National Programs Aquaculture

FY2004

National Program Annual Report: FY 2004

• 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 enjoyed an exciting year with expanded program, new hires, scientific productivity, and recognition of scientific quality.  The FY 2004 appropriations increased aquaculture research in four of the seven research program component areas.  ARS implemented new program on Great Lakes Aquaculture at Milwaukee, WI.

The Aquaculture National Program was peer reviewed during 2004.  The program was organized into 26 projects that were submitted to two review panels.  I am proud to report that 70 percent of the projects were rated needing only minor revision or needing no revision.

Congratulations to Brian Bosworth, Mid-South Area and Ken Overturf, Pacific West Area for being named Early Career Scientists of the Year.

Welcome to 7 new permanent full-time scientists:

Shawn McNulty, microbiologist-Aquatic Animal Health, Auburn, AL

Sylie Quiniou, Molecular Immunologist, Catfish Genetics, Stoneville, MS

Peter Silverstein, Virologist, Catfish Genetics, Stoneville, MS

LaTonya Clay. Molecular Biologist, Catfish Genetics, Stoneville, MS

Cynthia Bower, Food Science/Microbiologist, Subarctic Agricultural Research. Fairbanks, AK

Philip Pearson, Agricultural Engineer, Aquaculture Production Systems, Pine Bluff, AR

Brett Dumbauld, Ecologist, Newport, OR

Two proposals for post-docs (Class of FY2005) were awarded to scientists (Camara and Bilodeau) in the Aquaculture National Program.

ARS scientists delivered six invitational scientific presentations at national and international conferences.  The Agency helped support symposia, workshops, field days or annual association meetings through partial funding, participation, sponsorship or hosting on various aquaculture research related topics.

Seven patents were filled or awarded in FY2004.  Les Torrans received Honorable Mention for Excellence in Technology Transfer from the Federal Laboratory Consortium, Southeast Region for the “Sock Saver” method to deliver oxygen to catfish.  He also received a Mid-South Area Technology Transfer Award.

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.

Five North American Atlantic Salmon stocks evaluated.  Development of a genetically improved North American Atlantic Salmon is important to survival of the Maine Salmon Industry. Atlantic salmon from 5 different sources was obtained from collaborators to initiate the breeding program at the ARS National Cold Water Marine Aquaculture Center, Franklin, ME.  Eggs were incubated, hatched, and fish reared as parr (juveniles) in indoor (greenhouse) tanks.  Early growth evaluation of the different genetic stocks indicate differences in growth between stocks  and individual families, an imperative result for genetic improvement. 

Broodyear lines established and the top families selected.  Evaluation of germaplasm and development of broodstock lines is critical to genetic improvement of economically important rainbow trout industry.  Scientist at the National Center for Cool and Cold Water Aquaculture in Leetown, WV, conducted the first generation of selective breeding, selecting the top 15% of 2002 broodyear families for breeding and generating 100 full sib families for 2004 broodstock (F1).  The 86 families from 2003 broodstock have been evaluated for growth and the top 10% of families are identified for breeding in Jan 2005.

Stress hormone (costisol) heritable.  Stress has a negative impact on many traits in fish that are important to aquaculture production, including growth rate, feed efficiency, disease resistance and reproductive performance.  Stress response, as measured by blood levels of the hormone cortisol was found to be highly heritable in other strains of rainbow trout, allowing lines of low and high responding fish to be generated by ARS scientists at the National Center for Cool and Cold Water Aquaculture, Leetown, WV.  Investigations into the performance benefits of altering stress response via breeding have been inconclusive.  Families of rainbow trout from  2002 broodstock development program that differ by about 2X in cortisol response to stress have been identified and increased stress response was correlated with increased growth and feed efficiency, two  selection criteria.  High and low stress broodstock families were bred to determine if the stress response is heritable in  fish. Positive correlation between stress response indicators and performance traits will provide the information on which to base selection to address the negative effects of stress in aquaculture production,.

