• Introduction
• Genetic Improvement
• Integrated Aquatic Animal Health Management
• Reproduction and Early Development
• Growth, Development, and Nutrition
• Aquaculture Production Systems
• Sustainability and Environmental Compatibility of Aquaculture
• Quality, Safety, and Variety of Aquaculture Products for Consumers

Introduction

The Aquaculture National Program continues to receive strong support from stakeholders. The FY 2006 appropriations increased aquaculture research in four of the seven program components at five locations. Construction for the National Cold Water Marine Aquaculture Center, Franklin, Maine began in the fall, 2005.

Two research scientists changed positions within ARS and two vacancies were filled. Ken Davis was selected for the Research Leader of the Catfish Genetics Research Unit, Stoneville, MS, and Brian Shepherd was selected to start the new research project on Great Lakes Aquaculture at Milwaukee, WI. Welcome to Keshun Liu, Research Chemist (cereal) and Gongshe Hu, Research Geneticist who joined the ARS aquaculture feeds research group at Aberdeen, Idaho.

Congratulations to Timothy Welsh, National Center for Cool and Coldwater Aquaculture, Leetown, WV for being awarded an Administrator’s Post-Doctural, Class of FY 2006 for his proposal entitled “Utilizing phage as targeted antibiotics in aquaculture”.

Craig Shoemaker, Joyce Evans, and Phil Klesius received the 2005 ARS Technology Transfer Award for Outstanding Effort and the 2005 FLC Southeast Region Excellence in Technology Transfer for catfish vaccines for prevention of the two major diseases of catfish. The Rapid Identification Assay for Channel Catfish Fillets was a product selected for supporting the ARS Budget presentation at the Congressional Hearing.

One U. S. patent was granted on modified live Flavobacterium columnare vaccine.

Scientists were active in holding customer workshops and field days, organizing and chairing professional scientific meeting sessions, and delivering local, national, and international invitational scientific talks.

Four scientists (Barrows, Hershberger, Silverstein, Rexroad, and Wolters) participated in a trilateral meeting between Norway, Canada, and the United States to determine shared goals and research priorities for genomics and breeding in aquaculture species. Follow-up conference calls will take place in January 2006 and the next meeting is planned to take place in Canada in 2006.

The Freshwater Institute, Shepherdstown, WV an ARS partner solved the problem of “what to do with market size research animals when the research is completed”. They made an arrangement to donate fish to the Virginia Federation of Food Banks and the West Virginia Mountaineer Food Bank as well as several local shelters Composting is often the only way to dispose of animals once the research is completed, but its a more expensive and wasteful solution.

Genetic Improvement 

Since there has been limited genetic improvement of aquaculture stocks, there are major opportunities for improvement through traditional animal breeding, broodstock development, germplasm preservation, molecular genetics, and allied technologies.  ARS research addresses improvement of growth rates, feed efficiency, survival, disease resistance, fecundity, yield, and product quality; genetic characterization and gene mapping; and conservation and utilization

North Atlantic Salmon Brood Stock  Progress is being made with an additional year-class (2004) of Atlantic salmon from 5 different sources was obtained from collaborators to continue the breeding program at the USDA, ARS National Cold Water Marine Aquaculture Center.  Eyed eggs were disinfected, incubated, hatched, and fish reared as parr (juveniles) in indoor (greenhouse) tanks.  Early growth evaluation of the different genetic stocks during the parr stage was completed and data are being analyzed.  Parr from the 2003 year-class were pit tagged, vaccinated, and stocked into replicated communal tanks for evaluation of growth to smolts.  Smolts from the 2003 year-class were transferred into sea cages at an aquaculture lease site operated by industry collaborators.  Fish will be reared through 2006 to market size, data collected on harvest weight, and data analyzed to determine broodstock to be spawned as a selected line.

Successfully cross-bred tetraploid rainbow trout.   First generation tetraploid male and female rainbow trout matured this year and produced a number of tetraploid and triploid crosses for further evaluation.  The tetraploid fish generated in this project by ARS scientists at the National Center for Cool and Cold Water Aquaculture, Leetown, WV offer the opportunity to produce 100% triploid offspring, which are desirable because they are sterile and potentially faster growing than typical diploid production animals. The offspring from these crosses provide (1) the initial generation of potential tetraploid lines for aquaculture and (2) the initial evaluation of the potential for the lines to produce superior triploid offspring for aquaculture production.  Each tetraploid female was crossed with (1) a tetraploid male to produce a second generation with four sets of chromosomes and (2) a diploid male to produce triploid offspring.  The tetraploid males were also crossed with diploid females to produce triploids from the reciprocal cross.  All crosses yielded the expected results with respect to ploidy level (100% tetraploids for the first crosses and 100% triploids for the latter two).  The triploids produced were analyzed in a growth study and initial results suggest they have a growth advantage from a very young age; this study is still ongoing.

