Looking Ahead

[Background 2](#background)

[Information Needs 2](#information-needs)

[Ecosystem Perspective 4](#ecosystem-perspective)

[Status of Research Program 7](#status-of-research-program)

[Question 1 - Physical Processes 8](#question-1---physical-processes)

[Question 2 - Nutrient Dynamics 10](#question-2---nutrient-dynamics)

[Question 3 - Plankton Blooms 11](#question-3---plankton-blooms)

[Question 4 - Seagrass Ecology 12](#question-4---seagrass-ecology)

[Question 5 - Higher Trophic Levels
13](#question-5---higher-trophic-levels)

[Progress on modeling 14](#progress-on-modeling)

[Focus on Restoration 16](#focus-on-restoration)

[Florida Bay Science Needs 17](#florida-bay-science-needs)

[Science in Ecosystem Restoration 18](#science-in-ecosystem-restoration)

[References 19](#references)

[Appendix: Unresolved Issues/Ongoing Research
20](#appendix-unresolved-issuesongoing-research)

[Physical Processes 20](#physical-processes-1)

[Water Quality 22](#water-quality-1)

[Plankton Blooms 23](#plankton-blooms-1)

[Seagrass Ecology 23](#seagrass-ecology-1)

[Higher Trophic Level Species 24](#higher-trophic-level-species-1)

#   {#section .unnumbered}

# Background

Since 1994, the Florida Bay Science Program has coordinated a program of
ecosystem research designed to shed light on the causes of ecological
changes that occurred in Florida Bay during the late 1980s and early
1990s, most visibly seagrass dieoff and algal blooms. These changes,
believed at the time to be chiefly precipitated by human forces, were
hypothesized to have altered historical patterns of circulation, water
quality and biotic communities in the Bay. The main goal of the Program
has been to understand the major driving processes and their
interactions that were responsible for these changes in the Bay, both
those that can be modified by human actions such as the flows of fresh
water into the Bay, and those solely to forces beyond management control
such as storms and sea level rise. This focus is reflected in the five
strategic questions that organize the research. The more general
objectives of the Florida Bay Science Program have been to develop this
knowledge and combine it with data on biological responses to help
define restoration goals, to predict system response to management
actions, and to establish success criteria.

Adoption of the Comprehensive Everglades Restoration Plan in 2000
establishes ecosystem restoration as the organizing principle for the
management of natural resources in South Florida. In many ways the
objectives and ideas employed by the cooperating agencies to establish
the Florida Bay Science Program have now been adopted as the general
basis for interagency cooperation throughout the region. However, CERP
represents a fundamental change in natural resource management within
which the Florida Bay Science must now function and deliver results.
Adoption of CERP refocuses attention of managers on future ecological
benefits to be achieved through restoration, and it establishes new
mechanisms for regional interagency planning and coordination. These
changes warrant a review of progress by the interagency Florida Bay
Science Program toward specific goals for research and an evaluation of
the Program's approach to pursuing its general objectives.

## Information Needs

The 1997 report of the Science Subgroup (Science Subgroup 1997) captures
the consensus of that time about how changes in quality, quantity,
distribution and timing of freshwater flows affect estuarine and marine
waters. The conceptual model shown in Figure 9.1 summarizes the
hypothesized causal relationships linking these to changes recently
observed in Florida Bay. Ecosystem research provides information needed
by resource managers in three areas: 1) confirm those linkages that are
not understood fully; 2) investigate and describe unrecognized links;
and 3) construct quantitative models managers require for detailed
planning and assessment of restoration projects.

Figure 9.1: General conceptual model linking quantity, quality, timing
and distribution of freshwater flows to observed changes in estuarine
and marine systems (Science Subgroup 1997). Yellow outlines highlight
changes in Florida Bay that were observed in the late 1980s and early
1990s. Connections in the model diagram represent hypothesized causal
links to the environmental effects of human activities, at the top of
the diagram, and to consequences elsewhere in the ecosystem, lower in
the diagram.

![](media/image1.wmf)

In response to this need, the Florida Bay Science Program formulated a
plan to develop and implement a research strategy designed to merge
scientific understanding of the Bay with management's decision-making
process (PMC 1997). Five central questions coordinate ecosystem research
(see box). These questions have continued until the present as the focus
of research. The strategic plan establishes the following additional
principal functions for the Program and describes activities to support
these functions:

-   facilitate a consensus-based process for determining science needs
    and priorities,

-   promote funding of critical science needs,

-   develop and maintain an open and scientifically sound review process
    for evaluating research results and for advancing the research
    program, and

-   communicate research results and program progress to the management
    and scientific community.

The strategic plan envisions that various modeling activities will
integrate results across the Program and deliver these to resource
managers. Conceptual models will synthesize our understanding of Florida
Bay and help formulate critical hypotheses about the Bay's response to
upstream hydrology, water quality or other restoration actions. Model
will identify information needs and assist in prioritizing those needs
and identifying research tasks. Ultimately, numerical models used in a
predictive mode will link research understanding of the Florida Bay
ecosystem to environmental management decisions by predicting the likely
outcomes of various management alternatives on the Bay. These
predictions then become hypotheses about the results of management
actions, which will be testable by observation through monitoring.

## Ecosystem Perspective

Resource managers need to understand the whole of the Florida Bay
ecosystem and its relationship to other ecosystems in South Florida. In
general, the characteristics of an ecosystem reflect the influence of
its regional geomorphic setting, hydrology, oceanography, and climate,
and the dynamic response of physical and biotic components within the
ecosystem to these large-scale driving processes. Geomorphic setting,
the underlying geology and associated geochemistry, serves as the
template on which the ecosystem develops. Climate and associated
environmental processes, especially the water cycle, drive ecological
processes and thus influence the structure and function of the
ecosystem. Singular events, such as large storms, flood, fire, etc. can
cause rapid change or disturbance, and characteristics of the ecosystem
might be defined by the gradual recovery from these events, i.e. through
succession. Human activities influence ecosystem structure and function
both directly and indirectly by altering the processes that drive
ecosystem functioning and by altering the geomorphic setting.

Each of the five central questions examine different characteristics of
Florida Bay and the relation of these to particular driving processes
and attributes of the geomorphic setting, Table 9.1. Similar tables in
the preceding chapters link specific results of the research program
with the ecosystem characteristics and functional relationships
addressed by each central question. Individual research projects
inevitably must focus on component parts and processes within the
ecosystem and the interrelationships between Florida Bay and adjacent
ecosystems. The five central questions distribute the research effort
across the elements of the ecosystem so that results of individual
projects provide the breadth of information needed to characterize the
entire ecosystem.

Questions 1 and 2 investigate the response of the physical and
biogeochemical characteristics of Florida Bay to variations in external,
driving processes. Question 2 also seeks to understand the influence of
nutrient fluxes across the boundaries of the Bay relative to processes
that cycle and redistribute nutrients within the ecosystem.