Transgenesis used to demonstrate disease resistance. Aquaculture production suffers large and variable losses to disease. Conveying disease resistance by selection is slow. Scientists at the University of Connecticut, Storrs, CN in collaboration with NCCCWA developed the P1 transgenic fish  in 1999 (Rbt-99)and a total of 6 families of F2 transgenic fish. This is the first time in this project that F2 transgenic fish are ready for disease challenge studies.  Animals from these six families were subjected to challenge studies with A. salmonicida, a potent bacterial pathogen of trout.  Results of the challenge studies showed animals from two families exhibited a significant protection from infection by A. salmonicida.  More F2 animals will be established from 8 additional families of F1 transgenic fish for further disease challenge studies and improve understanding of gene action.

Characterized a rainbow trout BAC library. Genome research requires the development of species-specific molecular genetic resources for organisms of interest.  Unfortunately, these resources are very expensive to construct and maintain, thus they are not available for every species.  ARS scientists at the National Cool and Cold Water Aquaculture Center at Leetown, WV, (NCCCWA) characterized a rainbow trout bacterial artificial chromosome library for use in genetic and physical mapping and sequencing DNA segments of interest.  The library, made up of ~135,000 base pair DNA segments retained in bacterial cells, has the equivalent of 10 times the amount of DNA of the rainbow trout genome.  This means that for any DNA segment of interest, there is a 95% probability of identifying at least one clone retaining that segment.  On average, each DNA segment is retained ~10 times as expected.  As rainbow trout have undergone an evolutionarily recent genome duplication, some DNA segments were retained 20 times.  Further DNA fingerprinting analyses revealed that these were actually two sets of clones retaining recently diverged duplicates of a single gene.   Mapping these copies has revealed homeologous segments of the genome expected to harbor similar genes.  These results have had an impact on strategies for constructing physical maps and the eventual sequencing of the rainbow trout genome.  The NCCCWA library is publicly available to the research community. 

Genes identified for early development of rainbow trout. Reproductive fecundity and early life forms survival are important traits for an aquaculture species. A high-quality cDNA library from rainbow trout oocyte has been successfully constructed and normalized by scientists at West Virginia University, Morgantown, WV in collaboration with NCCCWA.  A total of 20,160 EST sequences from the normalized library was generated.  The information of these sequences provides a global picture of genes expressed in trout oocyte and is important for identification of key genes essential for oocyte development, maturation, and early embryogenesis.

Calpain proteins characterized for rainbow trout.  Calpain proteins from rainbow trout muscle have been isolated and characterized by scientists at West Virginia University, Morgantown, WV in collaboration NCCCWA. These proteins are important in muscle texture development.  The cDNAs for calpain regulatory subunits of the two calpains were successfully cloned and characterized.  The expression of these genes in muscle during starvation has been determined. These determinations will improve the accuracy and reduce time in selective genetic improvement of rainbow trout. 

Performance rank order similar for trout in different systems. Domesticated strains of rainbow trout from flow-through culture environments were used as the founding population for the selective breeding program by ARS scientists at the National Center for Cool and Cold Water Aquaculture in Leetown, WV.  Individuals from each strain were reared in tanks receiving recirculated or single use water to examine the impact of culture environment on growth characteristics.  Surprisingly, fish reared in tanks receiving recirculated culture water gained more weight than fish reared in the flow-through tanks, even though water quality in the recirculating aquaculture system was poorer, with respect to ammonia and organic concentrations.  Additionally, the results indicated that the strains maintained the same rank order in terms of growth while being reared in either environment.  The implications of this work suggest that a single selective breeding program may be sufficient to improve performance characteristics of rainbow trout when reared in a recirculating or flow-through environment. 

