Category Archives: Ecosystem Assessment and Restoration

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.

A Light in the Fog: Shipboard Genetic Quantification of the Red Tide Alga Karenia brevis

By Alicia Hoeglund, Matt Garrett and Mary Harper

On January 11, on FIO’s new research vessel (R/V) the W. T. Hogarth, FWRI-HAB researchers assisted USF in deploying new infrastructure for oceanographic sensors and took advantage of this opportunity to test hand-held genetic sensors that can detect the red tide alga, Karenia brevis, in water samples collected while onboard. The genetic detection project, funded through a NOAA Prevention Control and Mitigation of HABs (PCMHAB) grant, utilizes a field-friendly approach that can provide genetic quantification of K. brevis in approximately one to three hours from the time of sample collection (see: Samples collected just west of the Skyway Bridge and off of Pass-a-Grille (Pinellas County) were tested during this trip and provided our researchers with some of the lowest field concentrations of K. brevis observed with this technology to date: approximately 108 cells L-1 and 42 cells L-1, respectively. The limit of detection using our routine light microscopy procedure is 333 cells L-1, making this a very promising find for the development of this project!

Syringes funnel the sampled water into a column that contains the filter to which the RNA binds.

Although this was intended to be a short-day trip, thick sea fog delayed both the departure and the return of the R/V W.T. Hogarth, with researchers spending an unanticipated night at sea. A short reprieve from foggy conditions allowed the port to reopen briefly early in the morning of the 12th, and sea fog continued to impact the area throughout that day. A subsequent trip completed the installation of USF’s oceanographic sensor system, and water current, meteorological, and wave data are now being reported every one to three hours (

Deployment of the real-time waves system and meteorological sensor: Once the concrete bottom mount and the Acoustic Doppler Current Profiler was dropped in the water by the ship’s crane, divers descended to remove the deploy cables and ensure the instrument was in the proper location and orientation.

CREMP Program

The Coral Reef Evaluation and Monitoring Project (CREMP) is one of the longest running coral reef monitoring projects along the Florida Reef Tract- the world’s third largest barrier reef system. FWRI biologists visited Dry Tortugas National Park to monitor the condition of coral reef and hardbottom habitats.

Top photo: A field of bipinnate sea plumes (Antillogorgia bipinnata) behind a woody barrel sponge (Xestospongia muta).

View Flickr set here:

Threats Assessments on the Peace and Withlacoochee River Watersheds

By Greg Knothe

By canoe, boat and airboat the threats assessment team (A.K.A. “The Bankfull Boyz”) are covering hundreds of river miles inventorying areas of habitat degradation on the Peace and Withlacoochee Rivers and major tributaries. Indicators of habitat degradation include:

  • active streambank erosion
  • streambank mass-wasting
  • sediment deposition
  • riparian zone degradation
  • channel alteration
  • potential areas of non-point source pollution

We are following a rapid assessment methodology developed by the United States Fish and Wildlife Service (USFWS) Panama City Ecological Services Office and David Rosgen’s Watershed Assessment of River Stability and Sediment Supply (WARSSS).

The whole project really boils down to sediment and river stability. So, why are we so fed up with sediment? The United States Environmental Protection Agency ranks sediment as the leading cause of water quality impairment in streams and rivers. Stream channel instability and accelerated erosion can have severe biotic impacts on food chains, habitat complexity, spawning and rearing habitats, instream cover and temperatures.

An example of a mass wasting bank assessed and inventoried during surveys on the Peace River.

The threats assessment project is a 3-year State Wildlife Grant funded study which is administered through FWC’s Florida’s Wildlife Legacy Initiative (FWLI). The project is match funded by FWC’s Aquatic Habitat Enhancement and Restoration Subsection (AHRE). The FWLI’s State Wildlife Action Plan listed the Peace and Withlacoochee as high ranking watersheds for habitat enhancement since they exhibit high potential for urban development, a high number of threats and a high number of Species of Greatest Conservation Need. The project is a joint venture with principal investigators within FWRI’s Ecosystem Assessment and Restoration (Freshwater Plants Program) and the Division of Freshwater Fisheries Management, and collaborators including the USFWS and AHRE.

