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Introduction
The Aquaculture National Program expanded in five of the seven research program component areas: Genetic Improvement; Integrated Aquatic Animal Health Management; Aquaculture Production Systems; Sustainability and Environmental Compatibility of Aquaculture: and Quality, Safety, and Variety of Products for Consumers.
In January 2002, Dr. Henry (Hank) Parker, former National Program Leader for Aquaculture, became the Associate Area Director for the ARS North Atlantic Area Office. Dr. Lewis (Lew) Smith became the current National Program Leader.
ARS and the State Cooperative, Research, Education and Extension (CSREES) planned a joint National Program Planning Workshop in St. Louis, MO, November 20-21, 2002.
In cooperation with the University of Maine and the Maine Aquaculture Industry, ARS continued the required program planning and design phases for a new ARS National Cold Water Marine Aquaculture Center to be constructed in Orono and Franklin, Maine,
The Harry K. Dupree Stuttgart National Aquaculture Research Center, Stuttgart, AR, hosted a workshop on Genetic Improvement and Selective Breeding for the Hybrid Striped Bass Industry on October 22-23,2002.
ARS provided partial funding support for the 4th International Symposium on Aquatic Animal Health in New Orleans, LA on September 1-5,2002 and the 2nd International Seafood Byproduct Conference in September, 2002
A patent for "Streptococcus iniae Vaccine" was issued April 30, 2002. Two other patents are being filed for the detection and quantification of pathogenic microorganisms in salmonids.
In February 2002, USDA and Mississippi State University completed a joint release of an improved catfish, under the commercial name NWAC103.
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 of important aquatic germplasm.
Expressed sequence tags (ESTs) completed for rainbow trout. The development of molecular genetic tools and reagents is vital to the application of genomic research technologies for the genetic improvement of aquaculture species. Scientists at National Center for Cool and Cold Water Aquaculture Research Center, Leetown, WV, analyzed 45,000expressed sequence tags (ESTs) that represented genes expressed in rainbow trout kidney, liver, spleen muscle, brain, and gill tissues. These were sequenced in cooperation with Dr. Christopher Koenig at Qiagen Genomics, Inc. The sequencing phase of this project has been completed and the bioinformatic analyses begun, with the assistance of Dr. John Keele, Meat Animal Research Center in Clay Center, NE. Completion of this research will greatly increase the number of rainbow trout gene sequences available to define how gene expression impacts important aquaculture production traits to enable improvement of these traits
Genetically selected trout strains for improved utilization on diets high in grain. The continued growth of aquaculture can only be sustained by the generation of improved genetic stocks of fish that can efficiently utilize grain-based diets that are both environmentally friendly and sustainable. Families of trout were tested and selected for their ability to grow and utilize a cereal grain based feed. ARS scientists at the Hagerman Fish Culture Experiment Station, University of Idaho, in collaboration with Small Grains and Potato Research and Germplasm Facility, Abderdeen, ID, made crosses with four strains of trout and the progeny were reared on 40% barley containing diets until they reached an age at which time they were selected, by family, as to their performance as judged by weight, length, and feed conversion ratio. All the individuals from selected families have been individually electronically tagged and genotyped for 10 distinct microsatellite markers linked to separate linkage groups while being analyzed for expression levels of growth and health related genes such as myosin, pyruvate kinase, lysozyme, and insulin-like growth factor. The genetically improved trout will provide farmers with rainbow trout that grow well on diets that are cheaper and more environmentally sustainable.
Catfish genetic improvement after the first release to industry Genetically improved catfish lines selected for multiple economically important traits are important for the viability and continued growth of the commercial catfish industry. The applied catfish breeding program at the Catfish Genetics Research Unit in Stoneville, MS, developed a genetically improved catfish line simultaneously selected for growth, feed consumption, processing yield, early sexual maturity, and bacterial disease resistance. Two generations of selective breeding was accomplished by combined family ranking from approximately 100 full and half-sib USDA103 line catfish families from 1999 year-class spawns and approximately 85 families from 2001 year class spawns to produce a select line. Parentage of spawning fish was obtained from inheritance of microsatellite markers, and this select line will be evaluated and compared to control line USDA103 fish to determine potential performance increases for each selected trait prior to future release to commercial producers and consumers.