State-of-the-art controlled facilities set-up for culture of oysters. Improved oyster germplasma with superior traits for growth, quality, and disease resistance is important for oyster farming. Molecular technology is needed to enhance selective breeding. The ARS scientist at Newport, OR constructed a large greenhouse with temperature controlled oyster rearing facilities and large algae-rearing containers in cooperation with the Oregon State University Molluscan Breeding Program. This accomplishment permits initiation of a large-scale genetic analyses. The new infrastructure for nursery and field stages of oyster culture will provide critical data and generate experimental materials for genetic mapping. Microsatellites will be the workhorse technology for oyster breeding efforts due to their high levels of polymorphism, ease of scoring, and transferability among laboratories, populations, and because very high throughput genotyping will be required. The ARS scientist optimized over 50 microsatellite loci for Pacific oysters and automated PCR setup using robotic liquid handling. PCR primer pairs published in the literature or provided by colleagues were tested using a matrix of reaction conditions and the best set of conditions was determined using a diverse panel of oysters. This accomplishment has permitted progress on the high throughput demanded by our research and will accelerate our progress and the transfer of our results to industry

Unique trait established for oyster breeding.  Ongoing international negotiations that limit cadmium content in seafood may impact the marketability of Pacific oysters, and there is need to know whether selective breeding can modify this character. The ARS scientist at Newport, OR collected oyster tissue samples for preliminary study of the heritability of cadmium concentration in Pacific oysters from an ongoing experiment setup by collaborators at OSU.  The research was accomplished by consultation and collaboration with OSU and other ARS researchers in Corvallis, OR.  This accomplishment will permit a critical evaluation of the feasibility of breeding to select for reduced cadmium accumulation, an issue of great concern to the shellfish industry.

Marker assisted selection of catfish.  Catfish families demonstrate variation in growth rate, but the mechanisms underlying genetic differences between families are unclear.  Levels of mRNA and protein of insulin-like growth factors (IGF) I and II were measured in slow and fast growing families of catfish by ARS scientists at the Catfish Genetics Unit, Stoneville, MS.  Fish in fast growing families demonstrated higher levels of plasma IGF-I and higher IGF-II mRNA expression compared to slower growing families.  The changes in protein levels of IGF-I supported IGF-I's role in growth regulation of channel catfish and provide evidence for a role of IGF-II in growth of channel catfish.  These gene products could be used as markers for selection of broodstock with superior genetic potential to increase the rate of improvement. 

Performance evaluation of several types of catfish shows advantage of blue catfish, Mortalities and reduction in growth due to diseases are an increasing problem for producers growing channel catfish, but blue catfish and channel x blue catfish hybrids are less susceptible than channel catfish for enteric septicemia and proliferative gill disease, two of the most prevalent diseases.  ARS scientists at the Catfish Genetics Unit, Stoneville, MS  conducted a comparison of production traits of blue catfish, channel x blue catfish hybrids, and two channel catfish strains (Norris and NWAC103).  Fingerling growth and survival were better for blue catfish and channel x blue catfish hybrids than for the channel catfish strains.  Feed records indicate hybrids consumed the most feed, followed by blue catfish, then NWAC103s, and then Norris strain channel catfish during the fingerling to market weight portion of the study.  Results demonstrated that use of blue or channel x blue catfish hybrids could benefit producers through improved growth and survival.

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.

Rainbow trout pathogen sequenced.  Sequence analysis of Flavobacterium psychrophilum genes will be useful for developing diagnostic assays, identifying putative virulence factors and prototype vaccine candidates.  A low coverage (~3.4X) genome sequence of Flavobacterium psychrophilum strain CFS 259-93 was generated by ARS scientists at the National Center for Cool and Cold Water Aquaculture in Leetown, WV.  This strain was chosen as it is representative of disease causing isolates from Idaho and a challenge protocol has already been established by an industry collaborator.  A single virulent clone was isolated, genomic DNA extracted, and clones from a small-insert library sequenced.  The sequence has been assembled into 1,160 contigs ranging in size from 0.8-13.6 kb.  Computer analysis identified 2,420 potential open reading frames.  Of these, 53% could be assigned putative functions.  Based on this sequence analysis, Flavobacterium psychrophilum is predicted to have a relatively small genome compared to other microbial pathogens. 