The Peace River (106 miles) flows south from its headwaters in Green Swamp to Charlotte Harbor, Florida’s second largest open water estuary. The Peace River Watershed has experienced high levels of habitat degradation due to urbanization, agriculture, phosphate mining and altered flow regimes. While water quality in Charlotte Harbor is generally considered “good,” the Southwest Florida Water Management District expressed concern regarding reduced streamflow in the Peace River and areas within the river where water quality ranked “fair” or “poor.” The threats assessment team has located, scored and inventoried an alarming 353 impairment sites on the Peace River and major tributaries, to date. The highest concentration of impairment sites is located in the river corridor between Zolfo Springs and Gardner. Most impairment sites appear to be a result of poor cattle grazing practices. In part, we theorize that the uprooting of countless trees by Hurricane Charley in 2004, in combination with cattle grazing, led to deterioration of the riparian zone and high channel instability.

The Withlacoochee River (141 miles) originates in the Green Swamp and flows northwest through a diverse range of habitats to Withlacoochee Bay before flowing into the Gulf of Mexico. High urban development, pollution and altered flow regimes pose several threats to water quality within the watershed. Although the Withlacoochee River Watershed has been significantly altered through the construction of the Lake Rousseau Dam in 1909 and the Cross-Florida Barge Canal in the 1930’s, we have identified very few impairment sites (24 sites to date). This is largely due to the river and tributaries having an intact and vigorous riparian plant community, and there is little agriculture within the river’s riparian habitat. Another reason we are finding few impairment sites in the Withlacoochee River is because it was dammed. As a result, water levels were stabilized, which decreases stream power and shear stress, which in turn can decreases streambank erosion. So, while finding few impairment sites sounds like a positive thing, it’s a double-edged sword. The Withlacoochee River does not function like a free-flowing river and like the major issue with all reservoirs, we alter the natural flow regime of the system. Consequently, it’s common for rivers to be over widened above the dam due to backwatering and increased sediment, while being deeper and narrower below the dam since they are sediment starved (commonly called “Hungry Water”).

The Threats Assessment Team (from left to right Kyle Miller, Matthew Phillips and Greg Knothe) at the 2017 Charlotte Harbor National Estuary Watershed Summit.


The overall goal of the project is to develop a prioritized list of restoration projects for each watershed. Preliminary recommendations for proposed restoration actions include a passive approach of fencing out cattle from rivers and riparian habitat, and allowing degraded areas to naturally restore. In more highly disturbed areas, an active restoration approach would be required including re-grading high slope or mass wasting banks, creating a bankfull floodplain bench and re-vegetation of banks to prevent further erosion. In a worst-case scenario (i.e. highly degraded and incised stream with no connection to its floodplain), a new channel could be excavated at a higher elevation with bankfull benches and floodplain connectivity.

Gonad Staging

Photo Caption: Female in early developing oocyte with cortical alveoli. It is indicative of the transition from immature to mature in the
reproductive cycle.

By Catalina Brown

The FWH group’s research project, Monitoring Offshore Reef Fish Populations, includes a comprehensive gonad staging section. Gonad staging is incorporated along with a series of other organosomatic indices which will then be applied to increase knowledge of the overall health status of specific fish species. Organosomatic indices in fish can be modified by environmental stressors, nutrition, reproduction and age. Our objective is to assess reproductive maturation, distinguish groups between males, females and transitional hermaphrodites and eventually compare health indices between fish in the same phase of reproductive maturation to identify implications of life history.

We assigned two distinct phases for males: developing/regenerating and spawning capable. Females are multifaceted, and undergo several phases of maturation. Therefore, females are categorized as immature or mature, and mature females can be further divided into three distinct sub-phases: developing, spawning capable or regressing. These phases are based on morphological changes that occur through development. Health indices of fish that are of the same sex and reproductive phase will be compared to determine if individuals at each stage are allotting a comparable proportion of energy towards reproduction.

The relationship between Organosomatic indices and gonad developmental phases will eventually provide a clear correlation between life history and overall fish health.

Assessing Differences in Insect Diversity between Pastures, Restored Sites and Flatwoods

By Cherice Smithers

Things are buzzin’ for the botany team! FWRI’s Upland Habitat team is collaborating on an insect diversity study with Dr. David Kaplan and his PhD student Kevin Henson, who are members of the Environmental Engineering Sciences Department at the University of Florida. The study is investigating how differences in plant species composition between pastures, restored sites and native flatwoods communities translate to differences in insect species composition. Insects are a key puzzle piece missing from our understanding of how to achieve functional restoration of former agricultural and pasture land, and this study will help us fill that critical knowledge gap. The findings could be used to assess habitat quality as it relates to insect assemblages, which in turn could influence management decisions seeking to restore and conserve habitat for insect taxa that fill important roles within ecosystems.

