

**v ariable in a meta-analysis of faunal density in**  **Florida Bay, and faunal density in relation to seagrass type varied differently depending on faunal species.**  **No faunal species was identified that had pure T** 

**halassia as its sole affinity.** 

**Do bottom and shoreline habitats affect abundance and community composition?** 

**• Mangrove prop-root habitat in northeastern Florida** 

**Bay had significantly more fish larvae than did nearby open-water sites or nearshore areas without**  **mangroves, but it had a lower density and diversity of both forage fish and juvenile predator fishes than**  **found in similar habitat in the Bahamas and Puerto Rico, leading to the hypothesis that the low densi**  **ties were caused by isolation from offshore sources of larvae or juveniles.**  **• S eagrass density was a significant explaining vari** 

**able for density for 10 of 11 key forage species examined, and seagrass type was a significant ex**  **plaining variable for density of 9 of the 11 species.**

**Does fishing affect fish populations?**

**• According to a comparison of the length-frequency** 

**distributions inside and outside of an area in the park protected from fishing, recreational fishing in Ever**  **glades National Park affects the size structure of**
**gray snapper.**

**• Evidence of overfishing is seen in gray snapper and** 

**other species on the reef tract.**

**Is spatial variation in influencing factors (e.g., fresh**

**w ater inflow, tidal mixing) reflected in distinct regional**  **patterns in species distributions and community and trophic composition in Florida Bay?**  **• P eak concentrations of postlarval pink shrimp are**  **roughly an order of magnitude greater in passes leading into western Florida Bay than in channels to**  **Florida Bay through the Florida Keys. Movement into the bay occurs on the flood tide. The timing of**  **high immigration rates is more predictable when shrimp immigrate from the west than from the east.** 

**• Based on stable isotope analyses, the central bay** 

**has a strongly seagrass-based trophic structure, whereas the western bay has a more plankton-dom**  **inated trophic structure. The eastern bay offers a non-seagrass-based diet (likely more water-column**  **based).The trophic structure of the southwestern bay is based on macroalgae.**  **• Northern Florida Bay is probably not a significant**  **nursery area for red drum.**

**Is temporal variation in recruitment strength of spiny lob ster, snapper, and pink shrimp related to oceanographic**  **processes, especially to the Tortugas gyres?**

**• Spiny lobster postlarvae that recruit throughout the** 

**y ear had peaks of influx into the bay at the Middle**  **Ke ys coinciding with the presence of eddy and coun**  **tercurrent conditions.**

**• Larval duration of gray snapper varied from one** 

**y ear to the next and, within the first year, ranged from**  **35.50 to 41.45 days. • P**  **eak abundance of gray snapper larvae in Florida Ke** **ys channels occurred in summer 1997 and was co incident with a well-developed Loop Current (high lat**  **itudinal extent) favoring gyre formation off the Dry T** 

**ortugas, where gray snapper spawning aggrega tions occur.**  **• T emporal variability was observed in the influx of**  **pink shrimp postlarvae through two channels in the Middle Keys and may be related to the position of**  **the leading edge of the cyclonic eddies relative to the**

**c hannels. Pink shrimp larvae at the spawning**  **grounds seem to be retained by the circulation of the T** 

**ortugas gyre.**
**Are urban and agricultural sources, carried by the C 111 canal, responsible for high methylmercury in**  **Florida Bay and its biota?**

**• Sources of elevated mercury concentrations in fish** 

**from northeastern Florida Bay include (1) methylmer cury in runoff from the Everglades and (2)**  **in situ mer**  **cury methylation in sediments from both the mangrove transition zone and the open bay itself.** 

**• Mercury concentrations were higher along a Taylor** 

**River–Little Madeira Bay sampling transect than along a C-111 canal–Joe Bay transect, suggesting**  **that the urban and agricultural runoff that more strongly influences the C-111 canal–Joe Bay tran**  **sect is not the most important source of mercury to the bay and its biota.** 

**Did the former density of sponges in Florida Bay in fluence water quality to the extent that the sponge** **die-off that followed seagrass die-off led to water quality conditions that impeded the recovery of sea**  **grass?**

**• At pre-die-off (before 1992) densities, sponges in** 

**Florida Bay may have been capable of filtering the entire water column in 24 hours. Recovery of the** **largest and most abundant species has been ex tremely slow. At present densities, filtering takes an**  **estimated four days. Sponges are efficient filters of** Higher-Trophic-Level SpeciesHunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 119

**small (<5 μm) planktonic particles. Loss of sponges may have reduced water clarity and affected seagrass** 
**recovery.**
**Do predators seek areas of higher prey abundance?**

**• Bottlenose dolphin were found in areas of highest** 

**density of potential prey, supporting the working hy pothesis that they search out feeding areas with** **higher prey concentrations. Dolphin and prey den sities are higher in the east-central and south-cen**  **tral bay than they are in the northeastern bay. However, densities of both dolphin and prey are**  **lower in the east-central and south-central bay than they are in other coastal areas.** 


## Distribution of Species and Patterns of Abundance

**Spatial variation in the influence of environmental and physical factors shaping Florida Bay, especially**  **substrate, freshwater inflow, and degree of mixing with waters of the Atlantic and the Gulf of Mexico, have** **led to substantial regional differences in animal dis tributions within the bay. For example, the southern bay**  **is prime habitat for juvenile spiny lobster, which are found in few other parts of the bay. On the other hand,** **juvenile pink shrimp occur most densely in the west ern bay. Animal distributions have been used to define**  **distinct subregions of the bay, beginning with Turney and Perkins’ (1972) delineations based on mollusks.**  **Subregional delineations based on animals roughly correspond to those based on seagrasses (Zieman**  **et al., 1989) and water quality (Boyer, 1997). Short-term and** **long-term temporal variations in environmental vari ables accentuate regional differences in bay habitat (for**  **example, the northeastern bay has the most seasonally**

**v ariable salinities). Temporal variation also under** **mines efforts to better describe and understand re gional differences (for example, the northcentral bay** **can be hypersaline one summer and mesohaline an other, creating an entirely different environment for an**  **imals during the same time of year). Recent research has expanded our understanding of how animal dis**  **tributions vary spatially and temporally and the most likely reasons for the variation. Results of studies that** **address the spatial and temporal variations of a num ber of parameters follow.**  **Field studies have expanded the knowledge of spawning areas and spawning periods. Powell (2003)**  **and Powell et al.**  **(2002, 2004) determined that spotted seatrout spawning occurs primarily in western Florida**  **Bay. Spawning at Bradley Key and Palm Key had been observed historically, but spawning at Whipray Basin**  **and Little Madeira Bay was determined for the first time in 1994–1995 sampling. Based on collections and hatch**  **date estimates from 1995 collections, they determined that spawning occurred principally during the summer,** **with spawning peaks in May and June. Larvae were col lected over a wide range of bottom types with and** **without seagrass, in waters with temperatures be tween 20°C and 35°C (majority 26°–34°C) and salini**  **ties between 12 psu and 41 psu (majority 25–40 psu). Consistently high densities of larvae were collected at**  **Wh ipray Basin, which is located in the central portion** **of the bay and is a valuable juvenile nursery area de spite low seagrass above-ground standing crop and oc**  **casional (two occasions during sampling—40 psu and 41 psu) hypersaline conditions in 1998 and 1999.**  **Nursery grounds of several other gamefish species that occur in Florida Bay as adults are not yet docu**  **mented in Florida Bay. Recently Powell et al.**  **(2002) at tempted to locate Florida Bay nursery grounds of red**  **drum, which occur in Florida Bay and spawn in the nearby Gulf of Mexico. Based on the work of Peters and**  **McMichael (1987) in Tampa Bay, Powell et al.**  **(2002) concluded that northern Florida Bay was the only suit**  **able nursery habitat for red drum in the bay. Powell et**  **al. (2002) sampled intensively there, and concluded** **that limitations on larval transport from offshore wa ters was preventing red drum from using this part of** **the bay as nursery habitat. Colvocoresses (unpub lished data) found young juvenile red drum in the**  **East River of Little Madeira Bay and near the mouth of McCormick Creek, but the Powell**  **et al. (2002) work**  **suggests that the occurrence of red drum juveniles in northern Florida Bay is not a seasonally regular event.**  **Read et al.**  **(2001) studied bottlenose dolphin in the eastern half of Florida Bay and found that densities of**  **prey organisms in trawl samples were higher in areas where bottlenose dolphin had been feeding than in** **samples taken elsewhere. This supported their hy pothesis that dolphin seek out feeding areas with higher**  **prey concentrations.These investigators found a greater abundance of dolphins in the east-central and south** **central parts of the bay than they found in the north eastern bay. (Their study did not include the western**  **bay.) They suggested that the low abundance of dolphins in the northeastern bay might be related to the lower** **fish densities that have been reported there by other in**

**v estigators. In 20 surveys conducted in all four sea**  **sons, they encountered 23 groups of bottlenose dolphins, consisting of 133 individuals.They concluded** **that the entire bay area they surveyed contained rela tively few dolphins, corresponding to the low density** **and diversity of potential prey items overall. In all sea sons and areas, Read**  **et al. ’s**  **(2001) trawl catches were dominated by mojarras (family Gerreidae).**  Higher-Trophic-Level SpeciesFlorida Bay Synthesis Hunt and Nuttle

120 FWRI Technical Report TR-11 

## Effect of Ecosystem Characteristics on Growth and Survival

**W**

**ork on this topic addresses the principal question: How do growth and survival of individuals in each** **HTLS vary through the range of environmental con ditions defined by salinity, water quality, and benthic** **habitat found in Florida Bay? Major working hy potheses are as follows:** 

**• Salinity directly affects the growth and survival of** 

**HTLS; • T** **he carrying capacity of Florida Bay nursery areas**

**is related to the overlap of favorable salinity and fa**

**v orable bottom or shoreline habitat.** 



### Effect of Salinity on Growth and Survival

**Simulation models and associated experimental trials suggest that several Florida Bay species, each with op** **timal habitat in a different part of the bay, can be af fected by changes in freshwater inflow and the resultant** 

**c hanges in salinity patterns. Both pink shrimp and**  **spiny lobster could be adversely affected by the extreme high salinity that often occurs in the north-central part** **of the bay and sometimes spreads westward into op timal shrimp nursery habitat and southward into op**  **timal lobster habitat. Lobster and shrimp could both be adversely affected by low salinities in otherwise**  **suitable habitat and locations. T**  **he effects of salinity and temperature on the growth, survival, and subsequent recruitment and har** 

**v est of pink shrimp (** **F arfantepenaeus duorarum**  **) were ex amined via laboratory experiments and a simulation**  **model (Browder et al.,**  **2002). The pink shrimp is an ecologically and economically important species that** **has major nursery grounds in Florida Bay. Experi ments were conducted to determine the response of ju** 

**v enile growth and survival to temperature (15°–33°C)** **and salinity (2–55 psu), and the results were used to re fine an existing model (Browder**  **et al., 1999). Results of**  **these experiments (Figure 8.3a,b) (Browder et al.,**  **2002) indicated that juvenile pink shrimp can tolerate a wide**  **range of salinities in their optimal temperature range (20°–25°C), but the salinity tolerance range narrows**  **with distance from that range. Acclimation improved survival at extremely high salinity (55 psu) but not at**  **extremely low salinities ( i.e.,**  **5–10 psu). Analyses of the laboratory data suggested that growth rate in**  **creases with temperature until tolerance is exceeded beyond approximately 35°C. Growth is optimal in the** **midrange of salinity (30 psu) and decreases as salin ity increases or decreases. Potential recruitment and**  **harvests from regions of Florida Bay were simulated** Figure 8.3 **Response curves of survival, growth, and potential off shore harvest of pink shrimp in relation to salinity and tempera**  **ture (Browder et al.,**  **2002).** Higher-Trophic-Level SpeciesHunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 121 **based on locally observed daily temperatures and salinities.The simulations predicted that potential har** 

**v ests might differ between years, seasons, and regions** **of the bay solely on the basis of temperature and salin ity. Results indicated that harvests on the Tortugas** **shrimp grounds could be affected by spatial extent, lo cation relative to suitable bottom habitat, and duration** **of unfavorable temperatures within a favorable salin ity range.**  **Butler et al.**  **(2001a) explored the effect of changing salinity on lobster and hard-bottom habitat, especially**  **as it might relate to lobster microhabitat ( i.e.,**  **v arious** **species of sponges and octocorals). Salinity experi ments at winter temperatures have recently been com**  **pleted for several sponge species (Figure 8.4). The results indicate that there is reduced survival for an in** **creasing number of species as salinity decreases (But ler**  **et al., 2001a). None of the five species tested survived**  **at 15 psu. Field and Butler’s (1994) results concerning salinity and temperature effects on postlarval lobsters**  **suggested a salinity optimum of 35 psu. Survival rates at salinities other than 35 psu were low below 18°C and**  **above 33°C. P** 

