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ARS Home » Northeast Area » Leetown, West Virginia » Cool and Cold Water Aquaculture Research » Research » Research Project #437702
Research Project: Support the Viability and Expansion of Land-Based Closed-Containment Aquaculture

Location: Cool and Cold Water Aquaculture Research

2025 Annual Report


Objectives
Objective 1. Improve fish health, performance, and welfare in recirculating aquaculture systems. Sub-objective 1.1 Evaluate salmonids grown to market size in a semi-commercial scale freshwater RAS. a): Collaborate with NCWMAC to evaluate multiple strains of Atlantic salmon and their performance in a RAS environment. b): Assess genetic strain of steelhead (including USDA-strain rainbow trout) raised to 4kg in a RAS environment. Sub-objective 1.2 Assess environmental manipulation to reduce maturation in mixed-sex diploid Atlantic salmon. Sub-objective 1.3 Improve biological monitoring and management of salmonids in RAS through technological integration of next-generation biomonitors. Objective 2. Support land-based salmonid recirculating aquaculture systems production through increased technological and operational efficiencies and novel, supplemental revenue streams. Sub-objective 2.1 Evaluate methodologies to convert RAS waste to value-added products. 1a: Assess feasibility of new composting technologies of RAS waste solids and their capacity to generate sellable products. 1b: Assess feasibility of anaerobic digestion of RAS waste solids to generate biogas/energy. Sub-objective 2.2 Assess novel methods to improve RAS water quality, including optimized integration of membrane biological reactors. Sub-objective 2.3 Pilot and evaluate new computing technologies for RAS integration to optimize system operational efficiencies.


Approach
The domestic salmonid aquaculture industry is currently experiencing a significant departure from traditional farming practices, as evidenced by recent, substantial capital investment in large-scale land-based, closed-containment facilities utilizing water recirculation aquaculture system (RAS) technologies. While this is an encouraging evolution for U.S. aquaculture overall, this relatively new approach to raising market-sized Atlantic salmon, steelhead trout, and other economically important species is still a frontier in agriculture, remains largely untested at commercial scale, and requires significant refinement and optimization in technological, biological, and economic methods and strategies. The Conservation Fund Freshwater Institute (TCFFI), an extramural program of the USDA-ARS, has been at the forefront of RAS technology research and development for over two decades, and at present we are uniquely suited to continue serving this growing agricultural sector through focused, industry-relevant research and innovation. Our next 5-year project plan seeks to address critical areas that are necessary to support the sustainable growth of the U.S. land-based, closed-containment aquaculture industry; specifically, our objectives fall under two broad categories aimed at improving i) the biological performance of salmonids in RAS, and ii) the technical and economic efficiencies of land-based closed-containment operations. Research activities will include identifying genetic strains of Atlantic salmon and steelhead for optimal performance in RAS, assessing methods to reduce early sexual maturation and improve water quality, developing next-generation biomonitors and computing technologies to improve fish health management and RAS environmental control, and developing means for RAS producers to monetize waste streams for enhanced economic viability.