Determined that cadmium accumulation in oysters is under genetic control. The ARS scientist at Newport, Oregon, in collaboration with an ARS scientist in Corvallis, Oregon discovered significant levels of genetic variation for the bioaccumulation of cadmium in Pacific oysters. Ongoing international negotiations that could limit cadmium content in seafood may impact the marketability of Pacific oysters, and there is a possibility that selective breeding can modify this character. Oyster tissue samples were collected for preliminary study of the heritability of cadmium concentration in Pacific oysters from an ongoing quantitative genetic experiment originally setup by collaborators at Oregon State University. These results provide the first evidence for quantitative genetic variation in cadmium bioaccumulation and suggest that this trait could be manipulated by selective breeding.

The released line of channel catfish is further improved. The USDA103 line of channel catfish was developed and evaluated by ARS scientists at the Catfish Genetics Unit, Stoneville, Mississippi and released under the name NWAC103 to commercial producers in 2001.  After two additional generations of selectively breeding USDA103 channel catfish for rapid growth, a new experimental channel catfish line (USDA303) has been developed.  Research was conducted to assess growth improvements in the USDA303 line of channel catfish, and showed a marked improvement in growth.  Two generations of selection for increased growth resulted in a 21% increase in USDA303 channel catfish body weight compared to USDA103 catfish at the end of the study.  Continued improvements in growth through selective breeding will lead to more efficient production for U.S. catfish farmers.

Integrated Aquatic Animal Heath Management

Despite progress in aquatic animal health, significant losses to diseases still occur.  ARS research addresses improvement of survival, growth, vigor, and wellbeing of cultivated aquatic animal stocks through integrated aquatic animal health research, improved technologies and practices, such as population health management; and development of health management products, including vaccines and therapeutics, and disease detection/diagnostic techniques.

A patent awarded for the detection of Bacterial Kidney Disease. ARS scientists at the Small Grains and Potato Germplasm Research Unit, Aberdeen Idaho developed an assay that will be valuable to clinicians and researchers to evaluate the health of salmonids. This quantitative real-time PCR assay was devised to detect the presence of the bacterial genome and quantify its absolute copy number in infected tissue. This test will be useful to monitor fish health and precise pathogen levels for research protocols and commercial rainbow trout production.

A molecular method of aquatic epidemiology.  Restriction fragment polymorphism (RFLP) and sequencing methods of the 16S rRNA gene and the 16-23S rDNA spacer were developed by ARS scientists at the HKD Stuttgart National Aquaculture Research Center at Stuttgart, Arkansas as an epidemiological tool for bacterial columnaris (Flavobacterium columnare) outbreaks in aquatic species.  A technique does not exist to compare genotypes of this bacteria; this method has the advantage of being universal and capable of comparing the genotypes from different geographic locations.  The method was used to show the correspondence between the genotypes of isolates in North America to those in Asia and Europe, and for the first time demonstrate the presence of genotype III in the US.  With the global development of fish farming and the increased movement of fish between countries, this epidemiological tool will be useful to protect the US from possible introduction of new genotypes of this pathogen.

A new way to immunize fish shows promise.  ARS scientists at the Aquatic Animal Health Research Unit, Auburn, Alabama through an agreement with an animal health company  tested  their patented S. iniae vaccine formulated in feed for its efficacy in tilapia.  The results showed that tilapia were protected against experimental challenge with S. iniae.  The concept of using an oral vaccine feed appears to be a promising mass immunization method to protect fish against disease.

Developed a more relevant challenge model.  Scientists need ways to test reactions of individual animals to different treatments when raised in groups. Fish have been grouped by fish tank, because identifying individual fish within a tank(treated or untreated) has been difficult. ARS scientists at the Aquatic Animal Health Research Unit, Auburn, Alabama have come up with a solution. Fish were non-invasively and chemically marked   and cohabitated with non-marked fish.  The chemically marked fish were immunized and non-marked sham immunized.  Marked and non marked fish were challenged at the same time in the same aquarium and the efficacy of the vaccine determined by identifying marked and non-marked mortalities. The development of this cohabitation and immersion challenge model simulated production facilities and since each fish is an experimental unit, increased statistical power to assess vaccine efficacy.