**ow ell**  **et al. (2004) examined temperature-related**  **spatial and temporal variation in growth and survival of spotted seatrout between areas and months. They** **found a strong parabolic relationship between tem perature and the growth of juveniles (22–60 d) but no**  **significant relationship between temperature and the growth of larvae. They did not have an appropriate** **distribution of samples to look at spatial and tempo ral variation in relation to salinity.**  **In a laboratory experiment, Wuenschel et al.**  **(2001, 2002) found a significant interactive effect of temper** **ature and salinity on routine metabolic rates of spot ted seatrout.They found a biphasic metabolic rate that** 

**c hanged isometrically with body mass in early stages**  **of larval growth, approximating the exponential rela tionship near unity proposed in previous studies, and** 

**c hanged allometrically thereafter. Response surfaces**  **describing the effects of temperature and salinity on maximum consumption and growth rates were also de** 

**v eloped from laboratory experiments.**  **T he optimal salinity for spotted seatrout may dif**  **fer for each life stage. Schmidt et al.,**  **2001, 2002) found a negative correlation between annual average spot** **ted seatrout catch rates and indices of freshwater in puts to the bay. Johnson**  **et al. (2002a) found a low but**  **significant negative correlation between spotted seatrout catch rates and bay salinity but thought it** **could be the spurious result of fish concentrating dur ing hypersaline events in more limited favorable habi**  **tat with increased vulnerability to fishing. There is indirect evidence that hypersaline conditions reduce**  **survival of spotted seatrout in the early-settlement stage. Although larval concentrations suggest that cen** **tral Florida Bay is a major spawning ground for spot ted seatrout (Powell, 2003), juvenile spotted seatrout**  **appeared to extend their range into the central portion of the bay when hypersaline conditions were absent**  **(Thayer et al.,**  **1999; Powell, personal communication), but this has to be tested more rigorously. Citing Alshuth**  **and Gilmore (1994), Powell (2003) noted that spotted seatrout eggs do not float at salinities less than 15 psu,**  **so egg survival might be virtually zero percent at 0–15 psu. On the other hand, laboratory experiments of**  **spotted seatrout in Texas suggest that the species does not spawn at salinities greater than 30 psu (Wakeman**  **and Wolschlag, 1977; Taniguchi, 1980).**


### Effect of Water Quality on Growth and Survival

**T**

**he staff of Everglades National Park maintain a record of fish kills in Florida Bay (Schmidt, 1993b; Schmidt and** **Robblee, 1994).These deaths are believed to occur be cause of low dissolved oxygen in the water column.The**  **mass mortalities are usually reported in the Snake Bight area, where episodic low dissolved oxygen may**  **be caused by a combination of extremely shallow water, high summer temperatures, poor tidal and wind mix**  **ing, and high respiration rates. High ammonia levels recently reported by Boyer (personal communication)**  **are another possible source of mortality. Contaminants in Florida Bay biota have been in** 

**v estigated previously. Tissues of fish, macroinverte**  **brates, and birds were analyzed for concentrations of heavy metals, pesticides, and polychlorinated biphenyls**  **(PCBs) in fish and macroinvertebrates (Ogden et al.,** **1974). Concentrations of DDT, arsenic, and methylmer cury in marine animals were high enough to warrant**  Figure 8.4 **Survival of five sponge species at four salinities at winter**

**w ater temperatures for four weeks (Butler** 
**, 2005).**  Higher-Trophic-Level SpeciesFlorida Bay Synthesis Hunt and Nuttle

122 FWRI Technical Report TR-11**further investigation and led to later air-quality stud ies in ENP. As part of a larger study of the possible ef**  **fects of mosquito control in Monroe County, the Environmental Protection Agency (Anonymous, 1980)** **examined fish and shellfish tissues and water for con centrations of certain pesticides, including Naled and**  **Batex.They found negligible amounts of Naled in fish and shellfish, although oysters accumulated an aver** **age of 0.007 ppb of Naled. Batex was not found in de tectable amounts in either fish or shellfish. Results** **may have been biased on the low side by the dry-sea son conditions that prevailed.** **A multiyear study in the C-111 canal and associ ated sites in Florida Bay was undertaken in order to de**  **termine other contaminant risks that may exist in south Florida (Scott**  **et al., 2002). According to extensive sur**  **face-water data and results from analyses of sediment, tissue, and semipermeable membrane devices, canal**  **contamination seems to be derived from the extensive agricultural production that drains into the C-111**  **canal. The results of this study indicate that runoff from agricultural fields led to quantifiable pesticide**  **residues found in both canal and bay surface water, at levels that occasionally exceeded current water-qual** **ity criteria. The major pesticide of concern was endo sulfan, which was detected at 100% of the sites sampled.**  **T he decision to alter the C-111 canal flow and allow in**  **creased freshwater flow into the adjacent Everglades may result in discharges of pesticides through Ever**  **glades National Park and into Florida Bay. Endosulfan concentrations are highest in the northeastern part of**  **Florida Bay, where the special sensitivity of pink shrimp could cause mortalities. Low pink shrimp densities in**  **northeastern Florida Bay have been documented since at least the 1960s (Costello**  **et al., 1986). Other factors (**  **e.g., extreme and variable salinities, absence of broad banks,**  **sparse seagrass coverage) may limit the presence of pink shrimp in the northeastern bay, but no investi**  **gation of the possible effect of endosulfan on pink shrimp in the bay has been made.**  **Health advisories are now posted in eastern Florida Bay warning of elevated levels of mercury in some**  **higher-trophic-level fish. Thirty percent of spotted seatrout sampled from eastern Florida Bay exceed**  **Florida’s no-consumption advisory level of 1.5 μg/g –1**  **(Evans et al.,**  **2001). Jack crevalles also contain compa rably high mercury concentrations (Evans, personal**  **communication). Other species of gamefish and forage fish, although not as high in mercury as these two**  **species, have concentrations several times those found in the western bay or elsewhere in Florida.These high**  **concentrations may put humans, other mammals, birds, and reptiles at risk. Reduction in body burdens** **of mercury in top carnivores is one of the success cri teria listed by the South Florida Ecosystem Restoration**  **T**

**ask Force. Work is underway by Marnie Billie at FIU to assess the ecological risk of consumption of Florida**  **Bay fish by piscivorous ospreys in the bay. Planned restoration activities in the Everglades will change**  **freshwater deliveries to Florida Bay. These deliveries could alter the existing high levels of mercury in some**  **Florida Bay gamefish through enhanced mercury fluxes as well as altered productivity and food web struc**  **ture, which influence mercury bioaccumulation.**



### Effect of Benthic Habitat on Growth and Survival

**T his issue has generally been approached by relating** **benthic habitat to animal densities, which implies sur vival and growth, rather than by measuring habitat** **effects on growth and survival directly.The fact that fau nal densities are correlated with certain benthic habi**  **tats suggests that growth and survival are highest in the appropriate habitat. See section on effect of ben**  **thic habitat on abundance.** 

### Immigration, Growth, and Survival of Offshore-Spawning Fishes that Use Florida Bay as a Nursery

**In an effort to understand spatial and temporal patterns of variability in immigration, growth, and survivor**  **ship of upper-trophic-level fishes, Settle (unpublished data) examined these life history attributes in several**  **important species in the bay. Juvenile great barracuda using the bay as nursery habitat are the product of pro** **tracted spawning, which is centered during the sum mer but with nearly 15% occurring from late fall and**  **winter. Spawning during these later periods has not been previously reported in south Florida and may**  **suggest that either some spawning does occur in the region during those times or that some barracuda in** **the bay originate from elsewhere in the species’ dis tribution.The youngest individuals are found in the At**  **lantic transition, gulf transition, and western subregions of the bay, suggesting ingress from both the Atlantic**  **ch annels and the open Gulf of Mexico. Cohort-specific**  **growth rates of young fish (age 30–150 d) ranged from 1.44 to 2.65 mm d** **–1 during the 1990s. Over the same pe**  **riod, growth was significantly slower in two faunally depauperate subregions, the eastern and the turbid** 

**w estern bay. Relative condition (weight/length) of this**  **species over the period 1973 to 2000 declined during the early to mid-1990s and appears to be returning to** 

**va lues observed during the 1970s and mid-1980s.The** 

**ov erall instantaneous natural mortality rate was 0.02656.**  **Av erage survival was 97.38% d**  **–1**

**. Cohort-specific growth**  Higher-Trophic-Level Species**rates of juvenile lane snapper (age 30–242 d), which pri marily inhabit the gulf transition and western subre**  **gions, showed significant intra- and interannual**

**v ariation and ranged from 0.59 to 0.93 mm d**  **–1**

**. Snap**  **pers spawned during the spring and summer grew faster than those spawned during fall and winter, and**  **fish spawned during 1998 grew faster than those spawned in 1997. Instantaneous natural mortality both** 
**y ears was 0.03636, and average survival was 96.43% d** **–1**

**.** 

## Effect of Ecosystem Characteristics on Species Distribution and Community and Trophic Structure

**W**

**ork on this topic addresses the major questions: Do HTLS’ community composition or trophic structure**  **in Florida Bay vary in time and space, what factors are responsible for this variation, and what processes are**  **affected? Major working hypotheses are as follows: • T** **he abundance of HTLS is low in the northeastern**

**portion of Florida Bay because of high-amplitude**

**v ariation in salinity, low density of seagrass, lack of**  **extensive banks, restrictions on the immigration of postlarvae, or a combination of all of these factors;** 

**• Changes in community composition are related to** 

**c hanges in salinity, which can be influenced by water**  **management, although the effect of benthic habitat, tidal exposure, rainfall, and oceanographic events**  **may need to be filtered out to see these effects; • C**  **hanges have occurred in the species composition**

**of mollusks, foraminifera, and other sessile species in Florida Bay, and these changes reflect changes in** **salinity, water quality, and the cover and composi tion of benthic vegetation;** 

**• Spatial and temporal patterns in trophic pathways** 

**v ary depending on salinity, water quality, and abun**  **dance and type of benthic vegetation; • W**  **idespread sponge mortalities may affect both hard-bottom and seagrass communities;** 

**• Fishing reduces the number and size of some apex** 

**predators, causing shifts in community structure; and** 

**• Changes in community composition are related di** 

**rectly to changes in benthic habitat.**


### Effect of Salinity on Species Abundance and Community Structure

**Several studies suggest that hypersalinity affects the benthic fauna of Florida Bay. Schmidt (1977) reported**  **lower forage fish diversity, biomass, and numbers in northcentral Florida Bay in salinities greater than 45**  **psu. Johnson et al.**  **(2002a,b) noted that “evenness”(an index of community structure) among 11 dominant** **species, as estimated from statistical model predic tions, was lower in 1990, a year of extreme high salin**  **ity in the bay, than in 1995, a wet year. Lyons (1999) observed fewer species in the molluscan community**  **in the hypersaline part of Florida Bay. A simulation model based on experimental data (Browder**  **et al., 2002) predicted lower juvenile pink shrimp densities**  **and fewer potential recruits to the Tortugas fisheries from the hypersaline central part of Florida Bay. Based**  **on relative concentrations of smallest-stage seatrout postlarvae, Powell (2003) determined that central**  **Florida Bay is a major spawning ground for spotted seatrout; however, there is evidence that at salinities**  **greater than 45 psu, survival and growth of larval and juvenile spotted seatrout could be diminished (Wuen** **schel, 2002). The frequency and duration of hyper saline events in the central bay might, therefore, affect** **survival and growth of young seatrout and, conse quently, the abundance of this species. Powell (2002)**  **noted that densities of the postlarvae of many species collected with an epibenthic sled were higher in the** **central bay, indicating that many species may be dis proportionately exposed to hypersaline conditions in**  **an otherwise favorable nursery area. Sogard et al.**  **(1989) found lower species richness of both epibenthic and** 

**w ater-column fishes. Holmquist**  **et al. (1989) found a**  **lower species richness of macroinvertebrates in the central bay, which was characterized by low tidal range**  **and hypersaline conditions during their studies.They concluded that water circulation and salinity patterns** 

**w ere influential in structuring Florida Bay’s epibenthic**  **faunal communities.**

HISTORICAL DISTRIBUTIONS OF MOLLUSKS AS INDICATORS OF PAST SALINITY PA TTERNS **Historical records of salinity and bottom vegetation**

**w ere reconstructed based on molluscan assemblages** **in shallow sediment cores. An analysis by Brewster W**  **ingard et al.**  **(2001) suggested that molluscan as semblages in Florida Bay have undergone distinct** 

**c hanges over the past 100–200 years.**  **Brachidontes exus tus,**  **a euryhaline species tolerant of diminished water quality and a wide range of salinities, accounts for**  **more than 80% of the molluscan fauna in the upper portions of six cores. Four cores from central and east** **ern Florida Bay and one from Featherbed Bank in Bis cayne Bay suggest decreases in molluscan faunal**  **diversity and absolute abundance that began perhaps in the 1960s or earlier and reached a low in the early**  **1970s (Figure 8.5). T** **he dominance of Brachidontes**  **and the decreases in faunal richness and abundance are indicative of a**  Hunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 123 Higher-Trophic-Level Species**system under stress. Interestingly, the transition-zone cores from the mouth of Taylor Creek and in Manatee** **Bay do not show the decline in faunal diversity and ab solute abundance exhibited in the other cores. Based**  **on their analysis of molluscan epiphytic species within the cores, Brewster-Wingard**  **et al. (2001) concluded**  **that common factors are affecting the faunas and their associated bottom vegetation across eastern and cen**  **tral Florida Bay, despite the isolation of some of the basins.** 


