Category Archives: Marine Fisheries Research

Expansion of Estuarine Monitoring to the Florida Panhandle

By Myranda Clark and David Gandy

A portion of the Deepwater Horizon’s Natural Resource Damage Assessment (NRDA) settlement was earmarked for the construction and operation of a production-level fish hatchery in the Florida Panhandle. A partnership between FWC, DEP, and the City of Pensacola has designed a hatchery facility (Gulf Coast Marine Fisheries Hatchery and Enhancement Center) to be built in Pensacola, Florida. The release of hatchery-reared animals is ethical only when both the wild and hatchery-reared stocks are monitored to ensure that wild populations are not adversely impacted.

Accordingly, the Fisheries-Independent Monitoring Program (FIM), with its long history of working with the Stock Enhancement Research Facility in Manatee County, was tasked with developing a sampling program for estuaries in the Florida Panhandle. With the potential release of in-season Phase I (1.25 inches) Red Drum (Sciaenops ocellatus) and Spotted Seatrout (Cynoscion nebulosus) into five Panhandle estuaries (Pensacola Bay, Santa Rosa Sound, Choctawhatchee Bay, St. Andrews Bay, and St. Josephs Bay), it was determined that the most appropriate sampling approach would be the use of 21.3-m seines in shallow water habitats.

Historical data collected by the FIM program from Apalachicola Bay (1998-2015), and Choctawhatchee Bay/Santa Rosa Sound (1992-1997) were used to develop a sampling design that would use 21.3-m seines to assess wild populations prior to hatchery releases, and wild and hatchery-reared populations after releases are initiated. Sampling of wild stocks began in July 2017 in all five estuaries and will occur monthly from July through December each sampling year. The timing of this sampling coincides with peak young-of-year recruitment for both Spotted Seatrout (July – September) and Red Drum (October – December) into estuarine nursery habitats in Florida Panhandle estuaries. Aside from a shorter sampling season, this survey employs identical protocols that are currently used in several other estuaries throughout Florida; therefore, project-associated data will be comparable to 21.3-m seine data collected throughout the state, so data should quickly be useful in stock assessments.

Young-of-the-year estuarine-dependent fish, such as Red Drum and Spotted Seatrout, depend on suitable nursery habitat to provide critical foraging grounds, refuge from predators, and essential abiotic conditions necessary to optimize growth and survival to adulthood. The data collected from this survey will allow FWC to identify these essential habitats in Florida Panhandle estuaries, allowing for the release of hatchery-reared fishes where they will have the greatest chance for survival. Current sampling efforts are also identifying trends in recruitment variability for wild stocks. Sampling after releases begin will gauge the relative contribution of the hatchery to overall stocks and assess the efficacy of these stocking efforts.

Data from year one of this study will be summarized with a preliminary presentation occurring at the FWRI-FIM program’s annual meeting in St. Petersburg, January 24 – 26, 2018.

FIM Data and the Southeast Data, Assessment and Review Process

By Dr. Ted Switzer

The Southeast Data, Assessment, and Review (SEDAR) is the cooperative process by which stock assessments of federally-managed species are conducted in the Southeast Region of NOAA Fisheries. SEDAR was initiated to improve planning and coordination of stock assessment activities and to improve the quality and reliability of stock assessments.  SEDAR strives to provide an open and transparent approach for development and review of the scientific information on fish stocks that is critical to effective management and decision making, and includes participants from various sectors, including researchers, stock assessment scientists, managers, and stakeholders.

Figure 1. Indices of abundance (least square means ± SE) for age-0 and age-1 Gray Snapper collected during FWRI long-term and polyhaline seine and trawl surveys in northeastern Gulf of Mexico estuaries

Many research groups at the institute provide data critical to the SEDAR process, including data on landings and discards from the commercial and recreational fishery, discard mortality, and life history including age and growth, reproduction, and stock identification. Data provided by the FIM program typically include trends in relative abundance through identification. Data provided by the FIM program typically include trends in relative abundance through time as well as annual estimates of size/age composition. Because these data are meant to characterize fluctuations in managed fish populations through time, several years of data are often required before fishery-independent indices become useful. Nevertheless, FIM data are increasingly being used for the assessment of managed fishes, including the ongoing SEDAR 51: Gulf of Mexico Gray Snapper.

