Category Archives: Notes from the Field

Wrapping Up the Statewide Reddish Egret Survey

By Andrew Cox

The reddish egret (Egretta rufescens) is North America’s rarest heron and is state-listed as Threatened in Florida. In 2016 we visited 305 coastal islands during the first statewide survey of the species to document its distribution, estimate Florida’s population size, and learn more about its nest-site selection patterns. In 2017 we attended to the less glamorous side of our work – sitting at our desks, crunching numbers and writing.

Reddish egrets were primarily concentrated in four areas of Florida: in and near Merritt Island National Wildlife Refuge, Florida Bay, the Lower Keys, and the Tampa Bay area south to Marco Island. The species has continued to slowly expand northward on the Gulf coast, with nesting occurring in Cedar Keys National Wildlife Refuge. There were an estimated 480 (95% CI: 375–606) nesting pairs at the 58 sites where birds we found birds. The largest colony we found had 23 nesting pairs, which is fewer than the three largest colonies documented in Florida Bay during 1978. Half of all colonies had 3 or fewer pairs.

Reddish egret foraging behavior can be something of a spectacle as birds move throughout tidal flats and other shallow estuarine waters in a graceful, high-energy pursuit of prey. Foraging habitat is probably the largest limiting factor for reddish egret populations, and our nest-site selection analysis confirmed that it was the most substantial predictor of occupancy and abundance of nesting reddish egrets. These results confirm the importance of incorporating foraging habitat into our restoration planning and highlight the need to understand how the shallow flats upon which reddish egrets rely will be affected by sea-level rise.

The photo accompanying this article was taken by Anne Macias. Anne was a retiree in Bonita Springs and a strong advocate for Florida’s birds. She took great pride in the colony of nesting wading birds in her neighborhood and raised awareness of their importance within her community. Our jobs are made that much easier by people like Anne. Anne unfortunately passed away earlier this year and will be deeply missed.

Fish and Macroinvertebrate Monitoring in the Lower St. John’s River Basin in Support of the Jacksonville Harbor Deepening Project

By Russell Brodie and Tim MacDonald

The U.S. Army Corps of Engineers (USACE) in cooperation with the Jacksonville Port Authority (JaxPort) have conducted a comprehensive economic, engineering and environmental study to examine the effects of increasing the depth of the existing Federally-maintained shipping channel in the lower St. Johns River (LSJR) from the current depth of 40-feet to a maximum depth of 47-feet between the mouth (Mayport, Florida) and river mile 13 (Figure 1). The channel deepening will allow access of larger vessels (Panamax and New Panamax classes) to deliver cargo to existing JaxPort terminals around Blount Island. The initial phase of dredging began in February 2018.

Figure 1. Map of lower St. Johns River (LSJR) highlighting the area being dredged (river mile 0-13; orange line) and the select tidal tributaries (Trout, Arlington, and Ortega rivers) and the Mill Cove area included in this project funded by the USACE (purple shading). River miles (small circles) represent 1-mile increments along the marked channel. Red lines indicate existing bridges. Base map with river miles and inset created by the SJRWMD and adapted by the FWC FIM program to highlight the current project.

As part of the project evaluation, computer modeling scenarios were completed on the potential effects that the channel deepening might have on water quality, circulation patterns, salinity gradients, and a variety of ecological components (wetland vegetation, submerged aquatic vegetation, benthos, plankton, and nekton [macroinvertebrates and fish]) in the LSJR. Over 100 nekton species have been documented by the Fisheries-Independent Monitoring (FIM) program at the Florida Fish and Wildlife Conservation Commission’s (FWC) Fish and Wildlife Research Institute (FWRI) as using the estuarine portion of the LSJR and many of the species represent important commercial and recreational fisheries. During the evaluation, there were two specific areas the FIM program felt were in need of consideration with respect to nekton: 1) the potential effects of salinity changes on the spawning success, recruitment, and population dynamics of important recreational, commercial, and forage nekton and, 2) the potential effects of salinity changes on critical nekton habitat within the LSJR estuary.