Questions 3 and 4 investigate the variation in particular
characteristics of the ecosystem, i.e. plankton concentrations in the
water column and the distribution and composition of benthic
communities. In contrast to the first two questions, which can draw on
principles of physics and chemistry to a large degree, Questions 3 and 4
present researchers with challenge to uncover the unknown mechanisms and
related principles that govern the variation in plankton concentrations
and seagrass communities.

Finally, Question 5 investigates how higher trophic level species
respond to changes in ecosystem characteristic that subject of
investigation under the other central questions.

Table 9.1: Topics of ecosystem research in Florida Bay related to each
strategic question

+---------+------------------+---------------------+------------------+
|         | **Driving        | **Ecosystem         | **Geomorphic     |
|         | Processes**      | Characteristics**   | Setting**        |
+---------+------------------+---------------------+------------------+
| **Q     | -   Storms and   | -   Circulation     | -   Connectivity |
| uestion |     wind         |     pattern         |     to reef      |
| 1**     |                  |                     |     tract and    |
|         | -   Changing     | -   Salinity        |     Florida      |
|         |     freshwater   |     pattern         |     Shelf        |
|         |     inflow       |                     |                  |
|         |                  | -   Outflows to     |                  |
|         | -   Sea level    |     adjacent        |                  |
|         |     and tides    |     systems         |                  |
|         |                  |                     |                  |
|         | -   Patterns of  | -   Bathymetry      |                  |
|         |     evaporation  |                     |                  |
|         |     and rainfall |                     |                  |
+---------+------------------+---------------------+------------------+
| **Q     | > Nutrient       | -   Water quality   | -   Regional     |
| uestion | > loading from:  |     and sediment    |     geologic     |
| 2**     |                  |     geochemistry    |     sources and  |
|         | -   Everglades   |                     |     sinks for    |
|         |     runoff       | -   Internal        |     nutrients    |
|         |                  |     nutrient        |                  |
|         | -   Atmosphere   |     cycling, water  |                  |
|         |                  |     column/benthic  |                  |
|         | -   Keys         |     nutrient        |                  |
|         |     wastewater   |     exchanges       |                  |
|         |                  |                     |                  |
|         | -   Groundwater  | -   Nitrogen        |                  |
|         |                  |     fixation        |                  |
|         | -   Adjacent     |                     |                  |
|         |     coastal      |                     |                  |
|         |     waters       |                     |                  |
+---------+------------------+---------------------+------------------+
| **Q     | -   Changes in   | -   Internal        | -   Factors      |
| uestion |     nutrient     |     factors driving |     affecting    |
| 3**     |     loading      |     changes in      |     physical     |
|         |                  |     growth rates,   |     losses of    |
|         | -   Factors      |     grazing and     |     plankton     |
|         |     affecting    |     physical losses |     from the Bay |
|         |     water        |                     |                  |
|         |     residence    | -   Planktonic      |                  |
|         |     time in the  |     algal blooms    |                  |
|         |     Bay          |                     |                  |
|         |                  |                     |                  |
|         | -   Factors      |                     |                  |
|         |     affecting    |                     |                  |
|         |                  |                     |                  |
|         |    sedimentation |                     |                  |
|         |     and          |                     |                  |
|         |     resuspension |                     |                  |
|         |     rates        |                     |                  |
|         |                  |                     |                  |
|         | -   Blooms on    |                     |                  |
|         |     the Florida  |                     |                  |
|         |     Shelf        |                     |                  |
+---------+------------------+---------------------+------------------+
| **Q     | -   Climate,     | -   Seagrass and    | -   Sediment     |
| uestion |     storms       |     hardbottom      |     geochemistry |
| 4**     |                  |     communities     |                  |
|         | -   Fresh water  |                     |                  |
|         |     flow         | -   Temperature and |                  |
|         |                  |     salinity        |                  |
|         | -   Disease      |                     |                  |
|         |                  | -   Light           |                  |
|         |                  |     attenuation     |                  |
|         |                  |                     |                  |
|         |                  | -   Sediment        |                  |
|         |                  |     texture         |                  |
+---------+------------------+---------------------+------------------+
| **Q     | -   Factors      | -   Habitat         | -   Factors      |
| uestion |     driving      |     (salinity,      |     affecting    |
| 5**     |     change in    |     water quality,  |     movement     |
|         |     salinity,    |     benthic         |     between      |
|         |     water        |     habitat)        |     adjacent     |
|         |     quality, and |                     |     systems      |
|         |     benthic      | -   Higher trophic  |                  |
|         |     habitat)     |     level species   |                  |
|         |                  |                     |                  |
|         | -   Factors      |                     |                  |
|         |     affecting    |                     |                  |
|         |     movement     |                     |                  |
|         |     between      |                     |                  |
|         |     adjacent     |                     |                  |
|         |     systems      |                     |                  |
|         |                  |                     |                  |
|         | -   Fishing      |                     |                  |
+---------+------------------+---------------------+------------------+

# Status of Research Program

This section evaluates the degree to which the Florida Bay Science
Program has addressed each of the five central questions and reviews
areas of ongoing research interest identified in the preceding chapters.
The evaluation is based on information in three areas: 1) coverage of
the topic area, 2) the degree of synthesis achieved on the topic, and 3)
progress on development and verification of predictive models. Coverage
of the topic area is judged primarily based on the summary tables
developed for each question that associate individual results, i.e.
citations to journal publications, abstracts, etc., with the components
of the ecosystem, their response to driving factors and interactions
with each other, i.e. Table 9.1. The degree of synthesis achieved is
evaluated based on the hierarchy of "regional information synthesis"
described in NRC (2003, page 69; below), i.e. description, correlation,
mechanistic models, and hybrid simulation models. Model development
generally parallels the degree of synthesis, reflecting the integrative
and synthetic role of modeling. Evaluation draws on the information on
the state of model development on each central question that is included
as part of the preceding chapters.

"Several synthesis approaches that have been used to examine ecosystems
in the past are applicable to the South Florida ecosystem. These include
synthesis of descriptive data, correlations of ecological data with
changes in environmental conditions, mechanistic models to make
large-scale predictions, and a combination of these methods (Hobbie,
2000). Synthesis of descriptive data, the simplest form of synthesis,
might involve descriptions of changes in the characteristics of
ecosystems (e.g. organic matter accumulation) and in physical factors
(e.g. hydroperiod) over time. Statistical correlations between
biological responses and environmental factors may take the form of
periphyton response to phosphorous loading. \[\...\] Mechanistic
simulation models could be used to predict a single process (e.g., rate
of mercury methylation) or interrelated processes (e.g. wading bird
nesting coupled with a hydrological model). Sophisticated models that
combine simulation modeling with descriptive and correlative methods are
also possible -- e.g., the Everglades Landscape Model
([www.sfwmd.gov/org/wrp/elm/](http://www.sfwmd.gov/org/wrp/elm/)), which
combines hydrodynamics, nutrient transformations, and translocation with
plant production and community composition responses. Each of these
approaches offers opportunities to enhance our understanding of the
complex interactions of the physical, chemical, and biological factors
that characterize the greater Everglades ecosystem, ultimately
facilitating factors South Florida restoration activities by reducing
uncertainties about overall ecosystem response."

