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Project Work Plan

U.S. Geological Survey Greater Everglades Science Initiative (Place-Based Studies)

Fiscal Year 2004 Project Work Plan


Project Title: Geochemical Monitoring of Restoration Progress
Project start date: October 1, 1999 Project end date: September 30, 2004
Project Funding: USGS Place-Based Studies Initiative
Principal Investigator: Kimberly Yates
Email address: kyates@usgs.gov
Phone: 727-803-8747 ext 3059 Fax: 727-803-2031
Mail address: U.S.G.S., 600 Fourth Street South, St. Petersburg, Florida 33701

Other Investigator(s): Robert Halley, Nate Smiley, Chris Dufore, Iuri Herzfeld
Email address: rhalley@usgs.gov, nsmiley@usgs.gov, cdufore@usgs.gov, iherzfeld@usgs.gov
Phone: 727-803-8747 ext. 3020 Fax: 727-803-2031
Mail address: U.S.G.S., 600 Fourth Street South, St. Petersburg, Florida 33701

Project Summary:

The flow of freshwater from the Everglades to Florida Bay and the interaction of Bay water with the Gulf of Mexico and Atlantic Ocean are critical processes that have defined the Florida Bay Ecosystem. Reconstruction of historical changes in the Florida Bay Ecosystem using paleoecological and geochemical data from cores and historical databases indicates that significant changes in water quality and circulation (McIvor et al., 1994; Rudnick et al., 1999; Boyer et al., 1999; Halley and Roulier, 1999; Swart et al., 1999), and biological species composition and ecology (Brewster-Wingard and Ishman, 1999; Fourqurean and Robblee, 1999; Hall et al., 1999; Zieman et al., 1999) have been coincident with alteration of drainage patterns in the Everglades and construction of bridges linking the Keys. For example, historical salinity records and paleoecological information derived from cores suggest that salinity patterns changed in the early 1900's in response to railroad and canal system construction and again around 1940 in response to water management practices, and that average salinity and hypersalinity have increased recently (Halley et al., 1996; Robblee and Smith, 1999; Brewster-Wingard and Ishman, 1999). Paleoecological data from cores also indicates that changes in the abundance of seagrass and algae in the Bay have been coincident with salinity changes (Brewster-Wingard and Ishman, 1999), and that significant loss of seagrass on mud banks and basins has occurred over the last several years (Robblee et al., 1991; Carlson et al., 1998). Stable isotope data from sediment cores indicate decreased circulation in the Bay coincident with railroad building and early drainage in South Florida (Halley and Roulier, 1999).

Water management practices in South Florida are already being altered in an effort to restore the Everglades and Florida Bay. Resulting changes in water chemistry will first affect biogeochemical processes, and may, subsequently, result in changes in species distributions (such as seagrass, algae, etc.) in the Bay. An extensive water quality monitoring program for Florida Bay has been in operation for several years. Primary participants include ENP (fixed water quality monitoring stations), NOAA (salinity, chlorophyll, and transmittance bimonthly surveys), SFWMD (northeast Bay and north coast monitoring), and FIU (nutrient monitoring). These programs have provided detailed information on concentrations of water quality parameters in the Bay. However, in situ monitoring of key biogeochemical processes resulting directly from biological activity has not been undertaken. Monitoring changes in biogeochemical processes is critical to early identification of ecological response to restoration and predicting changes in species distribution within the Bay. Additionally, these processes may directly impact water quality. For example, production and accumulation of carbonate sediments may play a key role in the removal of phosphate from the water column due to binding of phosphate to sediments. Calcification, photosynthesis, and respiration directly affect dissolved oxygen, pH, dissolved inorganic carbon and a number of other chemical characteristics of the water column. This information will enable managers to evaluate the progress and success of South Florida restoration efforts.

This work plan is a continuation of a project that began in FY2000 to monitor changes in critical biogeochemical processes in Florida Bay relative to water quality changes as South Florida restoration proceeds. FY2000 and 2001 efforts focused on establishing baseline data from which to evaluate restoration progress. Continued geochemical monitoring efforts through FY2002 and 2003 will provide a measure of the progress and effects of restoration on environmental health and water quality, and complement biological monitoring of indicator species. This information is essential for identifying when successful restoration has been accomplished.

