110 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.**