-   quoted from Box 5-2, Tools for Learning; NRC 2003

## Question 1 - Physical Processes

How and at what rates do storms, changing freshwater flows, sea level
rise, and local evaporation/precipitation influence circulation and
salinity patterns within Florida Bay and outflows from the Bay to
adjacent waters?

### Coverage of topic

Research and monitoring of physical processes covers the driving
processes (i.e. winds and storms, precipitation, evaporation, surface
water inflow, groundwater, sea level and tides, and boundary currents)
and characteristics of the ecosystem (i.e. salinity patterns,
circulation patterns, and exchanges with adjacent waters). Some data
exist on each of the driving processes and ecosystem characteristics.
More work remains to fully characterize groundwater and evaporation. For
both, the available flux estimates vary over a significant range of
values. In the case of groundwater, a mechanistic model has yet to
emerge that can explain the magnitude of groundwater discharge to the
Bay that has been reported in the peer-reviewed literature. Elsewhere,
basic measurements of bathymetry, depth, and flow still have yet to be
done across the extensive mud banks that divide the inner portion of
Florida Bay.

Work remains to analyze the sensitivity of ecosystem characteristics to
the different forcing factors. On going observations and monitoring
aimed at constructing water and salt budgets for the Central region will
address this deficiency, but results are still preliminary. Meanwhile,
little attention has been paid to investigating the influence of sea
level fluctuations on circulation patterns and residence time in the
inner portion of Florida Bay. Sea level fluctuates about 20 cm within a
normal year. This represents a substantial change in the depth of the
water column for shallow portions of the Bay, such as the Central
region, and thus it can be expected to affect circulation and flushing.

### Level of synthesis

+----------------+-----------------------------------------------------+
| *              | ***Salinity*** -- paleoecological data and          |
| *Description** | historical data have been compiled and analyzed for |
|                | trends in salinity and variation in salinity        |
|                |                                                     |
|                | ***Circulation and Exchange*** -- ongoing           |
|                | monitoring on shelf region west of Florida Bay with |
|                | current meters and drifters, sporadic data exist    |
|                | for currents in passes between Keys and deeper cuts |
|                | within Florida Bay                                  |
|                |                                                     |
|                | ***Driving processes*** -- monitoring data on all   |
|                | except groundwater discharge and evaporation        |
|                |                                                     |
|                | ***Bathymetry*** -- lacking information on          |
|                | elevation (depth) of bank tops                      |
+----------------+-----------------------------------------------------+
| #              | ***Coastal oceanography*** -- correlation of        |
| ## Correlation | current patterns with seasonal winds                |
|                |                                                     |
|                | ***Salinity*** -- regression and time series models |
|                | link salinity with characteristics of Everglades    |
|                | hydrology on both long-term (paleoecological data)  |
|                | and short-term.                                     |
|                |                                                     |
|                | ***Sea level*** -- remains to be investigated,      |
|                | other combinations of driving processes and         |
|                | ecosystem characteristics are thought to not be     |
|                | significant based on physical reasoning.            |
+----------------+-----------------------------------------------------+
| ### Mech       | ***Salinity** --* mass balance models link salinity |
| anistic models | variation with net freshwater supply, including     |
|                | effects of runoff and evaporation -- but not        |
|                | groundwater. Understanding of the physical          |
|                | mechanisms that might support measured groundwater  |
|                | discharge rates is lacking.                         |
|                |                                                     |
|                | ***Circulation and exchange*** -- confident that    |
|                | physical mechanisms operating in other estuaries    |
|                | apply to Florida Bay, but there is not a generally  |
|                | accepted implementation of a hydrodynamic model for |
|                | the Bay.                                            |
|                |                                                     |
|                | ***Groundwater*** -- lacking an understanding of    |
|                | the physical mechanisms driving groundwater         |
|                | discharge into Bay except in case where differences |
|                | in head between the Bay and the Atlantic drive flow |
|                | under the Keys.                                     |
+----------------+-----------------------------------------------------+
| ### Sim        | (none)                                              |
| ulation models |                                                     |
+----------------+-----------------------------------------------------+

## Question 2 - Nutrient Dynamics

*What is the relative importance of the influx of external nutrients and
of internal nutrient cycling in determining the nutrient budget for
Florida Bay? What mechanisms control the sources and sinks of the Bay's
nutrients?*

### Coverage of topic

Some information has been developed on each the major components of the
nitrogen and phosphorous budgets of the inner portion of Florida Bay.
This provides a context for judging the influence of some nutrient
sources that have been seen as threatening the health of the Bay, such
as wastewater discharges from the Keys. However, uncertainty in
estimates of the larger fluxes and lack on information on their temporal
variation hampers our understanding of the significance and possible
role of other nutrient sources, such as in surface water discharge from
the Everglades and in groundwater. Information on internal nutrient
cycling has not yet been integrated with information on the Bay's
nutrient budget. The influence of seagrass community (composition and
density) and higher trophic level species (e.g. sponges) on nutrient
fluxes and internal cycling has not been determined.

### Level of synthesis

+----------------+-----------------------------------------------------+
| *              | ***Water quality*** -- extensive water quality      |
| *Description** | monitoring data exist, and these have been analyzed |
|                | to describe temporal trends and "zones of similar   |
|                | influence." There is some paleoecological data      |
|                | indicating a trend of increasing nutrients in the   |
|                | Bay since about 1980.                               |
|                |                                                     |
|                | ***Nutrient cycles*** -- work is still underway to  |
|                | describe major pathways, fluxes, rates of           |
|                | transformation and associated nutrient species in   |
|                | Florida Bay and in the adjacent mangrove wetlands.  |
+----------------+-----------------------------------------------------+
| *              | ***Everglades runoff*** -- analysis of nutrient     |
| *Correlation** | concentration/loading as a function of freshwater   |
|                | discharge has been done as part of work to          |
|                | investigate metabolism of coastal mangroves.        |
|                |                                                     |
|                | ***Eutrophication*** -- one hypothesis to explain   |
|                | plankton blooms invokes increased nutrient loading  |
|                | with increased inflow of freshwater through the     |
|                | 1980s and 1990s. This is supported by correlative   |
|                | arguments, but these correlations have yet to be    |
|                | tested rigorously.                                  |
+----------------+-----------------------------------------------------+
| **Mechanistic  | Mechanistic models of nutrient cycles are being     |
| models**       | formulated and investigated as part of the FCLTER   |
|                | research. Beyond this, little has been done to      |
|                | formulate and test mechanistic models that might be |
|                | able to explain the variation in water quality      |
|                | documented in the monitoring data.                  |
+----------------+-----------------------------------------------------+
| **Simulation   | Preliminary work has been done to adapt and         |
| models**       | calibrate a water quality model that supports       |
|                | simulation of plankton blooms and seagrass (Cerco   |
|                | 2000). Lacking supporting information from a        |
|                | coupled hydrodynamic model, this model cannot be    |
|                | fully calibrated and verified.                      |
+----------------+-----------------------------------------------------+

## Question 3 - Plankton Blooms

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

### Coverage of topic

Much of the work in this area has focused on the various effects of
nutrients either as the trigger for blooms or on nutrient limitations to
growth. Research describes the regional characteristics of plankton
blooms in Florida Bay and on the Florida Shelf west of the Bay,
including the dynamics of the \~annual bloom cycle in the Central and
West regions. Understanding the causes and dynamics of the apparent
sudden onset of intense blooms in the early 1990s remains speculative.
It is not possible to choose from among several hypotheses about the
cause of this phenomenon based on the results of research so far.
Research has not investigated the possible influence of variable grazing
rates and/or flushing (or residence time) on bloom occurrence and
intensity in Florida Bay.