Progress Report
In support of Sub-objective 1.1, two growout trials were conducted in Shepherdstown, West Virginia, in a semi-commercial scale recirculating aquaculture system (RAS) to determine the best performing strains of domestically available i) steelhead trout, and ii) Atlantic salmon. For the steelhead trial, clear differences in growth performance were noted among six strains assessed, with the USDA-ARS fillet yield-selected strains demonstrating the best overall growth performance up to the target harvest size of 3 kilograms. The Atlantic salmon strains trial was carried out simultaneously at The Freshwater Institute, the National Cold Water Marine Aquaculture Center (Franklin, Maine), and the Northern Aquaculture Demonstration Facility (Bayfield, Wisconsin), to investigate growth performance differences between USDA-ARS’s St. John River and Gaspe strains of Atlantic salmon. Results clearly indicated that the St. John River strain performs significantly better across the different RAS rearing environments, in terms of growth, survival, fillet yield, and reduced early maturation, versus the Gaspe strain. To follow up on this research, our next 5-year project – 8082-10600- 001-000D “Innovating New Technologies that Improve Efficiencies of Recirculating Aquaculture Systems” – includes research plans to investigate within-strain St. John River salmon families and whether superior performance in RAS is a heritable trait. In support of Subobjective 1.2, ARS scientists in Shepherdstown, West Virginia, performed a long-term experiment in replicated RAS to determine the impacts of rearing temperature (12 degrees C vs. 14 degrees C) on early maturation in mixed-sex diploid Atlantic salmon. Results indicated that significantly less early maturation occurred in the lower temperature treatment group; however, maturation in the lower temperature group still occurred at a level that would be unacceptable to stakeholders raising Atlantic salmon in RAS, and therefore other temperature options and/or genetic and/or environmental manipulation needs to be carried out to reduce maturation to acceptable levels. Furthermore, follow-up research in our next 5-year project will be carried out to provide additional insights into early maturation, specifically through investigation of the impacts of rearing temperature (11 degrees C vs. 14 degrees C) and dietary energy levels on early maturation in all-female diploid Atlantic salmon. In support of Subobjective 1.3, ARS scientists in Shepherdstown, West Virginia, completed a 6-month experiment in replicated RAS to determine the impacts of nitrate-nitrogen concentrations on Atlantic salmon post-smolt performance, specifically with the use of next-generation surgically-implanted heart rate biomonitors. Analysis of heart rate data indicated that concentrations of nitrate-nitrogen up to 150 mg/L appeared to have little impact on fish stress, and growth performance, feed conversion, survival, and other performance outcomes were unaffected. Heart rate was increased above 150 mg/L (up to 250 mg/L maximum nitrate-nitrogen concentration) indicating a stress response; however, measured performance metrics were unaffected, and blood analysis indicated physiological compensation for the elevated nitrate-nitrogen. These results are important to stakeholders producing Atlantic salmon in RAS, as establishing a higher nitrate-nitrogen threshold will equate to greater water savings. Establishing such thresholds will also reduce energy for pumping makeup water or for denitrification water treatment processes. To follow up on this research, our next 5-year project includes plans to investigate nitrate-nitrogen concentration thresholds for an additional commercially important salmonid species (i.e., coho salmon). In support of Sub-objective 2.1, ARS scientists in Shepherdstown, West Virginia, carried out a range of laboratory- and pilot- scale experiments to determine the feasibility of converting RAS waste solids (feces, mortalities, waste feed) into additional revenue streams through conversion to compost or biogas using composting and anaerobic digestion processes, respectively. Regarding composting, our studies demonstrated that RAS waste solids can be successfully converted to compost, although the addition of wood shavings was required as a bulking agent. Analysis of the compost produced from RAS solids waste demonstrated that the product met the requirements to be classified as a Class A biosolids, indicating it is