Location: Subtropical Plant Pathology Research
2025 Annual Report
Objectives
The U.S. has tremendous capacity for meeting the domestic demand for seafood by expanding aquaculture in federal waters and land-based recirculating systems. As the largest importer of seafood products, expanding domestic production will reduce our reliance on imports and the trade deficit. This project will support the U.S. aquaculture industry by developing technologies that will ensure a steady supply of warm water marine fish seedstocks that are optimized for commercial production.
1. Develop year-round spawning strategies for captive broodstock and larviculture methods for seed production of marine finfish.
2. Develop methods for genetic improvement of warm water marine finfish for optimum production efficiency.
3. Increase understanding of fish physiology and enhance production efficiency through improved management strategies.
Approach
Aquaculture producers need access to seedstocks that are available year-round and optimized for the production environment. Research is needed to develop seedstocks that are bred for maximum production efficiency and have minimal impacts on the environment and native populations. Research in the disciplines of genetics, fish health, nutrition, reproductive biology, and physiology will contribute to the development of seedstocks that meet these criteria.
Progress Report
This is the FY2025 report with Florida Atlantic University’s Harbor Branch Oceanographic Institute (HBOI) cooperators.
Lab spaces were upgraded and renovated. This included completing a 96-tank temperature controlled closed recirculating aquaculture system (2 separate systems) to conduct studies on early juvenile finfish. This not only increases the capacity to conduct more replicates/treatments and studies but also allows direct comparisons of fish performance between different environmental conditions (e.g. salinity, temperature, pH, etc). Additionally, a biosafety lab II has been approved for occupancy that consists of separate wet and dry labs to conduct disease challenge studies and diagnostics. Set up a12 single tank loop systems equipped with grow lights to do macroalgae and off-flavor work.
One of the four new broodstocks systems has been completed and the other 3 systems are around 75% complete. F1 redfish broodstock fish (spawned from east coast and west coast wild fish) will be moved to these new RAS systems as soon as they are completed. Two of the 4 selective breeding grow out systems have been completed. The remaining two grow out systems are 25% complete. Larviculture room systems are around 25% complete that will consist of 8 RAS larval systems with 12 tanks per system (96 tanks total). Construction of all these systems will continue into the next fiscal year and new broodstock will be collected.
An ARS scientist from Fort Pierce, Florida and HBOI cooperators are working with farmers and researchers to develop a predictive model for egg quality using Raman spectroscopy that rapidly measures the fatty acid composition. This will allow farmers to assess quality in seconds, rather than weeks. This model is being developed for various marine finfish including red drum, pompano, Almaco jack, Yellowtail and Atlantic croaker. Additionally, scientists are comparing the egg quality between artificially and naturally spawned Yellowtail in collaboration with Hubbs-Seaworld Research Institute.
The feasibility of raising Atlantic croaker was conducted based on farmer’s interest for diversification in Texas. This included captive spawning using hormones, larviculture over a one-month period using live feeds, an 8-week feeding management study on early juveniles and evaluating the growth performance and gonadal maturity (every 2 weeks) over one year in a closed recirculating aquaculture system.
Research demonstrated that bioflocs produced from integrated multi-trophic aquaculture (IMTA) systems can replace up to 50% of fish meal in red drum diets if an amino acid mixture is used. Research demonstrated that Ulva lactuca (‘sea lettuce’) produced from IMTA can replace up to 25% fish meal in red drum diets. A HBOI Masters student is currently investigating ways to improve the nutritional value of Ulva using different processing methods.
Research demonstrated that 25% of fish meal can be replaced by black soldier fly larvae (BSFL) in red drum diets in collaboration with Stratium, LLC, the Florida Costal Conservation Association and Duke Energy Crystal River Mariculture Center.Ways to further enhance the nutritional value of BSFL are being conducted based on using IMTA by-products.
Two separate 8-week feeding trials were conducted on pompano, which are based on problems experienced by a local farmer. One was on dietary binders to investigate if solid waste can be more efficiently removed in a closed aquaculture system. The other was on dietary starch (sorghum and whole wheat) with or without being gelatinized (molasses-based diet acted as a control). This was done in collaboration with the United Sorghum Checkoff Program. Diets were extruded to represent commercial dietary manufacture in Bozeman, MT at a USDA-ARS station. The data from these studies are being analyzed and manuscripts being prepared for journal submission.
Research demonstrated that the starch source can significantly affect pompano growth, feeding efficiency and overall health based on immunological measurements, intestinal microbiota, and gene expression including pathways for carbohydrate utilization. Results were published in a scientific journal after peer-review.
USDA-ARS lead scientist is writing a literature review on pompano nutrition, in collaboration with scientists at NOAA and Mississippi State University, to assist farmers and feed manufacturers in designing and formulating diets specific to pompano.