### Effect of Water Quality on Species Abundance and Community Structure

**Ortner et al.**  **(2001), who examined possible relation ships between chlorophyll, zooplankton, and anchovy** **from January 1994 through January 1999, found no ev idence that phytoplankton blooms were causing a fun**  **damental shift in community structure and trophic d** 

**ynamics in Florida Bay. Copepod concentrations were not related to chlorophyll concentrations, and anchovy**  **density was not related to copepod concentrations. On the other hand, Johnson**  **et al. (2002a) found a sig**  **nificant relationship between bay anchovy density and**

**c hlorophyll**  **a concentrations. Intermittent high an**  **cho vy densities might be due to the attraction of an**  **cho vies to unvegetated bottoms and high turbidity**  **(Patillo et al.,**  **1997). Peebles’ (2002) study of bay an cho**  **vy egg densities in the Manatee River suggests that structured, spatially and temporally intensive** **sampling of bay anchovy eggs may reveal relation ships with prey abundance, salinity fronts, and fresh** 

**wa ter inflow not obvious from previous sampling in**  **Florida Bay.**


### Effect of Benthic Habitat on Species Abundance and Community Structure

FISH DISTRIBUTIONS IN MANGROVE PROP–ROOT HABITAT **Dennis and Sulak (2001) found that prop-root sites in northeastern Florida Bay had significantly more fish lar** 

**v ae than did nearby open-water sites or nearshore**  **areas without mangroves. However, the densities of both forage fish and juvenile predator fishes were**  **lower among mangrove prop-root habitats in Little Madeira Bay, Trout Cove, and Manatee Bay than in**  **prop-root habitats in the Bahamas and Puerto Rico. Th**  **ey proposed that isolation from offshore sources of** **larvae or juveniles was the reason for the low densi ties. In support of this conclusion, they found that the** **concentration of larval fish was much greater on the lee**

**wa rd**  **side of Key Largo than at their northeastern Florida Bay mangrove prop-root sites. Fish density** **and biomass were greater in mangrove prop-root habi tats than in adjacent fringing seagrass areas. In a pre**  **vious study by Thayer et al.**  **(1987), they determined that the mangrove prop-root habitat in Florida Bay and** **nearby areas was occupied by a distinct faunal as semblage.** 

C

ANOPY–DWELLING FISH AND MACROINVERTEBRATE ASSEMBLAGES IN RELATION TO SEAGRASS **Densities of many macroinvertebrate and fish species in Florida Bay are higher inside seagrass beds than out**  **side them (Holmquist et al.,**  **1989; Sogard et al.,**  **1989; Th**  **ay er and Chester, 1989; Thayer**  **et al., 1999; Matheson**  **et al., 2001). Johnson**  **et al. (2002a) analyzed the combined**  **data of 6 field studies (including those cited above) and quantified the relationship between animal density**  **and seagrass density for 11 key forage species. They found that of the 10 species whose densities were sig**  **nificantly related to seagrass, 5 were densest in dense** Florida Bay Synthesis Hunt and Nuttle

124 FWRI Technical Report TR-11 Figure 8.5 **Historical view of the dominance of a molluscan**

**w ater-quality indicator in the molluscan fauna (Brewster-Wingard**  **et al., 2001) at three Florida Bay locations.**  **Brachidontes toler** **ates conditions that other mollusks cannot. Experiments are un derway to better define the conditions tolerated by**  **Brachidontes.** Higher-Trophic-Level Species**seagrass, 4 were densest in moderately dense sea grass, and 1 was densest in sparse seagrass. Bottom or**  **seagrass type was a significant variable explaining the densities of 10 forage species.Three species were dens**  **est in Syringodium,**  **three were densest in Halodule,**  **two**

**w ere densest in mixed grasses with**  **Syringodium, and**  **one was densest in mixed grasses with T**  **halassia. One,**  **bay anchovy, was densest in areas without seagrass.**

SHIFTS BETWEEN BENTHIC AND PELAGIC ZOOPLANKTIVORES **A prevailing hypothesis has been that the seagrass die-offs and phytoplankton blooms experienced be**  **ginning in the late 1980s provoked a trophic shift in**

**w estern Florida Bay from a system based principally**  **on benthic production to one based principally on**

**w ater-column production.This hypothesis grew out of** **comparisons of the fish and macroinvertebrate com munity compositions in 1984–1985 to those in 1994–1995.**  **Thay er**  **et al. (1999) compared the fish assemblages of**  **1984–1985 to those of 1994–1995 in three regions of the bay and found that canopy-dwelling species had de**  **clined and that pelagic zooplanktivores dominated the fauna. Robblee**  **et al. (2001) compared benthic veg**  **etation, fish, and macroinvertebrate assemblages found in Johnson Key Basin in 1985 to those found there in**  **1995. They observed a decrease in T**  **halassia and**  **Sy ringodium**  **and an increase in Halodule**  **and bare bottom. Th**  **ey found a decrease in**  **F arfantepenaeus duorarum**  **(pink shrimp), seagrass-associated caridean shrimps (–65%), and seagrass-associated fishes (–81%) and con**  **cluded that the decline in seagrass-associated species**

**w as a result of seagrass die-off.**  **T he hypothesis that loss of seagrass would result**  **in a trophic shift of fish was discounted by sampling data beyond 1995.The juvenile and small-resident fish**  **assemblage in collections of Powell et al.**  **(2001b) made during 1996–2000 (especially 1998) differed markedly**  **from that in 1994–1995 and resembled the assemblage observed in 1984–1985. The change from canopy**  **dwelling to pelagic zooplanktivores from 1984–1985 to 1994–1995 was followed by a change back to canopy**  **dwellers in 1998–1999. The investigators concluded that the recovery of an assemblage of fish species dom**  **inated by seagrass canopy dwellers cannot be wholly explained by recovery of seagrasses because there is** **no evidence of seagrass recovery on a subdivision wide basis in 1999–2000 relative to 1994–1995. In fact,**  **seagrass densities in 1999–2000 were much lower than in 1984–1985 (Powell**  **et al., 2001b).**  **Ortner et al.**  **(2001) also refuted the hypothesis of a trophic shift related to loss of seagrass coverage and**  **an increase in phytoplankton blooms.They concluded that the recent history (1994–2000) of phytoplankton,**  **zooplankton, and planktivorous fish abundances pro vides little or no support for the concept of a funda**  **mental, persistent shift from a demersal benthic-based food web to a pelagic water-column-based food web.**  **Furthermore, there seems to be no clear relationship between plankton bloom incidence or intensity and the**  **abundance of zooplanktonic herbivores, nor is there a relationship between the abundance of the bay an**  **cho vy and its preferred copepod prey.** **An alternative hypothesis for the observed fluc tuation in dominance between demersal and water-col**  **umn species is that the density of the small-juvenile and small-resident canopy-dwelling fish assemblage**  **is influenced by the sporadic dominance of pelagic zooplanktivorous clupeiforms that might be related to** 

**w ater column chlorophyll**  **a concentrations (Powell**  **et al.,**  **2001b). Another alternative hypothesis is that the estab** **lishment of a more heterogeneous bottom habitat, oc cupied by**  **Halodule and**  **Syringodium as well as some**  **T**

**halassia, might be responsible for the recovery of** **canopy-associated species after 1995 (Robblee, per sonal communication) An exploratory principal com**  **ponent analysis revealed four PCs, each of which could be interpreted to relate to a vegetation component:**  **T**

**halassia (PC1),**  **Halodule (PC2),**  **Syringodium (PC3), and**  **macroalgae (PC4) (Robblee et al.,**  **2001). Pink shrimp cor related with PC2 and PC3.The rainwater killifish was**  **correlated with PC1. Affinities of various species to certain types of seagrass habitat might lead to greater** 

**ov erall abundance if seagrass habitat diversity in**  **creases.This is supported by the work of Johnson et al.** **(2002a), who found that densities of various species var ied, depending upon the type of seagrass they were**  **found in and that no species was found at highest density in pure**  **T halassia**  **beds.This result is especially**

**v aluable because Somerfield**  **et al. (2002) concluded** **that even large faunal effects of seagrass habitat het erogeneity might be difficult to detect. This hypothe**  **sis might explain the recovery of canopy-dwelling species after 1995 but not the fluctuations in bay an**  **cho vy density.**  **P**

**eebles’ (2002) study of bay anchovy egg abun dance in the Manatee River provides insight on the bay**  **anchovy fluctuations in Florida Bay. Using a spatially and temporally intense sampling strategy, Peebles** **(2002) found that nighttime bay anchovy egg abun dance in Manatee Bay was positively related to**  **Acar tia tonsa**  **abundance the previous day. Bay anchovy appeared to spawn immediately upstream from salin**  **ity fronts (which he defined as a change of 1 psu/km) that concentrated their prey. The effect of freshwater**  **inflow on bay anchovy egg abundance was non-linear. P** 

**eak abundance occurred when salinity fronts formed** Hunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 125 Higher-Trophic-Level SpeciesFlorida Bay Synthesis Hunt and Nuttle

126 FWRI Technical Report TR-11 **near the river mouth. Egg abundance declined when these fronts advanced seaward of the river mouth but** 

**w as lowest when fronts were weak or absent during**  **low-flow periods.The presence of a salinity front was associated with relatively low mean salinity and high**  **standard deviation in salinity. In their analysis of a data set compiled from several studies, Johnson**  **et al. (2002a) found a significant relationship between bay an**  **cho vy density and salinity (negative relationship), stan**  **dard deviation in salinity (positive relationship), and freshwater inflow index (positive relationship) in**  **Florida Bay. Peebles’ (2002) study might explain the mechanisms behind these relationships.** 

EFFECTS OF MACROALGAE ON ANIMAL ABUNDANCE **Th e pattern of settlement of spiny lobster postlarvae** **in southwestern Florida Bay may be highly depen dent on the location of red macroalgae (**  **Laurencia ),**  **crevice shelters and planktonic postlarval abundance (Herrnkind and Butler, 1994). Mud banks that restrict**  **transport, unfavorable salinity, and scarcity of hard-bot tom settlement habitat may severely restrict the pres**  **ence of spiny lobster in the interior bay (Field and Butler, 1994).** 

EFFECT OF SPONGES ON JUVENILE SPINY LOBSTER **Butler et al.**  **(1995) documented widespread sponge mortality coinciding with months-long, extensive** 
**cy anobacterial blooms in the south-central part of**  **Florida Bay in the early 1990s (1991, 1992, 1994). They showed with field experiments that the loss of sponges**  **affected the distribution of spiny lobster juveniles, which use crevices beneath sponges as nursery habi**  **tat. Use of artificial shelters increased following the sponge decline. Juvenile spiny lobster abundance de** **clined 23% at sites without artificial substrates and in creased 76% at sites with artificial substrates. The** **long-term effect of sponge mortality on lobster abun dance is not known, but shelter such as that provided**  **by sponges reduces the risk of predation (Herrnkind**  **and Butler, 1994). Based on their results, the authors suggested that loss of shelter might lead to increased**  **predation on animals that remain in areas without shelter or are in search of shelter. Loss of area with shel**  **ter may cause crowding and resource limitation in areas of remaining shelter (Butler**  **et al., 1995). Other an**  **imals that use sponges as habitat include stone crabs (** **Menippe mercenaria ), spider crabs (** **Mithrax spp.), toad**  **fish ( Opsanus beta**  **), and octopus ( Octopus**  **spp.).**

SPATIAL VARIABILITY IN TROPHIC RELATIONSHIPS **T he relative importance of seagrass and phytoplank**  **ton in food webs differs across the bay, and neither is important in certain parts of the bay. Chanton**  **et al. ’s**  **(2001) evaluation of stable carbon (C), nitrogen (N), and sulfur (S) (**  δ **13 C,**  δ **15 N,**  δ **34 S) data for producers and con**  **sumers in Florida Bay indicated that the interior of the bay has a strongly seagrass-based trophic structure,**  **whereas the gulf (outer or western) sites in the bay shift toward a more plankton-dominated trophic system** **(Figure 8.6). It is not yet certain whether the shift in Fig ure 8.6 reflects natural spatial variation or a temporal**  **trend forced by changing environmental conditions in the bay. Stable carbon, nitrogen, and sulfur data in**  **Figure 8.7 from Evans et al.**  **(2001) confirm Chanton et**  **al. ’s**  **(2001) description of the trophic structure of the interior and western bay. In addition, the data suggest**  **a nonseagrass-based diet (likely a more pelagic-, or**

