Category Archives: Marine Fisheries Research

Gag Grouper: Where Have All The Cowboys Gone? Evaluating Spatio-Temporal Trends in Male Abundance and Reproductive Dynamics in a Sex-Changing Reef Fish

By Sarah Burnsed, Hayden Menendez, and Sue Lowerre-Barbieri

Gag grouper (Mycteroperca microlepis) are an iconic Florida fish that may be in trouble.  All fish begin as females in estuarine nursery grounds, but as they age they move further offshore, with the oldest, largest fish turning into males (Figure 1).  This life history and spatial ecology pattern makes it difficult to decide on the best measure of reproductive potential.  Based on females-only, the last stock assessment found them to not be overfished or undergoing overfishing. But the same assessment predicted only approximately 2-3% of the population was male and since then commercial fishermen have not been meeting quota, leaving fishermen and scientists concerned that this stock may not be as healthy as assumed.

Figure 1: Conceptual model of gag spatial ecology. Seasonal information is in parenthesis, yr = year, mo = month.

 Beginning in 2015, the Movement Ecology and Reproductive Resilience (MERR) Lab at FWRI began a series of gag studies to evaluate factors affecting gag reproductive potential. Empirical data derived from these studies, including estimates of fecundity-at-age, spawning frequency and sex ratios, and spatio—temporal patterns of sex change and sex ratio, will help to refine estimates of long-term biological productivity of the stock and in turn better manage this important fishery. We describe our three major gag program initiatives below.   

Our initial study (December 2015- May 2018) off the Florida Panhandle targeted the best-known gag spawning habitat ~50-100 miles off Panama City Beach.  Three areas were sampled, with varying protection from fishing: (1) Madison Swanson, an MPA (2) The Edges, open half the year to fishing (3) an open area. Twice monthly during gag spawning season (December-May), we departed lab headquarters in St. Petersburg to drive to Panama City and boarded chartered fishing boats for multiple day cruises. We captured gag using hook-and-line and recorded parameters of time landed, location, depth and ventral pigmentation. We collected video data using an unbaited camera array with a ~360° field of view to assess habitat, spawning behavior and abundance. We evaluated all gag for lengths, weight, genetics, mercury, age, sex, hormones and maturity. Data from our collections were integrated with data from FIM surveys, FDM, and a collaborating commercial fisherman to test assumptions about sex change and spatial management in gag. Results indicate overall gag abundance is low, MPAs do not protect all recruiting males (as previously assumed) and current regulations are not sufficient for males to recover to historic levels. To read more on this study, please see: Lowerre-Barbieri S, Menendez H, Bickford J, Switzer TS, Barbieri L, Koenig C (2020) Testing assumptions about sex change and spatial management in the protogynous gag grouper, Mycteroperca microlepis. Mar Ecol Prog Ser 639:199-214. https://doi.org/10.3354/meps13273.

To assess how these results might differ with location, a second study was begun in December 2018 (extending through May 2021).  This study uses similar methods but is focused ~100 miles offshore of Tampa Bay at (1) Steamboat Lumps, an MPA and (2) the Sticky Grounds, an open area south of Steamboat Lumps, originally brought to our attention by fishermen and confirmed as a spawning site by preliminary sampling. Both habitats are quite different from those in the Panhandle with Steamboat Lumps having considerably less relief than Madison Swanson and the Sticky Grounds characterized by patchy high relief in depths greater than sites sampled before.  Because gag spawn at these offshore sites in the windy winter months, it is not surprising previous sampling in this area has been limited due to uncooperative seas and day trips requiring 18 hour runs from shore. We are fortunate to again work with an impressive group of captains willing to safely execute these trips and share their knowledge of the gag fishery to increase our success.  By expanding the area of collection, we’ll be able to identify and quantify gag spawning aggregations, sex ratios, and reproductive potential off the West Central Florida Shelf and compare these parameters to those collected in the initial study to determine spatial and temporal differences within and between study areas.

Figure 2: MERR biologist Hayden Menendez sampling blood from the gills of a gag grouper during a directed offshore charter trip. Blood is drawn immediately after capture and processed as part of a companion study to assess if hormones can help indicate transitional fish, which are difficult to determine even with histology.