### Level of synthesis

+----------------+-----------------------------------------------------+
| *              | ***Trends** --* Water quality monitoring data       |
| *Description** | documents the timing and general extent of bloom    |
|                | phenomenon over the last 10 years or so.            |
|                | Paleoecological data documents possible periods of  |
|                | intense blooms as long ago as the early 1800s.      |
|                |                                                     |
|                | ***Species composition** --* Research characterizes |
|                | the different characteristics of blooms in the      |
|                | Central and West regions. Included are results      |
|                | documenting difference among dominant species in    |
|                | terms of nutrient uptake and growth rates.          |
+----------------+-----------------------------------------------------+
| *              | No results reported for correlative studies linking |
| *Correlation** | the onset and/or peak concentrations of blooms to   |
|                | water quality characteristics or to variation in    |
|                | driving processes.                                  |
+----------------+-----------------------------------------------------+
| **Mechanistic  | ***Bloom and plume*** -- quantitative research      |
| models**       | relates onset of bloom on Florida Shelf to a        |
|                | trigger provided by the input of silica in Shark    |
|                | River flow.                                         |
|                |                                                     |
|                | ***Central region*** -- results demonstrating the   |
|                | dominance of Synecocus in the Central region leads  |
|                | to a mechanistic model for this bloom based on some |
|                | of the unique characteristics of Synecocus, i.e.    |
|                | high nutrient uptake at low concentrations and      |
|                | variable buoyancy, but this model has not be tested |
|                | quantitatively.                                     |
|                |                                                     |
|                | ***Onset, persistence and fate*** -- general        |
|                | mechanistic model that blooms result from an        |
|                | imbalance between growth rate and losses due to     |
|                | grazing and flushing is invoked, but this model has |
|                | not been used quantitatively to investigate the     |
|                | observed dynamics of blooms in Florida Bay.         |
+----------------+-----------------------------------------------------+
| **Simulation   | Plankton is included as a component of the water    |
| models**       | quality model by Cerco (2000), but it is not known  |
|                | whether the mechanics of Cerco's model are          |
|                | consistent with either the detailed observations of |
|                | blooms in Florida Bay and the interpretation of     |
|                | these observations.                                 |
+----------------+-----------------------------------------------------+

##  Question 4 - Seagrass Ecology

What are the causes and mechanisms for the observed changes in seagrass
community of Florida Bay? What is the effect of changing salinity, light
and nutrient regimes on these communities?

### Coverage of topic

Research has documented the patterns and extent of dieoff associated
with the event that began in the late 1980s, recovery of seagrass
communities following that event, and the occurrence of several recent,
but more limited, occurrences of dieoff. Two complementary conceptual
models have been developed to explain the course of the original dieoff
event and conditions in the ecosystem leading up to and following the
event. Focused research has tested various elements of these models,
confirming some (e.g. sulfide stress contributing to primary dieoff) and
limiting the role of others (e.g. labyrinthula infection limited by
salinity). A seagrass unit (i.e. plot-scale growth and metabolism) model
is under development by two groups (Madden and Burd). Results of this
research should provide a quantitative test of the conceptual models for
dieoff; however these results are not reported as part of the synthesis
document. Research has yet to address some plant metabolic and community
responses to conditions in the ecosystem, such as sediment
characteristics, water temperature, salinity and light levels.

### Level of synthesis

#### 

+----------------+-----------------------------------------------------+
| *              | FHAP surveys of seagrass occurrence and             |
| *Description** | composition.                                        |
|                |                                                     |
|                | Zieman ongoing monitoring of seagrass               |
|                | growth/productivity at selected field sites.        |
|                |                                                     |
|                | Results of paleoecological studies suggest that     |
|                | seagrass periods of seagrass cover have alternated  |
|                | with periods of no seagrass over the last 100 years |
|                | or so at several sites studied in the Bay.          |
+----------------+-----------------------------------------------------+
| #              | Fourqurean model correlates community composition   |
| ## Correlation | with water quality characteristics.                 |
|                |                                                     |
|                | Zieman et al 1999 correlate changes in productivity |
|                | with environmental conditions                       |
+----------------+-----------------------------------------------------+
| ### Mech       | Unit models under development, but results not      |
| anistic models | provided in synthesis.                              |
+----------------+-----------------------------------------------------+
| ### Sim        | Landscape model under development.                  |
| ulation models |                                                     |
+----------------+-----------------------------------------------------+

##  

## Question 5 - Higher Trophic Levels

What is the relationship between environmental and habitat change and
the recruitment, growth, and survivorship of animals in Florida Bay?

### Coverage of topic

The potential scope of research on higher trophic level species in
Florida Bay is almost open ended. To limit the scope in a rational way,
research is limited to a set of species for which sufficient survey data
exist to begin immediately to answer questions about the influence of
environmental conditions in the ecosystem on species abundance and
community structure. For a few key species, research provides a fairly
complete coverage of issues raised by the central question, e.g. pink
shrimp. For other species, the analysis of available research results is
still underway.

### Level of synthesis

+----------------+-----------------------------------------------------+
| #              | In general, the data on higher trophic level        |
| ## Descriptive | species are sparse and usually highly variable.     |
|                | Therefore, simple description of the data holds     |
|                | little potential for progress on the question, and  |
|                | correlative studies are the primary level at which  |
|                | synthesis occurs.                                   |
+----------------+-----------------------------------------------------+
| #              | A large amount of work on correlative studies for a |
| ## Correlation | number of species and communities. Much of this     |
|                | work is summarized in Table 7.1.                    |
+----------------+-----------------------------------------------------+
| ### Mech       | Mechanistic models have been investigated for       |
| anistic Models | individual growth and survival response to salinity |
|                | and temperature, sometimes in combination with      |
|                | available habitat. In a few cases, such as shrimp   |
|                | and lobster, these individual-based models have     |
|                | been aggregated to investigate population response  |
|                | to changing conditions in the ecosystem. Mechanisms |
|                | controlling the recruitment (transport) of larvae   |
|                | into Florida Bay have been investigated.            |
+----------------+-----------------------------------------------------+
| ### Sim        | In the case of shrimp (and lobster) the aggregated, |
| ulation Models | population-level models have been driven by simple, |
|                | regression-base models linking Everglades hydrology |
|                | to salinity in the Bay, and these hybrid models     |
|                | have been used to investigate the sensitivity of    |
|                | the population (i.e. fishery yield) to water        |
|                | management activities.                              |
+----------------+-----------------------------------------------------+

## Progress on modeling

### Physical Processes

Although still not available as a management tool, steady progress has
been made toward developing a predictive capability for salinity and
circulation changes in Florida Bay and connecting coastal waters as
follows:

-   2-D hydrodynamic models with coarse grids have been developed for
    Florida Bay as pilot projects by J. Wang (finite element) and J.
    Hamerick (finite difference) that show encouraging salinity pattern
    results that are similar to observations.