**w ater-column-, based food web) in the eastern bay.** **Predominant food webs in the hard-bottom com munities of Florida Bay (mainly the southwestern bay)**  **and bayside hard-bottom communities in the Florida** Figure 8.6 **Summary comparison of consumer tissue** δ **13 C vs**  δ **34 S**  **from several Florida coastal ecosystems. Data illustrate the gradient in stable isotope values as trophic dependence shifts from seagrass**  **beds “benthic”,** δ **13 C-enriched,**  δ **34 S-depleted) to the water-column**  **(“planktonic”) (** δ **13 C-depleted,**  δ **34 S-enriched) (Chanton and Lewis,**  **2002).** Higher-Trophic-Level SpeciesHunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 127 **Ke ys are based on macroalgae rather than seagrass, ac** **cording to stable-isotope analyses (C, N, and S) con ducted by Behringer and Butler (1999).They sampled**  **macroalgae, seagrass, suspended particulate organic matter (POM), sediment POM, sponges, gastropods,**  **holothurians, bivalves, and spiny lobsters. With the exception of suspension feeders, the hard-bottom an**  **imals were trophically independent of seagrass. K** **oenig et al.**  **(2001) found spatial, temporal, and on togenetic dietary shifts in the major prey of red drum.**  **Th ey**  **speculated that the differences were due to dif ferences in prey availability. This is consistent with**  **observations about the abundance of various prey, which differs by region. They were not able to detect**  **spatial or seasonal differences in the diet of snook, possibly because of the lower resolution of the snook**  **diet data.**



## V

ariation in Ecosystem Characteristics

Effects of Animals on the Ecosystem

**Specific questions being addressed by this research are as follows: (1) how do animals affect their ecosystem,**  **and what are the consequences of change in animal abundance or distribution for the rest of the system?** **(2) What is the ecological role of sponges in the ecosys tem, and what does the loss of sponges in southwest**  **ern Florida Bay and an increasing fishery for some sponge species portend?** 

EFFECTS OF ANIMALS ON BENTHIC HABITAT**Benthic grazing animals in exceptionally high densi ties can adversely affect benthic vegetation in Florida**  **Bay. A dense aggregation of the variegated sea urchin (**  **L**

**ytechinus variegatus ) caused severe, localized defoli**  **ation of a seagrass bed in outer Florida Bay during 1997–1998 (Rose**  **et al., 1999). Macia and Lirman (1999)**  **described the population dynamics of this aggregation and Rose**  **et al. (1999) described the short-term effect** **of this aggregation on the benthic community. Subse quent monitoring of the aggregation during 1998–1999**  **revealed that urchin densities progressively declined, as did their effect on seagrass biomass. However, as of**  **2002, seagrass biomass in the area of the meadow that underwent the most severe defoliation remained dras**  **tically reduced compared to areas that had not been damaged by urchins (W. Sharp, personal communi**  **cation).**

ROLE OF SPONGES IN REGULATING WA TER QUALITY **T he working hypothesis is that the large-scale loss of**  **suspension-feeding sponges may have rendered the Florida Bay ecosystem susceptible to recurring phy**  **toplankton blooms (Peterson and Fourqurean, 2001). Sponges are capable of filtering large volumes of water**  **when feeding.Widespread sponge mortalities occurred in Florida Bay from 1992 to 1994. By 1995, total sponge**  **biomass was a fraction of its former level: there had been a 70% decline in the Long Key area and an 84.6%**  **decline in the Marathon area (Stevely and Sweat, 2001). Loss of sponge biomass in Florida Bay may be having**  **major ecological effects on water quality (Stevely and Sweat, 2001; Peterson and Fourqurean, 2001)**  **Sponges are a particularly dominant structural feature of Florida Bay seagrass and hard-bottom habi**  **tats, functioning as efficient filters of small (less than 5 μm) planktonic particles. Previous studies have il**  **lustrated that the grazing pressure of filter-feeding bivalves may control phytoplankton abundance. If the**  **presence of sponges increases light availability to the benthic plant communities, then sponges may reduce**  **the shading effects of phytoplankton blooms, and the loss of sponges in Florida Bay may have cascading ef**  **fects on the associated seagrass community (Peterson and Fourqurean, 2001).**  **Since the initial seagrass die-off in the late 1980s, blooms have swept over extensive portions of the bay**  Figure 8.7 **Stable isotope analysis of Florida Bay gamefish to support methylmercury studies in Florida Bay (Evans**  **et al., 2001).**  **T**

**he analysis complements the view of the bay in the previous figure by adding information on the bay’s eastern and northern tran**  **sition zones.** Higher-Trophic-Level Species**north of the middle Keys and have persisted for months.The proliferation of the cyanobacterium (**  **Syne**

**c hococcus**  **) and diatom ( Rhizosolenia**  **) blooms has caused widespread concern among scientists and water man**  **agers.These blooms have the potential for disrupting the ecology of the bay and harming benthic plant com**  **munities by depleting oxygen, producing toxins, and reducing the light levels in the bay. Some regions of** **Florida Bay exhibit high levels of algal and/or nonal gal suspended solids, resulting in low light penetration.**  **Although phytoplankton blooms were not likely the cause of the initial seagrass die-off, the reduction in**  **light caused by high phytoplankton standing crops may have contributed to poor seagrass recovery and**  **more recent seagrass die-offs. Prior to the widespread sponge mortalities that oc**  **curred from 1992 to 1994, Stevely and Sweat (2001) collected data on the abundance of commercial sponges**  **( Spongia**  **and Hippospongia**  **) and the entire sponge com munity at 15 locations in the Middle and Upper Keys**  **(4 locations were within Everglades National Park). Th**  **ey have been evaluating the recovery of the sponge**  **community annually since 1994 and have identified to family, genus, or species level approximately 95% of the**  **sponges counted. In general, recovery of the largest and most abundant sponge species (in the genera**  **Sphe ciospongia**  **and Ircinia**  **) has been extremely slow.The first significant indication of recovery of these species was**  **found at Marathon in 1999 and 2000, but recovery was still not apparent at Long Key by April of 2001. These** **large species represented 70% of the sponge commu nity biomass prior to the mortalities.** **Based on their data prior to the 1992–1994 mortal ities, Stevely and Sweat (2001) estimated that the mean**  **sponge abundance was 0.725 sponges/m 2**  **and mean sponge biomass volume was 364 ml/m**  **2**

**. Based on a** **sponge pumping rate of 10,000 times the sponge vol ume per day (Reiswig, 1974; Reiswig, personal com**  **munication), the sponge biomass could therefore pump 3,640 liters of seawater per square meter per day. Since**  **the water column in the study area was approximately three meters deep, sponge biomass could be expected**  **to pump the equivalent of the entire water column in 24 hours (Stevely and Sweat, 2001).The loss of 75% of**  **sponge biomass might be expected to lengthen the time required to pump the water column from one day**  **to four days. P** **eterson and Fourqurean (2001) speculate that system-wide trophic dysfunction caused by the sponge**  **die-off has potentially contributed to the magnitude of the nuisance phytoplankton blooms, and that the loss**  **of these organisms can explain why this system remains susceptible to recurrent blooms of phytoplankton and** 
**cy anobacteria.**  

### Oceanographic Effects on Larval Transport and Recruitment

**Major questions related to this topic are (1) What processes are involved in the transport of presettlement**  **stages of fish and invertebrates to the boundaries of Florida Bay, and what are their schedules? and (2)**  **W hat pathways do early life stages of offshore-spawned** **HTLS use to enter Florida Bay, what is the relative im portance and extent of penetration into the bay’s in**  **terior by these pathways, and what factors influence transport and settlement?**  **Many species associated with the reef tract and the southwestern Florida shelf spend some part of their**  **life cycle in Florida Bay. For example, Florida Bay is a major nursery ground for pink shrimp that are har** 

**v ested in waters off the Dry Tortugas, the most eco**  **nomically important pink shrimp fishing ground in the state. Florida Bay also contains important spiny lob**  **ster nursery habitat, and Everglades National Park is a fishing-free sanctuary for spiny lobster. Water flows**  **and animal movements connect Florida Bay not only to the upstream Everglades and coastal mangrove**  **areas but also to the Florida Keys, the reef tract, the southwest Florida shelf, and the Dry Tortugas. Many**  **HTLS range between the bay and coastal reefs within their life cycle. The development of scientific knowl**  **edge about HTLS of the bay, therefore, must extend beyond Florida Bay to address the greater ecosystem**  **that supports these species and the processes that affect their movements. For example, research should** **include the Loop and Florida currents and counter currents, the Tortugas Gyre, and coastal eddies.The ef**  **fect of these processes on larval transport and the distribution and abundance of HTLS in the bay must**  **be addressed to improve the ability to distinguish effects of changes in freshwater inflow.**  **Florida Bay lies between the Atlantic Ocean and the Gulf of Mexico and is connected to both of these bod**  **ies through regional-scale circulation and exchange processes and the oceanic boundary currents that in**  **fluence these processes. The southwest Florida Shelf to the west and the Keys coastal zone to the east and**  **south of Florida Bay interact with each other and the bay through the tidal channels between the Keys and**  **also by means of their boundary currents (Herrnkind and Butler, 1994; Lee**  **et al., 2001). A dominant process** **potentially affecting water transport and the trans port of eggs and larvae to Florida Bay is the strong, co**  **herent response to alongshore wind-forcing coupled with seasonal stratification in response to variations in**  **wind-mixing, air-sea exchange, and river runoff along the nearshore western shelf. Boundary current dy** **namics and eddy processes are also critical larval trans** Florida Bay Synthesis Hunt and Nuttle

128 FWRI Technical Report TR-11 Higher-Trophic-Level SpeciesHunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 129 **port mechanisms that operate both on the regional and local scales.Transport response to prevailing east**  **erly winds may vary along the Florida Keys as a result of the curvature of the coastline (Lee and Williams,**  **1999), but they are expected to favor onshore larval transport between the Lower Keys and the Dry Tortu** **gas, where the coastline is east-west oriented. On shore convergence of the Florida Current can also**  **facilitate transport into the coastal zone of the Keys, and this occurs mainly in the upper Keys where the shelf**  **narrows and curves northwards (Yeung and Lee, 2002). T** 

**he area of the Dry Tortugas is an important spawn ing site for penaeid shrimps, spiny lobsters, and some**  **species of snappers and groupers (Limouzy-Paris et al.,** **1997). Pink shrimp larvae were retained by the Tortu gas gyre circulation for a period of two weeks (Criales**  **and Lee, 1995). Coastal eddies originating from the Dry Tortugas and propagating downstream may be a**  **mechanism to deliver presettlement stages from spawning site to nursery sites on the reef tract and in**  **Florida Bay (Yeung et al.,**  **2001; Criales et al.,**  **2003).The lower southwestern shelf in the vicinity of the Dry**  **T**

**ortugas is a potential source of recruitment to the Florida Keys reef tract and Florida Bay for both reef fish**  **and pink shrimp. F**  **rontal eddies of the Loop Current in the Gulf of Mexico that propagate southward along the outer edge**  **of the western shelf may be trapped and develop into persistent gyres off the Dry Tortugas (Fratantoni**  **et al., 1998; Yeung and Lee, 2002). The subsequent arrival of**  **another frontal eddy or the abrupt retreat of the Loop Current may dislodge the gyre, which then moves**  **eastward along the southeastern shelf off the Florida Ke** **ys in the form of a transient coastal eddy. The Tor tugas gyre provides a mechanism for retaining larvae**  **for periods of weeks to up to three months (Lee et al.,**  **1994).**

EDDIES AND GYRES **W**

**orking hypotheses about the transport of larvae to the boundaries of the bay are as follows: (1) Presettle**  **ment stages are transported and detrained into the coastal zone of the Florida Keys by coastal eddies. (2)**  **Spawning and nursery sites for pink shrimp, spiny lobsters, and some snappers are linked through the** 

**ev olution of the coastal eddies from the Tortugas gyre.**  **(3) The formation of the Tortugas gyre is enhanced by a well-developed Loop Current (high latitudinal in**  **trusion) whose dynamics may be modulated by climatic shift. (4) Snapper larvae entering Florida Bay origi** **nate from spawning stocks that form seasonal aggre gations off the Dry Tortugas. (5) Year-class strength of** **six snapper species is enhanced by increased larval re tention and nutrient-enrichment of the pelagic larval**  **habitat via gyre-induced upwelling during spawning season off the Dry Tortugas (Criales and McGowan,**  **1994; Criales and Lee, 1995; Jones et al.,**  **2001; Yeung et**  **al., 2001; Yeung and Lee, 2002).** **Supply of early-life-stage recruits is a major lim iting factor of the year-class strength of aquatic species.**  **Presettlement stages of the spiny lobster, snapper, and pink shrimp that inhabit Florida Bay as juveniles and/or**  **adults enter the bay from the ocean through interisland**

