Location: Cool and Cold Water Aquaculture Research
2023 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 Subobjective 1.1, two strains of Atlantic salmon (St. John River and Gaspé, provided as eyed eggs from the USDA-ARS National Cold Water Marine Aquaculture Center, Franklin, Maine) were raised in a semi-commercial scale recirculation aquaculture system (RAS) for growout to a target harvest size of 4 kg. Regular data collection events have been carried out throughout the year, and harvest will commence in summer 2023. Final data on growth performance, survival, maturation, fillet yield, fillet composition, fin condition, deformities, and cataracts will be collected and compared between the two strains to determine which performs best in freshwater RAS. Additionally, some of these salmon have been PIT-tagged and fin-clipped to track genetic associations with performance and production metrics 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; performance data will be provided to Benchmark Genetics to assist with their breeding program. Additional progress towards Subobjective 1.1 included preparing and submitting a manuscript of the steelhead strain study (FY2021) for peer-reviewed publication.
Subobjective 1.2 has been completed, with all milestones met in FY2022.
Progress towards Subobjective 1.3 has included the completion of high (peak approximately 250 mg/L) versus low (100 mg/L) nitrate-nitrogen challenge of Atlantic salmon in six replicated RAS, with data collected and compared from surgically-implanted biomonitors, whole blood analyses, and growth performance and welfare sampling events. Findings indicate that high nitrate-nitrogen does affect Atlantic salmon post-smolt growth and health; however, trends in heart rate separation and elevated whole blood hemoglobin / hematocrit indicate a physiological response occurs at a threshold between 150-250 mg/L 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 and reduced energy for pumping makeup water or denitrification water treatment processes. A manuscript for peer-reviewed publication for this study is currently being prepared.
Progress towards Subobjective 2.1 has included (i) the analysis of microbial communities associated with the anaerobic digestion of RAS waste solids and its mixture with fish viscera, (ii) completion of the pilot-scale digester engineering design (heat energy requirements, mixing power requirements, and pump sizing/selection), (iii) peer-reviewed publication on the anaerobic digestion of RAS waste solids, and (iv) completion of a bench scale study on composting RAS waste solids. At the end of the incubation period within the anaerobic reactors, a higher relative abundance of ammonia and long chain fatty acid-tolerant microorganisms were observed, indicating acclimation of the microbiome to those conditions. The composting study highlighted the challenges associated with composting fish sludge at bench-scale due to higher heat losses to the environment, making thermophilic temperatures difficult to achieve; however, analysis of the finished material revealed a very stable and mature compost product (STA Certified Compost Standards) with heavy metal concentration below EPA limits and no detectable pathogens. Results from completed studies were presented at Aquaculture America 2023 conference in New Orleans, Louisiana, and at RASTech 2023 conference in Orlando, Florida. At the time of report submission, ongoing efforts in support of Subobjective 2.1 include (i) procurement of pumps, mixers, heat exchanger, and related accessories for construction of the pilot-scale anaerobic digester over the next 4 months, and (ii) recipe development and completion of a pilot-scale composting study with RAS waste solids by the end of 2023.
As discussed in previous annual reports, Subobjective 2.2 was conceived as follow-up research to a previous on-site USDA-ARS membrane biological reactor (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. Significant progress towards Subobjective 2.2 was made in FY2023, with design and construction of new replicated MBRs completed and the study fully underway at the time of report submission. The MBRs are operating well and performing as designed, with significant improvements in water quality (compared to RAS operated with no MBR) observed. Data will be analyzed and compared following the completion of the study later in 2023, and at least one manuscript will be prepared for peer-reviewed publication.
In support of Subobjective 2.3, a study aimed at developing a computer vision platform (RASense1.0) for non-invasive in-tank fish detection was completed in FY2023. RASense1.0 performed satisfactorily in detecting partial and whole fish under RAS rearing conditions, and the optimized one-stage fish detection model achieved satisfactory mean average precision (mAP) and F1 score of 86.5 % and 0.8, respectively. This study was published in both peer-reviewed and trade-press articles. Further efforts to support Subobjective 2.3 included the development of an Artificial Intelligence (AI) and Internet of Things (IoT)-enabled fish mortality detection and alert system (‘MortCam’) for use under RAS conditions. The proposed tool, employing AI and IoT, 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. The MortCam is currently deployed in a semi-commercial scale grow-out tank at The Conservation Fund Freshwater Institute (TCFFI), reliably generating email and text alerts to notify fish production staff of unusual mortality events. The details of the MortCam and validation results have been published in a peer-reviewed journal. Finally, additional work in support of Subobjective 2.3 include efforts in developing tools to rapidly detect off-flavor in RAS-raised fish, and a preliminary study is underway to test the feasibility of High-Field Asymmetric Waveform Ion Mobility Spectrometry (FAIMS) for fish off-flavor detection.