Within the estuary, channel deepening has the potential to affect salinity and water quality gradients, most likely by shifting distributions in these gradients within the estuary. These shifts may affect spawning and nursery habitats and ultimately influence the reproductive and recruitment success of estuarine-dependent nekton. Of particular concern are the tidal tributaries in the LSJR near and upriver from the area being dredged. These tributaries between river miles 15 and 30 (Trout, Arlington, and Ortega rivers; Figure 1) and the estuarine section between Julington Creek (river mile 40) and Palatka (river mile 82; Figure 2) are highly influenced by freshwater inflow and generally have lower salinities than other portions of the LSJR estuary. The freshwater influence in these sections of the LSJR provides low salinity habitats that many estuarine and marine nekton require during their early life history stages. Previously collected data in these tributaries suggests that many recreationally and commercially important estuarine-dependent species (i.e. members of the Sciaenidae family [i.e. red drum, spotted seatrout, atlantic croaker, spot], white shrimp, blue crab, and mullet) utilize these habitats and that these areas likely represent critical habitats for maintaining healthy stocks of these species in the LSJR estuary and adjacent coastal waters. Also of concern with regards to potential changes in salinity would be impacts on resident freshwater species, especially within the Trout, Arlington, and Ortega rivers. Salinity increases could decrease the availability of freshwater habitat, thereby reducing the abundance of freshwater species in these tidal tributaries. The Mill Cove area, although freshwater inflow is limited, is also of concern because the salinity modeling done by the Corps identified it as the area most likely to experience the greatest salinity changes. Young-of-the-year (YOY) and juveniles from numerous nekton species utilize this habitat during ingress, egress, and as nursery habitats.

Figure 2. Map of lower St. Johns River (LSJR) highlighting the long-term sampling area between Julington Creek (river mile 40) and Palatka (river mile 82; purple shading) previously funded by the SJRWMD and now funded by this USACE project. River miles (small circles) represent 1-mile increments along the marked channel. Red lines indicate existing bridges. Base map with river miles and inset created by the SJRWMD and adapted by the FWC FIM program to highlight the current project.

Since 2001, the Fisheries-Independent Monitoring (FIM) program has monitored nekton abundance and distribution in the LSJR estuary downstream of Julington Creek (river mile 40; Figure 1). Between 2005 and 2016, funding from the St. Johns River Water Management District (SJRWMD) enabled the FIM program to extend sampling upriver from Julington Creek (river mile 40) to Palatka (river mile 82; Figure 2). The FIM program uses a multi-gear approach in a stratified-random sampling design to collect data on nekton from a wide range of habitats and life history stages. Water chemistry, habitat, and physical parameters are recorded at each sampling site. The FIM program sampling was designed to monitor fishery resources in the estuary as a whole and, therefore, does not include individual tributaries as specific sampling strata, but instead includes them as portions of larger geographic strata. The spatial extent of the tributaries is very small compared to that of the entire estuary, so the individual tributaries are often underrepresented and inconsistently sampled in the current sampling design. Data from the existing FIM program design, therefore, are not sufficient to assess changes in nekton composition and abundance due to perturbations, such as a channel deepening, within specific areas (tidal tributaries and coves). Estimating impacts to the nekton assemblage from the channel deepening in these areas requires a sampling strategy that focuses on these specific areas of the LSJR estuary.

To gain a better understanding of the relationships between channel deepening, salinity, water quality, water flow, estuarine habitats, and the abundance of estuarine-dependent and freshwater-resident species that inhabit the identified areas of the LSJR, the FIM program and the USACE have developed a long-term monitoring project to determine the impact of the dredging activities on the spatial distribution and abundance of nekton within the LSJR. The long-term monthly sampling, which began in May 2017, and has the potential to run through 2035 (funding dependent), will increase the resolution of nekton data within the identified tidal tributaries (Trout, Arlington, and Ortega rivers) and the Mill Cove area (Figure 1) as well as continue the long-term sampling upstream of Julington Creek (Figure 2), for which funding from the SJRWMD was withdrawn at the end of 2016. This project will allow for the assessment of the effects of channel deepening on nekton assemblages in these critical LSJR estuarine habitats.