**c hannels.**  **T he eddy hypothesis of regional recruitment has** **important implications over larger temporal and spa tial scales. Because coastal eddies originate from the** **Dry Tortugas, they may constitute the essential trans port link between the spawning and nursery grounds.** **Moreover, eddy formation at the Dry Tortugas is asso ciated with Loop Current frontal dynamics, which are**  **in turn modulated by long-term climatic variability (Yeung**  **et al., 2001; Yeung and Lee, 2002).** **Observed larval distribution patterns of some crus taceans in the Florida Keys coastal zone corroborate**  **many of the predictions based on key coastal transport processes. Early-stage phyllosomata (less than 2 months**  **old) were concentrated within or at the boundaries of a gyre in the pattern hypothesized for passive drifters** **(Yeung and Lee, 2002).The abundance of strong-swim ming spiny lobster postlarvae was not highly correlated**  **with wind-driven currents that can affect the coastal transport of more passive drifters (Acosta and Butler,**  **1997). High concentrations of pink shrimp larvae were found in the Tortugas Gyre in late spring–early sum**  **mer (Criales and Lee, 1995). High densities of larvae and postlarvae of 10 different shrimp families were found** 

Figure 8.8 **Monthly mean influx density of spiny lobster postlarvae observed at Long Key and the predicted density (density**  **LK ) using**  **an index of countercurrent magnitude in a simple regression model (**  **r 2**  **= 0.50, F 1,16**  **= 17.90, P**  **< 0.0006) (Yeung et al.,**  **2001).The index is the average magnitude of the countercurrent component for the**  **periods two weeks prior to and three days during sampling taken at a current meter moored at Tennessee Reef in the middle Keys.**  **Satellite imagery confirmed that in most cases, enhanced coastal countercurrents coincided with the presence of a cyclonic mesoscale**  **eddy in the vicinity.** Higher-Trophic-Level SpeciesFlorida Bay Synthesis Hunt and Nuttle

130 FWRI Technical Report TR-11 **off Looe Key during the presence of a gyre (Criales and McGowan, 1993, 1994).**  **V**

**ariability in the supply of larvae may be related to the development of mesoscale eddies and their as** **sociated countercurrents on the oceanside of the chan nels. Peak influx of spiny lobster postlarvae into the bay**  **through the middle Keys coincided with the presence of eddy and countercurrent conditions (Figures 8.8,**  **8.9) (Yeung et al.,**  **2001; Yeung and Lee, 2002). Te**  **mporal and spatial variability in the supply of spiny lobster postlarvae to Florida Bay nursery grounds**  **may interact with local nursery-habitat structure to influence recruitment and year-class strength. Butler**  **et al. (2001b) used an individual-based model to address** **this question. They tested eight scenarios of variabil ity describing postlarval supply (Uniform, Volumet**  **ric, Gradient, Broken Stick–Static, Broken Stick– Va**  **riable, Pulsed, Aggregated, and Random).Their re sults indicated that random variation in the arrival of**  **postlarvae among regions of the Florida Keys leads to the highest recruitment, whereas persistently patchy**  **settlement ( i.e.,**  **pulsed and aggregated scenarios) yields the lowest. Analyses of field data suggested that the ran**  **dom supply was the most realistic scenario. Field data**

**w ere based on artificial collectors positioned at eight**  **sites in the Florida Keys. Eddy transport processes may also affect supply**  **and nutritional condition of pink shrimp and snapper presettlement stages entering Florida Bay through the**  **Florida Keys. Influx of early-life-stage recruits was monitored monthly on the new moon for two years at**  **two tidal channels on opposite ends of the middle Ke** **ys: Whale Harbor (east end) and Long Key Channel (west end). Back-counted birth dates based on counts**  Figure 8.9 **Example of a sequence of satellite SST images used to infer gyre displacement and progression down the Straits of Florida (Yeung**  **et al., 2001). Warmer waters are red, cooler waters are blue. The centers of each of two gyres (**  1 **and** 2**) present during this period are indicated. On March 5, a gyre (**  1**) was centered off the Dry Tortugas; by March 14, it had begun moving downstream; and by March 25, the upstream frontal eddy (**  2**) responsible for its displacement is clearly evident.** Higher-Trophic-Level SpeciesHunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 131**of otolith daily increments suggested that snapper lar**

**v al duration during the first year varied across species**  **and ranged from 35.50 to 41.45 days (Jones et al.,**  **2001). Preliminary analyses of Year-2 samples suggested that**  **larval durations differed from those of Year 1. Peak abundance of snapper larvae in the channels occurred** **in the summer of 1997 and was coincident with a well developed Loop Current (high latitudinal extent) fa** 

**vo ring gyre formation off the Dry Tortugas, where**  **snapper spawning aggregations occur. Criales et al.** **(2003) showed that the temporal pattern of immigra tion of postlarval pink shrimp differed substantially be**  **tween Long Key Channel and Whale Harbor Channel (Figure 8.10).The influx of postlarvae at Long Key chan** **nel was lower in magnitude but steadier than the in flux at Whale Harbor. Long Key channel showed the**  **highest postlarval influx in late spring–summer, whereas the postlarval influx through Whale Harbor**  **(downstream from Long Key in terms of the Gulf Stream and associated shelf gyre processes) showed**  **both spring–summer and winter peaks. The winter peak may be associated with the countercurrent gen**  **erated by eddies (Figure 8.10). This high variability**

**ov er small spatial scales suggests the influence of**  **mesoscale processes.**

MOVEMENT INTO AND WITHIN FLORIDA BAY **Other working hypotheses that relate principally to movement of postlarvae into the bay are as follows: (1)** **Pink shrimp postlarvae enter Florida Bay from two di rections: west (across the southwestern shelf) and**  **southeast (through the Lower Keys).The western and southeastern pathways vary in importance and are af**  **fected differently by physical oceanographic factors and tides. (2) Sufficient numbers of pink shrimp larvae** **enter the bay’s interior for the interior bay to be a sig nificant nursery ground and source of recruits to the** **fishery during years of favorable conditions. (3) Snap pers settle outside Florida Bay but near the boundary**  **and enter Florida Bay as juveniles. (4) The abundance of bay-dependent species that are spawned offshore**  **is lower in northeastern Florida Bay because of weak transport across the bay.**  **T**

**ransport across the lower and middle Keys has previously been the most recognized pathway of lar** 

**v al transport to Florida Bay because past studies (Cri**  **ales and McGowan, 1994; Yeung, 2001) have shown that local winds, Florida Current flow, and coastal ed** **dies interact to influence the onshore transport and re circulation of larvae in the Florida Keys. New work,**  **based on synchronized sampling of postlarvae on both sides of Florida Bay, indicates that the dominant path** 

**wa y of influx of postlarval pink shrimp into Florida Bay**  **is from the west (Browder et al.,**  **2002). Peak concen trations of pink shrimp postlarvae in water moving**  **into the bay from the west (through Sandy Key and Middle Ground channels) were substantially larger**  **than in water moving into the bay from the southeast (Whale Harbor Channel). The temporal pattern from**  **the west consisted of one large, sustained summer peak (Figure 8.11). In contrast, peak concentrations at**  **W hale Harbor were observed in February, May, and**  **Ju ly**  **and were smaller (Figure 8.11). Prior studies ex amined the influx of pink shrimp postlarvae from the**  **southeast (Allen et al.,**  **1980) and west (Tabb et al.,**  **1962; Roessler**  **et al., 1969; Robblee**  **et al., 1991), but these**  **studies were not designed in a way that would allow us to make comparisons now.**  **Pink shrimp nursery grounds are on the western** Figure 8.10 **Mean monthly postlarval influx of pink shrimp has different temporal patterns in channels of the middle Florida Keys**  **(Criales et al.,**  **2003). At Long Key Channel (the two upper graphs), larval concentrations are associated with surface temperature. At**  **Whale Harbor Channel, larval concentrations were associated with the coastal countercurrent flow.**  Higher-Trophic-Level SpeciesFlorida Bay Synthesis Hunt and Nuttle

132 FWRI Technical Report TR-11 **side of the bay (Robblee et al.,**  **1991), not in the east (Costello**  **et al., 1986).The larvae spawned north of the**  **Dry Tortugas on the relatively shallow shelf may escape from the strong flow of the Florida Current and move**  **northeast toward the bay with the winds and tidal**
**currents.**



### Effect of Human Activities

**T his topic was approached by addressing three major**  **questions: • W**  **hat are the potential effects of water management and other human activities on recruitment, growth,**  **and survivorship of HTLS? • W**  **hat is the potential effect of water management on bioaccumulation of mercury?**  **• H ow**  **does fishing, both within the bay and outside**

**the bay, affect fishery populations and our ability to detect effects of water management on recruitment,**  **growth, and survival?**

**Some critical working hypotheses relative to these questions were as follows:**  **• T he timing and amount of freshwater releases to** 

**coastal wetlands adjacent to Florida Bay affect the nesting success of wading birds in northeastern**  **Florida Bay.**

**• Changes in water management that affect the spa** 

**tial coverage, intensity, and duration of hypersalin ity affect shrimp, lobster, and other species.** 

**• Abrupt and out-of-season releases of large volumes** 

**of fresh water into Florida Bay and coastal waters ad**

**v ersley affect benthic fauna and fish, shrimp, and lob**  **ster recruitment.**

**• Increased freshwater inflow to northeastern Florida**  **Bay will increase the load of mercury entering the bay and the body burden of mercury in bay HTLS.** 

**• Fishing on the reef tract, in the Tortugas, and through** 

**out the bay affects the population structure and abundance of predator fish species in Florida Bay.** 

WA TER MANAGEMENT AND W

ADING–BIRD NESTING SUCCESS **Linkages of water management, fish production, and roseate spoonbill nesting success in wetlands adja**  **cent to northern Florida Bay have been quantified in studies by Lorenz (2001a,b). Other investigators have**  **proposed that fish availability to wading birds during their nesting season in south Florida is influenced by**  **two main factors: the extent to which water covers**

**w etlands during the wet season and the consistency of** **the decrease in water depth and water coverage dur ing the following dry season. Lorenz (2001b) demon**  **strated the effectiveness of the process of expansion and contraction of water area in enhancing prey availabil**  **ity to wading birds in the coastal marshes immediately north of eastern Florida Bay. He determined that fish**  **density during the wet season is positively related to**

**w ater depth in the marsh and the length of time in**  **which depths in the marsh are greater than 12.5 cm. He found that concentrations of fish in topographic lows**  **occur—and reach roughly twice dry-down density— when water depths in the adjacent marsh decline**  **below 12.5 cm. Roseate spoonbills that nest on islands in northeastern Florida Bay feed in these coastal**  **marshes during the nesting season, which coincides with the usual dry season. Lorenz (2001b) examined**  **their nesting record in relation to water-level data and determined that, in general, mean water levels at his**  Figure 8.11 **T he temporal pattern of monthly pink shrimp postlarval influx on the western side of the bay (upper-graph) differs from**  **the Middle Florida Keys stations (lower-graph) but is similar to that at Long Key Channel the two previous years (Figure 10, upp er graphs,**  **(Criales et al.,**  **2003).** Higher-Trophic-Level SpeciesHunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 133 **fish-sampling sites in the coastal marshes were lower than 12.5 cm during successful roseate spoonbill nest**  **ing periods and higher than 12.5 cm during failed nesting periods. Furthermore, prey availability at the**  **sites during successful nesting periods was twice that during failed nesting periods. On the other hand, nest**  **ing failed to occur during several recent years that might have been expected to support successful nest**  **ing. This failure may be explained by out-of-season**

**w ater releases from the nearby C-111 canal.These re**  **leases have been shown to raise water levels in the coastal wetlands. Such releases during spoonbill nest**  **ing periods could cause prey to become dispersed and result in nesting failure.**  **T he coastal marshes north of Florida Bay were**  **principally oligohaline prior to the extensive drainage and water diversion that occurred with water man**  **agement (Egler, 1952). Since the time that hydrologic modification was begun, mangroves have encroached**  **inland, and there are other indications that the coastal marshes have become more saline (Ross**  **et al., 2000).**  **Lorenz’s (2001a) study of coastal fish populations demonstrated that fish densities were substantially**  **greater and that community composition in the coastal**

**we tlands immediately north of northeastern Florida**  **Bay resembled that of an oligohaline marsh in recent**
**y ears of exceptionally high rainfall, when conditions**  **approximated predrainage conditions. Fish densities**

**w ere substantially greater in the years of oligohaline**  **conditions.This study demonstrated that it is possible to regain wetland productivity with restoration of more**  **natural hydrologic responses to rainfall. Several time series are being developed for birds**  **in Florida Bay.The database on nesting activity in bald eagles extends back to the late 1950s and continues.The**  **osprey database is also lengthy, albeit interrupted, and continues. Monthly data on the abundance and activ**  **ity of water birds in Florida Bay is five years in length and still growing.These databases provide the oppor**  **tunity to analyze bird activity in the bay in relation to freshwater inflow and other conditions that might af**  **fect these birds’ food supply. This information also is**

**av ailable for use in trophic network models. Informa** **tion on the diet of water birds in Florida Bay is very lim ited and largely anecdotal.** 

EFFECTS OF WATER RELEASES ON RECRUITMENT AND BENTHIC FAUNA**Some statistical studies have directly connected abun dance indices from fishery data to indices of freshwa**  **ter flow to Florida Bay and the southwestern coast. T** **hese freshwater flows are affected by water releases to ENP at the Tamiami Trail and by the management** **of water levels and releases in the South Dade Con vey** **ance system on the eastern border of ENP. Changes in catch rates in fisheries can provide a rough index of** 