-   Better estimates of surface and ground water inflows are available
    from the recent measurements and hydraulic model results of USGS and
    SFWMD.

-   Improved estimates of evaporation are available from recent studies
    by R. Price, P. Swart, W. Nuttle, and N. Smith.

-   Improved estimates of precipitation patterns and quantities are
    available from calibrated NEXRAD measurements (P. Willis).

-   Measurements of interior basin circulation and exchange processes
    are available to improve understanding of Bay dynamics, quantify
    residence times and help validate and improve hydrodynamic models
    (T. Lee, E. Johns, V. Kourafalou, and N. Smith).

-   Modeling Terms of Reference were established by the PST and approved
    by the PMC.

-   A Standard Data Set has been established for model use (J. Pica).

-   An interagency nested model program has been formulated using
    regional hydrodynamic and hydrological models to provide boundary
    conditions for the Florida Bay model (SFWMD, NOAA, USGS).

### Water Quality

The water quality model (Cerco et al. 2000; Fig. 5.14 and 5.15) linked
modules including water-column eutrophication, seagrass dynamics,
sediment diagenesis, solids and nutrient resuspension, and benthic algal
production. To our knowledge, this is a first for Florida Bay. In fact,
we know of few systems that presently have a model application to rival
the current effort in Florida Bay. The model does require substantial
upgrading, however, to fully represent processes in the Bay.

Interpretation of results from the water quality model was severely
compromised by lack of a verified hydrodynamic model operable on the
same time scale as the water quality model. The major uncertainty in the
system nutrient budget is transport across the western boundary and
through the Keys passes.

### Plankton Blooms

This simulation model will be a component of a water quality model.

### Seagrass Ecology

Statistical modeling was commissioned by the Restudy consistent with
recommendations from the 1998 Seagrass Modeling Workshop (Fourqurean et
al. in press). The goal of this work is to seek relationships between
water quality variables and seagrass species composition and abundance,
which if sufficiently strong, can be used to predict the effects of
various alterations in Florida Bay salinity regimes. The statistical
models developed in this project will be used in conjunction with output
from other models to predict the effects of Restudy scenarios on the
benthic habitats of Florida Bay. The statistical model will not address
mechanisms or degree of change in water quality that result from Restudy
scenarios; other models (like the NSM, FATHOM, and the Florida Bay
salinity transfer function models currently employed by the Restudy)
must simulate water quality changes across Florida Bay that will provide
the input to the new models developed in this project. As a consequence,
it is anticipated that the benthic habitat change predictions of the
statistical models will be the most reliable in the regions most closely
coupled with water management practices, i.e. in the enclosed,
mangrove-lined estuaries on the fringe of Florida Bay.

In addition, other seagrass modeling efforts have recently been
initiated. These include the development of both seagrass unit models
for *Thalassia* and *Halodule* and a landscape model that will take
output from the unit models.

### Higher Trophic Level Species

Two 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 incorporating population dynamics, to
examine the sensitivity of individual organisms to varying
characteristics of their habitat, such as bottom cover and salinity.

Statistical Models

#### Exploratory General Additive Models

Johnson et al. (2001, 2002a, 2002b) assembled a database for Florida Bay
that integrated six independent forage fish/macro-invertebrate studies
conducted between 1974-1997. General additive models were used to
determine which major forcing functions and habitat factors control
their abundance and distribution. Hindcasts of density distributions
across the Bay were made with these models and used to compare density,
biomass, and evenness in wet seasons and dry seasons of a representative
wet (1995) and dry (1991) year.

#### 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 monitoring well P35.
Later Sheridan (1996) developed a statistical model that related annual
Tortugas catches to Everglades well and rainfall data, as well as air
temperature and Key West sea level, the previous spring and summer. The
Sheridan model, which was updated every year with new data, successfully
predicted Tortugas catches for the upcoming year for a number of years.

More recently, Browder (2000) developed a statistical model relating
annual average Tortugas catch rates to the rainfall of several prior
months. A second empirical model was prepared (Browder 2000) to test
alternative configurations of the water management system proposed in
the "Restudy" that developed the Comprehensive Everglades Restoration
Project. This model related Tortugas catch rates of recently recruited
shrimp to releases of fresh water into Everglades National Park at its
northern boundary immediately downstream from the leveed Everglades
Water Conservation 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 temperature and salinity in Florida Bay
    (Browder et al. 1999). The model was recently refined with data from
    new laboratory experiments (Browder et al. 2002). A spatially
    explicit individual-based model for Caribbean spiny lobster
    (Panulirus argus) was developed 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
    recruitment of a massive loss of nursery habitat structure due to a
    sponge die-off (Butler et al. in press), (2) the

-   Table 7.1: Summary of forage fish models and significant factors
    consequences of temporal and spatial variation in post larval supply
    on recruitment (Butler et al. 2001), (3) the effect of nursery
    habitat structure and geographic specificity on recruitment (Butler
    et al. 2001), and (4) the direct and indirect consequences of
    altered salinity on recruitment (M. Butler, pers. comm.).

-   Richards (in prep.) examined the relationships between temperature
    and salinity and growth rate in crocodiles (Crocodylus acutus), by
    tracking 30 radio-tagged hatchlings in the vicinity of the Turkey
    Point Power Plant for up to several weeks.

-   Substantial progress has been made in the development of a
    bioenergetically based individual larval spotted seatrout model to
    simulate metabolic rate, consumption, and growth as a function of
    temperature and salinity (Wuenschel 2001).

-   A spatially explicit prey-predator model for spotted seatrout and
    pink shrimp coupled to physical processes was developed for Biscayne
    Bay (Ault et al. 1999; Ault et al. 2003; Wang et al. 2003). The
    spotted seatrout component of the model was individual-based.

# Focus on Restoration

What role can the Florida Bay Science Program play in the restoration of
the Bay and in CERP? What information on the ecosystem will be most
useful to resource managers, and what should the Program do to develop
this information and deliver it to the resource managers in the
cooperating agencies and to the interagency groups established to guide
CERP?

Restoration focuses attention on the relationship of Florida Bay to
Everglades hydrology and on evaluating the effects of alternative water
management practices. The Working Group of the Interagency Task Force
identifies three overarching goals that guide ecosystem restoration in
South Florida. These are 1) get the water right, 2) restore and enhance
the natural system, and 3) transform the built environment (Working
Group 1998). The most important goal for restoration of Florida Bay and
adjacent marine systems is to get the water right. This means providing
freshwater flows with the right quality, quantity, timing and spatial
distribution. Determining the "right" quantity, quality, timing, and
distribution of freshwater will require specific scientific information.
Goals for restoration define the need for scientific information;
however the specific information that is needed will change over time as
restoration progresses and our understanding of the natural systems
increases.

