Category Archives: Ecosystem Assessment and Restoration

Monitoring and Assessment of Eastern Oyster Growth on Created Oyster Reefs in Tampa Bay

By Dr. Ryan P. Moyer

Oyster reefs, constructed primarily by the eastern oyster (Crassostrea virginica), provide critical ecosystem services to nearly all of coastal Florida. Over many years, multiple generations of oysters settle upon one another, constructing a large reef structure that stabilizes sediment and provides a hard substrate that is utilized as habitat by other species. Oyster reef habitats are crucial components to coastal ecosystems and provide substrate, habitat, and/or food sources to numerous species of gastropods, crustaceans, sponges, worms, fish and birds. Thus, their ability to support recreational and commercial fish species, improve water quality through filtration, and reduce shoreline erosion highlights their significance as critical species within estuarine ecosystems.

In Tampa Bay, continued coastal development, dredging, and historical harvests have led to a reduction in suitable hard substrate for oyster recruitment. Beginning in the early 2000s, several public and private organizations initiated the installation of artificial oyster reefs to mimic the natural substrate oysters need for settlement and growth. These reefs were constructed from shell, concrete domes and mesh shell bags, and were placed throughout Tampa Bay to increase available oyster habitat and oyster populations. In collaboration with Tampa Bay Watch and the Tampa Bay Estuary Program, the Florida Fish and Wildlife Research Institute (FWRI) Coastal Wetlands Research Program implemented a study to assess and monitor oyster growth on old (>5 years), moderate-age (2-5 years), and young (<2 years) constructed oyster reefs.

FWRI Coastal Wetlands staff perform oyster density counts as part of monitoring on a young created oyster reefs (foreground). At the same time ecological surveys are conducted, high-precision elevation surveys are conducted to assess elevation change in newly constructed oyster reefs (background)

Physical assessments of oyster growth (e.g., oyster density, shell height, associated fauna) are coupled with real-time kinematic (RTK) Global Positioning System (GPS) surveys resulting in high-resolution (cm) elevation control of both the reefs and associated shorefaces being sheltered by the reefs. To date, 16 constructed oyster reefs in Tampa Bay with variable substrates (shell bags, concrete domes and loose shell) and ages (old, moderate and young) have been assessed, with young-age reefs being monitored bi-annually. In addition, three nearby natural reefs have been identified to serve as controls, and the same metrics used on created reefs are measured there. Physical oyster growth and faunal information at the 16 sites will be correlated to elevation (depth below mean tide level) and age (young, moderate, old) to further understand how these reefs mature over time.

Oysters are tolerant to prolonged areal exposure, however in order to release toxins and feed they must be submerged; therefore, it is imperative to maintain tight elevation controls during reef construction to ensure proper placement of substrate within the water column. As a result, reef sections situated above, or below suitable oyster settlement depths may experience reduced settlement, increased predation and reduced growth. The conclusions from this study will be used to maximize oyster growth potential and inform adaptive improvement in the planning and design phase of future oyster restoration projects to ensure maximum recovery of healthy oyster populations in Tampa Bay and around Florida.

Evaluating Eelgrass for Restoration at Lake Apopka

By Jamie Richardson and Maggie Bass

Many of us are familiar with Lake Apopka – once known for its pristine waters and premier fishing, then known for its status among the most polluted lakes in the state. Pesticides and fertilizers from agricultural run-off were pumped into the lake from the 1940s to the 1990s. Over time this sandy bottomed, clear watered system turned into a muck bottomed, algae filled lake that appears green on every satellite image you see. Fish, wildlife, and plants all suffered negative impacts from these decades of dumping. Many efforts have been made over the years to improve and restore Lake Apopka to its former glory with slow and limited success. A recent effort taken on by the University of Florida (UF) in collaboration with the St. John’s River Water Management District (SJRWMD) and FWRI is an initiative to repopulate submerged aquatic vegetation (SAV) in the lake. Our Freshwater Plants Research team began an ongoing monitoring and research project of Lake Apopka’s SAV, with a specific focus on American Eelgrass (Vallisneria spp.) as FWC’s contribution to this initiative.

Maggie Bass takes a sediment core from Lake Apopka near historic pump house.