Scientists at FAU-HBOI submitted the first de novo genome assembly for Florida pompano to the National Center for Biotechnology Information (NCBI) GenBank database (Accession: GCA_040938265.1; BioProject PRJNA1128138). Since it was publicly released on 07/30/2024, our contig-level draft genome has provided a baseline for sequence composition and genetic variance data to develop genomic selection techniques that can reduce the breeding cycle, maximize genetic gain, and minimize inbreeding depression.
USDA-ARS lead scientist is a technical advisor to a farmer on biofloc technology to determine the efficacy of biofloc for baitfish. HBOI cooperators are measuring the nutritional value of three microalgae species for the same farmer as part of a live feed project.
Accomplishments
1. Atlantic croaker research. ARS researchers from Fort Pierce, Florida developed a new conditioning cycle for broodstock and determined they can readily spawn in captivity with hormone implants. It was determined that their larviculture is longer than red drum (a closely related species), which provides baseline information on their culture feasibility. A subsequent feeding management trial demonstrated that their growth and feeding efficiency is not influenced by feeding frequency and that the feeding efficiency is significantly better at lower feed rations.
Additionally, their growth begins to decrease when they approach 70 grams, which may be related to them maturing early in captivity. Histopathological analysis of the gonads will provide greater insight into their maturation status and the obtained data will help inform farmers including whether croaker is more appropriate as a food fish or bait fish (or for both). A manuscript is being prepared for journal submission from the feeding frequency study while data is currently being collected on their growth until market size to assess growth rates in a closed recirculating aquaculture system. Preliminary results indicate their high value as a baitfish but not as a foodfish.
2. Black soldier fly larvae (BSFL) as a partial substitute for fish meal. ARS researchers from Fort Pierce, Florida believe fish meal is by far the most expensive ingredient in fish feeds as well as becoming harder to obtain because this is a finite resource that is used in various food producing sectors. Thus, there is substantial interest in replacing fish meal with alternatives, especially in the diets of marine finfish due to their often high requirements for quality protein. There is interest in BSFL due to their high protein and lipid content but also relative ease of culture in which they thrive on various waste products unfit for human or livestock consumption. It was demonstrated that 25% of fish meal can be replaced by BSFL in red drum diets without affecting their growth or feeding efficiency. Inclusions of higher amounts led to reduced growth, possibly due to taurine deficiencies and/or excessive chitin. Results were published in a peer-reviewed journal and further research into improving the nutritional value of BSFL is being explored using IMTA by-products. The industry is using the data to seek Association of American Feed Control Officials (AAFCO) and the US Food and Drug Administration (FDA) approval of BSFL meal as an approved feed ingredient in fish feeds.
3. Biofloc as a partial substitute for fish meal in red drum diets. ARS researchers from Fort Pierce, Florida suggests bioflocs are a mixture of various microorganisms that convert otherwise toxic ammonia and nitrite into microbial biomass. The creation of bioflocs is often done by simply adding sugar to encourage heterotrophic bacterial growth and thus bioflocs help clean the water as well as being a nutritious supplement to various fish. Bioflocs have been an integral part of one of our systems for years and it was demonstrated that when these were captured and included in the diets of red drum at 50%, with an amino acid mixture, this led to similar growth as red drum fed a fish meal-based diet. Thus, this information provides an incentive for farmers on closed aquaculture systems to similarly capture bioflocs and include in diets. Results were published in a peer-reviewed journal. The use of bioflocs is currently being explored by a local baitfish farmer and we are providing technical assistance.
4. Ulva as a partial substitute for fish meal in red drum diets. Ulva lactuca, also known as ‘sea lettuce’, is commonly used in IMTA systems to remove excessive nitrate. Thus, Ulva helps clean the water for the fish and reduce or eliminate the need for water exchanges. It is necessary to periodically harvest Ulva due to their fast growth rates and the Ulva is often discarded. However, when included in the diets of red drum, it was shown Ulva could replace fish meal by 25%. In fact, an inclusion of 25% Ulva led to better red drum growth compared to a fish meal-based control diet. Higher replacement at 50% led to lower growth, which could be related to some antinutritional factors, such as trypsin inhibitors. ARS researchers from Fort Pierce, Florida are exploring ways to improve the nutritional value of Ulva through different processing methods to determine if higher inclusions are possible.
5. Exploring different starch sources in pompano diets. ARS researchers from Fort Pierce, Florida believe starches are included in the diets of fish to act as an inexpensive energy source as well as binder. Although the starch source can greatly affect growth in fish, this is not often investigated. Moreover, marine finfish tend to utilize starches more poorly than freshwater finfish. It was demonstrated that wheat starch led to significantly better growth in pompano than corn starch sources. This was likely related to improved digestibility of the wheat starch and preventing excessive glycogen/fat overload in their livers that would disrupt liver function. Currently, the industry relies on diets formulated for cold water marine finfish. This information paves the way towards designing diets more appropriate for pompano.