Data from long-term seine-surveys (initiated in 1996 – 1998, depending on estuary) and recently-implemented polyhaline seagrass seine and trawl surveys (initiated in 2008) were analyzed separately to generate indices of abundance for age-0 (≤ 100 mm SL) and age-1 (101 – 250 mm SL) Gray Snapper; a single index was developed for each by combining data from multiple estuarine systems. In general, indices for each age class were similar between surveys (Figure 1); index results documented strong interannual variability in age-0 recruitment, but a generally increasing trend in the relative abundance of age-1 Gray Snapper. Although the SEDAR Data Workshop recommended incorporation of the long-term index only to avoid duplication, future efforts to incorporate data fromboth surveys into unified age-0 and age-1 indices should dramatically increase the statistical power of these indices.

Figure 2. Relative standardized index (solid red line) with 2.5% and 97.5% confidence intervals (black dotted lines) and the nominal index (blue hashed line) for Gray Snapper in the FWRI West Florida Shelf Video Survey.

In addition, data from the FWRI video survey off Tampa Bay and Charlotte Harbor were analyzed to generate and index of abundance for subadult/adult Gray Snapper (generally ≥ 300 mm FL) from 2010 – 2015. Model results generally corroborate the increasing trend in abundance of Gray Snapper in recent years. Although useful, this model was ultimately not recommended for incorporation, as an additional model, it was developed utilizing data from FWRI, NMFS – Panama City, and NMFS – Pascagoula video surveys.

Spartina by the Numbers

By Chris Young

This September marked twenty years since the first harvest of Spartina alterniflora from the constructed treatment marsh at the Stock Enhancement Research Facility (SERF). This initial harvest was used for coastal restoration near City Island in Sarasota Bay. The 1.9-acre effluent marsh was constructed and planted with 20,000 Spartina sprigs from a local wetland nursery. The marsh is connected to a two-acre settling pond that works together to filter nutrients and solids from hatchery discharge.

9,300 Spartina plugs harvested from the SERF marsh were planted at Clam Bayou in Pinellas County, March 11, 2011. Photo by Brandt H.

Spartina are harvested from the SERF marsh by an army of volunteers coordinated by FWC and like-minded partners for coastal habitat restoration. Plants are dug from the marsh and separated into plugs of two or more culms (stems), then counted and packaged into plastic bags for transport to restoration sites. Shoots, or single stem Spartina, are separated at harvest for school nurseries. Five thousand Spartina plugs are planted to restore one-acre of coastal marsh. Since 1997, almost 1.2 million plugs were harvested by partners and given to 67 restoration sites. These plants often grow rapidly at these restoration sites (photo below). Approximately 411,282 Spartina shoots  were harvested from the FWC donor marsh and provided to establish 35 school nurseries for education and environmental awareness.

Revitalized Clam Bayou marsh in Pinellas County March 15, 2012 (Photo provided by Brandt Henningsen with the Tampa Southwest Water Management District).

Recently, the variety of marsh vegetation used for restoration has expanded to include Paspalum vaginatum, a saltmarsh grass. In a short period of time over 28,000 plugs of Paspalum have been donated for coastal uplands restoration. This demonstrates that effluent donor marshes for fish hatcheries are an effective approach for hatchery wastewater treatment while supplying valuable native plants for coastal habitat restoration.

Florida Forage Fish Coalition

By Tim MacDonald and Kevin Thompson

Managing Florida’s marine fishery resources requires cross-discipline research on fish biology and demographics, the marine and upland ecosystems and the human impacts of fisheries and economics. A key aspect in understanding how fish interact with other species in a complex ecosystem is determining predator-prey interactions.

The Florida Fish and Wildlife Conservation Commission (FWC) recognized the importance of forage fish as a prey-base in 2015 when it signed a resolution recognizing that forage fish are vitally important to the state’s commercial and recreational fisheries which annually contributing $12.3 billion to the state’s economy and supporting over 100,000 jobs. Building on this resolution, the International Game Fish Association, Florida Wildlife Federation, Pew Charitable Trusts, and The Snook and Gamefish Foundation banded together to form the Florida Forage Fish Coalition. The Coalition has teamed up with the FWC to improve the understanding of forage fish population dynamics, recruitment processes, and the dietary needs of predators through the Florida Forage Fish Research Program Fellowships. The goal of these fellowships is to use data collected by FWC’s Fisheries-Independent Monitoring (FIM) program to inform policy decision that better support ecosystem balance and sustainable fisheries.