This section compiles information about the restoration of Florida Bay
and research needs associated with it. Ecosystem restoration in South
Florida will affect Florida Bay in specific ways. These anticipated
effects point to areas where research can be particularly helpful
setting goals, reducing uncertainties, and documenting restoration
progress. The approach of adaptive management, which has been adopted to
guide restoration, establishes these roles for research and monitoring
as part of a new relationship between resource management and research
that is still evolving.

## Florida Bay Science Needs

A committee of the National Research Council (NRC 2002) identified
anticipated impacts of Everglades restoration on Florida Bay as part of
its examination of the role of the Florida Bay Science Program in
relation to CERP. Principal among these impacts are the following: 1)
increased freshwater flow reaching Florida Bay from the Everglades,
albeit from Shark Slough via a coastal current around Cape Sable rather
than through Taylor Slough; 2) increased loading of nitrogen associated
with freshwater from the Everglades and leading to more frequent and/or
more intense plankton blooms; and 3) resulting perturbation of seagrass
communities and decreased water clarity. This committee recommends that
a focused technical review should be carried out to evaluate these
potential impacts on the Florida Bay ecosystem more fully.

In order to support such a review and evaluation, the NRC committee (NRC
2002) identifies the following areas of needed research:

-   better information on components of the water budget for the Bay, in
    particular on groundwater discharge and surface water runoff;

-   information on the effects on nitrogen and phosphorous fluxes to the
    Bay of anticipated changes in the distribution and amount of
    freshwater runoff in the Taylor Slough/Craighead basin and in Shark
    Slough;

-   better understanding of nutrient loads contributed from different
    sources and of the bioavailability of these nutrients;

-   historical characterization of the Bay's water quality drawing on a
    variety of information sources, such as anecdotal accounts;

-   development and application of a hydrodynamic circulation model and
    a water quality model for the Bay;

-   application of statistical, time-series and "box model" mass balance
    calculations to estimate the influence of CERP projects on Florida
    Bay;

-   better definition of the potential effects on the ecosystem of
    "distant drivers" that are unrelated to, and largely beyond the
    influence of, CERP activities; these include phenomenon such as
    hurricanes, sea level rise, population growth, economic activities,
    etc.

Finally, the NRC (2002) report recommends that cooperating agencies
adopt a more formal approach to managing ecosystem research and
integrating the research with resource management. In particular, the
committee calls on agencies to execute a formal agreement that
identifies one modeling approach, from among several potential
approaches, that will function as the interface between the regional
hydrology model that supports restoration and water resource planning in
South Florida and a hydrodynamic model in Florida Bay.

## Science in Ecosystem Restoration

Stepping back from these specific research needs, another NRC committee
(NRC 2003) has reviewed the different ways in which scientific
information contributes to ecosystem restoration. This report is the
result of the Critical Ecosystem Studies Initiative, conducted in South
Florida by the Department of Interior, but it draws on experience
elsewhere in the United States (e.g. the Grand Canyon) for information
on the broader role of research and monitoring in ecosystem restoration.
Science contributes to defining restoration goals, conceptualizing (i.e.
modeling) the ecosystem, and as a tool for institutional learning and
the integration of new knowledge into ongoing restoration efforts. This
report also discusses some of the challenges that arise from the
conflict between objectives for research on one hand and on the other
decision-making related to water system design and management.

Science has already made significant contributions to restoration
decision-making in South Florida. Integrative environmental science has
injected essential new information, for example about water quality
requirements to maintain the Everglades ecosystem, into the relatively
staid, conservative practice of water management that prevailed just a
few years ago. Scientific information from monitoring that documents the
conditions and trends in the region's ecosystems have been persuasive at
key junctures in motivating a response to emerging problems and in
decisions on how to address these problems. In addition, the widely used
device of peer-review has been adopted to support management decision
making by assuring the quality of available information and analytical
tools. The present structure of the Florida Bay Science program reflects
an appreciation of these contributions and the intent to secure similar
benefits for the management of Florida Bay and adjacent marine systems.

The NRC (2003) report on the CESI program and a contemporaneous report
by GAO (2003) on science coordination in South Florida both make
recommendations on how to improve the management of research for
restoration and the application of the results of research and
monitoring to resource management activities, including CERP. These
recommendations call for more centralized and independent management of
the combined interagency science effort in the region. Both view
RECOVER, the coordinating body for research and monitoring within CERP,
as one component in a more comprehensive restoration and natural
resources science program. In light of these recommendations, it is
unclear what will be the future for the Florida Bay Science Program as a
distinct interagency effort. However, in the meantime as this future
unfolds the information contained in these recent reports (NRC 2002,
2003 and GAO 2003) can be used to help focus the interagency research in
Florida Bay on topics that are most relevant to ecosystem restoration in
South Florida.

# References

GAO, 2003. South Florida Ecosystem Restoration: Task Force Needs to
Improve Science Coordination to Increase the Likelihood of Success.
United States General Accounting Office, Washington D.C.

NRC, 2002. Florida Bay Research Programs and Their Relation to the
Comprehensive Everglades Restoration Plan. National Academies Press,
Washington, D.C. 53 pages.

NRC, 2003. Science and the Greater Everglades Ecosystem Restoration.
National Academies Press, Washington, D.C. 168 pages.

PMC 1997. Strategic Plan for the Interagency Florida Bay Science Program

Science Subgroup. 1997. Ecologic and Precursor Success Criteria for
South Florida Ecosystem Restoration. Report to the Working Group of the
South Florida Ecosystem Restoration Task Force.
*http://everglades.fiu.edu/taskforce/precursor/toc.html*

Science Subgroup. 1996. South Florida Ecosystem Restoration: Scientific
Information Needs. Report to the Working Group of the South Florida
Ecosystem Restoration Task Force.

*http://everglades.fiu.edu/taskforce/scineeds/index.html*

Working Group. 1998. Success in the Making: An Integrated Plan for South
Florida Ecosystem Restoration and Sustainability. South Florida
Ecosystem Restoration Task Force.

[*http://www.sfrestore.org/documents/success/01.htm*](http://www.sfrestore.org/documents/success/01.htm)

# Appendix: Unresolved Issues/Ongoing Research

The following is a synopsis of information on unresolved issues and
ongoing research from the chapters dedicated to each central question.

## Physical Processes

### Winds and Storms

A number of questions remain: What are the long-term effects of the
daily development of convergent wind patterns over the Bay? What are the
magnitudes and spatial and temporal scales of this mesoscale wind
forcing? How does it influence the south Florida seascape in terms of
water levels, evaporation and precipitation patterns, circulation and
exchange between water bodies, and surface and groundwater inflows to
the Bay? What is the effect of winds on residence times of the interior
waters of the Bay? It is not clear what changes may occur from intense
cyclones, nor how long these changes may persist. Predictive modeling of
different classes of tropical cyclones is needed to anticipate these
impacts.

### Precipitation

Do the spatial patterns of Bay surface salinities measurably change as a
result of the heterogeneity of precipitation? To what degree has
precipitation over the Bay been changing because of land use changes on
the peninsula?