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 (http://myfwc.com/media/3323422/Pyrodinium-bahamense-factsheet.pdf).

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!

Changes in Seagrass Within Indian River Lagoon System

By Renee Duffy

Modern methods of remote acquisition, image data processing and modeling have presented new opportunities to research and better understand the complexities of seagrass ecology. The high spatial and spectral resolution information provided by modern airborne sensors such as satellite imagery presents opportunities to monitor subtle yet ecologically important changes in seagrass abundance.

In 2016, FWRI’s Center for Spatial Analysis received funds from FDEP’s Coastal Management Program to quantify long term changes in seagrass cover within the Indian River Lagoon (IRL) system. The demand for improved mapping and monitoring submerged resources in the IRL was driven, in part, by unprecedented losses in seagrass resulting from several algal ‘super bloom’ events starting in 2011.

The study employed a supervised classification method to map seagrass percent cover by relating spectral values in the satellite image to percent cover observations collected at fixed station transects by the St. John’s River Water Management District (SJRWMD) and the Ecological Program at NASA’s Kennedy Space Center.

Worldview-2 satellite imagery and seagrass percent cover observations along a fixed station transect routinely monitored by the SJRWMD.

Results indicated considerable declines in percent cover between 2010 and 2016. The extent of seagrass loss, however, was spatially and temporally variable throughout the lagoon system. Throughout the study area, seagrass cover was highest in 2010 and 2011 just prior to the 2011 super bloom and then declined considerably in 2012. In several areas, there were signs of recovery with increased percent cover in 2013, however, seagrass declined in 2015 and was nearly absent in most areas by 2016.

Declines in seagrass percent cover were highest in the southern portion of the Indian River Lagoon and throughout the Banana River with as much as 100% loss of the densest seagrass (75-100% cover). While complete loss of seagrass was observed by 2015 and 2016 in some areas, there was a general pattern of “thinning” in seagrass percent cover throughout the study area. This pattern is characterized by replacement of dense seagrass (>50% cover) with sparse, low density seagrass (<25% cover). The extent of this variation was not detectable from small scale in situ transect monitoring nor from temporally limited aerial photography. Results of the study emphasized the need for evaluating landscape-scale variability in seagrass percent cover using a variety of remote sensing technologies.

FWRI Researchers Catalog the José Torres Collection

By Jonny Veach

In response to the Deepwater Horizon disaster in 2010, USF Professor Emeritus Dr. José J. Torres spearheaded a study to assess the oil spill’s effect on deeper, mesopelagic and midwater species that were migrating vertically through oil plumes – “RAPID Deepwater Horizon Oil Spill: Impact of sub-surface oil plumes on mesopelagic fauna”.

The “RAPID Deepwater Horizon Oil Spill” study obtained a wide array of mesopelagic fauna, including the deep sea hatchetfish, as seen above. Specifically, the Deepwater study sought to document the effects of the oil spill on the highly diverse and vertically mobile fish and crustacean species of the water column, since most species reside at depths below 600 meters during the day, but migrate into the upper 250 meters at night. Because of this migration, a large portion of the mid-water community would be migrating through oil plumes. Because of a very deep well-head and extensive use of dispersants, the chances that these organisms would encounter petroleum hydrocarbons was very high. The data collected in this project provides a stable isotope baseline allowing for evaluation of present and future subsurface oil impact.

Various specimens being identified by FWRI researchers.

Researchers at the FWRI are currently in the process of determining exactly what species are present in the Torres collection. Some of the groups represented in the samples are diverse species of fishes, shrimp, jellyfish, amphipods, pyrosomes, salps and more. Many of these species have bioluminescent organs or other adaptations for living in the dark. One of our FWRI interns, Vang Thach, is working through the invertebrates to definitively identify which species are present.