**c hange in relative abundance. In an analysis of ENP**  **catch and effort data, Schmidt et al.**  **(2001) found that an index of freshwater runoff to Florida Bay and adja**  **cent coastal waters was positively related to snook catch rates but negatively related to spotted seatrout**  **catch rates. Change in harvests can provide a rough index of abundance when change in effort is taken** **into account. Browder (1985) found a positive rela tionship between pink shrimp harvests in the Tortugas**  **fishery and a freshwater inflow index (water levels at P35 in ENP). Analyses by Browder (2000) and Sheridan** **(1996) suggested that freshwater inputs as either rain fall or runoff influence pink shrimp catch rates. Brow**  **der’s (1985, 2000) work suggested that the timing of freshwater inputs affects harvests and catch rates.**  **J ohnson**  **et al. (2002a) found that water releases at the**  **Ta miami Trail were a significant variable explaining the** **density of 9 of 11 dominant species in Florida Bay’s for age fish assemblage (Table 8.2).** 

SPATIAL PATTERNS OF MERCURY AND METHYLMERCURY **Wi despread patterns of elevated mercury (Hg) con** **centrations in game fish and forage fish have been ob served in eastern Florida Bay (Evans**  **et al., 2001).Within** **this region, highest concentrations of both methylmer cury and total mercury have been observed in water**  **and sediments in the mangrove transition zone near the inflows of Everglades freshwater through Joe Bay**  **and Little Madeira Bay (Rumbold et al.,**  **2003). Incuba tion studies with stable mercury isotopes revealed**  **substantial in situ**  **methylation in open-water bay sed iments as well. Inputs of bioavailable Hg(II) may be a**  **critical-determining factor driving this methylation. Concurrent seasonal variations in both methylmer**  **cury and total mercury concentrations were observed in sediment, water, and forage fish, with peak con**  **centrations occurring during the warm rainy season near the coast, where Everglades runoff enters the** **bay. No significant long-term temporal trends in mer cury levels in gamefish can be observed as yet for the** **period 1996–2001. From these results, it has been con cluded that the sources of elevated mercury concen**  **trations in fish from northeastern Florida Bay include (1) methylmercury in runoff from the Everglades and**  **(2) in situ**  **mercury methylation in sediments from both the mangrove transition zone and the open bay itself**  **(Rumbold et al.,**  **2003). Mercury concentrations seem to be higher along a Taylor River–Little Madeira Bay sam** **pling transect than along a C-111 canal–Joe Bay tran sect, suggesting that the urban and agricultural runoff**  **that most strongly influences the C-111 canal–Joe Bay** Higher-Trophic-Level SpeciesFlorida Bay Synthesis Hunt and Nuttle

134 FWRI Technical Report TR-11 **transect is not the most important source of mercury to the bay and its biota. All of these processes could** 

**c hange with restored Everglades freshwater flows and** **might be further altered by changes in nutrient in puts and trophic processing.** 

EFFECT OF FISHING ON AGE STRUCTURE AND ABUNDANCE OF PREDATORS **F aunce**  **et al. (2002) provided evidence that fishing in** **areas of northern Florida Bay open to recreational fish ing affects target fish populations there. The modal**  **length of gray snapper ( Lutjanus griseus**  **) along man grove shorelines is substantially larger in the Croco**  **dile Sanctuary of Everglades National Park, where fishing has been excluded since 1980, than in other parts**  **of Florida Bay in Everglades National Park and the nearby Biscayne National Park, where fishing is al** **lowed. Modal lengths were 25–30 cm TL in the Croco dile Sanctuary vs. 15–20 cm TL elsewhere. Future work**  **may be needed to clearly separate effects of fishing from effects of differences in habitat. Ley**  **et al. (1999) found**  **a similar pattern. Other studies (Bohnsack et al.,**  **2001; A** **ult et al.,**  **2002a,b) suggest that fishing affects reef fish populations, some of which spend part of their life** 
**cy cle in Florida Bay. On the other hand, Schmidt**  **et al.**  **’s (2001, 2002) recent analyses of Everglades Na**  **tional Park creel census data shows that catch rates were positively correlated with fishing rates for four target**  **species—spotted seatrout, red drum, snook, and gray snapper—suggesting that fishing pressure was not af**  **fecting overall abundance.**


## Modeling Change in Higher-Trophic-Level Species

**Tw o types of models have thus far been applied to**  **HTLS research in Florida Bay. Empirical, statistical models have been used to explore data for patterns that**  **suggest the major processes driving variation in species abundance and community structure. Complementing** **these models are simulation models, often incorpo rating population dynamics, to examine the sensitiv**  **ity of individual organisms to varying characteristics of their habitat, such as bottom cover and salinity.** 



### Statistical Models

EXPLORATORY GENERAL ADDITIVE MODELS **J ohnson**  **et al. (2001, 2002a,b) assembled a database for**  **Florida Bay that integrated six independent forage fish/macroinvertebrate studies conducted between**  **1974 and 1997.The database was used to examine the d** 

**ynamics of 11 key forage species. General additive models were used to determine which major forcing**  **functions and habitat factors control the abundance and distribution of these key forage species. The most**  **widely influential variables explaining abundance and** T able 8.2 **Summary of forage fish models and significant factors. S = the factor was significant for that species. NS = factor was not significant. A number following an S means the significant effect was lagged by that many months.**  **T**

**he bottom row represents the number of species where that factor is statistically significant.**

Seagrass Seagrass Tidal Species Gear Month Temp. Depth Salinity Habitat Type Density Amplitude Sea Level Wind Rain Flow

**T**

**ransitory species F.**  **duoraram S NS S NS**  **NS S S* S S S-3 NS NS NS** **L. rhomboides NS S S S NS NS S S S NS NS S-1 S-1**  **Mojarras S NS S NS**  **NS S S* S S S-2 S-2 S-2 S-2**

**P**

**elagic species A. mitchilli**  **S S S S S S S S S NS S-2 NS S**  **Resident species O. beta**  **NS S S NS S S NS S S NS S-3 NS S-3 G.**  **robustum S S NS S NS S S S**  **S NS NS S-2 S-1**  **F. carpio**  **S NS NS NS S S NS N S NS NS S**  **NS S-2 S. scovelli**  **S S S SS S S S S N S NS NS**  **S-2 M. gulosus**  **S NS NS NS S S S S S NS**  **NS NS S-2 L. parva**  **S NS NS NS S S S S S NS**  **NS S-3 NS H. zosterae**  **NS S NS NS S S S S S NS NS NS S-2 Significance 8 6 6 4 7 10 9 10 10 2 4 4 9** 

*** The significant effect occurred only between presence vs. absence of seagrass.** Higher-Trophic-Level SpeciesHunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 135 **distribution were seagrass density, habitat, and tidal amplitude, which were significant variables for 10** **species, followed by seagrass type and freshwater in flow to the bay (9 species), salinity (7 species), and**  **temperature and month (6 species). Depth, wind, and rainfall (4 species each) and sea level (2 species) were**  **less important variables in predicting the abundances of forage species (Table 8.2).The**  U **-shaped relationships of three species (**  **Gobiosoma robustum, Floridichthys car pio,**  **and Lucania parva**  **) to salinity suggested they might be adapted to extreme conditions (high and low salin**  **ities).The majority of species were positively correlated with seagrass density, with the exception of the pelagic**  **bay anchovy ( Anchoa mitchilli**  **), F.**  **carpio, the toadfish (**  **Op sanus beta**  **), and the gobies Microgobius gulosus**  **and G.**  **robustum, which were more abundant in sparse sea** **grass.The specific types of bottom cover were impor tant for seven animal species, as follows:**  **Syringodium (** **M. gulosus, Lagodon rhomboides, Hippocampus zosterae, and**  **L. parva ),**  **Halodule (**  **F arfantepenaeus duorarum, Syn**  **gnathus scovelli ),**  **T halassia**  **( G.**  **robustum ), and no seagrass**  **( A. mitchilli**  **).Three taxa ( F.**  **duorarum, L. rhomboides, and**  **Eucinostomus spp.) that spawned outside of the bay**  **showed relationships with tidal amplitude, sea level, and/or wind, which suggests that transport mecha**  **nisms may affect abundance.**

FORECASTS OF THE TORTUGAS SHRIMP FISHERY **Several empirical statistical models have been used to relate Tortugas catches or catch rates to indices of**  **freshwater inputs to Florida Bay. Browder (1985) found a statistical relationship between quarterly Tortugas** **catches and the average water level in ENP monitor ing well P35. Later, Sheridan (1996) developed a sta**  **tistical model that related annual Tortugas catches to Everglades well data, rainfall data, and air tempera**  **ture and sea level measured at Key West the previous spring and summer. The Sheridan model, which was** **updated every year with new data, successfully pre dicted Tortugas catches for the upcoming year for a**  **number of years. More recently, Browder (2000) developed a statis**  **tical model relating annual average Tortugas catch rates to the rainfall of several prior months.Two mod** **els were developed, one for recruits to the fishery (as sumed to be shrimp in the 68-count per pound** **category) and another for larger shrimp. These mod els were designed to make rainfall-based predictions**  **of catch rates that could be compared with observed catch rates to separate effects of south Florida’s highly** 

**v ariable rainfall from effects of change in water man**  **agement. Modeling results suggested that timing as**

**w ell as quantity of rainfall influence catch rates.The two**  **rainfall-based models, which were based on data for biological years (July–June) 1964–1965 through**  **1994–1995, had high r**  **2 (0.89 and 0.76, respectively), but**  **their predictions differed greatly from observations in five subsequent years, when few if any water man** **agement changes had occurred (Browder, 2001, un published report).** **A second empirical model was prepared (Brow der, 2000) to test alternative configurations of the water**  **management system proposed in the “Restudy”that developed the CERP.This model related Tortugas catch**  **rates of recently recruited shrimp to releases of fresh**

**w ater into Everglades National Park at its northern**  **boundary immediately downstream from the leveed Everglades Water Conservation Areas. The model,**  **based on data for the period 1964–1965 through 1994–1995, explained 92% of the variation in average**  **annual catch rate. Total monthly water releases for several months of the year explained more than 57%**  **of the variation in catch rate.The rest of the explained**

**v ariance was due to other variables. These included**  **large-shrimp catch rates the previous year and monthly average Key West air temperature (as a proxy** **for water temperature) for several months. The rela tionship between catch rate and water flow was pos**  **itive for some months and negative for others, suggesting that timing as well as volume is important.**  **W hen used in alternative testing, the model predicted**  **consistently higher annual catch rates for the “Natural System”than for the “1995 base case”or any alterna** **tive, suggesting that south Florida’s predrainage hy drologic system provided the best conditions for pink**  **shrimp production. To make these predictions, the output of hydrologic models served as input to the**  **shrimp model. Another analysis examined pink shrimp recruit**  **ment to the Tortugas grounds in relation to observed salinity in the western and central bay (Browder, 2000).**  **Because of limitations in available salinity data, the time series analyzed was very short compared to that avail** **able for relating recruitment to rainfall and water re leases to Everglades National Park. A weak, but**  **significant, relationship was found between monthly recruitment and time-lagged monthly average salin**  **ity in both areas.**



### Simulation Models

**A simulation model was developed to predict survival, growth of juvenile pink shrimp cohorts, and potential** **harvests from these cohorts as a function of tempera ture and salinity in Florida Bay (Browder**  **et al., 1999).**  **T**

**he model was recently refined with data from new lab oratory experiments (Browder**  **et al., 2002).The model**  Higher-Trophic-Level SpeciesFlorida Bay Synthesis Hunt and Nuttle

