National Program 106 Aquaculture Annual Report for 2014

The vision for ARS aquaculture research and technology transfer is to support a thriving 

domestic industry based on improved genetic stocks and scientific information on 

biotechnologies and management practices to ensure a high quality, safe supply of healthful 

seafood and aquatic products.

Mission: The mission of the Aquaculture National Program is to conduct high quality, 

relevant, fundamental and applied aquaculture research, to improve the systems for raising

domesticated aquaculture species, and to transfer technology to enhance the productivity and 

efficiency of U.S. producers and the quality of seafood and other aquatic animal products.

The aim of the ARS Aquaculture Program, as described in the National Program 106 (NP 

106) Action Plan:

http://www.ars.usda.gov/SP2UserFiles/Program/106/NP106_Action%20Plan%2011-03-

08_FINAL.pdf, is to support a safe and affordable domestic supply of seafood products for 

the 330 million U.S. consumers, that is produced in a healthy, competitive, and sustainable 

aquaculture sector; a sector supported by more than 3000 aquaculture farmers producing in 

excess of $1.35 billion worth of goods annually. This year the USDA National Agricultural 

Statistics Service published the Census of Aquaculture (2013) updating these statistics for the 

first time since 2005. The report details many features of aquaculture in the United States, 

and shows that since 2005, the overall number of farms has dropped (from about 4300 to 

3090) and the sales have increased from just over $1billion to over $1.37 billion in 2013.

Fiscal year 2014 was the fifth and final year of externally-reviewed five-year project plans

(2010-2014). The aquaculture laboratories and the aquaculture scientists were involved all 

year in developing the new five year plan which has just begun and will run from 2015-2019. 

The new Aquaculture Action Plan is available at:

http://www.ars.usda.gov/SP2UserFiles/Program/106/NP%20106%20Action%20Plan%20201

5-Final2.pdf. Although these project plans guide most of the efforts of the laboratories, we 

remain flexible to respond to unanticipated challenges and opportunities. NP 106 research 

covers the spectrum from fundamental to applied research, and is focused on solving

problems through long term high impact research. NP 106 scientists published over 100 

articles over the past two years in peer-reviewed scientific journals.

NP 106 People in 2013

During 2014, we added two new scientists to the NP 106 roster, Miles Lange, Ph.D. was 

hired at the Harry K. Dupree Stuttgart National Aquaculture Research Center, Stuttgart, 

Arkansas. Miles is a research microbiologist and has extensive research training and 

experience in immunology. Miles completed his Ph.D. at Kentucky State University and has

post-doctoral experience working with primary B-cell development and B-cell immune 

response to HIV infection and immunization.
Allyn Spears, Ph.D. joined our ARS team at the University of Wisconsin-Milwaukee. Allyn 

is a research molecular biologist with considerable experience in virology. Allyn came to 

Milwaukee from a post-doc with ARS at the National Animal Disease Center in Ames, Iowa. 

This year we had three retirements. Phil Klesius, Ph.D. retired in January 2014, after an 

extremely productive 42 years of Federal service with ARS. Phil achieved Super-grade (ST) 

status as a scientist and served as Research Leader of the Aquatic Animal Health Research 

Unit and Location Coordinator in Auburn, Alabama, for 26 years. Dr. Klesius’ team research 

on discovery, patenting, and licensing of vaccines for bacteria pathogen control in fish has 

been recognized repeatedly in technology transfer awards from ARS and the Federal 

Laboratory Consortium (FLC). Phil retired with 356 publications, book chapters, and

proceedings including 177 original and referred publications and 16 patents. Joyce Evans, 

Ph.D. and Natha Booth, Ph.D. retired from our Stoneville, Mississippi, Warmwater 

Aquaculture Research Unit (WARU). Joyce started with ARS in 1998 and worked at the 

Chestertown, Maryland, worksite of the Auburn, Alabama, Aquatic Animal Health Research 

Unit. In 2012 she transferred to WARU. Throughout her career with ARS, Joyce contributed 

expertise involving vaccine development, pathogen identification, diagnostic tool 

development, and immune responses of fish. She was author and co-author on over 100 

publications and contributed to 7 patents related to vaccine development. Natha began at 

WARU as a post-doc in 2006 where she focused on physiological and immunological studies 

on catfish, and research contributing to the breeding program.

