Location: Cool and Cold Water Aquaculture Research
2025 Annual Report
Objectives
Objective 1: Optimize genetic x environmental interactions for Atlantic salmon performance in recirculating aquaculture systems.
Sub-objective 1.A: Assessing U.S. strain Atlantic salmon performance, health, & welfare in RAS.
Sub-objective 1.A1: Family-based evaluation of St. John River strain Atlantic salmon.
Sub-objective 1.A2: Assessing heritability of RAS-derived off-flavor uptake, retention, and depuration in St. John River strain Atlantic salmon.
Sub-objective 1.B: Optimizing early rearing environmental conditions for triploid Atlantic salmon: Assessing diet impacts on musculoskeletal deformities in triploid Atlantic salmon at two different temperatures.
Sub-objective 1.C: Improving water quality for salmonid production in RAS: Evaluating the effects of RAS water quality on the production of the common off-flavor compounds, geosmin and 2- methylisoborneol.
Objective 2: Develop strategies to reduce the impacts of early maturation in Atlantic salmon on growth and production efficiency.
Sub-objective 2.A: Evaluating the effects diet energy content on the onset of early maturation in all- female Atlantic salmon reared in freshwater RAS at two different temperatures.
Objective 3: Develop precision aquaculture strategies to improve recirculating aquaculture system production efficiencies.
Sub-objective 3.A: Investigating the feasibility of hyperspectral imaging for the early detection of salmonid maturity in a semi-commercial scale freshwater RAS.
Sub-objective 3.B: Investigating alternative and low-cost off-flavor detection technologies for rapid tank-side detection of off-flavor in RAS cultured Atlantic salmon.
Objective 4: Develop and optimize methods to transform recirculating aquaculture system waste products to valuable, alternative revenue streams.
Sub-objective 4.A: Evaluate (i) anaerobic digestion (AD) and (ii) microalgae production for energy and nutrient recovery from RAS waste streams.
Objective 5: Optimize recirculating aquaculture system parameters for coho salmon.
Sub-objective 5.A: Investigating the impact of water temperature on post-smolt coho salmon in freshwater RAS.
Sub-objective 5.B: Evaluating the effect of water exchange rates on water chemistry and coho salmon growth, health, and welfare in replicated RAS.
Approach
Over the past decade, the U.S. farmed salmon industry has demonstrated significant growth and substantial capital investment in large-scale land-based, closed-containment operations utilizing water recirculation aquaculture system (RAS) technologies. There are numerous advantages to land-based RAS compared to more traditional farming methods; these advantages include increased environmental control of fish culture conditions for optimized and biosecure fish production, the ability to strategically locate farms close to markets or regions supplying inexpensive power, and the enhanced ability to capture wastes to reduce environmental contamination significantly. As a relatively new approach to salmon farming, however, there remains considerable room for improvement in refining and optimizing the technological, biological, and economic aspects of RAS production. The Conservation Fund Freshwater Institute (TCFFI), an extramural research program of the USDA-ARS, has been at the forefront of RAS technology research and development since the 1990s, and we continue to be uniquely suited to serve this growing agricultural sector through focused stakeholder-driven research and innovation. Our next 5-year research plan will focus on critical areas and knowledge gaps hinder growth in the U.S. land-based, closed-containment RAS salmon industry. Specifically, we aim to 1) identify genetic and environmental factors that can improve salmon performance in freshwater RAS, 2) develop strategies to reduce early maturation and consequent product devaluation in RAS-raised salmon, 3) innovate and refine precision aquaculture technologies to provide RAS farmers with accurate, real-time data to inform management decision-making, 4) develop viable supplemental revenue streams for RAS farmers through converting waste materials to sellable products, and 5) assist industry diversification through alternative salmonid species (e.g., coho salmon) culture environment optimization. We anticipate that public dissemination of our research findings to key stakeholders will significantly and positively impact the growth of the nascent U.S. RAS salmon industry.
Progress Report
In support of Subobjective 1.B, all-female triploid Atlantic salmon eyed eggs were received from Benchmark Genetics (Iceland) and incubated on-site at <6 degrees C. Once hatched, fry were transferred to our new early rearing recirculating aquaculture systems, with six tanks operating at 11 degrees C and the remaining six tanks operating at 14 degrees C. Within the twelve tanks, six randomly selected tanks are currently being fed a triploid- specific diet while the remaining six tanks are being fed a standard commercial salmon diet. At the time of report submission, fry are approximately 2 g in mean weight; data collection on growth performance, survival, deformities, and other important production metrics will be carried out for the remainder of FY2025 and throughout FY2026, in order to determine the performance impacts of diet type at the two study rearing temperatures.