High density genetic linkage map started. Use of marker assisted selection (MAS) to more efficiently develop strains of rainbow trout with improved production traits requires the development of a high density genetic linkage map. Researchers at the National Center for Cool and Cold Water Aquaculture, Leetown, WV, are participating in an international collaboration to develop these maps. We have developed about 380 microsatellite markers from microsatellite enriched libraries, about 130 from expressed gene sequences and about 10 from physically mapped bacterial artificial chromosome clones. The development and characterization of these markers contribute to the construction of high-density linkage maps that will be utilized to identify and define quantitative trait loci (QTLs) that are important to the genetic improvement of production traits in rainbow trout and other salmonid species.
Transgenic rainbow trout developed with genes for improved resistance to infection and flesh color. One of the most important factors affecting the economics of rainbow trout aquaculture is loss due to disease outbreaks. An alternative approach to the use of antibiotics for disease control is the production of fish containing the genes for antimicrobial peptides. Scientists at the University of Connecticut Biotechnology Center have produced seven F1 families from transgenic fish that contained the gene for the antimicrobial peptide cecropin; in addition, two F1 families were produced with fish containing the gene for ß-ketolase, a factor in meat coloration, and more than 100 fish per family were produced. The results of these studies should lead to the development of new strains of rainbow trout resistant to infection to pathogenic organisms and that exhibit more red colored flesh.
Progress on high-density genetic map of catfish. The identification of genes controlling important traits is more efficient with the use of a high-density genetic map, but the current catfish genetic map does not have enough markers for efficient detection of linkage between genes and performance traits. Scientists at the Catfish Genetics Research Unit, Sonteville, MS, determined the DNA sequence of several thousand genes expressed in the catfish brain. A large percentage of these genes contained polymorphic sequences termed microsatellites that facilitate addition to the existing catfish genetic map. These sequences will enhance the precision of the genetic map for linkage analysis and marker-assisted selection, and allow researchers and breeders to compare the catfish map with those of other species to identify candidate genes important for catfish production.
Identification of immune function genes. Infectious disease in channel catfish causes significant losses to the U.S. catfish industry. Scientists at the Catfish Genetics Research Unit, Stoneville, MS, are performing high-throughput DNA sequencing to identify genes in molecular libraries produced by researchers at the University of Mississippi Medical Center. This ongoing genomics project has led to the identification of several catfish genes involved in immune function. The genes identified in this project will be useful to researchers examining genetic control of immune function in channel catfish and help breeders identify brood stock with enhanced innate disease resistance.
Integrated Aquatic Animal Health 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.
Approval near for copper sulfate. Research was directed toward gaining FDA approval of new chemicals and drugs for disease control in the culture of food fish. ARS scientists at the Harry K. Dupree Stuttgart National Aquaculture Research Center, Stuttgart, AR, conducted research to demonstrate the margin of safety of copper sulfate for use as an aquaculture therapeutant. A report of results was presented to the CRADA partner for submission to FDA to gain approval for use of copper sulfate for fish disease control. The data package is critical in obtaining formal FDA approval for use of this chemical in fish disease control and making it commercially available to fish farmers.