These studies, and the integration of their results with the larger sampling efforts of the FIM reef fish survey and FDM, changed our understanding of where and when gag change sex.  Previously, it was believed that this occurred only on the spawning grounds and that spawning ground MPAs would protect males.  However, we found fish transitioning from females to males not only on the spawning grounds but also in pre-spawning female-only aggregations. Thus, there is a need to better understand pre-spawning aggregations, their seasonal cues, and spatial consistency, as well as sex-specific movement ecology.  Research on these questions was started in December 2017 when the same fisherman who provided samples from a gag pre-spawning aggregation site for our first study began working with us to dart tag and release gag at his nearshore site. 

 In 2019 and 2020 we increased this effort to include scientific sampling of pre-spawning gag aggregations, dart tagging a larger number of fish, and beginning a program to acoustically tag females (Figure 3 and cover image). Our recaptures so far suggest very high site fidelity of females to pre-spawning aggregation sites, as well as much higher catch per unit effort at these sites than on the spawning grounds. We expect recapture rates at these sites to decrease as fish begin moving offshore. In addition, acoustic tag detections will help us understand where these females move to once they leave these sites. Our ability to detect them throughout the Gulf is made possible because of the iTAG (Integrated Tracking of Aquatic Animals in the Gulf of Mexico) network, which enables researchers to share detections on their receivers that are not their study species.  This network and the data exchange are FWRI initiatives, with the digital exchange developed and maintained by the FWRI Information Science and Management section. These telemetry detections along with dart tag recaptures and reproductive  data will collectively enable us to better understand how this species’ spatial ecology affects vulnerability to fishing and the measures needed to allow more males to recruit to the population, hopefully in turn keeping this valuable fish on dinner plates across the state.

Figure 3: The incision used to insert the acoustic tag is stitched up with one stitch and a series of three knots.

FIM’s Marine Fish Mercury Program — Indian River Field Lab

By Richard Paperno and Deb Leffler

The Florida Fish and Wildlife Conservation Commission’s Fish and Wildlife Research Institute (FWC-FWRI) Mercury Program conducted by the Fisheries-Independent Monitoring (FIM) Program is one of the most comprehensive efforts in the United States for monitoring mercury concentrations in marine and estuarine fishes. Mercury is a toxic metallic element that has been shown to bioaccumulate in fish tissue. Humans and wildlife that consume fish can potentially ingest significant levels of mercury in their diet. In 1989, the FWC-FWRI began to examine total mercury levels in fish muscle tissue from many economically and ecologically important species to better understand mercury contamination in Florida’s marine fishes. With analytical cooperation from the Florida Department of Environmental Protection, the program’s initial goal was to document mercury levels in Florida’s commercial and recreational fishery species to assist the development of regional Fish Consumption Advisories. In 2006, the FWC-FWRI began analyzing mercury samples in-house at the Indian River Field Laboratory. This addition expanded the program’s analytical capabilities and its focus to now include ecologically important predator and prey species in marine and estuarine habitats.  Currently, the Indian River Field Laboratory is responsible for all analyses of marine fish mercury samples within the waters under Florida’s jurisdiction.  

To date, we have examined the concentration of total mercury in more than 113,000 fish representing over 350 species. These species represented all major trophic groups from primary consumers (e.g., anchovies, herrings, mullets) to apex predators (e.g., mackerels, tunas, billfish, sharks). Most individuals we examined contained low concentrations of mercury, but concentrations in individual fish varied greatly within and among species. Overall, fish concentrations ranged from 0.001 ppm to 32.0 ppm, yet only 10% of all individuals analyzed had tissue concentrations above the U.S. EPA “Choices to Avoid” consumption guideline of approximately 0.47 ppm. Species with very low average mercury concentrations tended to be those that feed on plankton, detritus, invertebrates, or small fishes. Apex predators typically had the highest mercury concentrations. In most species, mercury concentration increased as fish size and age increased.

