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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

2022 Annual Report

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.

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
Progress towards Subobjective 1.1 has included early rearing culture, smoltification, and stocking of two USDA strains of Atlantic salmon (St. John River and Gaspe) into a semi-commercial scale recirculation aquaculture system (RAS) for growout to a target harvest size of 4 kg. A portion of these salmon have been PIT-tagged and fin clipped to track genetic associations with growth performance over the course of the study, in collaboration with USDA-ARS scientists at the Leetown, West Virginia, and Franklin, Maine, laboratories. Additional salmon from Benchmark Genetics (Iceland) are also stocked as “filler fish” for the growout trial, i.e., additional biomass to maintain commercial densities. At the time of report submission, the salmon are in the 0.5-1.0 kg range in weight, and regular performance and welfare assessments will be carried out for the remainder of the growout trial, including data collection on length, weight, fin condition, deformities, condition factor, coefficient of variation, and survival. Final performance assessment (including early maturation) and product quality data will commence when a 4 kg mean weight is achieved. Additional progress towards Subobjective 1.1 included analyses of steelhead strain performance data from the previous growout trial (FY2021) and preparation for a peer-reviewed manuscript of the steelhead strain study, to be submitted by the end of 2022. In support of Subobjective 1.2, all data analyses have been completed for the assessment of early maturation of Atlantic salmon and its association with RAS rearing temperature, i.e., 12 degrees C vs. 14 degrees C. Furthermore, dissemination of these results has been made through a peer-reviewed publication and scientific presentations at two conferences, Aquaculture 2022 (San Diego, California) and RASTech 2022 (Hilton Head, South Carolina). In support of Subobjective 1.3, heart rate biomonitors have been successfully surgically implanted into the coelomic cavities of 35 Atlantic salmon post-smolts, and initial pilot evaluation has determined that data quality is high and heart rate is noticeably associated with induced stressful conditions. The salmon population has now been stocked into six replicated experimental-scale RAS, and at the time of report submission experimental conditions of high vs. low nitrate in these systems are being established. Baseline blood chemistry data have been collected for the acclimation period and will continue to be collected at two further time points during the study period. The study will conclude at the end of FY2022, and data from biomonitors in addition to performance, health, and welfare data will be analyzed. Progress towards Subobjective 2.1 has included completion of a bench-scale study on the anaerobic co-digestion of fish viscera mixed with RAS waste solids. Preliminary results show that total methane production increased by 35-125% when different fractions of these two waste substrates are digested, when compared to RAS waste solids as an individual substrate. Fish viscera, as an individual waste substrate, produced 150% more methane compared to RAS waste solids as an individual substrate. At the time of report submission, ongoing efforts in support of Subobjective 2.1 include (i) investigating the change in the digester microbiome when fish viscera are mixed with the RAS waste solids, with plans to analyze the concentrations of inhibitory long chain fatty acids in the waste mixture after study completion, (ii) designing the pilot-scale anaerobic digester for construction at TCFFI (flow rate, hydraulic retention time, etc. have been calculated, and calculations are ongoing for heat energy requirements, mixing power requirements, and pump sizing/selection), and (iii) analyzing the microbial community associated with the anaerobic digestion of RAS waste solids, in collaboration with the Center for Aquaculture Technologies, San Diego California; these data will provide an understanding of which bacterial and archaeal genera are more acclimated to the high ammonia environment in a digester containing RAS waste solids. As discussed in our previous annual reports, Subobjective 2.2 was conceived as follow-up research to a previous on-site USDA-ARS MBR study and was initially planned to be carried out during the first half of 2020. However, assessment of the experimental-scale MBRs revealed that significant maintenance and retrofitting were required to begin this study, and we requested a postponement in study commencement in order to carry out the necessary infrastructure changes. We anticipate that the MBRs will be brought back to operational status in late 2022, with study commencement scheduled for January 2023. In support of Sub-objective 2.3, a computer vision platform (RASense1.0) was developed with four off-the-shelf sensors customized for underwater image acquisition. Data were acquired under two light conditions (i.e., ambient and supplemented), and the images were annotated, augmented, and trained using a custom YOLOv5 ML model. Sensor selection significantly affected model precision, recall, and mean average precision (mAP); however, light condition did not demonstrate a considerable effect on model accuracy. There was a substantial improvement in model performance while increasing the size of the image datasets up to 700 images. Similarly, image augmentation improved model accuracy for a smaller dataset. The model detected whole and partial fish in real-time with satisfactory mAP and F1 score of 85% and 0.8, respectively. At the time of report submission, the model is being further optimized by including training data from various growth stages and water quality conditions to improve the robustness of RASense1.0, which will be further utilized to estimate fish biomass and study fish behavioral responses under various environmental conditions. Additionally, a journal manuscript focusing on initial RASSense1.0 research has been submitted for peer-review.