acceptable for use in residential areas and for food crops. The compost product was tested for per- and polyfluoroalkyl substances (PFAS), and all 40 analytes tested were below the limit of quantification (with a majority below the limit of detection). Concerning anaerobic digestion, we reviewed the challenges associated with this process using RAS waste solids; subsequent studies revealed that RAS waste is a promising substrate for biogas production and energy recovery, with potentially more biogas production compared to traditional wastes. The low carbon:nitrogen ratio of the waste solids resulted in an extended lag phase during the start-up of lab-scale bioreactors, but microbial community analysis revealed that the relative abundance of the methanogenic archaea shifted to a more ammonia-tolerant community. Additionally, co-digestion of fish viscera with waste solids resulted in increased biogas production. A pilot-scale anaerobic digester was constructed to assess the feasibility and operational challenges associated with the long-term operation of the process at scale. However, due to the low temperatures during the winter months, biogas production was low. To follow up on this research, our next 5-year project includes plans to further investigate and refine anaerobic digestion of RAS waste solids, specifically through optimizing organic loading rate, temperature, and hydraulic retention time, to increase biogas production; a recirculating mixing pump, boiler, and heat exchanger system will be incorporated for more efficient operation. Additionally, nutrient recovery from RAS wastewater and anaerobic digestate will be assessed through the use of microalgae. In support of Sub-objective 2.2, ARS scientists in Shepherdstown, West Virginia, designed and constructed replicated multi- vessel membrane biological reactors, and their integration into replicated RAS for the purposes of water quality improvement was assessed during a long-term experiment. Results indicated that membrane biological reactors are indeed a viable approach to RAS water treatment, rainbow trout performance was unaffected by including membrane biological reactors in RAS, and reusing membrane biological reactor permeate reduced RAS water use by 94%. In support of Subobjective 2.3, ARS scientists in Shepherdstown, West Virginia, initiated a research focus on precision aquaculture, through the application of cutting-edge computer vision, artificial intelligence, and machine learning to RAS fish culture activities to increase operational efficiency and provide producers with accurate, real-time data. Research began with the development of a computer vision platform (RASense1.0) for non-invasive in-tank fish detection; this platform performed satisfactorily in detecting partial and whole fish under RAS rearing conditions, and the optimized one-stage fish detection YOLO model achieved satisfactory mean average precision (mAP) and F1 score of 86.5 % and 0.8, respectively. Additionally, to support rapid and low-cost AI model training, a computer-simulation method was tested to generate virtual training images simulated for RAS environment. The mixed model trained with 630 virtual and 70 real images (virtual to real image ratio: 90:10) achieved mAP and F1 scores of 91.8% and 0.87, respectively, with substantially lower training time cost. Subsequent precision aquaculture research focused on developed an artificial intelligence and Internet of Things-enabled fish mortality detection and alert system (‘MortCam’) for use under RAS conditions, which provides round-the-clock mortality monitoring and triggers an alarm when mortality thresholds are exceeded; the optimized mortality model achieved a mAP and F1 score of 93.4 % and 0.89, respectively. Finally, an experiment was carried out to develop an artificial intelligence-enabled handheld device (‘FilletCam AI’) for precise, repeatable, rapid, real-time, and objective color and defect evaluation of fish fillets. The model demonstrated robust performance in terms of detecting fillet and reference color palettes, achieving a mAP of 99.5% and an F1 score of 0.99 at 100 epochs. Additionally, gaping defect model achieved mAP of 90.4% and Precision of 85.5%. FilletCam outperformed traditional fish fillet color and defect evaluation methods. To follow up on this research, our next 5-year project includes plans to investigate the feasibility of hyperspectral imaging for the early detection of early salmonid maturation in freshwater RAS.