The data generated by the FWC-FWRI Mercury Program have been used to inform the public and to weigh the potential risks and health benefits of consuming common fishery species in Florida. These data have also advanced scientific research regarding ecological tracers and ecosystem function. Indian River Field Laboratory scientists have shared Florida mercury results through numerous professional presentations at scientific conferences, technical reports, and more than 20 publications in scientific journals. Ongoing cooperative collaborations regarding mercury with researchers within and outside of the FWC-FWRI currently involve stable isotope applications, point- and non-point source identification, ecosystem-wide assessments, and evaluation of mercury effects on marine fishes at the sub-cellular level.  Sampling in Florida waters is continuing, and FWC-FWRI research relating mercury to fish age, feeding ecology, and the trophic structure of Florida’s marine and estuarine ecosystems will help us better understand concentrations of this element in marine fishes and their habitats.

Coral Creek Restoration Monitoring – Investigating Juvenile Sport Fish Nursery Habitats

By Courtney Saari, Dave Blewett, and Tim MacDonald

Fisheries scientists from FWRI’s Fisheries-Independent Monitoring (FIM) and Fish Biology section have been collaborating with scientists and managers from the Southwest Florida Water Management District (SWFWMD), Bonefish Tarpon Trust (BTT), Florida Department of Environmental Protection (FDEP) and FWC’s Habitat and Species division (HSC) to assess restoration techniques for fish nursery habitats in the Charlotte Harbor Estuary. This partnership formed almost a decade ago when SWFWMD was in the initial phase of the Coral Creek Ecosystem Restoration project and biologists observed large numbers of juvenile Tarpon in a small section of the relic man-made canal system that was next in line for restoration. After this discovery, fisheries scientists from BTT and FWRI and restoration scientists from SWFWMD all agreed that the next phase of restoration presented a unique opportunity to examine different restored habitat designs as they relate to juvenile sport fish habitat use.

Figure 2. The relic man-made canals prior to restoration.

The Coral Creek Ecosystem Restoration project is taking place in the Charlotte Harbor State Preserve on the Cape Haze Peninsula (cover image). The project consists of several phases of hydrologic and habitat restoration of approximately 2,600 acres of degraded and impacted wetlands within the preserve (SWFWMD 2010). One phase of this project converted six relic man-made canals into marsh ponds with varying degrees of connectivity to the open creek (Figure 2). A limited connection to the estuary is an important feature commonly observed in nursery habitat studies involving tarpon and common snook, where tidal flow and access is restricted seasonally (ex., rain flooded marshes meet summer high tides) or driven by weather events (ex. tropical storms and hurricanes). Restricted access seems to be important for recruitment and likely helps separate the juvenile fish from large predatory fish that cannot access these habitats or tolerate harsh wetland conditions. Therefore, the restoration of the canals used an experimental design with habitat connections in mind. Four of the canals were designed to be marsh ponds with an earthen sill at the entrance to limit tidal exchange and access by predatory fish, while the other two were designed as marsh ponds open to tidal flow. The constructed canal sills were augmented with bagged and loose fossilized shell to achieve desired elevations. In addition, within each connection type, the marsh ponds have varying depth contours, with the presence/absence of a deep hole habitat.

The entrance to one of the restored marsh ponds.

A 3-year project to follow up on these restoration efforts, made possible through Charlotte County’s RESTORE Act funding (Charlotte County 2015), is currently underway, where FIM staff are characterizing fish assemblages and juvenile sport fish use of 1) the restored marsh ponds, 2) natural marsh ponds in the nearby landscape, and 3) the associated tidal creek (Coral Creek) into which the restored ponds discharge and two adjacent reference creeks. Concurrently, our partners at BTT are tagging juvenile sport fish and tracking movements of these fish in and around the restored marsh ponds and FWRI is tracking juvenile sport fish movements in the natural ponds. Characterizing the physical attributes of these restore and natural marsh ponds (e.g., depths, frequency of tidal inundation) and the dynamics of fish use (e.g., fish density and movement between ponds) will inform future restoration and preservation efforts for juvenile sport fish habitat.