In November 2018 our team, affectionately known as the “Action Snackers,” began monitoring a thriving patch of eelgrass located on the North Shore of the lake. Each month we note the changes we observe; record water depth, Secchi disk transparency and water chemistry data; and collect sediment cores from in and around the patch for analysis. The sediment cores are then processed and sieved down to very fine sediment components to reduce the sample material to the particle size of eelgrass seeds. Our sieved samples are then housed at the Eckerd College greenhouse in St. Petersburg for monitoring of germination.

Although our crew was oftentimes met with hurdles such as fast-approaching thunderstorms, extreme summer heat on breezeless days, or arriving to our collection site only to realize we were experiencing some equipment malfunction, our dedication and teamwork paid off. The results show that an eelgrass seed bank is present and possibly expanding. Our greenhouse data show an emerging pattern of seasonal highs and lows for eelgrass germination. Understanding this information will be important to restoration efforts, such as deciding which months planting would be most successful. The project is ongoing, and all data and results are being shared with UF and SJRWMD to assist management decisions to repopulate Lake Apopka’s SAV.

Maggie Bass checks an eelgrass specimen for reproductive parts.

30,000 Fish Kill Reports is a Big Deal

By Cat Brown

July 24, 2019 was a momentous day for Fish and Wildlife Health (FWH). It looked like another day, until Pete Wenner from DEP sent Theresa Cody an email reporting water discoloration in the Hillsborough River near the Buchman Bridge. Pete described floc-like orange masses, possibly indicating the presence of iron-reducing bacteria where the water had pooled. DEP staff planned to investigate and possibly even use their newest acquired iolight field microscope. However, it was soon discovered that the discoloration was apparently normal. The surrounding pine flatwoods soils comprises acidic sands over a clay layer from which iron oxides may naturally leach with the rise and fall of ground water. And so, this particularly not very exciting report, that did not even have dead fish associated with it, turned out to be the FWC’s Fish Kill Hotline’s (FKH) 30,000 report.

Since the hotline’s inception in September 1995, in addition to responding to over 30,000 calls, the FWH group has investigated 988 sites, provided 4837 data information requests and emailed over 5000 educational brochures. Through the FKH, FWH staff document and track reported fish kills and disease events, initiate governmental event response as needed, provide expert information to the public on fish health related issues and respond to information requests. We have long depended on citizen scientists to help track fish kills and monitor aquatic animal diseases in state waters. We have worked to increase public awareness of the FKH and associated web‐site through various outreach activities.

Monitoring fish kills around the state allows us to recognize important epizootics and opportunistically collect biological samples.  Our database can be queried online to help interested parties determine the status and the historical trends for reported fish disease and mortality events. The FKH is a unique tool for FWC that allows citizens and scientists to communicate and work together for the good of Florida’s natural resources.

Assessing Insect Communities and Plant-Pollinator Networks in Fire-Maintained Sandhills

by Johanna Freeman

The arthropod fauna of xeric longleaf pine savannas has been conservatively estimated at 4,000 to 5,000 species.  This diversity virtually guarantees that insects play numerous and complex roles in the functioning of longleaf pine sandhills, but little is known about sandhill insect communities and how they are affected by land management activities.  In particular, fire effects on plant-pollinator interactions are poorly documented, and at present there are few management recommendations regarding pollinators in fire-maintained sandhills. 

The Upland Habitat research group is working on a project designed to collect baseline data on sandhill insect communities, as well as identifying areas in which fire management can influence insect species diversity and plant-pollinator networks.  In collaboration with University of Florida community ecologist Dr. Benjamin Baiser and his students, we are sampling 24 1-hectare research plots at 9 fire-maintained sandhill preserves once a month from March to October 2019.  The study sites have been chosen carefully in order to provide adequate replication of a variety of environmental variables (soil moisture, soil texture, and elevation) and standardize others (time-since-fire), which will enable us to sort out anthropogenic sources of variation from natural environmental gradients.  We are also collaborating with Dr. Eben Broadbent of the University of Florida spatial ecology lab, who will be using a combination of LiDAR and high-resolution aerial imagery to quantify landscape-scale structural and spatial variables surrounding the research plots. 

Butterflies pollinating Cirsium horridulum. Photo by Cherice Smithers.