1. Integration of precision agriculture technologies into recirculating aquaculture systems. Application of precision agriculture and precision technologies in the U.S. aquaculture industry is presently minimal. These technologies in aquaculture can eliminate the stress and negative impacts on fish welfare associated with the traditional, hands-on methods for estimating population biomass. ARS scientists in Shepherdstown, West Virginia, have developed an artificial intelligence (AI)-aided computer vision system for real-time fish monitoring in recirculating aquaculture systems (RAS). Underwater images and videos were acquired to train an AI fish detection model, and the developed vision system detected whole and partial fish in the field of view with satisfactory model performance of greater than eighty five percent precision. These findings demonstrate the capability for precision technology to assist non-invasive fish condition monitoring and biomass estimation, benefiting fish health, welfare, and production efficiency.

2. Identification of barriers to anaerobic digestion of aquaculture waste. The U.S. aquaculture industry has been moving towards intensive land-based systems to meet the ever-increasing demand for fish protein, but this intensification also leads to the generation of waste streams from these facilities. Anaerobic digestion can be a carbon-neutral biological technique for simultaneous waste treatment and renewable energy generation (heat and electricity). Extramural ARS scientists in Shepherdstown, West Virginia, have identified components of waste streams that negatively affect anaerobic digester effectiveness. These include low solids, high salt concentration, low carbon to nitrogen ratio, high fat content, and high sulfur content. These problems can be mitigated by co-digestion of multiple waste streams to balance the carbon/nitrogen ratio, the use of pre-selected microbial communities adapted to these harsh conditions, and using innovative techniques to simultaneously capture sulfur and boost energy production. These findings will provide farmers with opportunities to troubleshoot and optimize anaerobic digestion performance, thereby improving the sustainability and reducing the environmental impact of land-based aquaculture systems.

Review Publications
Crouse, C., Davidson, J., Good, C. 2022. The effects of two water temperature regimes on Atlantic salmon (Salmo salar) growth performance and maturation in freshwater recirculating aquaculture systems. Aquaculture. 553(2022):738063.
May, T., Good, C., Redman, N., Vinci, B., Xu, F., Østergaard, L., Mann, K. 2022. Efficacy of BioRas® Balance (an enzyme product) to break down hydrogen peroxide following routine treatment applications in aquaculture. Aquaculture Research.
Davidson, J.W., Summerfelt, S., Grimm, C.C., Fischer, G., Good, C. 2021. Effects of swimming speed and dissolved oxygen on geosmin depuration from market-size Atlantic salmon Salmo salar. Aquacultural Engineering. 95:102201.
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. Bioresource Technology. 354:127144.
Ranjan, R., Sinha, R., Khot, L.R., Whiting, M. 2022. Thermal-RGB imagery and in-field weather sensing derived sweet cherry wetness prediction model. Scientia Horticulturae. 294:110782.
Ranjan, R., Sinha, R., Khot, L.R., Hoheisel, G., Grieshop, M.J., Ledebuhr, M. 2021. Effect of emitter modifications on spray performance of a solid set canopy delivery system in a high-density apple orchard. Sustainability. 13(23):13248.