A rapid specific test for Edwardsiella ictaluri.   A rapid (less than 1 hour) detection assay (loop-mediated isothermal amplification method, LAMP) was developed by ARS scientists at the Aquatic Animal Health Research Unit, Auburn, Alabama for the detection of E. ictaluri, the most important disease agent in the catfish industry.  LAMP was shown to be rapid, accurate and sensitive (about 10 bacteria/sample) for the detection of E. ictaluri.  This assay has the potential to be used for rapid and specific detection of E. ictaluri of catfish in hatcheries and ponds.

Bacterial genome for cold water disease sequenced. Bacterial cold water disease caused by Flavobacterium psychrophilum, is a serious problem for rainbow trout aquaculture.  Conventional approaches to vaccines have been ineffective and development of antibiotic resistance is of concern.  ARS scientists at the National Center for Cool and Cold Water Aquaculture, Leetown, WV addressed this major health problem by sequencing the complete bacterial genome in order to identify targets to develop an effective vaccine.

Reproduction and Early Development

Reproduction and early development are important aspects of species domestication and sustainability.  ARS research on this component interacts with several of the other components of the Aquaculture National Program.  The selection below exemplifies the multi-disciplinary character of husbandry research.

Gene related to reproduction identified in catfish. Reproductive efficiency is important for the sustained production of channel catfish; however, the hormonal and genetic regulation of catfish reproduction is not understood.  ARS scientists at the Catfish Genetics Research Unit, Stoneville, Mississippi have identified several genes with the potential to regulate catfish reproductive efficiency.  One gene in particular, steroidogenic factor-1 (SF-1), was identified in reproductive tissues of mature channel catfish and has the potential to control the production of steroids important for successful reproduction.  Identification of factors regulating reproductive development will allow for the genetic selection of superior broodfish and provide information toward the development of tools for spawning induction

Growth, Development, and Nutrition

There are substantial opportunities to improve the growth, development, and nutrition of cultivated aquatic organisms.  ARS research addresses improving survival, growth rates, feed conversion, environmental tolerances, and feed formulations and feeding strategies to reduce dependence on marine fish-based protein in aquaculture diets.

An inexpensive form of methionine with soybean meal can reduce cost of shrimp diets. Different forms of methionine (including L-methionine, DL-methionine and HMTBA [(2-hydroxy-4-methylthio) butanoic acid]) were shown to be equal in their ability to meet the needs for dietary methionine of shrimp grown in low-water exchange pond-like conditions.  A trial was conducted in order to find an inexpensive form of methionine (HMTBA) that could be used to improve the nutritional quality of diets containing high levels of soybean meal, which is an inexpensive source of protein but contains a low level of methionine.  In this trial, the growth rate of shrimp fed a control diet containing low methionine (high soybean meal) was compared with the same diet supplemented with a fixed level of each of three forms of methionine.  Use of HMTBA could enable formulation of commercial shrimp feeds with higher levels of soybean meal to replace fish meal and meet the nutritional needs of the shrimp.

New Method to evaluate fish diets. Understanding the genetic components of nutrient utilization in trout is critical for the US aquaculture industry to remain competitive particularly in the face of higher feed costs, due to limited natural protein resources, and stricter environmental standards. Scientists at the Small Grains and Potato Germplasm Research Unit, Aberdeen, ID. measured differential gene expression relating to growth, health and  metabolism of trout reared on formulated cereal grain and commercial feeds. Rainbow trout of distinct lineage were separated and reared on either a commercial diet or a diet containing a high level of barley (32%) for one year after which, tissue samples were taken and the changes in gene expression were evaluated using quantitative real-time PCR for several genes and microarray hybridization. This method will be valuable for selecting more broodstock for improved performance fed diets containing nutrients from plant sources.

Taurine identified as a required nutrient for growth of rainbow trout. Taurine was identified as a previously unidentified growth factor present in fishmeal that is not present in plant-derived ingredients. ARS scientists at the Small Grains Germplasm Research Unit, Aberdeen, Idaho conducted research that demonstrated taurine supplementation is required by rainbow trout if fed diets containing protein from only plant-derived ingredients. The supplementation of taurine to these diets improves growth rates, feed conversion efficiencies, protein retention efficiencies and energy retention efficiencies.