Project Objectives and Strategy:

Carbonate environments such as Florida Bay are characterized by three primary biogeochemical processes including 1) carbonate sediment production by calcifying organisms and dissolution, 2) photosynthesis and 3) respiration (referred to collectively as productivity). These processes are sensitive to changes in water quality including salinity and nutrients, and show distinct rate changes before visual evidence of environmental disturbances such as seagrass die-off, algal blooms, and shifts in ecosystem success indicator species. Therefore, measuring changes in these processes relative to changes in water quality (such as salinity and nutrients) provides a mechanism for monitoring restoration progress. This project employs geochemical analytical techniques, salinity, pH, and dissolved oxygen surveys to measure current rates of productivity in Florida Bay, and to monitor changes in productivity during implementation of restoration plans to assess progress and effects of restoration in South Florida on environmental health.

FY2000 efforts focused on measuring current seasonal rates of productivity (including carbonate sediment production, photosynthesis and respiration) in Florida Bay to establish baselines for these parameters from which to monitor restoration progress. Productivity and geochemical monitoring was continued through FY2001, 2002 and 2003. Project objectives include 1) productivity monitoring to assess restoration progress and its effect on critical environmental processes in the Bay, 2) performing Bay-wide, bimonthly salinity, pH, dissolved oxygen, total carbon and air:sea CO2 gas flux surveys to measure changes in these parameters during implementation of restoration, and to identify sustained water quality changes that may result in ecosystem stress, and 3) comparison of results from productivity monitoring efforts to historical cycles of salinity change, carbonate sediment accumulation, and distribution patterns of subaquatic vegetation and indicator species to help identify when restoration has been accomplished. Each of these objectives will be addressed as tasks described below.

Potential Impacts and Major Products:

Productivity monitoring efforts will allow resource managers to evaluate progress and success of restoration efforts. Geochemical productivity monitoring provides a mechanism for measuring early response of the Florida Bay ecosystem to environmental perturbations. This will enable resource managers to identify ecological responses to restoration and to evaluate the need for alteration of restoration procedures prior to the onset of visual shifts in sub-aquatic plant and animal populations. Geochemical survey data will provide information on the extent and magnitude of salinity shifts in the Bay due to freshwater inflow from the Everglades and the effects of freshwater inflow on other parameters critical to environmental health in the bay including dissolved oxygen, pH, and carbon speciation. Presenting resource managers and decision makers with a comparison of monitoring data to historical cycles in sediment accumulation rates, shifts in indicator species, and salinity changes will assist them in defining restoration criteria and identifying when restoration has been accomplished.


  1. Productivity database for Florida Bay - information from this database has been accumulated through the duration of the project. The database will be submitted to the SOFIA website at the end of FY03.
  2. Bimonthly salinity, dissolved oxygen, pH, carbon speciation and air:sea CO2 gas flux maps of Florida Bay.
  3. Scientific publications on results of monitoring.
  4. Educational outreach materials including web-site products

Project Time Frame:

WORK PLAN (Time line FY 2000 to project end):

Time Line






FY00: Productivity Baselines


Task 1: Seasonal Productivity Monitoring


Task 2: Bimonthly Geochemical Surveys


Task 3: Historical Comparisons



Department of Interior, U.S. Geological Survey, Geologic Division
Contact: Dr. Lynn Brewster-Wingard

Florida, State Agencies, Fish and Wildlife Conservation Commission - FMRI
Contact: Dr. Paul Carlson

Florida, State Agencies, Florida Department of Environmental Protection
Contact: Penny Hall


Department of Interior, National Park Service, Everglades National Park
Contact: Bob Zepp

Florida, County Agencies, Dade County Department of Environmental Resource Management
Contact: Susan Markley

Florida, County Agencies, South Florida Water Management District
Contact: David Rudnick

Department of Defense, U.S. Army, U.S. Army Corps of Engineers
Contact: Steve Traxler


Title of Task 1: Productivity Monitoring
Task Funding: Place Based Studies
Task Leaders: Kimberly Yates
Phone: 727-803-8747 ext. 3059
FAX: 727-803-2031
Task Status (proposed or active): Complete
Task priority: na
Time Frame for Task 1: See timeline above
Task Personnel: na