### Evaporation

What is the mean rate of evaporation in Florida Bay? What is the spatial
and temporal variation of evaporation? How reliable are long-term
estimates of evaporation? How much additional precision can be gained by
refinement of stable isotope methods? Other questions regarding
evaporation include: To what degree does the seasonality of evaporation
need to be considered in evaluating the effect upon salinity patterns of
different water management scenarios? What is the effect of the Bay's
bank and basin topography upon evaporation? The rate of evaporation over
the extensive, shallow banks may be different from the average estimates
used to date.

### Surface water inputs 

Simulation models under construction by the United States Geological
Survey (USGS) and the SFWMD in conjunction with their ongoing
measurement programs are expected to resolve any remaining uncertainty
concerning surface water discharges into Florida Bay.

### Groundwater inputs

Clearly many unresolved questions remain concerning not only the
absolute amount of groundwater input to Florida Bay but also its
temporal and spatial variability and the resulting salt and nutrient
flux. The consensus at present is that the water quality implications of
groundwater input from either the southern Everglades or Florida Keys
may be more significant than its physical consequence unless the larger
estimates prove to be correct.

### Sea level and Tides

No major unresolved issues remain concerning tides. Studies are underway
concerning the effects of sea level differences on inter-basin exchange
and upon flow through the passages between the Florida Keys. It is also
not clear how long-term sea level differences between the Gulf and
Atlantic affect the observed mean southeastward flow that transports
water to the Florida Keys reef tract.

The depth over many of the banks is approximately equal to or less than
the range of seasonal fluctuations in mean sea level. What consequences
might this have for rates and patterns of inter-basin water exchange in
the interior portion of the Bay? What are the rates and pathways of
exchange between the interior basins and across the banks in the
western, central, and eastern regions of Florida Bay and with the
southwest Florida shelf?

### Salinity 

Although the spatial and temporal variability of salinity in Florida Bay
is well documented and continues to be monitored both with field surveys
and fixed instruments, a number of unresolved questions remain, such as:
How is the salinity of Florida Bay influenced by atmospheric forcing on
time scales from daily to inter-decadal, including significant transient
meteorological events such as hurricanes and tropical storms? How do the
spatial patterns of evaporation, precipitation and basin residence time
affect Bay salinity distributions? For example, does hypersalinity occur
where it does because evaporation is greater over broad shallow banks
than in the rest of the Bay, or because exchange with lower salinity
water is restricted? How do the salinity records inferred from
paleoecological data compare with salinity values measured over the past
45 years? Is there a statistical transfer function sufficient to
adequately describe the effect of fresh water flows on salinity for the
purposes of predicting the effect of restoration scenarios upon Bay
salinity? If so, over what spatial domain does it apply?

### Circulation

A better understanding of flow across banks, and bank characteristics in
general (e.g. cover, elevation, salinity, and temperature), will be
necessary for successful hydrodynamic and ecological modeling of the Bay
interior.

It is essential to better describe and understand the net southward flow
that couples the eastern Gulf and Atlantic coastal region of the Keys in
order to aid future model development and facilitate informed management
decisions. What is the influence of the Loop Current or synoptic winds
over the west Florida shelf on driving this flow? Are topographic
constraints on the southwest Florida shelf important? How is the flow
related to observed southward flows farther north on the west Florida
shelf that appear to diverge away from the coast before reaching the
southwest shelf (Yang et al., 1999)?

### Exchanges with Adjacent Waters

There is evidence from the large-scale hydrographic surveys that at
times these high salinity waters can form a near-bottom salty layer in
the Hawk Channel region. However, very little is known about this
process. How are the salty bottom layers formed? What are their spatial
extent and transport pathways? What are their durations?

Transports across the western boundary are very uncertain at this time;
however, field research is planned to improve understanding of transport
processes and help quantify this exchange. Can the bank \"overtopping\"
process explain the observed net outflow from the central part of the
Bay.

More effort is needed to quantify and monitor Mean Gulf to Atlantic
flows through western Florida Bay to the Keys coastal zone to better
understand the physical processes involved. Is it related to the
position and configuration of the Loop Current as Gulf models and
satellite observations suggest? Coupling of a large-scale model that
includes the Gulf and Straits of Florida to a finer scale Florida Bay
model is needed to address this issue.

## Water Quality

We need to accurately predict the sensitivity of the Bay\'s nutrient
cycles to changing fresh water flow to the Bay, and the resultant change
in the Bay\'s salinity regime. For much of the Bay, any factor that
increases P availability either by increasing sources or decreasing
removal is likely to exacerbate the current problems of the Bay. We also
need thorough understanding of the Bay\'s nutrient cycles, particularly
with regard to the fate and effects of dissolved organic nitrogen inputs
from the Everglades. Questions that the future program should address in
order to meet these needs are as follows.

1\. What are the sources of nutrients that sustain algal blooms?

2\. How will changing fresh water flow directly and indirectly alter the
supply and availability of nutrients in the Bay? What effect does
changing salinity have on nutrient availability in the Bay?

-   How will the quality and quantity of nutrient outputs from the
    Everglades change with restoration?

-   What is the fate and effect of dissolved organic matter from the
    Everglades and how will this change with restoration?

-   What effect does changing salinity have on nutrient cycling and
    availability in the Bay?

3\. What effect does a change in seagrass community structure have on
nutrient availability in the Bay? Has seagrass mortality only increased
nutrient availability by releasing nutrients from this detrital source,
or has seagrass mortality also caused other less direct changes, such as
a decrease in the capacity of the sediments to sequester nutrients?

4\. How do we deal with the spatial heterogeneity of internal nutrient
cycling in the Bay?

5\. What is the quantitative role of microphytobenthos in nutrient
cycling and how is this likely to change with Everglades restoration?

6\. To what extent is atmospheric deposition of nutrients contributing
to ecological changes in Florida Bay? What is temporal variability
(including long-term trend) of this nutrient source?

7\. Is ground water an important nutrient source in Florida Bay? If so,
what is the spatial and temporal pattern of this input?