There is currently no active research involving these specimens, but by cataloging and inventorying the collection, they will be made available for research purposes. FWRI received the collection from Dr. Torres in April 2013. The Torres collection is particularly noteworthy because the FWC doesn’t normally collect at these depths for usual monitoring programs. These deeper water specimens are very valuable in part because of the expense of physically collecting these specimens. The Torres collection is here to stay as a permanent collection item for the FWRI, to serve as an important looking-glass into mesopelagic gulf species for the future.

Florida Bonneted Bat Roost Selection: Implications for Conservation

By Elizabeth Braun de Torrez

The Florida bonneted bat (Eumpos floridanus), which occurs only in Florida, is federally endangered and extremely rare. These bats can traverse extensive areas to forage but their distribution may be restricted by the availability and security of roosting sites. However, we know very little about what types of natural roosts the bats use or whether tree roosts are readily available across the landscape. In our current study, we are working to identify and characterize previously unknown roost locations in conservation areas across southwest Florida. This information will allow us to protect existing roost structures and to develop guidelines for conserving or enhancing roosting habitat for this species.

Building upon research started with the University of Florida, we are using a combination of acoustic surveys, mist netting and radio-telemetry. Florida bonneted bats are notoriously difficult to capture in mist nets due to their high-altitude flight, and prior to our recent research this species had only been captured once away from known roost sites. Using a technique we developed involving an acoustic lure that broadcasts conspecific social calls to attract this species to nets, we now have the ability to capture free-flying individuals, attach radio-transmitters and track them back to unknown roost sites using radio-telemetry.

Florida bonneted bat with VHF radio-transmitter attached to break-away collar.

To capture bats, we erect a triple high mist net system (9 m high) coupled with an acoustic lure. Upon capture, we identify the individual’s species, sex, reproductive status and take standard measurements (e.g., mass, forearm length). We also collect a 4mm wing biopsy and guano sample for genetic and diet analysis. For adult, non-pregnant Florida bonneted bats, we secure a VHF radio-transmitter attached to a break-away collar and track the bats to roost structures using a combination of aerial and ground-based radio-telemetry. Due to the suspected distance that these bats are capable of flying between foraging areas and roost sites (ca. 25 miles) and the challenges of navigating throughout the south Florida terrain, aerial telemetry is essential to locate roost sites!

Once we locate a potential roost, we verify occupancy and colony size by counting the number of Florida bonneted bats that emerge around dusk, and measure characteristics of the roost tree (e.g. height, size and orientation of roost opening). We also measure characteristics of the surrounding vegetation (e.g., tree density, canopy height, canopy cover) in a plot around the roost tree and at four random tree plots.

Royal palm snag in Fakahatchee Strand Preserve State Park containing 80 Florida bonneted bats. This is the largest known colony for this species.

We are in the process of compiling data from natural roosts that we have located, in conjunction with our research partners, over the last several years. In total, we have located 17 roost trees, with 5 new roosts located in 2018. The roosts include enlarged woodpecker cavities, cavities formed from decay, and spaces under loose bark, and they occur in live and dead long leaf pine, slash pine, royal palm and cypress trees. Colony sizes range from 1 individual to a new record of 80 bats in a recently discovered royal palm roost in Fakahatchee Strand Preserve State Park in May 2018. Of these 17 roost trees, 6 have since been damaged or destroyed by fire or hurricanes. Ultimately, we will use the data collected on new Florida bonneted bat roost structures to examine patterns of roost site selection relative to a variety of local and landscape-scale variables, and make appropriate habitat management recommendations.

Bar Hopping: Searching for Imperiled Species in the Escambia River

By Kayla Smith and Chelsea Myles-McBurney

Our freshwater fisheries biologists in the panhandle are working on an imperiled species trawl survey in the Escambia River. Crystal darter (Crystallaria asprella), Gulf sturgeon (Acipenser oxyrinchus desotoi), saddleback darter (Percina vigil), pallid chub (Macrhybopsis sp. cf aestavalis), southern logperch (Percina austroperca) and river redhorse (Moxostoma carinatum) are listed as species of greatest conservation need, and are not routinely sampled during long-term fish monitoring surveys. These species share an important aspect of their life history: the use of gravel substrate is required at some point in their lifetime, making them gravel obligate species.