Task Summary and Objectives:

The objective of task 1 is to monitor seasonal rates of productivity and site specific nutrient concentrations as restoration is implemented to provide a measure of restoration progress and its effects on biogeochemical processes. Rates of productivity are determined from precise, in situ measurements of alkalinity, pH, dissolved oxygen, temperature, conductivity, sulfides, and air:sea CO2 and O2 gas fluxes (Smith and Key, 1975; Millero, 1979; Barnes, 1983; Gattuso et al., 1993; Millero et al., 1993). Productivity on mudbanks will be determined by measuring spatial geochemical changes along transects across mudbanks using techniques modified from Smith (1973) and Frankignoulle and Disteche (1984). Productivity in basins will be determined by measuring temporal geochemical changes in water masses isolated over the bottom using techniques developed by Halley and Yates (1999) employing a large environmental incubation chamber (Submersible Habitat for Analyzing Reef Quality, or S.H.A.R.Q.). Comparison of productivity monitoring data to productivity baselines established in FY2000 and geochemical survey data from task 2 will provide a measure of the response of biogeochemical processes to changing water quality in the Bay. Since these processes respond quickly to environmental stress, productivity monitoring results will provide the first indication of ecosystem response to changing water quality. This information will assist the seagrass research team (P. Hall (FMRI), P. Carlson (FMRI), M. Durako (UNC), et al.) in targeting areas for biological monitoring of seagrasses and other benthic community indicator species. Condition/response data from productivity monitoring will be incorporated into a productivity database. Rates of photosynthesis and respiration associated with seagrass monitoring stations will complement seagrass monitoring data in characterizing ecosystem health, and will be examined as a mechanism for evaluating seagrass performance.

Work to be undertaken during the proposal year and a description of the methods and procedures:

Task 1 was completed during FY03. No additional work will be performed on task 1 during FY04. Data and information will be synthesized during FY04 as described in task 3. The following describes the work that was completed in task 1 during FY03:

Fiscal year 2003 activities focused on continued monitoring of production rates at monitoring sites established during FY2000 (Russell Bank, Manatee Key Basin, and Buchanon Basin). Productivity rates were determined by measuring rates of calcification, photosynthesis, and respiration associated with representative substrate types including seagrass beds, hard bottom communities and mud bottom communities. Biological characterization of geochemical monitoring sites by FMRI and USGS will provide critical information used for hind-casting production rates based on historical information from cores. Rates of productivity at each site were measured for 24-hour periods, during field expeditions to establish daily, seasonal, and annual rates of production in the Bay. These data will be compared to baseline productivity data established in FY2000 to identify changes in ecosystem health.

Calcification, photosynthesis, and respiration were measured using the SHARQ incubation system developed by Yates and Halley (in press). Geochemical parameters including pH, dissolved oxygen, fluorescence, and temperature were measured continuously through the SHARQ's flow-through analytical system throughout the duration of incubation periods (from 20-28 hours). Water samples were removed from sample ports every 4 hours for alkalinity measurements via the Gran titration method using methods of Millero (1979). Dissolved oxygen, pH and alkalinity data were used to calculate rates of net calcification, photosynthesis, and respiration for each 4-hour interval between alkalinity measurements during incubation periods. Productivity parameters were calculated using the alkalinity anomaly technique (Smith and Key, 1975) and carbonate system equations of Millero (1979), whereby delta concentration of each parameter/deltaT x SHARQ volume/SHARQ surface area = g C m-2s-1. Sample interval rates will be used to calculate net daily production rates that were then used to derive average hourly rates of calcification, photosynthesis, and respiration. Photosynthetically active radiation (PAR) was measured in the air at the water's surface and on the seafloor at monitoring sites during all monitoring exercises.