Hybrid striped bass (HSB) fry survival improved with organic fertilizer. ARS scientists at the HKD Stuttgart National Aquaculture Research Center, Stuttgart, Arkansas found a relationship between fertilization method, water pH, and survival of hybrid striped bass (HSB) fry that may increase production in commercial fry ponds. Fry ponds are fertilized to stimulate the growth of live food organisms; however, when producers use chemical fertilizers the fry often die when pH levels become too high. HSB fry ponds were treated with chemical or organic fertilizers, or commercial baking soda (sodium bicarbonate) and the change in pond acidity (pH) and fry survival were measured. Adding baking soda failed to prevent lethal increases in pH during algae blooms but use of organic fertilizers were not accompanied by increased pH. These results show how commercial HSB hatcheries can significantly improve year-round production of HSB by using only organic fertilizers during most of the fry phase.

Vitamins C and E essential for healthy catfish.  Vitamins C and E are dietary nutrients that are essential for growth and maintenance of normal immune function. ARS scientists at the Aquatic Animal Disease Unit, Auburn, Alabama fed channel catfish juveniles practical diets supplemented with graded levels of both vitamins for 12 weeks. Vitamin E presence in soybean-based diets is sufficient to promote good growth but supplementation of 100-500 mg/kg diet is needed for maintaining normal blood parameters, improving white blood cell superoxide anion production and maintaining high liver storage levels. Vitamin C supplementation (100 mg/kg diet) is required for good growth, normal bone formation, improving immune responses and increasing liver storage of both vitamins C and E. Although supplementation of vitamin E to practical diets is not required for normal growth, it is recommended that grow-out diets for catfish should be supplemented with vitamins E and C, each at 100 mg/kg diet for optimum growth, improving immunity and increasing liver storage levels of these vitamins. Since minimal feed is offered for fish held through winter months, much higher levels of these vitamins may be required for winter to maintain levels of these vitamins in early spring.

Aquaculture Production Systems

There are opportunities to improve the performance of aquaculture production systems through development and application of innovative engineering approaches and technologies.  ARS research addresses development and successful application to aquaculture of new technologies as well as relevant existing technologies and engineering presently employed in other sectors of the economy.

Accurate prediction of algal biomass.  Timely and accurate assessment of algal biomass is required to assure optimal conditions for fish grown in high stocking densities. ARS scientists at the Catfish Genetics Research Unit, Stoneville, Mississippi, Mississippi collaborated with University of Nebraska to develop specific remote sensing models for the highly turbid productive waters found in catfish production ponds. This new model provided greater accuracy of algal biomass estimation than previous models by over 15%.  This model has application in all inland waters and is particularly useful for rapid assessment of algal biomass in aquaculture systems.

Feeding practices affect on profitability started. Feeding practices have marked impacts on fish growth, production, feed efficiency, and profit in channel catfish farming. Mississippi State University scientists initiated a long-term study to compare 1) feeding to apparent satiation once daily; 2) feeding to apparent satiation once every other day; 3) feeding once daily to no more than 90 kg/ha under a multiple-batch cropping system. Results from the 2004 growing season showed that fish fed once daily to satiation were fed more feed and gained more weight than those fed once every other day to satiation or those fed once daily to no more than 90 kg/ha. There were no differences in the amount of feed fed and weight gain between the latter two feeding regimens. No differences were observed in carcass, fillet, and nugget yields among the three feeding regimens. Based on the first-year growth data, feeding channel catfish grown from advanced fingerlings to market size once daily to apparent satiation provides maximum growth. Feeding the fish once every other day to satiation resulted in growth rate similar to those fed once daily to no more than 90 kg/ha.

Sustainability and Environmental Compatibility of Aquaculture

The overall goal of ARS research in this area is to protect and conserve the nation's water resources and natural environments by conducting research and technology transfer to improve the sustainability and environmental compatibility of aquaculture production systems.

First step in Integrated Pest Management of Burrowing Shrimp. Information was needed to establish a basic understanding of geospatial relationships between estuarine ecology and commercial aquaculture enterprises.  Aerial photography of Willapa Bay,  the most significant site of Pacific Northwest commercial oyster aquaculture, was completed by the ARS scientist at Newport, Oregon. These aerial photographs will provide the basis for future mapping of aquaculture beds, other estuarine habitats, and shrimp and predator/parasite populations. This research establishes the framework that will be used by the ARS program and university researchers to develop integrated pest management strategies to control burrowing shrimp that threaten commercial oyster aquaculture in the region.

Improved feeding strategies for hybrid striped bass production. Diet recommendations for summer and winter culture of hybrid striped bass (HSB) were developed at the HKD Stuttgart National Aquaculture Research Center, Stuttgart, Arkansas collaboratively with commercial Hybrid Striped Bass producers. Seasonal extremes in pond temperatures reduce feed consumption and result in deterioration of water quality, wasted feed, stress, disease, and increased cost. The research determined the influence of different diet protein and energy levels on feed consumption and growth at temperatures simulating summer (32 C) and winter (8 – 25 C). This work provided essential information for improved production efficiency during summer and winter production in ponds and is now being used the industry.