In a competitive process refereed by the coalition and FIM program staff, two fellowships, totaling $10,000 each, have been awarded for the 2017/2018 academic year. The two fellowships were awarded to Meagan Faletti at the University of South Florida and Dr. Edward Camp at the University of Florida.

Dr. Camp, a post-doctoral researcher at the University of Florida will use diet data gathered by the FIM program for juvenile and adult Red Drum and juvenile Gag. He will be identify patterns in diet from estuaries throughout Florida’s Gulf Coast for these two critical species. He will be using emerging analytical techniques to illustrate how prey resources vary through space and time and how that relates to observed predation by these two species. This will provide insight into the importance of particular forage fish as prey, and how the prey are used by predators in relation to abundance. This represents a critical step in understanding these complex ecosystems and how forage fish support larger economically more valuable species.

Meagan Faletti is pursuing her graduate degree at the University of South Florida as a student of Dr. Chris Stallings. Her fellowship involves a new technique that analyzes eye lenses to identify where a fish lived during different life history stages. Concentrations of carbon (δ13C) and nitrogen (δ15N) isotopes in eye lenses reflect the environment in which the fish lived when the eye lens was deposited. Once deposited in the lens, these concentrations do not change, and the environmental concentrations of these isotopes follow latitudinal (δ15N) or depth (δ13C) gradients. By identifying the concentrations of these isotopes, Meagan will be able to determine spawning locations and movements of Pinfish throughout their life history. She will be looking at lenses from Pinfish in four different estuaries (Charlotte Harbor, Tampa Bay, Cedar Key, and Apalachicola Bay), allowing her to compare and contrast these processes between estuaries. This will provide information that can be used to protect ecosystems that are critical to Pinfish during various life history stages.

Hatchery Outreach and Education Program

By Gina Russo

The Stock Enhancement Research Facility (SERF) hosts several outreach and education programs annually to educate youth, students, and stakeholders about marine aquaculture, fisheries stock enhancement research, and the benefits of Sport Fish Restoration.

Aquaculture in the Classroom is a state-wide program designed for students from fifth grade through college. SERF provides participating schools juvenile hatchery-reared red drum (Sciaenops ocellatus) along with starter feed and technical advice on how to raise the fingerlings. Students are given the opportunity to design their own aquaculture (fish-raising) systems, perform daily husbandry (care) and conduct research projects such as salinity tolerance tests, feed studies, and water quality/chemistry investigations. This year nine schools and one Marine Life Center participated in this program.

Stock enhancement research internships and limited volunteer opportunities are available to university students and stakeholders interested in marine aquaculture and research. Student interns and volunteers assist hatchery biologists with raising red drum, zooplankton, and phytoplankton.

Tours and special opportunity fishing events are provided upon staff availability to give guests an opportunity to learn about hatchery operations and to catch marine sport fish from the 2-acre detention pond. This catch-and-release-only fishing pond, which is a settling pond for treating hatchery waste water, is home to many different species such as black drum, red drum, snook, spotted seatrout, tarpon, pinfish, toadfish and even blue crabs.

Staff also partner with angling clubs and nonprofit organizations to host Fish Camps during the summer which includes a presentation about the hatchery and hands-on instruction on how to become ethical anglers and stewards of our natural resources. This is followed by lunch onsite and a special opportunity fishing experience. This summer, fish campers from the Florida Aquarium, Hillsborough County Parks and Recreation, and Tampa Police Department RICH House kids participated in these camps.

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.

Red Drum Broodstock and Biosecurity at SERF

By Chris Young

Adult red drum purse-seined from the Gulf in September 2016 were moved into the hatchery building at SERF in January 2017. Maintaining these fish in ponds at SERF for several months provided ideal conditions for external parasites to find a reliable and healthy host. Two common parasites with direct life cycles (one host species is used for all life history stages), Amyloodinium ocellatum (dinoflagellate) and Caligus sp. (copepod), can cause mortality of marine fish, including red drum, maintained in recirculating aquaculture systems.

Before introducing the red drum to the hatchery maturation and spawning tanks the red drum were bathed in freshwater for 20 minutes to remove these parasites in particular.

Chad Young obtains a biopsy from a red drum while the fish is sedated during a
Freshwater bath at the Stock Enhancement Research Facility January 18, 2017.