Awards and Recognitions:

Scientists in the Aquaculture National Program were well recognized nationally and 

internationally over the past year, with successful grant applications for external funds, 

several cooperative research and development agreements (CRADAs), and many invited 

presentations. 

Dr. Benjamin Beck with the Stuttgart National Aquaculture Research Center, Stuttgart, 

Arkansas, was selected as the Early Career Scientist of the Year from the Southern Plains 

Area. Kevin Schrader and co-authors won honors for the best poster at the International 

Congress of Pesticide Chemistry. Steve Summerfelt, of the Conservation Fund Freshwater 

Institute, Shepherdstown, West Virginia, is a close collaborator in the Aquaculture program 

and was recognized with the 2014 “Award of Excellence” by the Aquaculture Engineering 

Society. The headquarters post-doctoral research associate program award went to Ken 

Overturf (Hagerman, Idaho) for Enhancing aquaculture sustainability by improving plant oil 

utilization and Peter Bechtel (New Orleans, Louisiana) for Postharvest processing to add 

value to catfish.

National Program 106 involves efforts in 10 different locations on 20 projects performed by 

approximately 85 scientists (41 ARS scientists and an equal number of collaborating 

scientists). Technology transfer activities included invention disclosures, 1 new patent 

application, and 18 new Material Transfer Agreements (MTAs). A number of additional 

activities to transfer technologies to other scientists and to industry partners were also 

completed. Among the outstanding examples is the ongoing effort to improve hybrid catfish 

production at Stoneville, Mississippi, where scientists are working closely with a number of 
hatchery operators in the Mississippi Delta region having tremendous success increasing the 

number of hybrid fry produced across the industry. Another example is the rapid 

development of numerous fish diets including new ingredients. The Trout Grains project has 

worked with multiple collaborators to improve, develop, and test new ingredients including 

pistachio and almond processors, leading to new feed formulations and opportunities for 

ingredient manufacturers. In addition, the Atlantic salmon industry on the East Coast of the 

United States and Canada use the improved germplasm developed at the National Coldwater 

Marine Aquaculture Center, Orono, Maine. Scientists’ research on kaolinic clays at Stuttgart 

National Aquaculture Research Center, Stuttgart, Arkansas, has had far reaching 

applications. See below for a sampling of some of the top research accomplishments from 

our scientists during 2014.

Across the program, researchers maintained beneficial collaborations with a number of 

international investigators and laboratories. Canada and Norway lead the list in terms of the 

active collaborations. Work ranges across cooperation on salmon breeding efforts and 

information sharing on recirculating aquaculture systems with Canadian counterparts to 

exchange with the Norwegian Aquaculture Protein Center on feed processing and with 

NOFIMA (Norwegian Institute of Food, Fisheries and Aquaculture Research) on fish health 

and well-being in recirculating systems. Our aim is to form real partnerships that have 

benefit to the United States and to cooperating countries. These relationships increase the 

depth of our intellectual capital with original ideas from different perspectives. 

Funding: During fiscal year 2014, total funding for aquaculture research at ARS was

approximately $30 million. Balancing the need for additional funding with the maintenance 

of our core mission is a constant challenge and the resulting dialog is a big part of the 

innovative process.

Research Results

The following section of the report summarizes the specific high impact research results 

addressing objectives in the current National Program Action Plan.

Genetic and Genomic Resources 

Atlantic salmon evaluated and selected for multiple traits. Commercial salmon producers 

in the United States use stocks that are not many generations removed from wild, unselected 

stocks. Because salmon are an endangered species, producers are legally required to culture 

certified stocks of North American salmon. ARS researchers at the National Cold Water 

Marine Aquaculture Center in Franklin, Maine, in collaboration with industry, generated a 

broodstock of fish with North American origin and compared the growth of 4-year classes of 

salmon from their breeding program with a control line of fish in commercial sea cages. 