Integrated management of fish health by multi-disciplinary approaches. Research on detection tools by ARS scientists at the Aquatic Animal Health Research Unit, Auburn, AL, has resulted in the development of polyclonal and monoclonal antibodies against the immunoglobulins of tilapia, hybrid striped bass, seabream and menhaden for the purpose of diagnostic tests. Tests for detection of Flavobacterium columnare, Streptococcus iniae, and the serum immunoglobulin levels in Atlantic menhaden were developed using these antibodies. A rapid polymerase chain reaction (PCR) - based detection test for Flavobacterium columnare was developed and evaluated using clinical isolates of F. columnare from fish collected from catfish farms and from catfish eggs that were experimentally inoculated with F. columnare. Columnaris disease is among the leading cause of catfish mortality. The detection test will be further validated to diagnose for Columnaris disease in catfish under field conditions.
Losses from fungus on eggs controlled. Egg loss due to fungus infections is a source of economic loss to channel catfish farmers. Safe, effective chemicals are needed to control these infections. Studies of the efficacy of copper sulfate for control of fungus on eggs were conducted by scientists at the Harry K. Dupree Stuttgart National Aquaculture Research Center, Stuttgart, AR. Copper sulfate at a concentration of 5 milligrams/L (5 ppm) in a 30-minute bath daily during the first 5 days of hatching practically eliminated egg loss due to fungus infections. The data will be submitted to FDA for consideration of a label claim for use of copper sulfate for this purpose.
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.
Closed-culture of southern flounder. Research was conducted to determine the feasibility of spawning captive and wild southern flounder brood stock under recirculating, closed-culture conditions. ARS scientists in collaboration with scientists at the Harbor Branch Oceanographic Institution, Ft. Pierce, FL, demonstrated captive and wild flounder spawning and the resulting larval fish were raised in closed recirculating systems. System and culture management protocols were established from the successful spawning and culture of larval fish raised in recirculating systems. This research provides evidence for culture of fingerlings in intensive, water re-use nursery systems, thus greatly enhancing the potential of commercial production of this important food fish.
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 fishbased protein in aquaculture diets.
An improved shrimp feed manufacturing process. A simple and economically efficient method is needed for processing shrimp feeds with excellent water stability. A modified pelleting process with reduced equipment requirements and fewer processing steps was developed using a commercially available pellet mill by scientists at the Oceanic Institute, Waimanalo, HI. The new pellet method was found to be easier and faster, and results have indicated that the pellets produced by this method had better water stability and a pellet durability index compared to conventional methods; if this modified process continues to produce good results after being thoroughly rechecked, verified, and documented, it has potential for a patent. This breakthrough in shrimp feed manufacturing is important because feeds with good water stability are needed for efficient feed utilization by shrimp.
Evaluation of genetically enhanced small grains as nutrient sources for trout feed. For aquaculture to maintain its rate of expansion it is necessary that fish feeds be derived from sustainable protein sources that have minimal negative environmental impact. This research was initiated to test cereal grain cultivars for use in fish diets. Scientists at the Hagerman Fish Culture Experiment Station, University of Idaho, in collaboration with the ARS scientists at the Small Grains and Potato Research and Germplasm Facility, analyzed several different barley and oat cultivars for amino acid, phytate phosphorus, protein, oil, beta-glucan, and other significant nutritional components, and for their digestibility by fish. During the last year important discoveries were found concerning grain phytate level and its effect on mineral retention, and the effect of grain protein levels in feed utilization by trout. As cereal grain-based fish diets become better understood, the use of these feeds by commercial industry will reduce feeding costs and reduce the release of phosphorus from production unit effluents while generating a new market for cereal grain farmers.
An alterative for fish oil in shrimp feeds. The effectiveness of alternative supplemental lipid sources in shrimp diets was investigated. Juvenile shrimp were fed for eight weeks in a flow-though system at the Oceanic Institute, using diets supplemented with either menhaden oil (control) or one of five vegetable oils or lard. Substitution of menhaden oil by vegetable oils or lard resulted in a significant reduction in growth of shrimp only in the diet containing canola oil (soybean oil showed the best response of the alternative sources). This finding will assist feed companies in selecting alternatives to replace expensive marine oil in formulating feeds for shrimp.