Title of Task 2: Bimonthly Geochemical Surveys
Task Leaders: Kimberly Yates
Task Funding: Place Based Studies
Phone: 727-803-8747 ext. 3059
FAX: 727-803-2031
Task Status (proposed or active): Complete
Task priority: na
Time Frame for Task 2: See attached timeline above
Task Personnel: na

Task Summary and Objectives:

The objective of task 2 is to measure salinity, conductivity, dissolved oxygen, pH, and carbon parameters bimonthly throughout the Bay to identify changes in these parameters during restoration. Carbon analyses will be performed on water samples taken from 24 sites distributed throughout the bay. Parameter maps and database will be accessible through the U.S.G.S. website shortly following each survey, and salinity data will contribute to the ENP salinity database. Comparison of bimonthly survey data from task 2 and NOAA surveys to historical water quality information from the ENP database will be used to identify locations of significant water quality change in the bay and potential new monitoring sites. Dissolved oxygen, pH, DIC speciation, and air:sea CO2 gas flux data from USGS surveys will play a critical role in identifying areas where significant changes in biogeochemical processes may be taking place. Survey data will be coupled with productivity monitoring data to establish condition/response criteria for biogeochemical processes. High frequency, bay-wide geochemical surveys will complement SFWMD water quality monitoring along the Bay's northern coastline, ENP water quality monitoring stations throughout the Bay, and NOAA bimonthly surveys to provide very detailed characterizations of water quality.

Work to be undertaken during the proposal year and a description of the methods and procedures:

Task 2 was completed during FY03. No additional work will be performed on task 2 during FY04. Data and information will be synthesized during FY04 as described in task 3. The following describes the work that was completed in task 2 during FY03:

Bay-wide geochemical surveys were conducted bimonthly throughout the year. Survey tracts targeted the perimeter of each of the smaller basins in the Bay, transected larger basins, and included sampling sites near canal and slough discharge areas. Salinity and conductivity (Orion instrumentation), temperature (Orion), pH (Orion Ross Electrodes and meter), and dissolved oxygen (YSI) were measured using a flow-through analytical system towed behind a small research vessel at a speed of less than 15 knots. Data from each of these parameters were logged approximately once every 4 to 8 seconds of travel resulting in collection of approximately 20,000 data points for each parameter throughout the entire bay over a three to four day time period. Water samples for total carbon analyses were collected from each of 24 sites distributed throughout the Bay. Analyses were performed using a carbon coulometer (UIC). Total carbon and pH data will be used to calculate carbon speciation using the CO2SYS carbon speciation program. Air:sea CO2 gas fluxes were directly measured at each of the 24 sample sites using a floating bell and a LiCor 6252 infrared CO2 gas analyzer. Data collected from each geochemical survey were contoured producing a GIS map layer for each chemical parameter. These maps have been posted on the SOFIA website. These data will establish the effects of alteration of freshwater flow to Florida Bay on critical geochemical parameters and assist in establishing links between changes in water quality, biogeochemical processes, and ecosystem health.

Title of Task 3: Historical Comparisons
Task Leaders: Kimberly Yates
Task Funding: Place Based Studies
Phone: 727-803-8747 ext. 3059
FAX: 727-803-2031
Task Status (proposed or active): Active
Task priority: high
Time Frame for Task 2: See timeline above
Task Personnel: Kimberly Yates, Chris Dufore, Nate Smiley

Task Summary and Objectives:

The objective of task 3 is to compare carbonate sediment and organic carbon production rates from monitoring to historical information on these parameters derived from cores and previous measurements. Data from cores and standing crop surveys on carbonate sediment accumulation (Robbins et al., Bosence, etc.), distribution of subaquatic plants and animals (USGS, L. Wingard), and organic productivity (Zieman, Fourqurean, Frankovich, Durako, etc.) will be used to estimate historical rates of production. Comparison of these estimated production rates to historical salinity data (ENP database; Brewster-Wingard and Ishman, 1999) will aid in establishing effects of water management practices on biogeochemical processes. This information provides a historical baseline for production in the Bay and helps identify criteria for defining successful restoration. Task 3 began in FY2003.