Salmon that were selected for greater growth, resistance to sea lice, and better fillet color, 

averaged approximately 90 percent larger than the control fish. Using improved salmon 

germplasm is increasing the cost-effectiveness, profitability, and sustainability of cold water 

marine aquaculture in the United States and providing a quality seafood product to 

consumers.
The development of a new tool to speed genetic improvement in rainbow trout. 

Technology to use genomic information for improving selective breeding in dairy cattle and 

poultry has not yet been developed for rainbow trout. ARS researchers at the National 

Center for Cool and Cold Water Aquaculture in Leetown, West Virginia, worked with 

international partners to develop a commercially available genetic marker tool (SNP chip) for 

rainbow trout. By incorporating genome information, this tool improves performance 

prediction accuracy for individual fish versus traditional family-based estimates. 

Commercial producers will find this information useful and it will accelerate genetic 

improvements in trout.

Improvement of catfish growth. Producers and processors of farm-raised catfish want to 

improve catfish growth. ARS scientists at the Warmwater Aquaculture Research Unit in 

Stoneville, Mississippi, have conducted a selective breeding program over several catfish 

generations to improve this trait, and showed that catfish in the breeding program were more 

than 25 percent larger at harvest than catfish that were not in the breeding program. These 

efforts are part of a long-term breeding program to improve channel catfish germplasm for 

release to the United States catfish industry.

Powerful genomic resources developed for blue catfish. The blue catfish, Ictalurus 

furcatus, is native to North America and serves as the paternal species of the blue x channel 

catfish hybrid that is highly valued for U.S. aquaculture production. Little was known about 

the extent of genetic diversity in blue catfish, which impeded genetic selection/improvement 

in this species. ARS scientists in Stuttgart, Arkansas, and Stoneville, Mississippi, 

collaborated with Auburn University researchers to identify genetic diversity between 

individuals and between populations. The research demonstrated many DNA sequence 

variants within and between five populations, and revealed potential shared ancestry among

populations. This research resulted in highly informative DNA markers useful for parentage 

and kinship determination in blue catfish and hybrid catfish populations.

 

Animal Performance, Well-being and Efficiency 

Lysine supplementation of fishmeal-free diets influences muscle genes. As part of a 

strategy to reduce feed costs, research on fish feeds is targeted at reducing reliance on 

expensive fish meal, and supplement diets directly with limiting amino acids. The 

mechanisms by which dietary amino acid supplementation affects nutrient utilization and 

muscle growth in fish is unclear, but elevations in amino acids in the blood after a meal have 

been shown to stimulate protein synthesis in the muscle. Researchers at the H.K. Dupree 

Stuttgart National Aquaculture Research Center, Stuttgart, Arkansas, demonstrated that 

dietary lysine supplementation of a commercial fishmeal-free diet influences the expression 

of two genes, myostatin, a growth inhibiting gene, and myogenin, a growth promoting gene, 

that contribute to muscle growth in hybrid striped bass. The relative expression of myostatin 

to myogenin was highly correlated to muscle protein accumulation. This is an important 

discovery of genetic markers that may be useful to select hybrid striped bass with improved 

growth performance on fishmeal-free diets.
Causes of variation in hybrid catfish growth rates. Hybrid catfish grow rapidly but not 

uniformly. This size variation is undesirable and some processors pay a discounted price for 

larger and smaller fish. A study was conducted at the Warmwater Aquaculture Research 

Unit in Stoneville, Mississippi, to examine the effects of size variation of fish on growth rates 

of hybrid catfish. Small fish raised in an ungraded (mixed sizes) population grow 15% 

slower than small fish raised in a graded (uniform size) population. Stocking graded 

fingerlings is an important aspect of producing a faster growing, more uniform sized 

population of harvest-sized fish.