We are focusing our assessment of insect diversity on two key functional groups thought to play a central role in ecosystem processes at different trophic levels: pollinators and predatory beetles. Native pollinators, including bees, wasps, moths, butterflies, and flies, sustain many of the plant species of natural communities and serve a critical role in food webs. Beetles of the family Carabidae fill a functional role as ground predators, with diets consisting primarily of herbivorous insects and other herbivorous arthropods. Since many herbivorous insects have co-evolutionary relationships with specific plant species, by extension Carabid beetles are also indirectly linked to particular plant species assemblages.

Our field sites are located at Triple N Ranch Wildlife Management Area (WMA), Half Moon WMA, and Caravelle WMA. At each WMA, we selected a bahiagrass-dominated pasture site (representing low plant diversity), a Native Groundcover Restoration (NGCR) site (representing medium plant diversity), and a reference flatwood site (representing high plant diversity). The NGCR sites are part of an ongoing restoration effort undertaken by the Division of Habitat and Species Conservation’s Wildlife and Habitat Management Section to restore formerly agricultural and pasture land to historic native flatwoods communities. As such, the NGCR sites represent the “middle phase” of an induced succession from pasture lands to flatwoods, and are regularly monitored by the Upland Habitat team.

The Upland Habitat team collected data on the understory species occurring at each of the study sites. In addition, we have collected data on the bloom phenology at each site to help understand pollinator species abundance cycles and feeding preferences. To sample for pollinators, we have set up a vane trap filled with propylene glycol at each point . In addition, a pitfall trap filled with formalin has been set up at each point to collect carabid beetles . Upon collection, insects are stored in ethyl alcohol until they are pinned and identified. The sampling is conducted for a period of one week per month from April through September.

We have collected a wide variety of insects to date, which are currently being identified with the help of Dr. Josh Campbell at the University of Florida Entomology Department. We are hopeful that the results of this study will shed light on ways that natural areas can be managed for the conservation of insect communities and the critical ecological roles they fill.

Measuring the Rate of Mangrove Encroachment into Tampa Bay

by Ryan Moyer

The FWRI Coastal Wetlands team is also evaluating the rate of mangrove encroachment into salt marsh habitats in Tampa Bay. As the atmosphere warms and sea level continues to rise, researchers have noticed an expansion of mangrove habitat into wetland areas formerly occupied by marsh habitats.

In Tampa Bay, mangroves have replaced salt marshes as the dominant coastal habitat type along most natural shorelines. However, habitat restoration efforts with the Bay focus on planting salt marsh grasses due to the low cost and high survivability of marsh plants vs. mangrove seedlings. However, many restoration sites that were planted as salt marsh have naturally converted to mangrove systems in the years following restoration. Although coastal resource managers have grown to expect this so-called habitat switching, a major gap in understanding is the rate of change in these ecosystems and how long it will take for a newly restored salt marsh to completely switch to a mangrove-dominated habitat.

To assess this, the Coastal Wetlands group has been measuring mangrove density in restored salt marshes of various ages across Tampa Bay at sites ranging from restored within the past 18 months to sites where restoration was completed over 20 years ago. The information gained from this study will help coastal resource managers better plan for future habitat switching and prioritize conservation in resilient systems vs. those that are expected to experience marsh-to-mangrove habitat switching over fairly short time spans (<5 years). Data from this study will also be used to support FWRI Fish and Wildlife Technician Emma Dontis’ graduate studies, where she is pursuing an M.S. in Environmental Science at the University of South Florida Saint Petersburg. FWRI Associate Research Scientist Ryan Moyer, Ph.D. and Biological Scientist III Kara Radabaugh, Ph.D. are co-managing the research project and co-advising Emma’s graduate research related to the project.

Tampa Bay Critical Coastal Habitat Assessment

by Ryan Moyer

The Coastal Wetlands research group at FWRI has recently partnered with the Tampa Bay Estuary Program (TBEP) to install four permanent coastal wetland monitoring transects on public lands in Pinellas and Manatee Counties. The project will also produce a written methods manual, accompanied by a short visual video manual to help train other agencies and organizations in hopes that similar monitoring protocols can be adopted for future wetland monitoring statewide. The work uses a continuous transect approach combined with random quadrat placement in order to quantify wetland vegetation along a gradient from open water to adjacent upland forest. High-precision elevation data was also collected along to the transect to establish the relationship of wetland elevation to mean sea level at each site. Pending the availability of future funding, each transect will be revisited every 3 – 5 years in order to document changes in plant community structure or ecological zonation in response to climate change, sea-level rise, or other ecosystem stressors.