136 FWRI Technical Report TR-11 **structure consists of three algorithms, which govern (1) physiological survival as a function of temperature**  **and salinity; (2) growth as a function of temperature, salinity, and total length; and (3) survival from preda**  **tion as a function of total length. The model is driven by**  **observed daily temperatures and salinities from specific locations in Florida Bay.The model simulates**  **juvenile densities in that part of the bay and potential recruitment (and related harvests) to the Tortugas fish**  **ery from that part of the bay. A spatially explicit individual-based model for**  **Caribbean spiny lobster ( P**  **anulirus argus ) was devel**  **oped in 1993 (Butler, 1994). Reformulations of the same model have been used to investigate a variety of** **issues, including (1) the potential effect on lobster re cruitment of a massive loss of nursery habitat struc**  **ture that was due to a sponge die-off (Butler, 2003), (2) the consequences of temporal and spatial variation in**  **postlarval supply on recruitment (Butler et al.,**  **2001b), (3) the effect of nursery habitat structure and geo**  **graphic specificity on recruitment (Butler et al.,**  **2001b), and (4) the direct and indirect consequences of al** **tered salinity on recruitment (M. Butler, personal com munication). The ecological aspects of recruitment**  **included in this model start with the arrival of spiny lobster postlarvae in the nearshore nursery and ter** **minate when larger juveniles begin to enter fisher men’s traps. The recruitment process is explicitly**  **incorporated into this model by superimposing on the model’s spatial landscape the daily ecological**  **processes faced by juvenile spiny lobsters: settlement, growth, shelter, selection, mortality, and movement.**  **T he model tracks each hypothetical lobster from set**  **tlement until recruitment to 50-mm carapace length. Settlement occurs once every 28 days, corresponding**  **to the lunar cycle. Growth is a discontinuous process involving molts. Daily mortality is a function of vari** **ous aspects of habitat and lobster-habitat interac tions. Simulations with the model were run for**  **observed extreme conditions: a wet year (1995) and a dry year (1993).The direct effects of salinity were lim**  **ited to approximately 20% of the lobster nursery area, where salinity varies naturally. Simulation results sug**  **gested that lobster recruitment during a very wet or dry year would be similar. In both cases, recruitment** **declined by approximately 25% in the area directly af fected by salinity changes, which resulted in an ap**  **proximately 5% decline in recruitment over the entire Florida Keys region, as compared to control simula** **tions where salinity was stable at 35 psu. Other sim ulations predicted that the lobster population would**  **be surprisingly resilient to sponge die-off. Although nearly the entire sponge community was decimated**  **ov er approximately 20% of the nursery area, this loss**  **of habitat was predicted to result in only a 16% decline in lobster recruitment in the perturbed region and a**  **2% decline over the entire Florida Keys region. The model allowed a follow-up analysis of “why this is**  **so.” Apparently the effect was not just because the supply of postlarvae was three times higher in the** **post-die-off year simulated, but mainly because ju**

**v enile lobster movement to nearby unaffected areas** **and shifts in shelter use on sites affected by sponge die off, a response supported by field evidence (Butler**  **et al.,**  **1995; Herrnkind et al.,**  **1997). Richards (2003) examined the relationships of tem**  **perature and salinity to growth rates in crocodiles (**  **Crocodylus acutus ) by tracking 30 radio-tagged hatch**  **lings in the vicinity of the Turkey Point Power Plant for up to several weeks.Water temperatures in habitats in**  **which the hatchlings were tracked were within the range 29°–35°C, a range in which temperature is not ex**  **pected to have a detrimental effect on growth (Mazzotti et al.,**  **1986). Richards found that temperature had no effect on most measures of growth. Although labora** **tory work has shown that salinity has a strong nega tive effect on mass in hatchling American crocodiles**  **(Dunson, 1982), field observations suggest that they can survive and grow in highly saline areas (Lang, 1975;**  **Mazzotti, 1983). Richards also found that salinity did not significantly affect growth rates, supporting these**  **field observations.Two of the individuals in very high salinities (approximately 60 psu) grew at the same rate** **as most individuals in low-salinity water. In the labo ratory, Mazzotti and Dunson (1984) showed that hatch**  **ling C.**  **acutus maintained in seawater (35 psu) grew well**  **if given periodic access to brackish water (4 psu). Richards observed that hatchlings used hollows in the** **banks of canals and ponds and also that four individ uals on five occasions (sometimes accompanied by**  **other hatchlings) moved out of their low-salinity pond and into the hypersaline canal areas at night and re** **turned to their pond the following day. These obser**

**va tions support the hypothesis that crocodiles may** **have behavioral adaptations for escaping adverse ef fects of salinity.** **Substantial progress has been made in the devel opment of a bioenergetically based individual larval**  **spotted seatrout model to simulate metabolic rate, consumption, and growth as a function of temperature**  **and salinity (Wuenschel et al.,**  **2004).The model follows the basic energy budget equation in which consump**  **tion equals the sum of metabolism, excretion, and growth, and each component is a function of fish size,**  **temperature, and salinity, where appropriate.The final model will incorporate variability for each component,**  Higher-Trophic-Level SpeciesHunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 137 **which will enable researchers to model a population of individuals, rather than just the average individual.**  **Laboratory experiments ( n**  **= 779, SL 4.5–39.5 mm) pro vided the basic information for the model.** **A spatially explicit prey-predator model for spot ted seatrout and pink shrimp coupled to physical**  **processes was developed for Biscayne Bay (Ault et al.,**  **1999, 2003; Wang et al.,**  **2003).The spotted seatrout com ponent of the model was individual-based.**  

## Ongoing Research
Projects

**At the time of the 2001 Florida Bay Conference, five new (or continuing) HTLS projects funded for two years by**  **the NOAA Coastal Oceans Program had barely started. Although these studies have made substantial progress**  **to now, their results were not presented at the Florida Bay Conference, and only a portion of these results** 

**we re available for this synthesis. These projects are**  **briefly described below.**

MODELING PINK SHRIMP RECRUITMENT FROM FLORIDA BAY**In this project, we are continuing to develop a simu lation model and the associated performance mea**  **sures to evaluate the potential effect that upstream**

**w ater-management changes resulting from efforts to**  **restore the Greater Everglades ecosystem have had upon Florida Bay.This work seeks to (1) clarify the ef**  **fects of freshwater inflow and seagrass habitat on Florida Bay’s pink shrimp nursery function, (2) deter**  **mine the major influences of meteorological and oceanographic processes on postlarval pink shrimp**  **and their recruitment to the fishery, and (3) improve the ability to predict recruitment to the Tortugas fish**  **ery in response to changes in water management. As part of this work, a spatially explicit recruitment model** **will be developed from the existing unit model; post larval immigration pathways, transport rates, and in**  **fluencing factors will be described and quantified; and historical data on pink shrimp density will be ana**  **l yzed and used to further refine and verify the model.** 

REGIONAL ASSESSMENT OF SPONGE DYNAMICS AND SPONGE FISHERY IMPACTS **T his project is part of a multiyear investigation of the**  **hard-bottom communities of Florida Bay and the Florida Ke** **ys. It combines modeling, laboratory experiments, and fieldwork to explore the relationship of spiny lob**  **ster population dynamics to spatiotemporal patterns in the structure of bottom habitat and environmental vari**  **ables.The current project focuses on sponges, but some elements also pertain to spiny lobsters and octocorals.**  **T**

**he four principal objectives of the project are (1) to de scribe size-specific population dynamics information**  **( e.g.,**  **growth and reproductive status) needed to model and manage commercial sponge species, (2) to deter**  **mine the effects of commercial fishing on sponges and the bycatch of the sponge fishery, (3) to experimen**  **tally test the tolerance ( e.g.,**  **survival, susceptibility to disease, changes in behavior) of selected hard-bottom**  **dwelling species ( e.g.,**  **five sponge species, two octoco ral species, and three size-classes of spiny lobster) to**  **different salinities and periods of exposure at winter (18°C) and summer (28°C) water temperatures, and (4)** **to incorporate new and existing information into a spa tially explicit simulation model to quantitatively com**  **pare the effects of potential management strategies on the sustainability of the sponge fishery and its effects**  **on hard-bottom community structure in the Florida Ke** **ys National Marine Sanctuary.**

POPULATION STUDIES, ABUNDANCE, HABITAT USE, TROPHIC DESCRIPTIONS, AND REPRODUCTIVE STATUS OF MARINE TURTLES INHABITING FLORIDA BAY **T he purposes of this study are (1) to capture and tag** **sea turtles in Florida Bay to continue long-term mon itoring of individual growth rates, foraging-site fi**  **delity, residency rates, health status, and trends in abundance, (2) to elucidate the trophic role of log** **gerheads as apex predators in Florida Bay, (3) to pro vide detailed descriptions of loggerhead habitat use**  **and behavior, and (4) to examine the sexual maturity and reproductive frequency of adult-sized logger**  **heads inhabiting Florida Bay.The principal study area is the central-western region.** 

REEF–FISH COMMUNITY DYNAMICS AND LINKAGES WITH FLORIDA BAY **T his continuing project will apply a visual sampling**  **strategy to quantify coral-reef fish community changes. T** **he project has the following goals: (1) to provide in tensive and precise spatial and habitat-specific fishery**  **independent assessment of reef fish communities; (2) to document trends in reef fish size and abundance**  **within and outside no-take zones in the Florida Keys reef tract; (3) to test specific hypotheses predicting**  **continuing changes in reef fish communities as the result of no-take protection; (4) to provide a precise and**  **spatially explicit database for assessing any future reef fish population changes resulting from Everglades** **restoration actions; (5) to provide managers with op tions for optimizing long-term survey design strategies**  Higher-Trophic-Level SpeciesFlorida Bay Synthesis Hunt and Nuttle

138 FWRI Technical Report TR-11**to identify reef-fish population changes; and (6) to cor relate the linkages between reef fish communities and**  **fishing, habitat, oceanographic, and other physical processes to guide appropriate experimental studies**  **on dynamic mechanisms and to develop predictive models.** 

DEVELOPMENT OF SPATIALLY EXPLICIT MODELS TO PREDICT GROWTH–POTENTIAL OF AGE–0 GRAY SNAPPER, LUTJANUS GRISEUS , IN FLORIDA BAY DURING RESTORATION OF FRESHWATER FLOWS **T he general goal is to examine patterns of growth in**  **juvenile gray snapper and develop a bioenergetic model of growth that is a function of temperature,**  **salinity, and fish size.This model will be extended into a spatially explicit calculation of potential fish growth** **using historical environmental data as well as pre dicted changes in the environment of Florida Bay** **under different water-management strategies. Spe cific objectives are (1) to quantify patterns in juvenile**  **gray snapper growth through a retrospective analysis of previously collected samples, (2) to examine the re**  **lationships between juvenile gray snapper growth and temperature and salinity using previously collected**  **samples and historical monitoring data, (3) to develop an individual-based bioenergetic model for juvenile** **gray snapper under a range of temperature and salin ity conditions, (4) to recalibrate and validate the bioen**  **ergetic model by comparing predicted growth with observed growth, and (5) to develop a spatially ex**  **plicit model that predicts growth-potential of young snapper throughout Florida Bay under various fresh** 

**w ater flow regimes.** 

UPSTREAM LARVAL SUPPLY TO FLORIDA BA Y—THE DRY TORTUGAS CONNECTION **T his project explores the pathways and transport** **processes for migration of larval fish, shrimp, and lob ster from the Dry Tortugas to Florida Bay. Emphasis is**  **on the role of episodic, mesoscale events, such as those involving eddies and the Tortugas gyre.The hypothe**  **sis to be tested is that the presence of a coastal eddy enhances the influx of presettlement recruits into** **Florida Bay. Densities of incoming recruits in the mid dle and lower Keys during the presence and absence**  **of an eddy are being compared.This is a continuation of a previous south Florida program project for which**  **substantial progress has been made in relating spiny lobster larval transport to eddies and gyres (Yeung**  **et al.,**  **2001). Planned work seeks to determine what hap pens closer to the origin of eddies at the Dry Tortugas** **and lower Keys and the importance of the western re cruitment pathway in connecting the Dry Tortugas**  **with Florida Bay over the southwestern Florida shelf. Coordinated sampling at Southwest Channel in the Dry**  **T**

**ortugas and bayside at Northwest Channel will at tempt to link the newly spawned snapper larvae to sub**  **sequent early-settlement stages.**

A

TLAS OF LIFE HISTORIES OF JUVENILE AND SMALL RESIDENT SPECIES IN FLORIDA BAY **T he atlas will include information on the range, re**  **production, diet, spatial and temporal abundance and distribution, and length-frequency distributions in the**  **bay. This work is being conducted with NMFS base funding.** 

A

TLSS MODEL OF COASTAL WETLAND FISHES **A spatially explicit model of the resident fishes of the coastal wetlands is being developed by Cline**  **et al. (2001) to further explore the relationships determined**  **by Lorenz (2001a,b). The model uses the object-ori**  **ented modeling framework provided by the Across T** 

**rophic Level System Simulation (ATLSS), which is now being applied to the Everglades. Development of the**  **coastal fish model will extend ATLSS into the coastal marshes and provide a basis for expanding the wad**  **ing bird elements of ATLSS into the coastal zone.**



### Unresolved Issues and Questions: Research Needs

**Criteria used to propose future research topics were as follows: (1) follow-up of promising recent research**  **expected to sharpen or broaden answers to Question 5; (2) addressing promising new hypotheses that re** **place failed hypotheses; (3) development of perfor mance measures based on species and communities** **most likely to be affected by CERP changes; and (4) ad dressing gaps in the current program when new in**  **formation suggests higher priority should be assigned. T** **he following series of topic areas fit one or more of these criteria.** 

LOCATION OF NURSERY AREAS OF MAJOR GAME FISH SPECIES **Many sought-after game fish species are found in Florida Bay as preadults and adults, but the current** **nursery grounds of most their populations are not de lineated.This includes red drum, snook, tarpon, bone**  **fish, and gray snapper. Recently, Powell (2003) delineated nursery grounds for spotted seatrout in** **central and western Florida Bay. Colvocoresses (un published data) found red drum juveniles in the East** **River of Little Madeira Bay at a salinity of 6 psu; how**