A disease challenge model for a rainbow trout pathogen. A standardized disease challenge model for the salmonid pathogen Yersinia ruckeri has been established by ARS scientists at the National Center for Cool Cold Water Aquaculture in Leetown, WV.  This accomplishment was a required first step for further studies of the pathogenesis of this bacterium and for the assessment of Yersinia ruckeri mutants.  Methods for the genetic manipulation of gram negative bacteria have been adapted for use in Yersinia ruckeri with the purpose of defining virulence factors.  

Rainbow trout immune gene identified. Immune system characterization has focused on identifying chemokine ligands/receptors and tumor necrosis superfamily ligands/receptors.  These families of genes were targeted by ARS scientists at the National Center for Cool and Cold Water Aquaculture in Leetown, WV because of their known roles in immune system signaling, activation, and memory.  They identified a number of putative family members in the Institute for Genomic Research (TIGR) rainbow trout, expressed sequence tag (EST) database.  Fifty-four unique cDNA clones were isolated for further characterization.

Virus found for a fish pathogen. ARS scientists at the National Center for Cool and Cold Water Aqauculture in Leetown, WV discovered a bacteriophage that specifically infects and kills the salmonid pathogen Yersinia ruckeri.  Methods for purifying this bacteriophage and assays for measuring its viability and antibacterial activity have been developed. This discovery could lead to new biocontrol technology to protect fish from pathogens.

A patent issued for Bacterial Kidney Disease diagnostic test. This test will be useful to evaluate the health of salmonids and document pathogen presence upon administration of a known dosage of a pathogenic bacterium. A quantitative real-time PCR assay was devised by the ARS scientist at Aberdeen, ID to detect the presence of the bacterial genome and quantify its absolute copy number in infected tissue. With this test there now exists a method to assay dietary effect on fish health status by administration and monitoring of precise pathogen numbers.

Efficacy of amoxicillin demonstrated for hybrid striped bass. Streptococcal infections can cause devastating mortalities in hybrid striped bass production.  The efficacy of amoxicillin for controlling Streptococcus iniae infection in tilapia was demonstrated using a laboratory disease model developed by ARS scientists at the HKD Stuttgart National Aquaculture Research Center, Stuttgart, AR.  This data could support the future approval of amoxicillin as an antibiotic to treat S. iniae infection in tilapia, which can be a devastating disease. Trials were run to show that amoxicillin is effective in decreasing the mortalities in infected fish from 96% to 6%.  The immediate impact of this accomplishment has been for the FDA to allow the continued temporary use of this compound for disease control of S. iniae in hybrid striped bass production.

Need to understand stress and disease susceptibility. The bacterial pathogen Edwardsiella ictaluri is a prevalent source of substantial economic loss to catfish farmers, and stress has been shown to increase E. ictaluri susceptibility. ARS scientist at the Catfish Genetics Unit, Stoneville, MS conducted trials to determine the effect of cortisol in the presence and absence of stress on mortality during an E. ictaluri challenge.  Increased plasma cortisol levels due to stress correlated to increased mortality; however, stress-free cortisol administration had no effect on mortality. These results suggest that although cortisol is considered the primary stress hormone in fish, it in itself is not immunosuppressive. Understanding the relationship between stress and disease resistance is crucial to the development of biomarkers and management strategies for improving disease resistance. 