Accomplishments
1. Utilizing artificial intelligence to detect fish mortalities in recirculating aquaculture systems. Early detection of elevated mortalities in aquaculture systems is crucial for timely management responses to prevent mortality escalation. Traditional approaches for mortality detection rely on observation and tracking by human operators, sometimes aided by underwater cameras; however, this approach can delay a mortality response, especially when personnel are mostly or entirely off-site, and may not be timely enough to prevent a significant mortality event. Additionally, higher stocking densities and water turbidity can obscure visual identification of mortalities in recirculating aquaculture systems (RAS). Extramural ARS scientists in Shepherdstown, West Virginia, have developed an Artificial Intelligence- and Internet of Things (IoT)-enabled fish mortality detection and alert system (‘MortCam’) that provides 24-hour surveillance under RAS culture conditions and reliably generates email and text alerts to warn fish production staff of elevated mortality events. This technology will provide RAS farmers with a critical tool for reliable early mortality detection and notification, providing for effective and timely treatments to prevent mortality escalation, improve fish welfare, and prevent economic loss.
2. Characterization of water quality and waste production during Atlantic salmon depuration. Microbial biofilms can accumulate over surfaces within a recirculating aquaculture system (RAS), and bacteria within these biofilms can produce and release off-flavor compounds. These compounds can be taken up by fish and impart objectionable flavors to fillets, thus requiring fish depuration, or the housing of fish into a separate, biofilm-free system prior to harvest to rid flesh of off-flavor compounds. At present, best management practices for depurating fish are still being developed in the RAS industry, as water quality and waste production during the depuration process have not been investigated. Extramural ARS scientists in Shepherdstown, West Virginia, performed the first comprehensive analysis of water quality and waste production in an Atlantic salmon depuration system. This study determined that residual waste production occurs in depuration systems fully stocked with Atlantic salmon, thus indicating that appropriate system management is required during the depuration period. As a result, a range of practical recommendations and procedural refinements were determined to optimize depuration system performance; these include 1) extension of the depuration period, 2) identification of the optimal location for adding depuration system water to RAS to mitigate solids and ammonia contribution, 3) integration of an internal solids removal process within the depuration system design, and 4) management of dissolved oxygen in depuration systems. These novel management strategies are central to optimize removal of off-flavor compounds and improve product quality of fish produced in RAS, thus contributing to industry sustainability through better tasting fish.
3. Optimizing carbon dioxide removal in recirculating aquaculture systems. Fish release dissolved carbon dioxide (CO2) as a normal product of metabolism, thus requiring management of this gas to maintain levels in culture tanks that are safe for fish. Diffused aeration basins are often used to remove CO2 in recirculation aquaculture systems (RAS), but management protocols for optimal basin performance have yet to be defined. Extramural ARS scientists in Shepherdstown, West Virginia, optimized protocols for the removal of CO2 using an aeration basin with diffused air as the stripping gas in a relatively shallow water column. Specifically, the effect of variables such as hydraulic loading rates, influent CO2 levels, diffused airflow rates, and water depths on CO2 removal efficiencies were characterized. These findings provide RAS farmers with management protocols for effective removal of dissolved CO2 using aeration basins in freshwater RAS, thus improving water quality, fish health, and production efficiency.
Review Publications
Redmen, N., Straus, D.L., Annis, E.R., Murray, M., Good, C. 2022. Assessing the toxicity of peracetic acid to early Atlantic salmon Salmo salar life-stages. Aquaculture Research. (53)14:5097-5104. https://doi.org/10.1111/are.15997.
Good, C., Redman, N., Murray, M., Straus, D.L., Welch, T.J. 2022. Bactericidal activity of peracetic acid to selected fish pathogens in recirculation aquaculture system water. Aquaculture Research. (53)16:5731-5736. https://doi.org/10.1111/are.16031.
Davidson, J.W., Reman, N., Crouse, C., Vinci, B. 2022. Water quality, waste production, and off-flavor characterization in a depuration system stocked with market-size Atlantic salmon Salmo salar. Journal of the World Aquaculture Society. (54)1:96-112. https://doi.org/10.1111/jwas.12920.
Choudhury, A., Lepine, C., Good, C. 2023. Methane and hydrogen sulfide production from the anaerobic digestion of fish sludge from recirculating aquaculture systems: Effect of varying initial solid concentrations. Fermentation. (9)2:94. https://doi.org/10.3390/fermentation9020094.
Davidson, J., Raines, C., Crouse, C., Good, C., Keplinger, B. 2023. Evaluating Brook trout egg and alevin survival at different temperatures in simulated karst environments with marl sedimentation. Southeastern Association of Fish and Wildlife Agencies Conference. 10:27-35.
Lepine, C.A., Redman, N., Murray, M., Lazado, C., Johansen, L., Espmark, A., Davidson, J., Good, C. 2023. Assessing Peracetic Acid application methodolgy and impacts on fluidized sand biofilter performance. Aquaculture Research. 2023:6294325. https://doi.org/10.1155/2023/6294325.
Ranjan, R., Sharrer, K., Tsukuda, S., Good, C. 2023. Effects of image data quality on a convolutional neural network trained in-tank fish detection model for recirculating aquaculture systems. Computers and Electronics in Agriculture. 205:107644. https://doi.org/10.1016/j.compag.2023.107644.
Ranjan, R., Sharrer, K., Tsukuda, S., Good, C. 2023. MortCam: An Artificial Intelligence-aided fish mortality detection and alert system for recirculating aquaculture. Aquacultural Engineering. 102:102341. https://doi.org/10.1016/j.aquaeng.2023.102341.