6. Development of genome selection tools. FAU-HBOI submitted the first de novo genome assembly for Florida pompano to the National Center for Biotechnology Information (NCBI) GenBank database (Accession: GCA_040938265.1; BioProject PRJNA1128138; https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA1128138). Since it was publicly released on 07/30/2024, our contig-level draft genome has provided a baseline for sequence composition and genetic variance data to develop genomic selection techniques that can reduce the breeding cycle, maximize genetic gain, and minimize inbreeding depression. ARS researchers from Fort Pierce, Florida have been using genome-wide SNPs to capture the additive genetic variance of alleles on whole segments and resolve phenotypic differences in growth performance among broodfish and seedstocks from Aquaco Farms (Fort Pierce, FL). However, our preliminary findings indicate a significant need to improve the contiguity of our reference genome assembly for T. carolinus. Currently, this is being achieved through numerous iterations of genomic polishing and scaffolding steps to correct base errors, misassemblies, and fill gaps. A tandem repeat-masked version of the more contiguous genome assembly is also being integrated with RNA-sequencing data to assemble transcripts and annotate functional genes. Access to a reference genome that is near chromosome-level will enable the identification of a subset of SNPs to accurately genotype selection candidates and predict genomic estimated breeding values. We plan to submit the new scaffolded genome assembly to NCBI GenBank prior to September 2025 and have started preparing a manuscript accordingly. Our genomic selection tools will contribute to an optimized selective breeding program for Florida pompano aquaculture, allowing producers to monitor trait introgression and maintain the genetic quality of commercial stocks.
7. Stakeholder meeting. Hosted an in-person and virtual stakeholder meeting on the HBOI campus that was attended by famers and academics where results were presented from the previous year’s work under this project. Thus, ARS researchers from Fort Pierce, Florida disseminated our findings as well as from our sub-contractors directly to stakeholders. This was followed by a question-and-answer session that was open to the farmers as well as to hear their main issues to help inform our research activities.
Review Publications
Paredes, J.F., Habte-Tsion, M., Riche, M., Mejri, S., Bradshaw, D., Sun Chin, L., Perricone, C., Wills, P.S. 2025. Effects of different carbohydrates on growth, hepatic glucose metabolism, and gut microbiome of Florida pompano (Trachinotus carolinus). Aquaculture. 600:742237. https://doi.org/10.1016/j.aquaculture.2025.742237.
Pimentel, O., Wasielesky, W., Brito, O.L., Roy, L.A., Romano, N.P., Krummenaeur, D. The fertilization of synbiotic system in intensive culture of Penaeus vannamei. Reviews in Aquaculture. 17(2):e13011. 2025. https://doi.org/10.1111/raq.13011.
Romano, N.P., Datta, S.N., Pande, G.J., Sinha, A.K., Yamamoto, F., Rawles, S.D., Webster, C.D. Preliminary assessment of the nutritive value of dietary exuviae from black soldier fly (Hermetia illucens) pupae in Mozambique tilapia. Journal of the World Aquaculture Society. 56(3):e70027. 2025. https://doi.org/10.1111/jwas.70027.
Singha, K.P., Abanikannada, M.F., Ma, J., Romano, N.P., Koutsos, E., Adams, D., Kumar, V. 2025. Complementing the high soybean meal diet with black soldier fly larvae meal as a functional feed ingredient to improve the performance, nutrient profile, and gut health of rainbow trout, Oncorhynchus mykiss. Aquaculture. 603:742405. https://doi.org/10.1016/j.aquaculture.2025.742405.
Romano, N.P., Wills, P.S., Paredes, F., Riche, M., Nilles, Z. Preliminary investigation on replacing fish meal with integrated multi-trophic aquaculture produced bioflocs in the diets of advanced Red drum (Sciaenops ocellatus, Actinopterygii) juveniles. Aquacultural Engineering. 111:102566. 2025. https://doi.org/10.1016/j.aquaeng.2025.102566.
Paredes, J.F., Riche, M., Bradshaw, D., Mejri, S., Chin, L.S., Perez, J., Popa, R., Romano, N.P., Wills, P.S. Evaluation of the effect of black soldier fly (Hermetia illucens L.) larvae meal in the diet of red drum (Sciaenops ocellatus) juveniles on production performance and feed palatability. Frontiers in Aquaculture. 4:1619878. 2025. https://doi.org/10.3389/faquc.2025.1619878.
Amirkolaei, A.K., Benito, M.M., Kumar, V., Romano, N.P., Hong, J., Small, B.C. Bile acid supplementation in alternative lipid-based diets: Effects on growth, histopathology and digestibility in rainbow trout (Oncorhynchus mykiss). Animal Feed Science and Technology. 319:0377-8401. 2024. https://doi.org/10.1016/j.anifeedsci.2024.116179.