Every month, the research team deploys five insect-trapping arrays in each plot for 24 hours.  The arrays consist of vane traps, pitfall traps, and bowl traps, each of which targets different types of insects.  Plant-pollinator interactions are also observed in each plot once a month.  Each 1ha research plot is divided into 4 quadrants, within which an observer walks a serpentine transect covering the entire quadrant over the course of 30 minutes, for a total of 2 hours sampling time per plot per month.  Every time the observer encounters an insect interacting with a flower, he/she captures the insect for identification and notes the plant species upon which it was encountered.  All flowering plant species within the 1ha plot are identified during the monthly visit, and flower abundance counts are conducted.  Back at the lab, research technicians have their work cut out for them sorting and pinning hundreds of insect specimens, which are being identified by entomologist Dr. Josh Campbell of Auburn University. 

The Upland Habitat group is grateful for all the support we have received in implementing this challenging field project.  It has been very much a team effort, requiring the input of several specialists and entailing a heavy schedule of monthly field work.  The project has been made possible by funding from the State Wildlife Grants program and the Fish and Wildlife Foundation of Florida, and the cooperation of the Florida Forest Service, Florida Park Service, St. John’s River Water Management District, Florida Fish & Wildlife Conservation Commission, and private landowner Nolan Galloway, Jr.  We look forward to analyzing the data and learning much, much more about this important component of sandhill ecosystems!

Employing New Technology to Indirectly Monitor Karenia Brevis

By Matt Garrett and Kelsey Marvin

Over 14,000 water samples were processed during the Karenia brevis bloom that began in November 2017 and ended in February 2019. Each of these samples represents a single moment in space and time, and both routine and event response sampling play a critical role in tracking blooms. Marine and estuarine environments –and blooms of K. brevis – are dynamic and can change rapidly over space and time. To help bridge gaps between sampling events, the HAB Group has been working to adapt a new passive sampling technology to monitor for brevetoxins produced by K. brevis in the Gulf of Mexico called Solid Phase Adsorption Toxin Tracking, or SPATT. SPATT uses tiny resin beads that passively adsorb free brevetoxins in the water. These beads are sealed in small mesh bags and can be deployed in various locations (on fishing piers, docks, buoy lines) for upwards to a month at a time, and once the bags are recovered, toxins can then be extracted and measured. Since this method only measures toxin exposure over time, it cannot be used to infer actual cell concentrations, like those provided on our weekly maps.  Instead, scientists can infer K. brevis’ presence and general concentration at a particular location and depth during the deployment period.

SPATT bags, which are nylon mesh bags filled with resin, are attached to a bouyed line at different depths, along with a temperature and light sensor attached at each depth. The SPATT bag on the left is seen just prior to deployment, while the image on the right is a bag harvested after one month.

Using SPATT bag analyses to detect toxins offshore and/or at depth is of particular interest, since sub-surface samples are beyond the reach of remote sensing, and most samples are taken within 0.5 m of the surface and/or in nearshore coastal and estuarine systems. Analyses of recently deployed SPATT bags have shown higher concentrations at depth, both when compared to concentrations at the surface and in previous months. These types of measurements are increasingly critical, as evidence points to bloom formation occurring at depth in the offshore environment. Information about bloom conditions at depth is particularly important to have for use in predictive models of bloom development and transport to the nearshore coast, where a bloom can become a severe red tide event.

Use of this technology in the lab and field has been very promising! In the future, the HAB Group hopes to be able to deploy SPATT bags in multiple locations spanning nearshore to offshore so that they can serve as an early warning sentinel system for K. brevis blooms. SPATT technology is currently used in other parts of the U.S. to monitor different marine and freshwater toxins, and FWRI HAB researchers also plan to determine how this method could be used to measure and track the multiple toxins produced by other HAB species in Florida waters.

New bouyed SPATT line prepped for deployment on 4/1/19.

Coral Rescue Update

By Stephanie Schopmeyer

Last month, 90 corals were transferred from Keys Marine Lab (KML) in Marathon, FL to their new home at Florida Aquarium’s Center for Conservation (FLAQ) in Apollo Beach–in response to the Stony Coral Tissue Loss Disease event currently affecting the Florida Reef Tract.  This transfer frees up space at KML to allow for upcoming rescue collections.

Since September 2018, FWC staff have been successfully caring for rescued corals, with more than 99% still alive and healthy.  View more images from the Coral Rescue efforts:

Fish and Wildlife Health Staff Investigate Ulcerative Skin Lesions in Lionfish

By Catalina Brown

In mid-August 2017, the FWC Division of Marine Fisheries Management’s lionfish group contacted the Fish and Wildlife Health Staff to confirm they collected lionfish (invasive Indo-Pacific lionfish Pterois volitans/miles complex) with significant ulcerative skin lesions approximately 30 miles off Pinellas County.