In the summer of 2016, transect sites were established at Harbor Palms park in Palm Harbor, Weedon Island Preserve in St. Petersburg, Fort DeSoto in Pinellas County, and Cockroach Bay in Manatee County, FL. The four sites established by the Coastal Wetlands team at FWRI compliment five additional sites that were installed and surveyed by TBEP in 2015 at various locations in Hillsborough County. Together, the nine permanent monitoring transects represent one of the most comprehensive ecosystem-scale wetland monitoring programs in the State of Florida. Field surveys were completed in December 2016, and work is currently focused on analyzing field data and producing the written and video training manuals.

Fish and Wildlife Health Outreach Efforts

By Catalina Brown

Fish and Wildlife Health (FWH) staff are committed to outreach projects that not only inform citizens about our role in the community regarding fish kills and disease, but also to promote the good work of other worthy, charitable causes associated with FWC.

Two outstanding outreach events that we participated in were the Steve Yerrid Kids Fishing Derby, in support of the National Cancer Pediatric Foundation, and the Tampa Bay Watch Open House.

FWH along with DMFM staff attended this year’s fishing derby to support the great work of this foundation. This annual event demonstrates that conservation and fishing are not independent. Attendees participated in a fishing rally and approximately a hundred kids went fishing with donated gear from local sponsors. FWH provided support and answered questions about habitat, fishing regulations and general “fish” questions.

On-Site Testing for Red Tide Alga

By: Katherine Hubbard

Water samples for harmful algal bloom (HAB) monitoring are collected throughout the state by numerous partners and shipped to FWRI  in St. Petersburg, where light microscopy is used to enumerate toxic species including the Florida red tide alga, Karenia brevis . These counts require expertise to discriminate K. brevis from morphologically similar, non-toxic species, and to provide critical information about the timing, extent and severity of the bloom for partners, managers and stakeholders.

Through funding from the NOAA Prevention Control and Mitigation of HABs (PCMHAB) program, researchers at FWC , the University of South Florida (USF), Mote Marine Laboratory and the Gulf of Mexico Coastal Ocean Observing System are working together to develop and test new hand-held genetic sensor technology to permit more timely and sensitive enumeration of K. brevis. The project team at USF developed this tool initially for the seafood industry – to differentiate grouper from other fish – and adapted it for HAB detection.

For the K. brevis assay, a seawater sample is collected, cells are concentrated and nucleic acids are extracted using a simplified,

Sensor amplification confirming K. Brevis after ~25 minutes

field-friendly approach. The extracted sample is then added to a cocktail of reagents including an enzyme and a fluorescent probe specific to K. brevis. These assays are placed in a battery-operated sensor, dubbed the “tricorder,” that conducts isothermal amplification of a targeted gene. The sensor measures the increases in fluorescence signal as the K. brevis-specific fluorescent probe binds to target K. brevis genes in the extracted sample. The assay has a limit of detection of approximately 800 cells L-1, is completed within an hour and the instrument displays changes in signal as the assay is running allowing confirmation of cells in as little as 5-10 minutes.

An ongoing bloom of K. brevis has provided the project team with several opportunities to conduct field trials, which have been successfully completed in Sarasota Bay (shown in the images), at Fort de Soto State Park and during a 24-hour cruise onboard the R/V Bellows. Samples collected at shore sites were processed rapidly while still on site, where microscopic and genetic counts detected similar concentrations of K. brevis. Rough seas prevented sample analysis while on the R/V Bellows and samples were instead processed in the lab after the cruise; however, future efforts aim to successfully analyze samples while onboard large or small vessels to provide timely information about bloom distributions and inform adaptive sampling.

Project team members conducting the first field trial


The project team is currently focused on simplifying and validating the K. brevis method further, and determining how variable gene copy number is across different strains of K. brevis and under different environmental conditions. This is a critical step in relating genetic and microscopic enumeration methods and automating genetic quantification, and in preparation for integrating this sensor technology into state  and citizen  monitoring programs in Florida and other states.