Citations

Charlotte County. 2015. RESTORE Act Advisory Board. https://www.charlottecountyfl.gov/boards-committees/raab/Pages/default.aspx

Southwest Florida Water Management District (SWFWMD). 2010. Peace River Basin Projects. https://www.swfwmd.state.fl.us/sites/default/files/calendar/others/peace_projects_dec.pdf

Reef Today, Gone Tomorrow

By Eric Weather

On October 10th, 2018, Hurricane Michael made landfall in the Florida panhandle as a Category 4 storm. This powerful hurricane caused over $25 billion in damages on land, but did the impacts end there?  Through collaborative efforts from FWRI Fisheries Independent Monitoring program (FIM) and the FWC Division of Marine Fisheries Management’s Artificial Reef program, scientists are setting out to assess the storm’s effects on Florida’s vibrant offshore environment and map changes to publicly accessible artificial reefs. 

A 50 ft tall steel structure in a water depth of 80 ft, moved about 400m, or a quarter-of-a-mile, by the strong waves and currents. The dark area represents a large depression in the sand where the tower had sat since 1993.

During a March 2019 cruise aboard the R/V Kimberly Dawn, FIM biologists utilized side- scan sonar to map over 50 square nm of sea floor near the eye path of Michael in the Northern Gulf.  The images are now being compared to previously identified reef habitat in the area, and at first glance it appears the huge waves created by the storm displaced many artificial reef structures and reshaped natural reef habitats.  This image shows a fifty-foot tall submerged radio tower that was dragged over 1,000 feet along the seafloor!  Understanding fish habitat is vital to properly managing Florida’s valuable fisheries, and this study will provide key insight into how large storm events affect these resources.

A 143′ Navy tugboat, the “Accokeek”, artificial reef site as seen on side-scan sonar.

Florida Keys Reef Fish Monitoring: Reef Fish Visual Census

By Alejandro Acosta, Jennifer Herbig, Jessica Keller, Danielle Morley and Colin Howe

In the Keys, the finfish team was hard at work during 2018, collecting data for the biennial reef fish underwater visual census. Underwater visual census methods are used worldwide to survey shallow aquatic habitats. These methods are suited to monitoring the abundance of coral reef fish because it allows for the collection of community level data without the disturbance inherent in other, more destructive sampling techniques. The finfish team monitors reef fish assemblages and benthic components with the objective of detecting changes in reef fish communities over time.

This is a multi-agency partnership that includes the National Oceanic Atmospheric Administration, National Park Service, and University of Miami-Rosenstiel School of Marine and Atmospheric Science and we rely on each other to complete the sampling. The RVC survey is a probability-based stratified random sampling survey that focus hard bottom habitat in depths less than 30m.  Sites are chosen by using a two-stage stratified-random sampling design based on depth and habitat.  Habitat with higher complexity has more fish, and therefore higher variance.  To improve sampling accuracy, more sites are allocated to habitats with higher complexity.    Targeting locations that represent important habitat for many fish species, scientists visit each of these sites to observe the size, species, and number of fishes within their sample location.

More than 4,000 individual fish surveys were conducted during the 2018 RVC season in South Florida, and the eight members of the finfish team conducted 452 of these surveys at 113 sites in the middle Keys.  They counted 89,464 individual fish, representing 187 species. FWC uses data from these surveys to help inform management decisions. For example, data from the RVCs were recently used to support the continuation of the Research Natural Area (a no-take marine reserve) in the Dry Tortugas for the next 20 years.  Data are also used in stock assessments, like the upcoming SEDAR 64 for Southeastern Yellowtail Snapper.  For more information, check the link. http://myfwc.com/research/saltwater/fish/research/fim-fl-keys-visual-sampling/

Sampling domain of the Florida Keys Reef Fish Monitoring. Each purple dot represents a survey conducted by the finfish team in 2018 in the middle Florida Keys.

Fine Tuning Reef Fish Surveys through the Incorporation of Hydroacoustic Technology

By Ryan Munnelly and Brett Pittinger

Stereobaited remote underwater video arrays (S-BRUVs) have become a standard gear used to sample fish distributions in aquatic systems around the world.  Over the past decade, the Fisheries-Independent Monitoring (FIM) program of the Florida Fish and Wildlife Conservation Commission (FWC) has used S-BRUVs like the array shown in Fig. 1 to study fish populations associated with natural and artificial reef habitats of the West Florida Shelf (WFS).  This effort has involved thousands of 30-minute deployments in waters 10–180 m deep, from Pensacola to the Florida Keys.