A crystal darter, freshly plucked from the Escambia River.

Prior to this project, only 11 crystal darters have been collected on the Escambia River since the 1970s. Crystal darters are known only to occur in the northern-most reaches of the Escambia River and little information exists on their distribution and habitat use. Using a mini-Missouri trawl, crystal darters and the other species mentioned above were targeted over gravel and sand bars. Since 2016, 357 trawls were conducted successfully. A total of 37 species were collected including five of the target species for the project. Although crystal darters are relatively rare, a total of 29 were collected during two years of sampling. These 29 individuals were all tagged using visual implant elastomer to determine if recapture was occurring.

Trawling was conducted both during the day and at night; however, researchers found that night trawling was much more successful at capturing crystal darters. In addition to the increase in crystal darters, researchers also captured a river redhorse, which had not been documented in the Escambia River since 1976. This individual was implanted with an acoustic tag and released. The movement of this fish will be monitored using Vemco VR-2 receivers to estimate site occupancy and assess population trend.

Small Investment, Big Returns

By Phil Stevens 

The acoustic telemetry research activities in the Finfish Biology subsection of Marine Fisheries Research continue to deliver . . . in surprising fashion.

Answering concerns expressed by Florida panhandle anglers about the status of cobia in the Gulf of Mexico, a pilot project was conducted in Pensacola, Florida seeking to connect cobia (Rachycentron canadum) research between Gulf and Atlantic waters. And connect it did!

Typically, cobia, a coastal migratory species, are abundant along panhandle beaches during spring. The popular paradigm is that cobia migrate from warm wintering grounds in south Florida towards the productive Mississippi delta. Northern gulf anglers have noted decreases in catches during recent years and tournament records appear to support these anecdotal observations. Partly in response to these concerns, the FWC reduced daily bag limits of cobia in state waters of the Gulf of Mexico. Researchers formed relationships with knowledgeable captains to facilitate this pilot project, creating important relationships upon which future research by FWC and other institutions will be based. Thanks to their eager cooperation, six cobia were tagged with acoustic transmitters off Pensacola and two acoustic receivers were deployed in April 2017.

Tequesta biologist Jim Whittington surgically implants an acoustic tag into a cobia.

The receivers were retrieved by Finfish Biology divers in late May 2018. Logic and experience suggest such a low saturation of transmitters and receivers would have a low probability of yielding meaningful results. But, half of the six cobia were detected on the Pensacola receivers within miles of where they were originally tagged. Another tagged cobia was harvested farther east at Destin, Florida on November 2, 2017. Surprisingly, one Pensacola tagged fish was detected on receivers deployed off Cape Canaveral along the Atlantic coast of east-central Florida!

But it gets even better. The two Pensacola receivers that were deployed detected two cobia that were originally tagged off Cape Canaveral during Aug. 3-4, 2016. One of these was detected on receivers in the Florida Keys, then was detected later at two stations off Pensacola in June and July, 2017. It then returned to the Ft. Pierce area in southeast Florida where it was harvested on December 3, 2017. The other cobia that was tagged at Cape Canaveral was detected on receivers in the Keys, and was last detected off Pensacola on May 1, 2018.

The results of this pilot project with its scant resources have been significantly more fruitful than expected. The boundaries of the Gulf of Mexico cobia stock include southeast Florida based on genetic analysis. What appear to be fairly regular movements of cobia between at least Pensacola and Cape Canaveral supports this stock delineation and provides information on the northern extent of the stock boundary in southeast Florida, which has been uncertain. Expanded research should continue to close knowledge gaps about this important gamefish.

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.