Accomplishments
1. Refinement of artificial intelligence technology for quality assessment of salmon fillets. The color and character of salmon fillets are key quality attributes that significantly influence consumer choice. Pale fillets and defects such as gaping or melanin spots can adversely affect perceived fillet quality. Salmon producers invest substantial effort in ensuring their products are visually appealing; however, traditional methods for assessing fillet color and defects can be unreliable. Previously, extramural ARS scientists in Shepherdstown, West Virginia, developed an artificial intelligence (AI)-enabled handheld device for rapid, accurate, and objective evaluation of salmon fillet color called FilletCam. Several enhancements were made to the device, including the integration of muscle gaping and melanin spot detection models, and the ability to assess a wider range of fillet sizes. With these improvements, FilletCam will provide salmon farmers and processors with a faster and more reliable tool for comprehensive fillet quality assessment.

2. Energy production from aquaculture waste solids through anaerobic digestion is a viable option for additional farm revenue. Anaerobic digestion is a biological process that breaks organic matter down in the absence of oxygen and produces methane-rich biogas. The biogas can then be used to produce heat and electricity or upgraded to natural gas. Farmers and wastewater treatment facilities typically use this process, but its use in aquaculture has received little attention due to limited opportunities to capture the waste. As recirculating aquaculture systems (RAS) allow for efficient capture and collection of the waste solids, extramural ARS scientists in Shepherdstown, West Virginia, investigated the feasibility of using RAS solids waste as a feedstock for anaerobic digestion to offset energy costs for farmers. The studies revealed that aquaculture waste is a promising feedstock, as its methane potential exceeded that of animal manure and sewage sludge. Conservative estimates demonstrated that fish farmers could offset up to 28% of their heat and electricity needs using this technology. As such, anaerobic digestion could provide a viable avenue for fish farmers to recoup more value from their waste streams.


Review Publications
Redman, N., Straus, D.L., Murray, M., Good, C. 2025. Assessing the toxicity of peracetic acid to parr, smolt, and post-smolt Atlantic salmon Salmo salar in RAS water. Aquaculture Research. 2025(1). Article e934217. https://doi.org/10.1155/are/9934217.
 Holan, A., Good, C., Powell, M. 2020. Health Management in Recirculating Aquaculture Systems (RAS). In: Kibenge, F.S.B., Powell, M.D., editors. Aquaculture Health Management Design Operation Approches. London, UK, San Diego, CA, Cambridge, MA, Oxford, UK: Academic Press. p. 281-318.
 Good, C. 2020. Chapter 29: Water recirculating aquaculture systems and the future for land-based, closed-containment salmon production. In: Goldberg, A.M., Wychgram, C., editors. Feeding the World Well: A Framework for Ethical Food Systems. Baltimore, MD: Johns Hopkins University Press. p.317-328.
 Davidson, Iii, J.W., Crouse, C., Lepine, C., Good, C. 2024. Evaluating the suitability of nitrate-nitrogen levels for post-smolt Atlantic salmon Salmo salar production in RAS with assistance from heart rate bio-loggers. Aquacultural Engineering. 107. Artcile 102461. https://doi.org/10.1016/j.aquaeng.2024.102461.
 May, T., Good, C., Reman, N., Vinci, B., Xu, F., Ostergaard, L., Mann, K. 2022. Efficacy of BioRas Balance (an enzyme product) to breakdown hydrogen peroxide following routine treatmentapplications in aquaculture. Aquaculture Research. 53(12):4556-4560. https://doi.org/10.1111/are.15927.
 Love, D.C., Fry, J.P., Cabello, F., Good, C., Lunestad, B.T. 2019. Veterinary drug use in United States net pen Salmon aquaculture: Implications for drug use policy. Aquaculture. 518. Article 734820. https://doi.org/10.1016/j.aquaculture.2019.734820.
 Stiller, K.T., Kolarevic, J., Lazado, C.C., Gerwins, J., Good, C., Summerfelt, S.T., Mota, V.C., Espmark, A.M. 2020. The Effects of Ozone on Atlantic Salmon Post-Smolt in Brackish Water—Establishing Welfare Indicators and Thresholds. International Journal of Molecular Sciences. 21(14). Article 5109. https://doi.org/10.3390/ijms21145109.
 Love, D.C., Fry, J.P., Cabello, F., Good, C., Lunestad, B.T. 2020. Veterinary drug use in United States net pen Salmon aquaculture:implications for drug use policy. Aquaculture. 518. Article 734820. https://doi.org/10.1016/j.aquaculture.2019.734820.
 Davidson, J., Grimm, C., Summerfelt, S., Fischer, G., Good, C. 2020. Depuration system flushing rate affects geosmin removal from market-size Atlantic salmon Salmo salar. Aquacultural Engineering. 90. Article 102104. https://doi.org/10.1016/j.aquaeng.2020.102104.
 Choudhury, A., Lepine, C., Witarsa, F., Good, C. 2022. Anaerobic digestion challenges and resource recovery opportunities from land-based aquaculture waste and seafood processing byproducts: A review. Journal of Bioresource Technology. 354. Article 127144. https://doi.org/10.1016/j.biortech.2022.127144.