An example of some of the sampled artificial habitat of the West Florida Shelf.

Some advantages of S-BRUVs are that they are minimally invasive to the fish community and habitat, they are less selective than other gears, and they provide behavioral information.  However, despite these advantages, it is difficult to determine the distance from which fishes are attracted to the bait during a deployment.  This complicates fish-habitat relationships observed in the video by adding uncertainty regarding the total area sampled and whether fishes observed were in fact associated with the habitat targeted.  Improving our current understanding of the range of attraction of fishes to an S-BRUV is an important step toward determining absolute species abundances.

Hydroacoustics use sound to detect fish in the water column in the same way that a typical fish finder works.  Hydroacoustics can be used to rapidly survey a large area and are even less invasive than S-BRUVs in that they do not influence fish distributions.  These features make hydroacoustics a complementary method to the S-BRUV surveys conducted by the FIM program.  Figure 2 shows the results from one survey designed to evaluate spatial redistributions of fishes that take place during an S-BRUV deployment relative to before the gear entered the water.  At this site located in 61 m water depth offshore of Panama City, fish abundance increased near the S-BRUV during deployment and decreased to the northwest of the site, where the current was oriented.  This information will be used to improve assessments of commercially targeted fishes, sportfish, and other ecologically valuable species throughout WFS waters.

Fig. 2. Mean volume backscatter in the lower 5 m of the water column from a hydroacoustic survey over several patches of low-relief habitat before (left panel) and during (right panel) deployment of an S-BRUV video array.  The dots represent data points that were interpolated throughout the 375 x 375 m survey grid, hashed areas are patches of previously identified habitat, and brighter colors indicate higher fish abundances.  The S-BRUV was deployed in the center of the survey grid and an arrow in the right panel shows the direction of the prevailing bottom current distributing the odor plume from the bait.

A Fond Farewell to Ed Matheson, FIM’s Top Taxonomist

By Sean Keenan and Theresa Warner, with much assistance from coworkers

Dr. Richard “Ed” Matheson Jr., an Associate Research Scientist at the Fish and Wildlife Research Institute (FWRI), is retiring after 32 years with the Institute. A Masters from the College of William & Mary and a Ph.D. from Texas A&M University provided Ed with the basis for a career focused on the systematics and ecology of fishes. Over the years, his research interests have included Gerreid systematics, seagrass-associated fishes, fishes of tidal-rivers, fish community structure in Florida Bay, seagrass die-offs, Everglades restoration, and fishes of the West Florida Shelf.

Starting with FWRI St. Petersburg in 1987, Ed has seen the Institute transition through several agencies and name changes to become what it is today. Initially hired into the Coastal Zone Management group with the Fish Biology program, Ed became the chief ichthyologist for the Fisheries-Independent Monitoring (FIM) program in the late 1990s. With FIM’s statewide, comprehensive sampling, rare or difficult to identify species are frequently encountered and they invariably come to Ed for verification.

Ed is seen here field sampling in Florida Bay.

The accurate identification of specimens is vital to evaluating distribution and abundance trends of native and exotic species. Ed has been instrumental in developing, maintaining and ensuring the near perfect fish identification proficiency of FWRI staff. He regularly creates and presents fish identification training sessions that focus on key sportfish and difficult to identify species groups like gobies, mojarras and sunfishes. His sessions always include a presentation, access to slides and identification keys, and typically include a ‘hands-on’ component that reinforces what staff learned in the presentation. Ed’s fish identification contributions beyond FWRI have been equally important. He frequently confirms identifications of specimens being cataloged in the Ichthyology Collection of the Florida State Board of Conservation and receives requests for assistance from other groups such as FWC Law Enforcement.

