Category Archives: Ecosystem Assessment and Restoration

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.

Coral Disease Outbreak

by Vanessa Brinkhuis

Colpophyllia natans colony with unknown “White Blotch” disease exhibiting several multifocal central and peripheral white lesions with bare exposed skeleton with turf algae.

Coral disease is recognized as a major cause of reef-building coral mortality and reef degradation. The first reports of coral disease in the Florida Keys and Caribbean emerged in the 1970’s. Since that time, worldwide reports have been increasing in frequency. From spring 2015 to present, coral disease outbreaks, which are greater than natural background disease levels, have been reported offshore Southeast Florida, within the Upper Keys and Dry Tortugas National Park. Initial reports in 2015 indicated disease outbreaks were occurring offshore Miami-Dade County. Since those initial reports, further disease outbreaks are being reported in areas north and south of the initial outbreak area.

Siderastrea siderea colony with unknown “White Blotch” disease. Multifocal to coalescing white-purplish lesions with exposed bare skeleton at the center of lesion.

During the Coral Reef Evaluation and Monitoring Project (CREMP)’s annual survey effort at Grecian Rocks in the Upper Keys in July 2016, the team observed what appeared to be multiple diseases on at least 11 species of scleractinian coral.  Species affected include Colpophyllia natans (Figure 1), Pseudodiploria strigosa (Figure 2),  Diploria labyrinthiformis, Meandrina meandrites, Dichocoenia stokesii (Figure 3), Siderastrea siderea (Figure 1), Montastraea cavernosa, Orbicella annularis, Eusmilia fastigiata, Undaria agaricites and Porites astreoides.  The diseases observed include what appear to be White Plague (Figures 2 and 3), the unknown white disease that is being called “White Blotch” (Figures 1 and 4), and other indistinguishable white diseases.  The CREMP team photographed affected colonies and prepared a summary report of the outbreak.

The following week, the CREMP team sampled coral colonies affected with the unknown White Blotch disease at the affected site and conducted prevalence surveys, which document the amount of coral colonies of the population affected by disease. For tissue sampling, four species were targeted, including M. cavernosa, S. siderea, C. natans and D. labyrinthiformis, for histopathology and molecular samples. Prevalence surveys (11, 10mx1m belt transects) revealed that 100% of M. meandrites colonies, 66.7% of D. labyrinthiformis colonies, 53.3% of M. cavernosa colonies, 50% of D. stokesii colonies, 50% of P. strigosa colonies, 42.3% of S. siderea colonies, 33.3% of C. natans colonies and 33.3% of E. fastigiata colonies were actively diseased or recently dead. An investigation is ongoing to determine the extent and etiology of the disease outbreak.

Studies of Turtle Grass Reproductive Success in Tampa Bay

By Sheila Scolaro and Mike Poniatowski, Ecosystem Assessment and Restoration

As part of a NFWF- funded study, we are investigating the reproductive success of turtle grass (Thalassia testudinum) in panhandle estuaries and in Tampa Bay.

Turtle grass and other seagrasses are land plants that moved back into the ocean over geological time. As a result, they produce flowers that look a lot like chickweed (Stellaria sp.) that appears in yards each spring. Seagrasses spread asexually by vegetative fragments (shoots and rhizomes) and sexually by seeds or, in the case of turtle grass, viviparous seedlings.  Male and female flowers are on separate Thalassia shoots, and pollination is haphazard.  Thirty years ago, FWRI scientists Mark Moffler and Mike Durako determined that seedling production was very limited here in Tampa Bay.

This study is important because, in many areas where seagrasses have been lost in the past, recruitment might limit seagrass recovery.  Our study is just beginning, but we have made some preliminary observations.

Here in Tampa Bay, flowering is very patchy in time and space and flowering activity is most common in spring. Interestingly, flowers are more common (or maybe more easily seen) in turtle grass beds with lower shoot densities. As reported by Moffler and Durako, we have also seen that successful production of fruits and seedlings is uncommon in Tampa Bay, but we don’t know why that’s the case.  As we continue this study in 2017, we will visit as many spots around Tampa Bay as we can to find Thalassia flowers and follow those plants through the summer to determine success in seedling production and establishment.  We will also carry out parallel studies in Panhandle estuaries.

Please record locations and email if you see turtle grass flowers next spring.