### Summary of Ongoing Research

1.  Continued monitoring of ambient water quality in Florida Bay

```{=html}
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```
1.  Continued monitoring of freshwater inflows and loads with expansion
    of network along Florida Bay and southwest Florida/Gulf coast
    beginning

2.  Continued monitoring of coastal circulation and biological and
    chemical parameters, with interpretation of transport and exchange
    of South Florida coastal waters

3.  Expanded research into nutrient cycling in wetland/mangrove areas
    and seagrasses/epiphytes

4.  Study of carbonate system - P - Fe relations

5.  Characterization of chemical structure of organic C and N from
    wetland/mangrove areas

6.  Assessment of microbial bioavailability of organic C and N from
    wetland/mangrove areas

7.  Expanded measurements of benthic nitrogen fixation, nitrification,
    and denitrification rates

8.  Measurements of phytoplankton N uptake rates

9.  Quantification of microbial loop parameters: heterotrophic bacterial
    numbers, bacterial production, nanoflagellate/protist grazing rates,
    and phytoplankton primary production

10. Effects on the coastal Everglades ecosystem of variability in
    regional climate, freshwater inputs, disturbance, and perturbations

11. Development of N and P mass balance models and measurements of
    nutrient cycling rates in Florida Bay

12. Assessment and monitoring of dissolved N in Florida Bay

13. Measurement of nutrient fluxes through Florida Keys passes

14. Monitoring of salinity and estimates of fluxes of water, TN, and TP
    across the southern Everglades mangrove zone

15. Development of an integrated hydrodynamic and water quality model to
    evaluate relationships with freshwater flow and oceanic/Gulf
    hydrodynamics and exchange is in a planning phase

## Plankton Blooms

(No information provided in synthesis chapter.)

## Seagrass Ecology

### Field Assessment

-   FHAP is continuing spring and fall sampling and has incorporated
    (since spring 2001) measurements of photosynthetic characteristics
    of *Thalassia* using PAM-fluorometry at each station, in addition to
    the Braun-Blanquet and standing crop measurements.

-   FMRI (Carlson) is continuously monitoring benthic light availability
    at fixed stations in several basins

-   Zieman is maintaining the long-term productivity measurements

### Experimental

-   SFWMD is funding a new study entitled "High salinity, nutrient and
    multiple stressor effects on seagrass communities of NE Florida Bay"
    (Koch and Durako). The results of this study are intended to help
    parameterize the unit model with data from Florida Bay seagrasses.

-   FMRI (Carlson) bucket experiments have been conducted to examine
    effects of multiple stressors (sulfide nitrogen and light) on
    seagrasses in situ.

## Higher Trophic Level Species

### Unresolved Issues/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
replace failed hypotheses; 3) development of performance measures based
on species and communities most likely to be affected by CERP changes;
and 4) addressing gaps in the current program where new information
suggests higher priority should be assigned. The following series of
topic areas fit one or more of these criteria.

*Location of Nursery Areas of Major Game Fish Species -* Many
sought-after gamefish species are found in Florida Bay as pre-adults and
adults, but the current nursery grounds of most their populations are
not delineated. This includes red drum, snook, tarpon, bonefish, and
gray snapper. These nursery areas need to be delineated so that the
potential effect of water management changes on salinity patterns,
nutrient inputs, and other conditions in these areas can be predicted.

*Influence of Habitat and Environmental Variables on Species Composition
and Trophic Dynamics* - The following non-mutually exclusive hypotheses
about factors influencing the abundance and relative abundance of water
column and seagrass canopy species should be explored.

Hypothesis 1: Density and abundance of bay anchovy is related to
salinity fronts.

Hypothesis 2: Density and abundance of canopy species is related to
seagrass diversity.

The database assembled by Johnson et al. (2001) provides the opportunity
to develop trophic network models for Florida Bay. Separate network
models should be prepared for the Bay's sub regions because of the major
differences in the food web base among sub regions suggested by Chanton
et al. (2001), Evans and Crumley (in review) (see also Evans et al.
\[2001\]), and Butler et al. (2001). Analysis and comparison of trophic
structure in the various regions of the Bay could be used to organize
information about higher trophic level species and assess affects of
salinity changes resulting from changes in water management.

Factors Affecting Postlarval Immigration:

-   Immigration into the Bay's Interior - To what extent 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 determination of potential benefits of
    improved conditions 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 interior of the Bay was initiated last year, opening new
    opportunities for collaboration.

-   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 southwest 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
    questions biological researchers need to know.

-   Effect of Larval Behavior and Freshwater Inflow on Larval
    Immigration Rates - Does the volume and timing of freshwater inflow
    influence that magnitude of influx of postlarvae to Florida Bay?
    Freshwater inflow may provide directional cues or otherwise
    influence the rate of larval immigration from offshore spawning
    grounds to nearshore nursery grounds.

*Effect of Salinity on Survival and Growth* - Integrated studies that
might include models, supporting field studies, laboratory experiments,
and statistical analyses should be conducted to quantify relationships
of survival, growth, and other processes to salinity. This includes
continued development and application of lobster, shrimp, gray snapper,
and spotted seatrout models.

*Quantification of Size-Related Predation Mortality* - Better
quantification of size-related predation mortality is needed to
adequately address the effect 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.

*Effect of Water Quality on Survival and Growth* - This question has not
been specifically addressed in current research in Florida Bay. Effects
of both nutrient enrichment and common chemical contaminants on Florida
Bay fish and macroinvertebrates may be relevant to determining effects
of changes in water management.

*Effects of Benthic Habitat on Settlement, Survival, and Growth* - What
characteristics of habitat lead to initial settlement? How do
characteristics of settlement habitat affect survival and growth? How
faithful are animals to the location 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* - The sensitivity of fish from the
mangrove ecotone of the entire Ten-Thousand Islands complex of southwest
Florida suggests the need for a monitoring program to establish mercury
concentrations in susceptible fish species and a research effort to
determine the mercury sources and responses to future CERP changes in
the volume and timing of freshwater flows.

### Ongoing Research

*Modeling pink shrimp recruitment from Florida Bay -* This project
continues development of a simulation model and associated performance
measure to evaluate the potential impact on Florida Bay of upstream
water management changes resulting from efforts to restore the Greater
Everglades ecosystem.

*Regional Assessment of Sponge Dynamics and Sponge Fishery Impacts -*
This project is part of a multi-year investigation of the hard-bottom
communities of Florida Bay and the Florida Keys. It combines modeling,
laboratory, and fieldwork to explore the relationship of spiny lobster
population dynamics to spatio-temporal patterns in the structure of
bottom habitat and environmental variables.

*Population Studies, Abundance, Habitat Use, Trophic Descriptions, and
Reproductive Status of Marine Turtles Inhabiting Florida Bay* - Purposes
of this study are to 1) capture and tag sea turtles in Florida Bay to
continue long-term monitoring of individual growth rates, foraging-site
fidelity, residency rates, health status, and trends in abundance; 2)
elucidate the trophic role of loggerheads as apex predators in Florida
Bay; 3) provide detailed descriptions of loggerhead habitat use and
behavior; and 4) examine the sexual maturity and reproductive frequency
of adult-sized loggerheads inhabiting Florida Bay. The principal study
area is the central-western region.

*Reef Fish Community Dynamics and Linkages with Florida Bay -* This
continuing project will apply a visual sampling strategy to quantify
coral reef fish community changes.

*Development of Spatially-Explicit Models to Predict Growth-Potential of
Age-0 Gray Snapper, Lutjanus griseus, in Florida Bay during Restoration
of Freshwater Flows* - The 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 predicted changes
in the environment of Florida Bay under different water management
strategies.

*Upstream Larval Supply to Florida Bay---the Dry Tortugas Connection -*
This project explores the pathways and enabling transport processes for
migration of larval fish, shrimp, and lobster 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.

*Atlas of Life Histories of Juvenile and Small Resident Species in
Florida Bay -* The Atlas will include information on the range,
reproduction, diet, spatial and temporal abundance and distribution, and
length-frequency distributions in the Bay.

*ATLSS 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, 2001b).