Scrapes of gill and skin from a representative number of fish were examined with the use of a compound microscope before the freshwater bath to provide a historical record of the parasite assemblage. The historical record informed staff to be aware of the signs of specific-parasite infestations and to be prepared for specific therapeutic measures to consider in the event that signs of parasite infestation appeared after the fish were put into maturation and spawning tanks. During the freshwater bath, the red drum were sedated to minimize harm to fish and staff when data was collected. Length, weight and sex were determined for each fish, a passive integrated transponder (PIT) tag was implanted to uniquely identify each fish, and a small tissue sample (fin clip) was obtained for genetic identification of each fish during the freshwater bath.

Chad Young holds a red drum while Josh Taylor (right) injects a passive integrated transponder (PIT) tag to mark red drum for broodstock research at the Stock Enhancement Research Facility January 18, 2017.

Genetic identifiers are used to assess parentage of hatchery offspring for hatchery and field studies. The latest group of red drum adults brought into the hatchery are being used for a second of three planned replicates to assess the effects of tank and population size on the spawning contribution of red drum – the aim is to improve stock enhancement operations efficiency and increase genetic diversity by using one 20-foot diameter tank for 30 red drum adults rather than five 12-foot tanks with six red drum each.

Nekton Community Structure and Habitat Availability for Dredge Holes within Tampa Bay

by Amanda Tyler-Jedlund and Tim MacDonald

Routine maintenance and dredging of boat basins and shipping channels by the U.S. Army Corps of Engineers (USACE) generates dredge material. Typically these materials are disposed of in spoil areas, but recently the USACE has been aggressively pursuing options for beneficial use of dredge materials. The Tampa Bay estuary has numerous subtidal borrow pits from which material was typically been removed for non-navigational purposes (dredge holes). It has been proposed that materials from routine maintenance dredging could be used to fill these dredge holes and restore shallow-water habitat that might be colonized by seagrasses

School of black drum on artificial reef material.

and serve as critical nursery areas for nekton (fish and macro-invertebrates). A 2004 study funded by the Tampa Bay Estuary Program (TBEP) and conducted by FWRI’s FIM program and the Hillsborough County Environmental Protection Commission found that the majority of the studied dredge holes represented habitats unique from adjacent shallow- and deep-water habitats.restore shallow-water habitat that might be colonized by seagrasses

Before a dredge hole can be selected as a sight for beneficial disposal of dredge material, its existing condition should be evaluated to define its ecological function and to determine the appropriateness of restoration. The goal of the current study is to determine available habitats and describe nekton distribution and abundance in eleven Tampa Bay dredge holes, ten of which have not previously been studied. The dredge holes being studied are distributed from the mouth of Tampa Bay into Hillsborough and Old Tampa bays, and have a high probability of appropriate dredge materials becoming available to fill them within the next ten years. Options for dredge hole restoration include retaining in current condition, filling with appropriate dredge material, or restoring in some other beneficial manner (i.e., artificial reef materials). In conjunction with TBEP’s Dredge Hole Advisory Committee, an implementation plan for restoration of the eleven dredge holes will be proposed.

Sponges and soft corals on artificial reef material.

Sampling with 6.1-m otter trawls and 21.3-m seines began in May 2016 and will continue through April 2017. Monthly samples are being collected at randomly selected sites within and adjacent to the eleven dredge holes. During the first month of sampling, it became apparent that the South Skyway dredge hole contained large concrete slabs and pilings.  This previously undocumented artificial reef material prevented deployment of our standard gears; a challenge that led to a great opportunity to assess hard bottom habitats within Tampa Bay. We constructed a small, easily deployable underwater camera stand with which we record GoPro camera video each month near the structural habitat within this hole.  The GoPro camera records 30 minutes of video with each deployment and two camera deployments are completed each month. Twenty minutes of each video are read back at the lab during which nekton are identified and counted.

So far we have had relatively good visibility overall and have seen large schools of Gray Snapper, Black Drum, Jacks, and baitfish. Other economically important species (Red Grouper, Common Snook, and juvenile Lane Snapper) have also frequently been identified. As confirmed in our earlier study dredge holes can provide valuable habitat and refuge.