Pre-spawning stress affects reproductive performance of channel catfish and 

subsequent progeny performance. Routine handling procedures like seining, 

transportation, crowding and handling may affect the quality of eggs that are stripped from 

gravid channel catfish. ARS scientists at the Warmwater Aquaculture Research Unit in 

Stoneville, Mississippi, determined the effects of pre-spawning handling on the performance 

of mature channel catfish and of their eggs and subsequent progeny. Gravid channel catfish 

females were exposed to lowered oxygen levels that are often experienced in commercial 

culture during warmer weather. Low oxygen stress reduced the hatching success of eggs by 

6.3 percent. Furthermore, offspring from treated parents had higher mortality in challenges 

of enteric septicemia of catfish (ESC) disease (9.6%). This research points to the importance

of careful pre-spawning handling procedures to improve reproduction and progeny 

performance.

Nutrient Requirements, Nutrient Composition of Feedstuffs, and Expanding Alternative 

Ingredients 

New processing method to improve nutritional value of ethanol production co-products. 

The primary method for producing fuel ethanol from grains results in a co-product known as 

distiller’s dried grains with solubles (DDGS), which is a low-value ingredient for animal 

feeds. The standard method results in distiller’s grains of high fiber and low protein 

digestibility, and only a single product being produced. These problems reduce the total 

revenue from ethanol production and limit the use of the co-product in animal feeds. To 

improve the value of this co-product, ARS scientists in Aberdeen, Idaho, determined the fate 

of many nutrients during traditional processing and devised a new method to recover 

multiple co-products, including a high-protein feed ingredient, a high-ash fraction for mineral 

supplementation, an oil fraction, and a glycerol fraction. Greater value of co-products from 

ethanol production increases the value generated by using renewable energy and provides 

valuable nutrients for animal production.

Improving water quality and lowering the price of diets for hybrid striped bass. 

Temperature and ammonia levels (ammonia is a waste product secreted by fish) often 

increase dramatically in ponds during summer production of hybrid striped bass in the 

southern United States. Extended periods of high ammonia result in fish stress, disease, 

mortality, and significant loss of feeding days as producers attempt to reduce ammonia to 

manageable levels by reducing feeding or using lower protein diets. Along with participants 

from the Trout-Grains Project, ARS scientists in Stuttgart, Arkansas, and Hagerman, Idaho; 

and U.S. Fish and Wildlife Service scientists in Bozeman, Montana, demonstrated better 
growth and nutrient retention by hybrid striped bass fed a 35 percent protein diet 

supplemented with limiting amino acids compared with fish fed a higher protein diet. 

Overall protein levels were decreased, whereas dietary nutrient retention increased, thereby 

lowering feed costs to producers and reducing negative environmental effects on water 

quality.

Method to produce a protein concentrate from barley is commercialized. Feeds costs 

are a significant production item in commercial aquaculture. Barley that is too high in 

protein to be used for malting has the potential to be developed as a protein-based fish feed. 

A method was developed and patented by ARS scientists in Aberdeen, Idaho, for producing a 

protein concentrate that can be incorporated into aquaculture feeds. Feeding studies with 

rainbow trout and Atlantic salmon demonstrated the concentrate is highly digestible and 

supports rapid fish growth, reducing the need for more expensive ingredients such as 

fishmeal. A pilot plant for barley concentrate production has been built and is delivering the 

product to commercial farms in Idaho. Two more plants are in development.

Improving Health

Development of a vaccination platform to protect catfish against Enteric Septicemia. 

Enteric septicemia is the most devastating disease affecting the catfish industry. The 

development of a new vaccine and feed-based delivery platform has resulted in providing 

exceptional protection against enteric septicemia of catfish with dramatic increases in 

production efficiency and economic returns. Mississippi State University scientists working 

in collaboration with ARS scientists developed a mechanized vaccine delivery system that 

consistently delivered target-immunizing doses in experimental pond trials. The vaccine 

delivery system was used in commercial field trials during the 2013 production season with 

excellent results; 2014 production season trials are ongoing. This vaccine will support 

catfish producers in efforts to control diseases and manage production costs.

