Location: Warmwater Aquaculture Research Unit
2025 Annual Report
Objectives
1. Improve oxygen delivery in ponds to minimize impacts of hypoxia on catfish physiology and improve growth.
1.A. Determine oxygen transfer performance of alternative aeration equipment other than paddlewheel aerators.
1.B. Introduce alternative dissolved oxygen (DO) automated control strategies in aquaculture tanks and ponds to improve monitoring and control of system dissolved oxygen distribution and concentration.
1.C. Evaluate sustainable production of stocker size catfish in low-head recirculating systems.
1.D. Measure effect of membrane lined ponds on fish production, water quality, and erosion.
1.E. Measure effects of hypoxia on catfish metabolism and gut-passage.
2. Identify factors that negatively impact product quality and develop mitigation strategies.
2.A. Develop genome resources for Marsh Ramshorn and Ghost Ramshorn snails.
2.B. Managing trematode risk in catfish ponds through control of host snails.
2.C. Evaluate microbial ecological conditions favoring cyanobacterial blooms.
2.D. Identify cyanobacterial species in catfish aquaculture ponds with the ability to produce off-flavors.
Approach
Most freshwater aquaculture production is from earthen ponds because capital costs are low, and the natural biochemical processes can provide an adequate environment for fish growth. Catfish is the largest freshwater domestic aquaculture industry that uses ponds with over 90% of production confined to Mississippi, Alabama, Arkansas, and Texas. Catfish production and acreage has contracted over 30% from its peak in the early 2000s. Adoption of intensive aeration, pond structural modifications, automated monitoring systems, and use of hybrids have helped increased per acre production and profitability of the industry since 2015. However, like other food production systems, the ecological sustainability of aquaculture pond production is threatened by a range of risks. The inflationary costs of labor, feed, and energy with climatic temperature changes and greater periods of drought necessitate innovative technology for the industry to remain competitive. Furthermore, production and product quality can suffer from environmental issues, such as disease, parasites, and off-flavor compounds produced by cyanobacterial species. Existing management strategies can present a significant cost to farmers and, in some cases, a risk to fish health.
The Project Plan aims to address pre-harvest production issues in three ways: 1) evaluate alternative production strategies that provide greater culture densities, reduces predation and environmental impacts, and has greater water use efficiency; 2) reducing the economic and ecological impacts of catfish disease by controlling important vectors; and 3) developing a better understanding of the pond conditions and microbial community characteristics that lead to production of off-flavor compounds by cyanobacteria. These technologies and strategies together will improve the economic, environmental, and social sustainability of the catfish aquaculture industry thereby enhancing food security, increase economic opportunities for inland underserved rural sectors, increase crop diversity, and be pro-active in accomplishing the USDA global warming goal with the 1.5°C constraint needed to minimize climate change impacts.
Progress Report
Under Objective 1A-C unit hatchery water reuse system components has been upgraded with new drain valves, drum filter screens, UV sterilizer bulbs, ballast, and sleeves, and sensors. The Cyclobio fluidized sand filter view port window repair has been completed and fresh sand installed. The water reuse system has been functional in maintaining MDEQ water parameters for several months. As a proof of concept to demonstrate the feasibility of the water reuse system, eight 200 gallon tanks in the hatchery were stocked with 10 g fingerlings and cultured on the recirculating water treatment system. The fingerlings were cultured for over 6 weeks and grew to 50+ g before being transferred to another research project. Little to no mortality was observed and all fish were healthy and disease free. Research evaluating the effect of stocking density on catfish performance has begun with one study being completed. Researchers in Stoneville, Mississippi measured the impact of stocking density on catfish performance in a flow-through indoor system where dissolved oxygen concentration was not a limiting factor. This study revealed that if their oxygen requirements are met, at the densities tested there was no impact of stocking density on catfish performance. Oxygen transfer and efficiency studies were conducted on several airlift design scenarios for 2-inch piping and 20 gpm flow as well as with air diffusers. Base studies resulted in airlift pump patent application. A commercial 10 hp Airmaster spray electric aerator was evaluated in a 0.1 acre pond providing oxygen transfer results similar to paddlewheel aerators. Additional aerators await testing once additional pond repairs are completed and reagents are acquired. Construction has started on small scale RAS units to evaluate system components (biofilters, drum filters) in the Engineering RAS bldg. Greenhouse construction is ongoing as rollup doors have been installed and contract bids have started for the electrical supply and connection.