Information on fish-eating birds communicated to U. S, Fish and Wildlife Service. ARS scientists at the HKD Stuttgart National Aquaculture Research Center, Stuttgart, Arkansas conducted aerial surveys in a fixed-wing aircraft for the fifth consecutive year to document double-crested cormorant, American white pelican, and other fish-eating bird numbers within the catfish production regions of southeastern Arkansas.  Trends in cormorant numbers, movements, and duration of use at roosting sites within catfish-producing regions of southeastern Arkansas were determined.  This information documented that bird numbers and numbers of roost sites are quite constant, with some variability in the time of year certain roosts are used.  This accomplishment provides the U.S. Fish and Wildlife Service (USFWS) reliable data to address and formulate new population estimates necessary for assessing the national cormorant management plan.

New Aquaculture Effluent Treatment Technology Provides Simultaneous Ammonia and Solids Removal.  More effective methods of waste control are necessary to remove total suspended solids and dissolved waste products from large, but relatively dilute, aquaculture effluents.  Scientists at The Conservation Fund’s Freshwater Institute (Shepherdstown, WV) demonstrated that the flocculating agent chitosan, when added to an aquaculture effluent pumped through fluidized sand biofilters, produced simultaneous removal of suspended solids and ammonia.  Adding only 0.5 mg/L of dissolved chitosan to the water entering the biofilters allowed the units to achieve suspended solids and ammonia nitrogen removal efficiencies of 65.1 ± 2.5 and 84.3 ± 1.3 %, respectively, and maintained mean suspended solids and ammonia nitrogen effluent concentrations of 1.60 ± 0.11 mg/L and 0.11 ± 0.01 mg/L, respectively.  The fluidized beds dosed with chitosan were shown to capture fine solids at the same time that the bed maintained effective nitrification.  The filter system never requires backwashing and shows great potential for significantly reducing solids and ammonia in relatively large but dilute aquaculture effluents.

Quality, Safety, and Variety of Aquaculture Products for Consumers

The overall goal of ARS research in this area is to improve the quality, safety, and variety of aquaculture products through research and technology transfer.  ARS research addresses improvement of the safety, freshness, flavor, texture, taste, nutritional characteristics, and shelf life of cultivated fish and shellfish, and development of new and improved value-added products and processes.

Milt meal from pollock and pink salmon. The potential to made milt meal from the large volumes available from the processing of pollock and salmon in Alaska is high. Today most of  the milt is included in the production of fishmeal or discarded. A study was conducted by a team of University of Alaska and ARS scientists at The Subarctic Agricultural Research Unit to develop an industrial scale extraction method for the production of high quality milt meal from both pollock and salmon. A process was developed and the meals were found to contain high concentrations of nucleic acids and there are a number of potential new uses for these meals in diets of fish, farm animals and pets.

Edible films from fish skin gelatins. Currently in Alaska fish skins are either used to make fish meal or discarded.  ARS scientists in Albany, California and Fairbanks, Alaska  evaluated unique permeability and tensile properties of films made from cold-water fish gelatins. In addition the feasibility of extracting gelatin from dried pollock skins with ultrasound was evaluated. This study identified unique permeability properties of the fish gelatin films and furthered the development of technologies to increase the yield of gelatin from dried skins. There are potential food applications for gelatin films from coldwater marine fish.

Dogs trained to detect off-flavor in catfish fillets. ARS scientists at the Aquatic Animal

Health Research Unit, Auburn Alabama in collaboration with scientists at Auburn University trained dogs to detect odors associated with off-flavors in catfish. This technology and the dogs with the ability to detect off-flavor compounds were transferred  to the Alabama Fish Farming Center in Greensboro, AL to determine the potential utility of canine detection of off-flavor in the field. Off-flavor (an earthy or musty taste) in catfish production costs the industry as much as $50 million annually. Dogs selected from a local animal shelter were trained to sniff water samples for the off-flavor compounds. Work this past year demonstrated that dogs were able to smell with 90% accuracy if a fish fillet was off or on-flavor. Use of trained dogs could reduce cost of marketing catfish.

Gene involved with off-flavor isolated from an cyanobacterium. ARS scientists at the Food Processing and Sensory Quality Research Unit, New Orleans, Louisiana cloned the sesquiterpene cyclase gene from O. splendida, a cyanobacterium. Use of this gene will be the basis of a new approach to study regulation of geosmin biosynthesis in off-flavor producing cyanobacteria.