Ross Boucek and iTAG

by David Westmark

It seems like just yesterday we were welcoming post-Doctoral fellow, Ross Boucek to the Fish Bio lab fold. But, though somewhat brief, during his stay Dr. Boucek has delivered boatloads of accomplishments. Last September Dr. Sue Lowerre-Barbieri charged Ross with amping up awareness of the collaborative iTAG effort in which FWRI is a leading participant.

iTAG deacronymizes to Integrated Tracking of Aquatic Animals in the Gulf (of Mexico). One of Ross’s biggest tasks was to use his prolific publishing skills, developed from building a prodigious bibliography, to write and publish a review article on the spatial ecology of key managed species in the Gulf of Mexico, expanding on key research needs for these species moving forward. The review is currently in progress and will be published in a special issue Sue and Ross are organizing in the Journal of Marine Science. Movement data derived from telemetry can inform ecosystem-based modeling, identify population structure and harvest management boundaries, as well as spawning sites and marine protected area (MPA) design.

Other work on behalf of the iTAG Steering Committee involved building awareness of the iTAG effort through outreach and social media. An extensive and vast network like iTAG produces significant orphaned data so in his “spare time”, Ross continues to help match the data to its appropriate recipient or project.

Finally, Ross and Sue have worked jointly on other local projects, examining fine scale space use by trout and snook of spawning sites in Tampa Bay, as well as using novel seascape metrics to predict where unknown trout spawning sites occur in Florida Bay. If you want to keep track of Ross, he will be devoting his talents to the telemetry work underway by the Tarpon and Bonefish Trust. Why not wish him well with a farewell post to the iTAG Facebook page?

Browse more information about telemetry research underway at FWRI.

Sheepshead Genetics

The sheepshead, Archosargus probatocephalus, is a marine fish that lives primarily in estuarine habitats from Nova Scotia, Canada, to Rio de Janeiro, Brazil. Sheepshead is the 10th most important recreational harvest making it a valuable fishery throughout the southeastern United States. In the Gulf of Mexico and the Atlantic combined recreational and commercial landings along Florida’s coast was the highest of all states until 2013.

Sheepshead have long been separated into three subspecies based on meristic traits, particularly counts of pigmented bars on the sides of the body. The ranges of two of the subspecies that occur in North America meet at Apalachee Bay, Florida. Members of the subspecies that occurs to the east of the Apalachee Bay boundary generally exhibit six bars on both sides of the body and are classified as A. probatocephalus probatocephalus. In contrast, most fish west of the boundary (to Campeche Bank, Mexico) exhibit five bars on both sides of the body and are classified as A. p. oviceps. The third subspecies A. probatocephalus aries occur from Belize to Bahia de Sepetiba, Brazil. No specimens from this subspecies were available for study.

The morphological differences of the sheepshead subspecies was expected to be associated with genetic differences, but initial genetic analysis did not show any genetic divergence between the described subspecies. For this reason, the sheepshead was assumed to be a single randomly interbreeding population that was found in both the Gulf of Mexico and the Atlantic Ocean.

Recently using sheepshead-specific microsatellite markers developed at FWRI, the genetic population structure of this fish was found to be composed of three population clusters demarcated in the western Gulf of Mexico, the eastern Gulf of Mexico and the Atlantic Ocean (see Figure). The two Gulf of Mexico clusters were separated by a genetic break located at Apalachee Bay, close to the boundary between the two morphologically defined subspecies. The second genetic break separated the eastern Gulf and Atlantic clusters and coincided with a discontinuity of estuarine habitat between Miami and Palm Beach that restricts gene flow between populations. Although this area had not been recognized as a genetic boundary for sheepshead populations in the past, it had been widely recognized as a boundary for many other near-shore fish species. The population structure discovered here cannot be equated to evolutionary divergence and does not serve to validate the morphological classifications of the sheepshead subspecies. That work would require the use of extensive single nucleotide polymorphism (SNP) analysis between the subspecies.

Because the population trend is stable, Sheepshead is listed as a species of “least concern” in the IUCN Red List of Threatened Species. At present, this fish is considered a perfect substitute species as others species become more limited through regulations. This situation is a potential concern since it could lead to a great stress on sheepshead fishery, eventually destabilizing the stable population trend.

In Florida, the management of this fish is not based on the definition of the subspecies as a baseline designation of stocks, but between Gulf and Atlantic populations. If changes were to be initiated in response to a changed status of this fish, one aspect of the fishery that will require attention would be the replacement of the present management policy on a par with the newly discovered fragmentation of the sheepshead into three clusters. This is of considerable interest to the state of Florida which is the only state where all three clusters exist and where most landings are made. This can be easily accomplished by adopting northwest Florida as a separate management unit within the Florida Gulf, which at present has not acquired such a status due to lack of adequate data.