Under Objective 1C/D, preparations have begun to measure the impact of pond liners on erosion and water quality in an intensively aerated catfish pond. Researchers in Stoneville, Mississippi began this project by taking ponds out of production so they can be renovated. Multiple suitable pond liner products and suppliers have been identified and the process to acquire the pond liners has begun. An indoor flow-through tank system suitable for conducting hypoxia production experiments has been constructed and tested. Researchers in Stoneville, Mississippi were able to maintain strict dissolved oxygen concentrations in 20 tanks for six weeks during an unrelated growth trial.
Under Objective 2A/B, research focused on identifying and mitigating factors that reduce the quality and quantity of catfish produced in earthen ponds. An inbred lineage of laboratory-reared snails has been developed for wild-type Marsh Ramshorn and Ghost Ramshorn snails, as well as an albino strain of the Marsh Ramshorn snail. These lineages will support genomic assemblies for both species, as well as providing better controls for laboratory testing of baits and chemical therapeutics. Scientists at Stoneville, Mississippi are using traps to monitor snail populations on commercial farms, these snails are known to serve as hosts for parasites that are detrimental to the catfish industry. Passively capturing snails from commercial facilities allows ARD Scientists to screen the snail for the presence of the parasite, refining the lifecycle timeline and helping inform pond treatments to a more specific period. This targeted treatment regimen will reduce the monetary cost of treatments, and shift treatments to earlier timepoints in the year, reducing toxicity risk to the fish during warmer months. The Scientists also evaluated more than 50 potential ingredients for use as bait in traps, including fruits, vegetables, and essential oils.
Under Objective 2C/D, research has begun to evaluate microbial ecological conditions favoring cyanobacterial blooms and identify cyanobacterial species in catfish aquaculture ponds. In May 2025, Researchers in Stoneville, MS began collecting weekly water samples from catfish ponds with cyanobacterial blooms, as well as adjacent ones without visible blooms. These samples have been processed via filtering and pelleting, and stored until sample collection ends, at which point DNA extractions will begin to enable sequencing-based pond water microbiome profiling. Additionally, cyanobacterial species have been isolated via culturing and will be cryopreserved.
Accomplishments
1. Airlift pump comparative studies for oxygen transfer, efficiency, and flow rates completed. Delivery of sufficient oxygen to catfish ponds is critical to production and is a significant economic factor in producer profitability. Scientists at Stoneville, MS, tested 2-inch air lift pumps to evaluate oxygen transfer efficiency and flow rates at different air flow rates. They also designed an air lift pump and compared it to a commercial pump unit and diffuser tubing. Results indicated the ARS design was as efficient as the commercial unit but at 1/10th the cost. Oxygen transfer efficiency for both air lift pumps was low compared to diffuser tubing indicating the pumps are best used for moving water while water aeration is an added benefit.
2. Characterizing ammonia removal in high-intensity catfish ponds. Catfish aquaculture production systems have been increasing production intensity (pounds of fish produced per acre) for the last two decades. However, if dissolved oxygen requirements are met, ammonia waste produced by the fish is the greatest limit to production. Scientists from Stoneville, MS, discovered that as feeding rates and production intensity increased, the amount of ammonia removed by nitrification also increased, keeping the production environment suitable for catfish. ARS researchers were able to produce catfish at almost quadruple the rates of industry averages. This study revealed that the production potential of earthen ponds is much greater than previously thought.
3. Determining the physiological effects of catfish digesting a meal. Catfish digestion not only plays a role in fish growth but is also an important factor in changing water quality. Following the consumption of a meal, an increase in ammonia production and oxygen consumption by catfish is expected. Scientists in Stoneville, MS, measured the timing and rates of post-feeding ammonia production and oxygen consumption of channel and blue catfish at cool and warm water. Both increased within two hours of eating a meal and peaked 6 to 12 hours later. Depending on the species and temperature, these physiological responses lasted 24 to 72 hours. The dramatic differences in ammonia production and oxygen consumption of catfish depending on their digestive status has extensive implications for research, optimizing production, harvest, and transport of catfishes.
4. Development of low-cost deployable ammonia and nitrate probes. The intensification of catfish aquaculture has renewed stakeholder interest in water quality, namely in how ammonia is removed. Monitoring ammonia is time-consuming and costly, thereby limiting ammonia sampling by researchers and stakeholders. Scientists in Stoneville, MS, and engineers from the University of Texas at Tyler have developed a low-cost ammonia and nitrate sensor that can continuously record ammonium, nitrate, temperature and pH values from aquatic environments. From this research, two patent approvals have been submitted. This research is the first step to providing powerful tools for ammonia and nitrate monitoring for both scientists and stakeholders.