Effects of the 36-year closure and opening of Joe Bay on fishes and recreational fisheries

By Kerry Flaherty-Walia and John Davis

Major portions of the coastal embayments in northeastern Florida Bay have been closed to public access, and thus to recreational fishing, since the creation of the Crocodile Sanctuary in 1980. The 2015 Everglades National Park (ENP) General Management Plan called for the opening of Joe Bay, which is part of the Crocodile Sanctuary, to public, non-motorized access and catch-and-release fishing. The Fish and Wildlife’s Research Institute’s Fisheries Biology and Fisheries-Independent Monitoring (FIM) programs are involved in a cooperative study with Florida International University, the Snook and Gamefish Foundation, the Audubon Society, and the National Park Service to examine the effects of the 36-year closure and subsequent opening of Joe Bay to catch-and-release fishing.

Locations of Little Madeira Bay, Joe Bay and Long Sound in Florida Bay.

To examine the effects of the closure on fish and macroinvertebrate (nekton) community metrics and recreationally important fish species, fisheries-independent and -dependent sampling methods are being employed across three embayments from 2016-2019 (Figure 1). Two of the embayments are in the Crocodile Sanctuary; Little Madeira Bay has been and will remain closed to fishing while Joe Bay was opened to fishing in November 2016. A third embayment, Long Sound, is not in the sanctuary and has been open to fishing the entire time.  Although the three coastal embayments appear similar in size and function, there are substantial environmental differences among the basins. Freshwater inflow into Joe Bay is much greater than the other two basins, and sediment depth and the amount of submerged aquatic vegetation (SAV) are quite low. Long Sound also has a very thin sediment layer but typically had the highest salinity, and in recent years, has experienced an increase in SAV cover. Little Madeira Bay has both a thick sediment layer and a consistently high percentage of SAV cover that includes Thalassia, indicative of a climax seagrass community. These existing spatial and habitat relationships will affect the prey base and recreational fishes and will be considered in assessing the effectiveness of the new management strategy.

Fisheries-independent surveys are being conducted during wet and dry seasons by FWC using small (21.3-m) and large (183-m) seines and by FIU using baited remote underwater video systems (BRUVs) using GoPro technology (Figure 2). In the first year of seine sampling, nekton communities differed significantly among basins; relative abundance of nekton was greatest in Little Madeira Bay, and the most numerous species were small-bodied fish that serve as the prey base, such as killifishes, mojarras, gobies, and schooling fish (silversides and anchovies), collected by the small seine. Unfortunately, the large seine technique (which collected the majority of recreationally important species) was only used in Long Sound and Little Madeira Bay because the depths and substrate in Joe Bay are not suitable to this sampling gear. The BRUVs, however, were deployed in all basins, and in contrast to the seine sampling, indicated that community composition was similar across basins.  Recreationally important species were most frequently observed in Little Madeira Bay in seines, but in Joe Bay on BRUVs. Sharks were seen frequently on video in Little Madeira Bay and may be affecting BRUV observations there. Trophic groups (small prey, large prey, mesoconsumers, and top predators) appeared stable over time as compared to previously collected seine data using the same methodology from 2006-2009, but there was preliminary evidence of species-specific differences within basins and over time.

Three methods are used to determine the effects of the fishing closure: A. BRUVs, B. Seines, C. Angler Reporting System.

Fisheries-dependent information is being obtained through an angler reporting system developed in conjunction with FIU, the Snook and Gamefish Association, and the Audubon Society (Figure 2, paper surveys and a mobile application). So far, the angler reporting system has a good response rate, but visitation to the recently opened no-motor zone in Joe Bay was low.

Two more years of sampling are ahead for this project, so more comprehensive data analyses incorporating hydrological and habitat dependencies are planned.  Seine and BRUV nekton community data will be compared between gears and across estuaries, and the long-term trends in visitation and angler experiences documented by the angler reporting system will be examined. This project will provide useful data for developing a long-term protocol for fisheries monitoring in these embayments into the future and demonstrates the advantage of collaborative research to reach a common goal.