Work to be undertaken during the proposal year and a description of the methods and procedures:

During FY03, average rates of carbonate sediment production derived from FY00 through FY03 monitoring exercises (Task 1) were used to estimate average sediment accumulation rates for various representative substrate types identified by Prager and Halley (1997). In FY04, this information will be compared to historical sediment accumulation rates derived from dated sediment cores and sediment thickness data. Carbonate sediment production rates from monitoring exercises will be compared to salinity data collected via geochemical surveys to identify potential salinity impacts on sediment production rates. A similar comparative exercise for organic productivity (rates of carbon fixation) from seagrass and other substrate types will be performed in FY04. Data sets from this study will be coordinated with data sets of Wingard, Zieman, Fourqurean, Frankovich, Durako, and Orem. Productivity data will be made available through a database on the SOFIA web site.

GIS map products have been generated for all water quality parameters from bimonthly geochemical surveys. Correlation statistics will be used to identify links between specific water quality parameters, and other physical parameters (such as bottom type, etc.) to aid in the identification of processes controlling water chemistry. Data used to generate map products will be incorporated into a database, and will be made available on the SOFIA website. All map products will also be made available as USGS open-file reports. It is anticipated that two to three additional scientific manuscripts will result from this study.

Planned Outreach:

Outreach activities will be coordinated through the Sea Grant/Florida Bay Outreach Group. Specific activities will include:

1. Public presentation of project and results to date at South Florida Restoration Science meetings

2. Project overview/highlight and database accessible to the public on the USGS SOFIA website


High-resolution water quality data from bimonthly surveys enables calibration of salinity and ecologic response to hydrologic condition models, and provides baseline water quality data from which to measure change and assess restoration impacts. Similarly, productivity monitoring of representative benthic habitats in Florida Bay provides baseline process rates from which to measure ecological response to water quality change. Specifically, carbonate sedimentation and seagrass growth play a key role in maintaining the unique physical structure of mud banks in Florida Bay that support the variety of benthic habitats in the Bay. Changing freshwater inflow to Florida Bay will inevitably change water quality parameters (such as pH, carbon speciation, etc) that impact carbonate sediment production directly. Knowledge of the current rates of sedimentation and processes that impact sediment production and accumulation are required to assess the impact of water quality change on sedimentation and the physical structure of Florida Bay. This project provides current carbonate sediment production rates for representative benthic habitats in Florida Bay and provides insight into potential controlling factors for production and accumulation. Seagrass has traditionally been identified as a critical ecological indicator for estuarine health. The metabolism of vegetation and fauna is typically impacted during environmental perturbations long before visual evidence of stress is observed. This project provides current rates of seagrass, hard-bottom, and mud-bottom community metabolism (photosynthesis and respiration) and information on the dependence of photosynthesis on light availability. This information is required for ecological modeling of the impact of water quality (including clarity) on benthic habitats. Continued monitoring of community metabolic processes throughout restoration could be used as an early indicator of environmental impact. The science objectives in the "USGS science plan in support of Everglades Restoration" document targeted by this project are listed below:

Restoration goal 1A, SO1 - What are the sedimentation rates?

Restoration goal 1B, SO3 - What are current water quality conditions across the South Florida environment?

Restoration goal, 2A, SG3 - What is the current baseline condition for habitats and landscapes within the ecosystem?

Restoration goal 2B, SG3 - What is the current status of the ecosystem and what are trends and variability of important ecosystem indicators.


Barnes, D.J. 1983. Profiling coral reef productivity and calcification using pH and oxygen electrodes. Journal of Experimental Marine Biology and Ecology 66:149-161.

Boyer, J.N., Fourqurean, J.W., and Jones, R.D. 1999. Seasonal and long-term trends in the water quality of Florida Bay. Estuaries 22(2).

Brewster-Wingard, G.L. and Ishman, S.E. 1999. Historical trends in salinity and substrate in Florida Bay: a paleoecological reconstruction using modern analogue data. Estuaries 22(2).

Carlson, P., Landsberg, J., and Blakesley, B. 1998. Seagrass mortality and recovery on Florida Bay mudbanks: year 1 progress report covering the period August 1, 1997 - July 31, 1998. Prepared for Everglades National Park.

Hall, M.O., Durako, M.D., Fourqurean, J.W., and Zieman, J.C. 1999. Variations in water clarity in Florida Bay from 1985 to 1997. Estuaries 22(2).

Halley, R.B. and Roulier, L.M. 1999. Reconstructing the history of eastern and central Florida Bay using mollusk-shell isotope records. Estuaries 22(2).