In support of Subobjective 1.C, a source population of Atlantic salmon is currently being raised in replicated recirculating aquaculture systems (RAS) for a non-USDA-funded study. Once this project is complete (summer, 2025) 600-800 salmon (average weight 1 kg) will be moved to a separate building and grown to 2.5-3 kg, after which (in FY2026) these fish will be stocked in replicated RAS for the planned experiment examining ammonia concentrations and their impacts on geosmin and methyl-2-isoborneal (off-flavor compounds) production from RAS biofilms and associated uptake in the edible portions of Atlantic salmon.
In support of Subobjective 3.A, hyperspectral imaging (HSI) combined with machine learning has been used to non-invasively assess maturity status in RAS-raised Atlantic salmon. A snapshot hyperspectral camera was configured to acquire images across 164 spectral bands spanning 350–1000 nm. At harvest, a total of 52 euthanized Atlantic salmon were manually evaluated for their sexual maturity status followed by hyperspectral imaging. The regions of interest (ROIs) were extracted from the HSI hypercubes and reflectance spectra were
extracted and analyzed. Spectral ratio analysis and principal component analysis (PCA) revealed class-dependent spectral variation, particularly in the visible and near-infrared regions. Multiple classification algorithms were tested on full-spectrum and feature-reduced datasets, with features selected using Random Forest importance and Jeffries–Matusita (J-M) distance. Ensemble models, particularly Extra Trees and Random Forest, achieved the highest classification accuracies, with Extra Trees reaching 81.8% on the full dataset. Key wavelengths contributing to class separation were consistently identified around bands in range of 400–456 nm. These findings demonstrate the potential of HSI as a non-invasive tool for maturity detection and provide a foundation for developing real-time, multispectral sensing solutions for precision aquaculture (i.e., a data-driven approach to aquaculture that uses technology and automation to optimize fish farming operations for increased efficiency, sustainability, and animal welfare). Our ongoing experiments for FY2025 are focused on evaluating the feasibility of HSI for early maturity detection in coho salmon, with data collected at different life stages. Underwater assessment of HSI maturation detection will also be evaluated in the remainder of FY2025.
In support of Subobjective 4.A, efforts by waste-to-value scientists at The Freshwater Institute have included ordering a) a centrifuge to harvest the microalgal cells from the solution, b) peristaltic pumps to supply the photobioreactors with a constant supply of nutrient-rich wastewater for the microalgae, and c) a control panel for automating the anaerobic digester's daily operations. Three variable-frequency drives have also been procured and installed to allow greater flexibility in controlling the speed of the three anaerobic digester pumps. Discussions on optimal photobioreactor setup and experimental designs for the studies based on the most up-to-date research on microalgae are ongoing. A literature review on microalgae production using wastewater from aquaculture is in progress.
In support of Subobjective 5.A, all-female coho salmon eggs were received from Riverence (Rochester, Washington) and grown in replicated RAS under two treatment regimes, i.e. 14 degrees C versus 17 degrees C. The fish are currently approximately 1.4 kg mean weight, and several growth performance, health, and welfare data collection events have been carried out. This experiment is set to conclude at the end of July, 2025. Preliminary results indicate that there are no major differences in growth performance and welfare metrics between the two treatment regimes; however, survival has been significantly worse in the higher temperature group. Final data analysis and summaries will be carried out during the remainder of FY2025 and FY2026.
Accomplishments
Review Publications
Amogi, B.R., Ranjan, R., Pukrongta, N., Khot, L.R., Sallato, B.V., Mogollón, M., Torres, C.A. 2025. Localized sensing data-driven efficacy evaluation of heat stress mitigation techniques in ‘Honeycrisp’ apple cultivar. Scientia Horticulturae. 341. Article 113992. https://doi.org/10.1016/j.scienta.2025.113992.
Ranjan, R., Shroff, H., Sharrer, K., Tsukuda, S., Good, C. 2024. FilletCam AI: A handheld tool for precise fillet color profiling of Atlantic salmon and rainbow trout. Journal of Agriculture and Food Research. 18. Article 101461. https://doi.org/10.1016/j.jafr.2024.101461.