The professional impact of Ed’s work at FWRI is immeasurable. He has been the lead author on five peer-reviewed manuscripts and he has co-authored over 20 manuscripts and over 10 reports. He has served as adjunct faculty at the University of South Florida (USF) and as a graduate committee member for students at USF and the University of Central Florida. Ed has participated in innumerable one day estuarine sampling trips, eight multiday research cruises, and dove in the Johnson Sea-Link submersible to 1,100 feet. He is a member of the American Society of Ichthyologists and Herpetologists, American Fisheries Society and Sigma Xi. Ed has served as a reviewer for scientific journals including Bulletin of Marine Science, Estuaries, Southwestern Naturalist and Fishery Bulletin.

Ed is one of the friendliest and most approachable scientists at FWRI. His sense of humor, pleasant demeanor, and professional expertise have made him an invaluable and irreplaceable asset to FWC.

Best Fishes, Ed! We will miss you.

Recruitment of Juvenile Gag Grouper in the Eastern Gulf of Mexico

By Ted Switzer

Gags (Mycteroperca microlepis) support extensive commercial and recreational fisheries in the eastern Gulf of Mexico. A 2016 stock assessment did not support earlier assessments that indicated that gags are currently overfished and continue to undergo overfishing (South East Data Assessment and Review 33 update). Considering the status of Gag in the eastern Gulf of Mexico, it is especially important to improve understanding of its juvenile recruitment processes.

Study area of polyhaline seagrass habitats sampled in estuarine systems in the panhandle (St. Andrew Bay, Apalachicola Bay), Big Bend region (St. Marks, Econfina, and Steinhatchee), and peninsula (Tampa Bay and Charlotte Harbor) of Florida, USA (Schrandt et al. 2018).

Past research has shown that juvenile Gags generally occupy structured polyhaline (18-30 practical salinity units) habitats such as seagrass beds and oyster reefs for several months before emigrating to nearshore reefs (Figure 1). The reliance of Gags on estuarine nurseries, combined with a brief period of estuarine occupancy, greatly facilitates the accurate characterization of the strength of juvenile recruitment.

A comprehensive examination of long-term (10+ years) FWC/FWRI fisheries-independent data was conducted to characterize habitat selection and recruitment of juvenile Gags. Results from Apalachicola Bay, Tampa Bay and Charlotte Harbor habitat suitability analyses indicated that juvenile Gags selected polyhaline habitats with sloping bottoms and extensive seagrass coverage. These analyses indicated that the near shore, deeper water polyhaline seagrass habitats had been under sampled (Switzer et al. 2012).

A multi-gear survey (183-m haul seine and 6.1-m trawl) was designed to supplement long-term, fisheries-independent survey data on estuarine-dependent reef-associated fishes. The supplemental survey design specifically considered juvenile Gag recruitment ecology and thus targeted the deep, polyhaline (>18 psu) seagrass habitats that are used by age-0 Gags. Potential sampling sites were limited to generally polyhaline waters that contained at least 50% bottom coverage of seagrass, had a measurable slope and were between 1.0 and 7.6 m deep.

Gag begin their life offshore in a pelagic environment where they spend their first 30-60 days. Eventually they settle out onto shallow water seagrass beds, where they spend the summer months feeding and growing. In the fall they migrate to nearshore hard-bottom habitat. As they mature, they eventually migrate to deeper water reefs and as mature adults they form spawning aggregations and spawn during the winter months. Gag are hermaphrodites. They are born as females and as they grow eventually transition to be male.

This supplemental sampling was initiated in 2008 and polyhaline seagrass beds were sampled by bottom trawls (6.1-m otter trawl) and haul seines (183-m haul seines) in seven estuaries along Florida’s Gulf coast (Figure 2). Apalachicola Bay, Charlotte Harbor and Tampa Bay have been routinely sampled since the late 1990s; St. Andrew Bay and three estuaries in the Big Bend region between Cedar Key and Cape San Blas (St. Marks, Ecofina, and Steinhatchee), where Gag recruitment had been documented, were added for this study and have become part of the continuing survey.