5. Apple snail management in rice-crawfish systems. Invasive apple snails in the rice-crawfish industry of Louisiana cause loss of productivity by clogging traps and increasing labor costs. These snails also pose human health risks due to toxic compounds found in the ovary and eggs, and serving as host to a parasite that can fatally infect humans if consumed. The snails are likely to invade catfish ponds as their range continues to expand northward. A team of scientists from APHIS, ARS, USGS, Louisiana State University, and Mississippi State University, are working to develop an integrated management plan for the invasive pests. Aerial application of copper sulfate as a chemical therapeutic was inconsistent, particularly during the “pull-up” phase at the end of the field to avoid applying copper on adjoining fields. Submerging egg clutches in water (knocking eggs into the water is current standard practice) was inconsistent in reducing hatching success. However, the application of vegetable oil to fresh egg clutches significantly reduced egg hatching success. This technique may be useful depending on the developmental stage of the eggs, and the length of submergence. Additional research has found the chemical composition of snail shells suitable for applications in bio-lime production and synthesis of other natural polymer products.
6. Effect of antibiotic, prebiotic, and probiotic on channel catfish gut microbiome. Antibiotics are used in aquaculture to combat bacterial infections, including those caused by Edwardsiella ictaluri in catfish. These antibiotics indiscriminately kill or inhibit growth of bacteria, thus non-pathogenic gut microbes can be affected and lead to substantial shifts, or dysbiosis, of the gut microbiome. Depletion of healthy or innocuous bacteria may put fish at risk for subsequent infections. Scientists in Stoneville, MS, in collaboration with Mississippi State University researchers found oxytetracycline, one of the antibiotics approved for use in catfish, had minimal effects on the bacterial communities present in the digesta of juvenile channel catfish raised indoors. After a 10-day course of oxytetracycline, fish were offered either a control diet, or a diet containing a prebiotic or probiotic to assess their ability to assist in gut microbiome recovery. There were only mild effects of prebiotics and probiotics on the gut microbiome, however fish fed the prebiotic diet following oxytetracycline administration demonstrated lower survival upon challenge with Edwardsiella ictaluri. These results provide insight into how oxytetracycline, prebiotics, and probiotics may affect the channel catfish microbiome and susceptibility to E. ictaluri infection.
Review Publications
Older, C.E., Goodman, P.M., Reifers, J.G., Yamamoto, F.Y. 2025. Differences in the bacterial communities along the intestinal tract of channel (Ictalurus punctatus) and hybrid (I. punctatus × I. furcatus) catfish. Physiological Genomics. 57(5)299-307. https://doi.org/10.1152/physiolgenomics.00008.2025.
Rosser, T.G., Meaux, A., Woodyard, E., Stilwell, J.M., Richardson, B.M., Robison, L.R., Hudnall, J.B., Mcnulty, K., Nguyen, J.A., Rose, D., Moore, D., Peterman, B., Reichley, S.R., Lawrence, M. 2025. Systematic revision of the genus Orchidasma and description of Orchidasma orchilobata n. sp. from the loggerhead (Caretta caretta) and Kemp’s ridley turtle (Lepidochelys kempii). Systematic Parasitology. 102(44). https://doi.org/10.1007/s11230-025-10243-x.
Yamamoto, F.Y., Older, C.E., Khoo, L.H., Romano, N., Richardson, B.M., Ott, B.D., Wise, D.J., Ware, C., Goodman, P.M., Reifers, J.G., Griffin, M.J. 2024. Dietary iron fortification did not affect the intestinal microbiome for channel catfish (Ictalurus punctatus) juveniles, but decreased their resistance against Edwardsiella ictaluri. Journal of Fish Diseases. Article 14060. https://doi.org/10.1111/jfd.14060.
Older, C.E., Griffin, M.J., Ware, C., Ott, B.D. 2025. Development of qPCR assays for nitrification and denitrification genes in catfish aquaculture ponds. Applied and Environmental Microbiology. e03088-24. https://doi.org/10.1128/spectrum.03088-24.
Ott, B.D., Torrans, E.L., Tucker, C.S. 2024. Fish Production, Water Quality, and the Importance of Nitrification as an Ammonia Removal Process in Intensively Aerated Hybrid Catfish Ponds. Journal of the World Aquaculture Society. 55(6)e13094. https://doi.org/10.1111/jwas.13094.