Increased expression of toll-like receptors for increased disease resistance, Little is known of host-response mechanisms that are activated when catfish are infected by the bacteria Edwardsiella ictaluri, which causes enteric septicemia of catfish (ESC).  The genes encoding toll-like receptors 3 and 5 (TLR3, TLR5) were identified by DNA sequencing and changes in the expression levels (using real-time PCR) were measured in liver, kidney, and spleen tissue in non-exposed fish and fish challenged with virulent Edwardsiella ictaluri by ARS scientists at the Catfish Genetics Unit, Stoneville, MS.  Expression of TLR5 was higher than TLR3 in all tissue types sampled and was elevated in liver tissue compared to non-exposed fish throughout experimental challenge.  This indicates TLR5 is involved in the innate immune response to E. ictaluri. Understanding factors influencing the expression of toll-like receptors that are related to disease resistance in catfish could benefit catfish producers and consumers by leading to the development of catfish with higher levels of innate resistance to ESC.

Intestinal shedding may be a factor in ESC transmission, Factors influencing transmission of enteric septicemia of catfish (ESC) are not well understood. Researchers at Mississippi State University, in collaboration with ARS scientists at the Catfish Genetics Research Unit, Stoneville, MS measured changes in pathogen levels in gut and intestinal contents of catfish infected with ESC to quantify levels of bacterial shedding during ESC infection. Evidence of bacteria in intestinal samples indicated bacterial shedding may be one mechanism of disease transmission. Ongoing research will address the issue of bacterial shedding and improve understanding of factors influencing disease transmission.

Fish vaccines being commercialized. Vaccines against Flavobacterium columnare, Edwardsiella tarda and Streptococcus agalactiae, all fish pathogens were developed and U.S. patent applications filed by ARS scientists at the Aquatic Animal Health Research Unit, Auburn, AL.  Intervet, Inc. is currently licensing a previous developed F. columnare vaccine that may be used in 7-10 day old fry and a U.S. patent was approved, and a divisional application has been filed.  Schering-Plough is licensing a previously patented S. iniae vaccine.  The availability of these vaccines is expected to increase fish farming profits by $80-$100 million annually.

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. 

Technology to produce sterile fish refined.  Sterile fish are important to aquaculture for production efficiency, risk reduction of escapes and protection of germplasm. In order to effectively make rainbow trout strains with four sets of chromosomes (tetraploids) to cross with normal diploids and produce sterile triploids, it is necessary to define the timing of the first cell division in fertilized eggs.  Scientists at the National Center for Cool and Cold Water Aquaculture in Leetown, WV.determined the time to first cleavage in embryos from individual females of a number of rainbow trout strains.  Results from the analyses revealed that at a given incubation temperature the time until first cleavage varied by as much as 40 min. among the strains.  Knowledge of this variation allows the development of a treatment protocol that will increase the production of tetraploids from different strains and may be an indicator of genetic differences in embryonic development rate that can be utilized for selection. 

A first step toward domestication of pompano. Florida pompano can be subjected to broodstock maturation procedures and successfully induced to spawn. Growth and expansion of the US mariculture industry depends on development of methods for sustainable reproduction and larviculture of target species such as Florida pompano.  ARS scientists at the Harbor Brabch Oceanographic Institute, Ft Pierce, FL collected pompano from the wild, acclimated them to indoor culture conditions, transferred them to a commercial diet, and successfully spawned them over a four-month period.  Results suggest the potential for year-round production of pompano seedstock for commercial farmers.

Artifical insemination-spawning of flounder and pompano.  Procedures were developed for the collection, handling, and refrigerated storage of sperm from two marine fish species, Southern flounder and Florida pompano by ARS and Harbor Branch Oceanographic Institute scientists, Ft. Pierce. FL. Utilization of refrigerated sperm improves hatchery techniques, by allowing efforts to be focused on maintaining female broodstock, monitoring ovarian development, and increasing efficiency during the strip-spawning process.  Sperm that were collected from domesticated southern flounder and wild Florida pompano retained motility for 10 d at 4 C when the sperm were suspended in diluted calcium-free Hanks' balanced salt solution (200 and 300 mOsmol/kg). This study demonstrated that southern flounder and Florida pompano sperm can be stored for short-term repeated use in the hatchery needed to support an industry.