An enzyme important for carbohydrate utilization verified in white shrimp. A comparative study sought to investigate whether the enzyme laminarinase was present in the digestive gland of juvenile Pacific white shrimp, Penaeus vannamei. Scientists investigated whether there was any difference in the specific activity of laminarinase between shrimp grown in an indoor clear water system and an outdoor zero-water exchange shrimp culture system. Laminarinase, a carbohydrate-digesting enzyme, hydrolyses beta-1, 3 glucans (laminarin), which are common carbohydrate storage products in marine microalgae. Specific activity of laminarinase was nearly 7 times higher in shrimp grown in the outdoor zero-water exchange system, compared to shrimp grown in the indoor clear water system, thereby indicating the possibility of substrate specificity. If, as this study suggests, laminarinase is present in the shrimp digestive gland, this enzyme may have an important role in the digestion of microalgae and other sources of beta-1,3-linked glucans present in shrimp pond water and soybean meal.
Assays developed for evaluating gene expression. Evaluation of genetically enhanced fish strains requires assays specific to monitoring individual aspects of the quantitative trait that is under selection. ARS scientists at the Hagerman Fish Culture Experiment Station in Hagerman, Idaho, developed assays utilizing real-time polymerase chain reaction for measuring gene expression for a number of metabolic, health, immunological and growth factors. These assays have been used to correlate nutrition and growth with selection for improving the utilization of cereal grain based fish feeds by rainbow trout. These assays, which should also prove useful in evaluating fish health, are aiding in the generation of improved trout strains that can utilize a diet that should be cheaper than most existing diets and will generate less harmful waste.
Reducing the cost of fish diets. One reason fish diets are expensive is that not enough is known about potential alternative feedstuffs to safely substitute them in existing diet formulations. Scientists at the Harry K. Dupree Stuttgart National Aquaculture Research Center, Stuttgart, AR, in collaboration with scientists at Texas A&M conducted research to determine the availability of nutrients in 19 common feedstuffs for hybrid striped bass and red drum using diets that were extruded with commercial methods and equipment. Digestibility values for protein, lipid, energy, 20 essential amino acids, and several fatty acids were determined in both species of fish. Results were made available to feed mills and producers that greatly expanded both the choice and accuracy of nutrient values for practical ingredients in hybrid striped bass and red drum diets and simultaneously reduced cost of diets.
A water treatment to reduce transport stress. Handling fish induces physiological stress, which can reduce growth, increase susceptibility to disease, and cause mortality. The tolerance of hybrid striped bass to several water additives and to combinations of additives and physical stress was tested at the Harry K. Dupree Stuttgart National Aquaculture Research Center, Stuttgart, AR, to determine which treatment reduced the stress response. Metomidate was the most effective in reducing cortisol secretion (an indicator of stress), and tricainemethanesulfonate (MS222) with and without sodium chloride was also effective in reducing stress and promoted rapid recovery to pre-stress conditions. Refinements of water treatments for handling fish will allow a greater density of fish to be transported with greater survival and less stress.
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.
Intensive aquaculture systems adopted. Expansion of aquaculture is significantly constrained by the interaction of production systems with the external environment through biological and nutrient exchanges. Cool and cold-water finfish production systems that utilize intensification and water recycling consistent with sustainability objectives have been designed and evaluated by scientists at the Freshwater Institute, Shepherdstown, WV. Production system technologies have been developed that minimize environmental interactions and biological exchanges through water recirculation, improved environmental control and biosecurity management. A broad range of commercial fish farm operations producing Atlantic salmon smolts, Arctic char, ornamental fish, tilapia, rainbow trout, walleye, yellow perch and hybrid striped bass have adopted production systems designs and altered management based on this research.