Ulcerated lionfish were also documented offshore Pensacola by local divers on Aug. 5. Following these initial reports, lionfish presenting with ulcers have also been reported in waters of the, East Florida Shelf, the Florida Keys, and the Bahamas as well as throughout the Caribbean Sea, including offshore of the Cayman Islands, Bonaire and Belize. FWC’s Fish and Wildlife Health group are collaborating with UF and Okaloosa County to obtain specimens and conduct necropsies to determine the etiology of the disease. In conjunction with UF, FWC have evaluated the specimens for parasitic infection as well as bacterial, fungal and viral infection.

This ongoing research is critical because the pathogen could be non‐specific and impact other marine sport fish species. Histological analysis has demonstrated tissues that appear to be healing. A causative agent has not been identified, but FWC continue to receive periodic reports of ulcerated fish and try to get specimens for analysis as they become available.

National Rivers and Streams Assessment

By Jamie Richardson

From the vast blackwaters of the Suwannee River to a braided creek in Pensacola to a pin-straight residential canal in the greater Miami area, our NRSA crew has been everywhere, man (cue Johnny Cash). For three months, personnel of the Freshwater Plants Research Program travelled all over Florida to sample a variety of unique ecosystems using multiple standardized sampling techniques. For shallow systems, like Pole Branch Creek in rural Calhoun County, our team of 5-7 samplers packed in all our gear and our backpack electrofishing unit and waded through the sites to complete our surveys. But for deeper and wider systems like the extensive Kissimmee River, we conducted our surveys via two boats loaded down with sampling equipment – one for our habitat crew, the other for our fish crew. On every system we recorded observations about habitat type and condition of the banks. We used specialized equipment and techniques to evaluate characteristics like slope, discharge and fish community assemblage. We also collected samples of water, algae, benthic macroinvertebrates, and fish tissue. All samples and data were recorded and sent to the U.S. Environmental Protection Agency (EPA) for analysis.

The National Rivers and Streams Assessment (NRSA) is a nationwide survey designed by the EPA that takes place in all lower 48 states. Rivers, streams and canals all over the country have been randomly selected for sampling. The resulting data provide an unbiased representation of our nation’s flowing waterways for comparing these systems with others in their region. This is part of a major ongoing effort by the EPA called the National Aquatic Resource Surveys. The purpose of these surveys is to assess the conditions of our nation’s waterbodies and to track them over time. NRSA is just one aspect of the big picture and takes place over two consecutive summers, occurring every 5 years. This season was the first of their 2018-19 sampling event.

As our season is wrapping up, we proudly look back at all we have learned, experienced, and accomplished this summer. This project has provided us the opportunity to use new tools and techniques, such as densiometers to measure canopy coverage and stadia rods or sonar to document channel depths and substrate type along thalwegs. It has also encouraged us to connect with other FWC offices, Water Management District personnel, and local land owners or managers. With the help of their local knowledge and expertise we have successfully completed half of the selected survey sites during this first year. We look forward to continuing this work next summer as we prepare to tackle the rest of our sites which include larger river ecosystems such as the Escambia and Apalachicola Rivers.

Our NRSA Sampling Crew included: Jamie Richardson, Kyle Miller, Emily McPartlin, Amanda Christensen (volunteer), Greg Knothe, Siobhan Gorham, & Craig Mallison. A special thanks to: Travis Tuten, John Knight, Kate Harriger, Chelsea Myles-McBurney, Kayla Smith, & Jason O’Connor for their assistance.

Bivalves to the Rescue: Can Bivalve Grazing Outpace HAB Growth?

By Cary Lopez, Sugandha Shankar and Steve Geiger

FWRI HAB and molluscan fisheries groups are collaborating on a one-year project funded by the Tampa Bay Estuary Program to investigate if the creation of shellfish nurseries as part of restoration efforts could have the added benefit of interfering with Pyrodinium bahamense bloom development. P. bahamense is a toxic dinoflagellate that forms high biomass blooms in Old Tampa Bay, the Indian River Lagoon (IRL), and other systems in Florida each summer. These blooms can cause shellfish harvesting area closures due to presence of paralytic shellfish poisoning (PSP) toxins (

A hard clam extends its siphon to filter-feed when exposed to a dense culture of Pyrodinium bahamense in our most recent experiment. The algal cells are seen as light brown clusters above the clam.