**ev er, efforts by Powell (2002) to find red drum nursery**  Higher-Trophic-Level Species**grounds in northern Florida Bay were unsuccessful, possibly because the appropriate salinity was not pre**  **sent during sampling. Efforts need to be directed at the southwestern mangrove estuaries of Everglades Na**  **tional Park, the most likely place to find the type of red drum habitat described by Peters and McMichael (1987)**  **( i.e.,**  **low-energy, low-salinity [range = 0–25 psu, mean = 7 psu], turbid, backwater environments “...of a river** **at the head of the bay”). Odum and Heald (1972) col lected many red drum juveniles in the Whitewater**  **Bay system (North River), and this system could be a nursery area for red drum found as adults and sub**  **adults in Florida Bay.Tabb et al.**  **(1962) found early-set tlement-stage bonefish and tarpon in the Buttonwood**  **Canal–Flamingo area.There has been no follow-up to better define the nursery areas of these species. Early**  **settlement-stage snook have not been found south of Chokoloskee (T. Schmidt, personal communication), al**  **though similar habitat appears to occur between Chokoloskee and Cape Sable.The settlement grounds**  **for gray snapper that enter the bay are not well defined, although Rutherford**  **et al. (1989) identified mixed sea**  **grass beds of Syringodium-Thalassia-Halodule**  **in west ern Florida Bay as best settling-out habitats for juvenile**  **gray snapper. The nursery areas of some of these species are likely to be in the front lines of changes** **caused by new water-management structure and op erations.These nursery areas need to be delineated so**  **that the potential effect of water-management changes on salinity patterns, nutrient inputs, and other condi**  **tions in these areas can be predicted.**

INFLUENCE OF HABITAT AND ENVIRONMENTAL VARIABLES ON SPECIES COMPOSITION AND TROPHIC DYNAMICS **T**

**he following nonmutually exclusive hypotheses about factors influencing the abundance and relative abun**  **dance of water column and seagrass canopy species should be explored:** **Hypothesis 1—Density and abundance of bay an cho**  **vy is related to salinity fronts. Hypothesis 2—Density and abundance of canopy**  **species is related to seagrass diversity. Regional trophic-web models should be devel**  **oped to integrate existing and future information on food webs and trophic structure in Florida Bay. Infor**  **mation on water birds and large marine vertebrates (sharks, rays, bottlenose dolphins, and sea turtles)** **should be incorporated into the models.The trophic**

**w eb models should be viewed as precursors to an**  **ecosystem model to be developed in a subsequent funding phase. The work should include the use of** **stable isotope analyses, including use of museum spec imens (assuming the work to develop methods for**  **processing museum material has been completed). Statistical analyses of historical resource survey** **data should be expanded and the results used to de sign and quantify trophic-web and ecosystem models.**  **T he database assembled by Johnson**  **et al. (2001) pro** **vides the opportunity to develop trophic network mod els for Florida Bay. As a result of major differences in**  **the food-web base, separate network models should be prepared for each of the bay’s subregions (Butler**  **et al., 2001b; Chanton**  **et al., 2001; Evans**  **et al., 2001; ). Network** **models previously prepared for the bay by R. Ulanow icz (University of Maryland) and A. Acosta (Florida’s**  **Fish and Wildlife Research Institute) would provide a starting point for a new effort. Acosta (personal com**  **munication) observed that network modeling suffered from a lack of biomass information on benthic organ**  **isms. This is still a serious deficiency, although some data on sponge biomass have been gathered. Mollus**  **can samples collected by W. Lyons and archived at the Fish and Wildlife Research Institute could be used to**  **develop data on molluscan biomass. Analyses and comparisons of trophic structure in the various re**  **gions of the bay could be used to organize information about HTLS and assess effects of salinity changes re**  **sulting from changes in water management.**

FACTORS AFFECTING POSTLARVAL IMMIGRATION

**IMMIGRATION INTO THE BAY’S INTERIOR HTLS researchers, building on the work of physical**  **oceanographers, have gained some knowledge about the pathways, mechanisms, and oceanographic fac** **tors influencing immigration of offshore-spawned lar**

**v ae and postlarvae to the eastern edge of Florida Bay.**  **However, little information exists on physical processes that influence the immigration of postlarvae onto po** **tential nursery grounds in the bay’s interior. This in formation is highly relevant because it would better** **elucidate the ecological importance and potential eco nomic importance of reducing the frequency, dura**  **tion, and intensity of hypersaline conditions in the interior of the bay.To what extent is and how much of**  **the interior of the bay is accessible to offshore-spawned species? What factors cause the accessibility of the** **inner bay to vary? This information would allow re searchers to determine what benefits of improved con**  **ditions might bring to these species. Greater coordination of biological and physical research on**  **the movement of water and early-life stages into the bay’s interior is needed. Physical research in the inte**  **rior of the bay was initiated last year, opening new opportunities for collaboration.**  Hunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 139 Higher-Trophic-Level SpeciesFlorida Bay Synthesis Hunt and Nuttle

140 FWRI Technical Report TR-11 **IMMIGRATION TO FLORIDA BAY Recent research suggests that the major pathway for**  **transport of pink shrimp postlarvae from the Tortugas to Florida Bay may be across the southwestern Florida**  **shelf. Research on larval immigration to Florida Bay nursery grounds from the west is hampered by a lack** **of physical oceanographic work that addresses ques tions biological researchers need to answer. For ex**  **ample, what dynamic, physical structures might enable early-life stages spawned near the Dry Tortugas to** **reach the bay from the west? Net flows across a hypo thetical boundary of the bay stretching from Cape**  **Sable to Marathon have been described (Smith, 2000), but the flow characteristics along the bay boundary**  **(boundary of the bay proper) that stretches from Cape Sable to Long Key are less known. Water movement**  **across this boundary from both the west and the south needs to be studied by oceanographers in integrated** **studies with biologists studying immigration of early life stages onto Florida Bay nursery grounds.** 

EFFECT OF LARVAL BEHAVIOR AND FRESHWATER INFLOW ON LARVAL IMMIGRATION RATES **F reshwater inflow may provide directional cues or oth** **erwise influence the rate of larval immigration from off shore spawning grounds to nearshore nursery grounds.**  **T**

**his topic has not been explored with respect to Florida Bay species since Hughes (1969a,b) conducted experi** **ments suggesting that presettlement pink shrimp post larvae move vertically in the water column in response**  **to salinity gradients. He proposed that this behavioral response resulted in net shoreward transport of post**  **larvae on flood tides. Hughes’results raise questions that have never been addressed regarding the possible role**  **of freshwater inflow in postlarval immigration of pink shrimp and other species: Do the volume and timing**  **of freshwater inflow influence the magnitude of influx of postlarvae to Florida Bay?** 

**EFFECT OF SALINITY ON SURVIVAL AND GROWTH** **Integrated studies that might include models, sup porting field studies, laboratory experiments, and sta**  **tistical analyses should be conducted to determine the relationships between salinity, survival, growth,**  **and other biological processes. For example, the shrimp model should be applied to assessing potential nurs** **ery grounds in the mangrove estuaries of ENP and ex amining the possible effects of alternative management** **strategies on the larger Florida Bay system that in cludes these areas. Another needed application is in** **interpreting juvenile density data in relation to post larval immigration and fisheries data. A spotted**  **seatrout individual-based model should be developed to integrate all the recently acquired new information** **about this species in the bay. Questions about the im pact of hypersaline conditions in the central bay on** 
**y ear-class strength of spotted seatrout need to be ad** **dressed.The lobster model should be expanded to in tegrate new information on salinity tolerance of lobster**  **and living components of lobster habitat. Following up on modeling results, field experiments should attempt** **to quantify the effect on growth and survival of move ments away from undesirable conditions (**  **i.e., h** **yper salinity or hyposalinity).** 

QUANTIFICATION OF SIZE–RELATED PREDATION MORTALITY**Better quantification of size-related predation mor tality is needed to adequately address the effects of**  **salinity on survival through the effect of salinity on growth.This issue is especially pertinent to pink shrimp,**  **spotted seatrout, gray snapper, and lobster. Results are needed to refine and quantify simulation models.** 

EFFECTS OF WATER QUALITY ON SURVIVAL AND GROWTH **T his question has not been specifically addressed in** **current research in Florida Bay. Effects of both nutri ent enrichment and common chemical contaminants**  **on Florida Bay fish and macroinvertebrates may be relevant to determining the effects of changes in water**  **management.**

EFFECTS OF BENTHIC HABITAT ON SETTLEMENT, SURVIVAL, AND GROWTH **W hat characteristics of habitat lead to initial settlement?** **How do characteristics of settlement habitat affect sur vival and growth? How faithful are animals to the lo**  **cation of first settlement? What causes movement and where do animals go? Information on these questions**  **is needed to further refine simulation models.**

IDENTIFICATION OF OTHER SOUTH FLORIDA COASTAL AREAS WITH ENHANCED MERCURY BIOACCUMULATION IN FISH **Previous work (Rumbold et al.,**  **2003) identified the transitional mangrove ecotone in northeastern Florida** **Bay as a region of enhanced mercury and methylmer cury concentrations in water, sediments, and fish. In un**  **published data, Evans found concentrations of mercury in red drum and crevalle jack from Whitewater Bay that** 

**w ere comparable to those found in the same species** **in northeastern Florida Bay.Whitewater Bay is a man grove-dominated embayment just north of western**  **Florida Bay that receives some runoff from the Shark River, an area of known mercury contamination in**  Higher-Trophic-Level SpeciesHunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 141 **fish. It seems likely that other estuarine recipients of Shark River drainage could support fish with high**  **mercury concentrations.The sensitivity of fish from the mangrove ecotone of the entire Ten Thousand Islands**  **complex of southwestern Florida suggests the need for a monitoring program to establish mercury concen**  **trations in susceptible fish species. A research effort to determine the mercury sources and responses to fu** **ture CERP changes in the volume and timing of fresh**

**w ater flows should be made.** 



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# Fish and Wildlife Research Institute T

echnical Report Series

TR-1 **Sargent, F. J., T. J. Leary, D. W. Crewz, and C. R. Kruer. 1995. Scarring of Florida’s Seagrasses: Assessment and Management Options. Florida Marine Research Institute**  **Tec hnical Report TR-1. iv + 37 p. + appendices.** 

TR-2 **W itherington, B. E., and R. E. Martin. 2000. Understanding, Assessing, and Resolving**  **Light-Pollution Problems on Sea Turtle Nesting Beaches. Second Edition, revised. Florida Marine Research Institute Technical Report TR-2. vii + 73 p.** 

TR-2 **W itherington, B. E., and R. E. Martin. 2003. Entendiendo, evaluando y solucionando los**  **problemas de contaminación de luz en playas de anidamiento de tortugas marinas. Florida Marine Research Institute Technical Report TR-2, traducción de la Tercera Edición inglesa,**  **revisada. (In Spanish.) vii + 75 p.** 

TR-3 **Camp, D. K., W. G. Lyons, and T. H. Perkins. 1998. Checklists of Selected Shallow-Water Marine Invertebrates of Florida. Florida Marine Research Institute Technical Report**  **TR-3. xv + 238 p.**

TR-4 **National Oceanic and Atmospheric Administration, Florida Fish and Wildlife Conserva tion Commission, and Florida Keys National Marine Sanctuary. 2000. Benthic Habitats of**  **the Florida Keys. Florida Marine Research Institute Technical Report TR-4. v + 53 p.**

TR-5 **McBride, R. S. 2000. Florida’s Shad and River Herrings ( Alosa**  **species): A Review of P** 

**opulation and Fishery Characteristics. Florida Marine Research Institute Technical Report TR-5. iv + 18 p.** 

TR-6 **Adams, D. H., and R. H. McMichael. 2001. Mercury Levels in Marine and Estuarine Fishes of Florida. Florida Marine Research Institute Technical Report TR-6. ii + 35 p.** 

TR-7 **W eigle, B. L., I. E. Wright, M. Ross, and R. Flamm. 2001. Movements of Radio-Tagged**  **Manatees in Tampa Bay and Along Florida’s West Coast, 1991–1996. Florida Marine Research Institute Technical Report TR-7. ii + 156 p.** 

TR-8 **Wak eford, A. 2001. State of Florida Conservation Plan for Gulf Sturgeon (**  **Acipenser oxyrinchus desotoi**  **). Florida Marine Research Institute Technical Report TR-8. ii + 100 p.**

TR-9 **Adams, D. H., R. H. McMichael, Jr., and G. E. Henderson. 2003. Mercury Levels in Marine**  **and Estuarine Fishes of Florida 1989–2001. Second Edition, Revised. Florida Marine Research Institute Technical Report TR-9. ii + 57 p.** 
TR-10 **McDonald, S. L., and R. O. Flamm. 2006. A Regional Assessment of Florida Manatees**  **( T** 

**richechus manatus latirostris ) and the Caloosahatchee River, Florida. Fish and Wildlife**  **Research Institute Technical Report TR-10. ii + 52 p.**
TR-11 **Hunt, J. H., and W. Nuttle, eds. 2007. Florida Bay Science Program: A Synthesis of Research on Florida Bay. Fish and Wildlife Research Institute Technical Report TR-11.**  **iv + 148 p.**