Engineering sustainable marine aquaculture systems. Research was conducted to determine the feasibility of spawning captive and wild southern flounder broodstock under recirculating, closed-culture conditions. ARS scientists in cooperation with Harbor Branch Oceanographic Institution scientists at Ft. Pierce, FL, evaluated captive and wild flounder placed in broodstock conditioning units for hormonal and temperature manipulation. Broodstock were successfully spawned and resulting larval fish reared under recirculating systems. This research provides evidence that it is possible to culture fingerlings in intensive, water re-use nursery systems, thus greatly enhancing the potential of commercial production of southern flounder.
Production economics favorable for larger catfish. Minimum size of channel catfish accepted at processing plants has increased, yet farmers lack basic production information for growing larger (> 1.25 lb) food fish. In collaboration with a University of Arkansas at Pine Bluff Aquaculture/Fisheries Center of Excellence researcher, a study was undertaken at the Aquaculture Systems Research Unit, Pine Bluff, AR, to quantify growth, feed conversion, and production economics to produce channel catfish of greater than 1.25-lb average weight. Results showed that channel catfish grow rapidly to average individual weights of 1.3, 1.6, 2.0, 2.5 lb, that feed-conversion efficiency was maintained across size classes, that gross yield of catfish increased from 5,400 to 10,100lb/acre as fish size increased, and that the incremental cost of production per pound decreased as average fish weight increased above 1.3 lb. Catfish farmers can use this production and economic information on growing larger-sized food fish to modify farm production strategies to produce larger fish in a cost-effective manner.
Metabolic information improves shipping. Golden shiners are sold and shipped live from Arkansas all over the United States as baitfish for recreational and sport fishing. The accumulation of ammonia during transport is toxic and limits the distance fish can be shipped. Research was conducted to determine ammonia excretion rate of golden shiners at three different water temperatures by scientists at the Aquaculture Systems Research Unit, Pine Bluff, AR, in collaboration with researchers from the University of Arkansas at Pine Bluff. Ammonia excretion rate for golden shiners ranged from 2.9 mg per kg fish per hr at 15 C to 15.0 mg per kg fish per hr at 25 C, which allows for design of zeolite filters for ammonia removal during fish transportation. The golden shiner ammonia excretion rates quantified in this study provide information for the design of effective ammonia removal methods during fish transport increasing transport time or the biomass of fish transported.
Sustainability and Environmental Compatibility
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.
Control of bird predation on farmed fish. Double-crested cormorant predation on cultured fish cause major economic losses for the aquaculture industry. Using multiple catfish production facilities across a large area within southeastern Arkansas, ARS scientists conducted research at the Harry K. Dupree Stuttgart National Aquaculture Research Center, Stuttgart, AR, to determine the effectiveness of a low-cost, physical barrier system. Overall, the physical barrier significantly limited double-crested cormorant access to aquaculture ponds by 4 to 5 fold, as well as limited the duration cormorants stayed on a pond. Some farmers have already adopted this economical and easy-to-set-up apparatus reducing losses of cultured fish to double-crested cormorants and to other fish-eating birds.
Design criteria established for aerobic lagoons to treat effluents. Aquaculture facilities that incorporate technologies to thicken waste solids generate a secondary waste stream that should be easily treated to remove dissolved nutrients, thereby reducing the environmental impact. Scientists at National Center for Cool and Cold Water Aquaculture Research Center, Leetown, WV, in collaboration with those at the Freshwater Institute, Shepherdstown, WV, examined the effluent quality from tanks operated at different retention times to determine the efficiency of aerobic treatment. Dissolved carbon and nitrogen constituents were readily removed at all retention times; however, phosphorus remained relatively unchanged. These results will provide the engineering design basis for aerobic lagoons used to treat effluents from aquaculture facilities.