As filter feeders, bivalves can clear particles from over a liter of water every hour for each gram of dry body weight when feeding optimally. Clams can have up to ~ 5 grams of tissue, so that’s a lot of algae consumption! The goal of this research project will be to investigate how well targeted bivalve molluscs can feed on toxic P. bahamense. Molluscs that consume P. bahamense become toxic and cannot be consumed by humans, but they still play a critical role in healthy estuaries. We are conducting our first set of experiments with hard clams (Mercenaria spp.), and the next focus will be eastern oysters (Crassostrea virginica). If successful, these experiments may be scaled up to mesocosms once ideal species are identified.

Check out this video illustrating clam feeding efficiency!

Assessing the Impacts of Hurricane Irma

By Dr. Ryan P. Moyer

The Coastal Wetlands research group at the Florida Fish and Wildlife Research Institute (FWRI) received a grant from the National Fish and Wildlife Federation (NFWF) to assess the impacts of Hurricane Irma to coastal wetland habitats of southwest Florida. Since 2014, the FWRI Coastal Wetlands group along with partner organizations, has been working in coastal marshes and mangroves across Southwest Florida, including Tampa Bay, Charlotte Harbor, Ten Thousand Islands, Biscayne Bay, and the lower Florida Keys. All pre-existing field sites were located within 50 km of Hurricane Irma’s eye path, with a few sites in the lower Florida Keys and Naples/Ten Thousand Islands region suffering direct eyewall hits. Since all locations include active field sites, a wealth of pre-storm data exists, and these locations are uniquely positioned to evaluate and quantify post-hurricane damage to standing biomass and ecosystem services across a wide geographic area.

Map showing the location of field sites in proximity to the path of Hurricane Irma. Pre-existing study sites are given for each area in the inset boxes at right.

Initial Post-Irma field assessments focused on qualitatively assessing and photographically documenting damage (e.g. defoliation, downed trees, redistribution of sediments, etc.). Upon identification of the habitats that experienced the most damage, storm impacts were then categorized as low-, moderate-, and severe-impacts based upon physical habitat damage and distance from eyewall path, height of storm surge, and maximum wind speed experienced during the hurricane. Quantification and monitoring of aboveground damage included measurements of indicators of defoliation (canopy coverage), mortality (recently felled trees and branches), plant community structure (tree diameter or height), and recovery (seedling percent coverage or density). Recovery of mangrove forest was assessed by subsequent visits to long-term monitoring plots in the six months following Hurricane Irma. Sedimentary impacts were also examined and included elevation change, shoreline erosion, and geochemical characterization of storm-derived sedimentary deposits.

Example of severe damage to a mangrove forest in the Ten Thousand Island due to Hurricane Irma. This site was directly under Irma’s eye path as Category 3 storm and was found to have complete loss of leaves in the canopy (defoliation) and numerous downed trees. Canopy cover is typically 80-100% in non-impacted forests.

Preliminary findings indicate a reduction in mangrove canopy cover from 70-90% pre-storm, to 30-50% post-Irma, and a reduction in tree height of approximately 1.2 m. Although signs of forest recovery and shows signs of slow regrowth, mangrove seedling density has significantly increased in the six months post-Irma. A sedimentary layer of fine carbonate mud up to 10-cm thick was imported into the mangroves of the lower Florida Keys, Biscayne Bay, and the Ten Thousand Islands. A siliciclastic mud layer up to 5-cm thick was observed in the marshes of Charlotte Harbor. All sites had imported tidal wrack consisting of a mixed seagrass and mangrove leaf litter, with some deposits as thick as 6 cm. In areas with newly opened canopy, a microbial layer was coating the surface of the imported wrack layer. Overwash and shoreline erosion were also documented at two sites in the lower Keys and Biscayne Bay and will be monitored for change and recovery over the next few years, pending subsequent funding. Due to changes in intensity along the storm path, direct comparisons of damage metrics can be made to environmental setting, wind speed, storm surge, and distance to eyewall. This information will help provide direct evidence of hurricane impact and recovery trajectories in coastal wetland ecosystems in Florida. The data will be shared with coastal ecosystem managers in order to enhance management and response planning for large natural disasters in Florida such as hurricanes.

Project partners included the U.S. Geological Survey, University of South Florida Saint Petersburg, Rutgers University, Nanyang Technical University, the University of Rhode Island, Tufts University, University of South Florida College of Marine Science, and the US National Park Service.