Halley, R.B., and Yates, K.K. 1999. Sediment production is critical to reef restoration. International Conference on Scientific Aspects of Coral Reef Assessment, Monitoring, and Restoration, Program and Abstracts, Ft. Lauderdale, FL, April 14-16, 1999.

Halley, R.B., Smith, D., and Hansen, M. 1996. Florida Bay salinity maps, surface and bottom salinity, 11/94; 1, 4, 6, 8, 10, 12/1995; 2,4,6/1996: USGS Open-File Report 95-634.

Fourqurean, J.W. and Robblee, M.B. 1999. Florida Bay: a history of recent ecological changes. Estuaries 22(2).

Frankignoulle, M. and Distéche, A. 1984. CO2 chemistry in the water column above a Posidonia seagrass bed and related air-sea exchanges. Oceologica Acta 7(2):209-219.

Gattuso, J.P., Pichon, M., Delesalle, B., and Frankignoulle, M. 1993. Community metabolism and air-sea CO2 fluxes in a coral reef ecosystem (Moorea, French Polynesia. Marine Ecology Progress Series 96:259-267.

McIvor, C.C., Ley, J.A., and Bjork, R.D. 1994. Changes in freshwater inflow from the Everglades to Florida Bay including effects on biota and biotic processes: a review. In: Everglades the Ecosystem and it Restoration, S.M. Davis and J.C. Ogden (Eds.), St. Lucie Press, Delray Beach, FL, chap. 6.

Millero, F.J. 1979. The thermodynamics of the carbonate system in seawater. Geochimica et Cosmochimica Acta 43:1651-1661.

Millero, F.J., Zhang, J., Lee, K., and Campbell, D.M. 1993. Titration alkalinity of seawater. Marine Chemistry 44:153-165.

Prager, E. and Halley, R.B. 1997. Florida Bay Bottom Types. U.S.G.S. Open File Report #97-526.

Robbins, J.A., Holmes, C.W., Halley, R.B., Bothner, M., Shinn, E., Graney, J., Keeler, G., tenBrink, M., Orlandini, K.A., and Rudnick, D. in press. First-order time average fluxes of 137Cs, Pb and 239+240Pu to 210Pb dated sediments in Florida Bay. Journal of Coastal Research.

Robblee, M.B., Barber, T.R., Carlson, P.R., Durako, M.J., Fourqurean, J.W., Muehlstein, L.K., Porter, D., Yarboro, L.A., Zieman, R.T., and Zieman, J.C. 1991. Mass mortality of the tropical seagrasses Thalassia testudinum in Florida Bay (USA). Marine Ecology Progress Series 71:297-299.

Robblee, M.B. and Smith, D.T. 1999. Salinity pattern in Florida Bay: a synthesis. U.S. Geological Survey Program on the South Florida Ecosystem. Proceedings of South Florida Restoration Science Forum, May 17-19, Boca Raton, Florida.

Rudnick, D.T., Chen, Z., Childers, D.L., Boyer, J.N., and Fontaine, T.D. 1999. Phosphorous and nitrogen inputs to Florida Bay: the importance of the Everglades watershed. Estuaries 22(2).

Smith, S.V. 1973. Carbon dioxide dynamics: a record of organic carbon production, respiration, and calcification in the Eniwetok reef flat community. Limnology and Oceanography 18(1):106-120.

Smith, S.V. and Key, G.S. 1975. Carbon dioxide and metabolism in marine environments. Limnology and Oceanography 20:493-495.

Swart, P.K., Healy, G., Greer, L., Lutz, M., Saied, A., Anderegg, D., Dodge, R.E., and Rudnick, D. 1999. The use of proxy chemical records in coral skeletons to ascertain past environmental conditions in Florida Bay. Estuaries 22(2).

Yates, K.K. and Halley, R.B. in press. Measuring coral reef community metabolism using new benthic chamber technology. Coral Reefs.

Zieman, J.C., Fourqurean, J.W., and Frankovich, T.A. 1999. Seagrass dieoff in Florida Bay (USA): long-term trends in abundance and growth of Thalassia testudinum. Estuaries 22(2).

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