Effective vaccine candidates to prevent Aeromonas disease in catfish. From 2009 to the 

present, outbreaks of motile aeromonad septicemia (MAS) in market-size catfish have 

occurred in western Alabama and eastern Mississippi with losses estimated to be greater than 

$12 million. Currently, there are no methods available, such as vaccination, to prevent MAS, 

but they are urgently needed. ARS scientists in Auburn, Alabama, identified secreted 

extracellular proteins of the bacterium that trigger protective immune responses. Their 

results show that catfish immunized with the extracellular proteins are resistant to infection 

and that this immunity persisted for at least 7 weeks. This research provides the foundation 

for developing an effective vaccine to prevent MAS disease and may help catfish producers 

contain production losses.

The development of a molecular test for the detection of significant catfish pathogens in 

environmental and tissue samples. Researchers from Mississippi State University (MSU), 

Mississippi Agricultural and Forestry Experiment Station (MAFES), and the College of 

Veterinary Medicine (CVM)), working with ARS, have developed and validated highly 

sensitive assays for the detection and quantification of numerous pathogens. These assays 
provide a reliable method for the detection and quantification of pathogens in pond 

environments and are being used for rapid diagnostic evaluations and evaluation of treatment 

efficacies associated with recommended disease management strategies and research. In 

addition to their diagnostic benefits, these assays provide a means to conduct epidemiological 

and environmental studies and evaluate how management strategies alter pathogen loading 

rates in commercial catfish ponds. This novel and proactive strategy is being used to 

optimize disease management practices aimed at maximizing production efficiencies and 

economic returns.

Standard protocol for determining Flavobacterium columnare type. Flavobacterium (F.) 

columnare is the causative agent of columnaris disease which severely impacts channel 

catfish production in the United States and is emerging in the rainbow trout industry. The 

assay previously used to identify different genetic types of F. columnare was found to be 

flawed. Research at the Aquatic Animal Health Research Unit in Auburn, Alabama,

developed a protocol for the genetic typing of F. columnare. The knowledge obtained from 

this research allows for the proper assignment of an unknown isolate to a genetic type, which 

is important because there is an association between genetic type of F. columnare and 

virulence.

Production Systems and Products

Scaling up recirculating aquaculture systems. Although production of Atlantic salmon in 

land-based recirculating water systems offers an environmentally sustainable approach to 

meeting domestic demands for seafood, some off-flavors can develop in such systems, and 

harvest strategies must be developed that ensure the product quality that consumers expect. 

Researchers at the Conservation Fund’s Freshwater Institute in Shepherdstown, West 

Virginia, working with an ARS researcher in Oxford, Mississippi, determined that concerns 

about off-flavor in 4-kg Atlantic salmon can be eliminated with a purging step in which fish 

are transferred to tank systems pre-disinfected with hydrogen peroxide and that do not 

contain hard-to-clean locations, such as aeration media, during the final 6–10 days of fish 

rearing. Compounds associated with off-flavor were consistently reduced to levels that are 

below human tasting limits. These standard operating practices maximize product quality for 

Atlantic salmon and other species that have been cultured in water recirculating systems.

Minimal impacts of oyster aquaculture to eelgrass at the landscape scale. Submerged 

aquatic vegetation such as eelgrass provides valuable habitat for fish and invertebrates in 

estuaries, particularly for juvenile salmon on the west coast of the United States. ARS 

researchers in Newport, Oregon, used layers of geographic information on tidal heights, 

cumulative wave stress, salinity, distance to the river mouth, and distance to the nearest 

channel to quantify the distributions of eelgrass and bivalve aquaculture in Willapa Bay, 

Washington. The effect of bivalve aquaculture on eelgrass at the landscape scale was 

measured over a period of 5 years. Although oyster harvest methods had demonstrable 

effects on eelgrass over time at the individual bed scale, oyster aquaculture reduced eelgrass 

cover by less than 1 percent in any given year over the entire estuary. This information 
promotes sustainable shellfish culture and is enabling managers and regulators to evaluate the 

potential effects of existing and expanded oyster aquaculture on estuarine habitat.