An inexpensive harvesting and grading tool developed. Large tank-based production systems could reduce production costs if inexpensive, efficient and portable fish handling equipment was available to reduce the labor requirement for grading and harvesting large circular culture tanks. To reduce the cost of handling and grading fish, and to minimize the stress on fish during harvest, the Freshwater Institute staff developed a portable and relatively low cost airlift fish pump and grader box to remove fish from large circular tanks and then sort the fish according to size and condition. A lightweight, compact, and inexpensive air-lift driven fish pump, dewatering box and fish sorting table was developed to assist fish harvest from intensively stocked circular rearing tanks. The portable fish pumping and sorting equipment will reduce the labor requirement for grading and harvesting large circular culture tanks and may improve final product quality by reducing handling stress.
Treatments evaluated that improve phosphorus removal from effluents. Phosphorus discharged by aquaculture systems, one of the nutrients of high regulatory concern due to its impact on receiving bodies of water, is primarily contained in the filterable or settle able solids fraction discharged from fish farms. Standard jar test studies were conducted by scientists at the Freshwater Institute, Shepherdstown, WV, to evaluate the effectiveness of several commonly used coagulation-flocculation aids at removing both suspended solids and phosphorus from the solids thickening tank overflow at the Freshwater Institute. Dosages, mixing speed and time, and flocculation conditions for applying alum, ferric chloride, and high iron concentration acid mine drainage (AMD) sludge amendments were optimized to effect maximum removal of both suspended solids and phosphorus from fish manure thickening tank overflows. The application of the coagulation-flocculation chemicals will improve capture of fine solids and total phosphorus in the overflow from aquaculture bio-solids thickening and settling treatment systems.
Quality, Safety, and Variety of 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 value-added products and processes.
Collagenases in fish processing wastes. The goal of this research was to identify high-value constituents like proteolytic enzymes in the processing by-products of Alaskan whitefish, including collagenases, other proteases, and lipases. Wash water from Arrowtooth flounder (Atheresthes stomias) processing and cod (Gadus macrocephalus) stomachs was collected from local processing plants to test for collagenases. Relatively high collagenase activity did occur in the stomach tissues of Gadus macrocephalus. The activity in cod stomachs is sufficiently high that a crude extract of cod stomachs can probably be employed to reduce the tensile strength of salmon ovarian skeins. An available source of collagenase will be important to improve the efficiency of fish egg recovery for caviar.
Aerial drift of Diuron from rice field application can be harmful to fish. Herbicides, applied aerially to control weeds in row crops that are adjacent to aquaculture ponds are potentially detrimental to fish production. A study done at the Harry K. Dupree Stuttgart National Aquaculture Research Center, Stuttgart, AR, in cooperation with the University of Arkansas at Pine Bluff determined the effect of Diuron, a rice herbicide, on plankton and water quality. Amounts of this herbicide at concentrations obtainable from drift during spraying depressed dissolved oxygen levels in ponds sufficiently to harm fish. These results indicate precautions must be taken to avoid drift to adjacent areas during aerial application of the herbicide.
Management information to control off-flavor. The rapid growth of the aquaculture industry during the past 25 years has resulted in little pond management information concerning reworking ponds, and the industry practice is to rework ponds when erosion of levees necessitates. ARS scientists at the Catfish Genetics Research Unit in collaboration with scientists at Mississippi State University, sampled ponds ranging in age from 1-25 post construction for normal physical/chemical parameters. Statistical analyses separated ponds into two groupings, with 4-5 years as the breakpoint. This research suggests ponds should be reworked every 4-5 years to minimize off-flavor.
A new selective algicide field-tested. The two algicides registered for use to control off-flavor in catfish lack selectivity and, in the case of copper sulfate, may accumulate in the environment after repeated treatment. Mississippi State scientists in cooperation with scientists at the Natural Products Research Unit, Oxford, MS, conducted research to identify and evaluate new algicides for use in managing algae-related off-flavors. One promising compound, a modified quinone, identified in laboratory screening was tested in outdoor mesocosms and found to be selectively algicidal to odor-producing blue-green algae, thereby reducing levels of odorous compounds in water. Successful research with this compound will lead to the development of another compound for managing off-flavors in commercial ponds.
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