Analyses of the data collected in the long-term and supplemental surveys (2008-2012) demonstrated the effectiveness of this sampling approach. The size ranges of Gags collected in both studies were similar, but age-0 individuals were captured more frequently and the catch-per-unit-effort (CPUE) was significantly higher in the supplemental surveys (Switzer et al 2015). These analyses will not only enhance our understanding of recruitment processes for juvenile Gags in the eastern Gulf but will also provide valuable insight into observed patterns of habitat use and the relative importance of various habitat types. Nevertheless, additional information on habitat availability, combined with a better understanding of the estuarine systems’ relative contributions to nearshore Gag populations, will be required to maximize the utility of these data in predicting fisheries productivity.

Strong Gag year-classes have been documented as persisting as the fish grow and enter the fishery. Accordingly, accurate estimation and prediction of juvenile recruitment is critical to the effective assessment and management of at-risk fisheries. Variability of estuarine nekton assemblages is valuable as an indicator of environmental quality.  Therefore, the patterns discerned from the supplemental sampling have important implications for fisheries managers.

Vessel Use Patterns in the Florida Keys National Marine Sanctuary

By Casey Butler, Maria Cooksey, Gabrielle Renchen and Emily Hutchinson

The Keys Fisheries Research program took to the skies in partnership with the Florida Keys National Marine Sanctuary (hereafter Sanctuary) management team to conduct an aerial survey of vessel use in the Sanctuary. Within the boundaries of the Sanctuary lie nationally significant marine resources, including hundreds of uninhabited Keys, the world’s third largest barrier reef, hard-bottom habitat, seagrass beds, mangrove trees, and more than 6,000 species of marine life. The Florida Keys are home for ~79,000 year-round residents and provide a destination for ~5 million visitors annually. Over the last few decades the number of registered vessels has increased, but the activities of these boaters and how their use of Sanctuary resources have changed over time is not well known. Understanding the patterns of boating activity in the Sanctuary is vital to evaluating the sustainable use of the valuable marine resources of the Sanctuary.

Whale Harbor Sandbar is the most popular sandbar in the Keys (331 boats were observed on the Sunday of Memorial Day Weekend 2016).

FWRI scientists flew in small planes over the breathtaking waters of the Keys and recorded the type, location, and activity of every boat, personal water craft, kayak, paddleboard, etc. Over the course of 29 flights in 2016, we counted 52,107 boats. The number of boats peaked at nearly 5,000 during the opening days of lobster season and summer holidays. On average, 19% of boats were involved in fishing, 19% were involved in diving, 13% were anchored (with no visible activity), and 9% of boats were at sandbars. Many of the boats we observed (29%) were in transit at the time; however, these boats likely participated in other activities throughout the day. In addition to diving and fishing, other watersports (e.g., kayaking, paddle boarding, jet skiing) and partying at sandbars were popular among the Sanctuary’s visitors and reflect alternative ways in which people enjoy Florida Keys waters. Our research team conducted a similar aerial survey in 1992, and the comparison of vessel use data between 1992 and 2016 shows that there has been a major increase (~400%) in the popularity of watersports (e.g., kayaking, paddle boarding, jet skiing) and partying at sandbars.

The 1992 aerial survey took place prior to the establishment of the Sanctuary Preservation Areas (Figure 1, SPAs). Establishment of the SPAs in 1997 limited consumptive activities within these areas and was intended to reduce conflicts between fishermen and divers. Because these areas were open to fishing during the 1992 aerial survey – including hook-and-line, recreational lobstering and commercial fishing, this allows us to examine how SPA implementation affected stakeholder activity. Currently, we are evaluating changes in dive and fishing boat spatial distributions after the SPAs were established.

Sombrero Reef, a Sanctuary Preservation Area (SPA) off of Marathon hosts many divers and snorkelers throughout the year.

Besides providing an outstanding office view for our scientists, this project provided essential information to the Florida Keys National Marine Sanctuary managers regarding vessel use in the Sanctuary and how that use has changed over time, which should aid in future management decisions regarding Sanctuary resources.

Watch our video for a glimpse of the scenery from the Florida Keys National Marine Sanctuary aerial survey project:  https://www.youtube.com/watch?v=TxQH3zRdYzk

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.