Additional nitrogen improves fry survival. Catfish fry survival to fingerling stage averages around 60%, and is affected by the availability of natural food resources in the ponds - particularly zooplankton.  ARS scientists at the Catfish Genetic Research Unit determined the effect of catfish fry pond fertilization to optimize plankton composition in collaboration with Mississippi State University researchers.  Industry practices do not provide sufficient nitrogen for growth of desirable algae, thereby limiting zooplankton population size in ponds.  Optimal fertilization practices have been assessed on commercial ponds and management recommendations adopted by fingerling producers.

Large zooplankton important in catfish fry. The objective of zooplankton research is to help catfish farmers adopt management practices that maximize profitability of fry culture through utilization of natural pond productivity and reduced feed costs.  Zooplankton are more important to catfish fry culture than previously thought.  Catfish fry actively forage on large zooplankton taxa (i.e., copepods and cladocerans); large bodied zooplankton from catfish nursery ponds meet or exceed all nutritional requirements for channel catfish fry (65% protein, 9% fat).  Mississippi State scientists at the National Center for Warm Water Aquaculture, Stoneville,MS conducted preliminary laboratory studies that indicate zooplankton, in conjunction with commercial feed, have a positive effect on fry growth, survival, and general fish health.  In several trials, vaccinated fry fed zooplankton performed better when challenged with ESC than vaccinated fry not fed zooplankton and non-vaccinated fry.  This research may have major implications regarding management decisions.  Ponds should be managed to increase the numbers of large sized zooplankton.

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.

New hormone involved in growth. ARS scientist at the National Center for Cool and Cold Water Aquaculture in Leetown, WV identified a new regulatory path controlling secretion of growth hormone, and an important hormone controlling growth in fish.  They determined that a new compound stimulated growth hormone release in tilapia and channel catfish.  This provided the first evidence for the presence of 'ghrelin', a recently discovered molecule and growth hormone regulator, in these species.  Their continued research in rainbow trout found that ghrelin stimulates growth hormone release and increases feed intake in this species.  This research may result in novel ways to promote growth, feed efficiency and immunity in commercially important fish.

Large Variation in nutrient utilization among groups.  Nutrient utilization not only influences the cost of production, but nutrient retention has become very important for reducing phosphorus and nitrogen excretion to the environment.  ARS scientists at the National Center for Cool and Cold Water Aquaculture in Leestown, WV are conducting research  to identify fish with superior nutrient utilization efficiency and measure the genetic component of this trait.  Significant strain variation for this trait was identified.  Significant variation between families within strains was also detected.  Importantly, a significant correlation between efficiency measured on individually reared fish and efficiency of groups of their siblings was detected.  This result suggests that feed efficiency measured on groups may be an adequate selection criterion to improve performance of the population.

Technique developed to measure palatability of shrimp feed.  There is a need for a simple  efficient test for quantifying the effectiveness of shrimp feed attractants and palatability aids. Attractants can enhance the value and use of nutrient sources otherwise unpalatable to animals A testing system was developed by scientists at the Ocean Institute in collaboration with NOVUS, Inc. consisting of a series of tanks each equipped with two feeding bowls in which shrimp were allowed to choose between a neutral control diet, and a control diet spiked with an attractant. After vigorous testing several putative attractants were ranked according to their effectiveness.  This methodology will be useful to reliably screen attractants and palatability aids for shrimp, and can be used to develop nutritious, inexpensive feeds containing high levels of  protein from plant sources in place of fish meal.

Differential gene expression related to source of nutrients. Understanding the genetic components in trout involved in diet utilization is critical for US aquaculture industry to remain competitive particularly in the face of higher feed costs, limited marine protein resources, and stricter environmental standards. ARS scientists at Aberdeen, ID measured differential expression relating to trout growth, health and metabolism of trout reared on diets containing cereal grain and commercial feeds. Rainbow trout of distinct lineage were separated and reared on either a commercial diet or a diet containing cereal grain for one year after which, tissue samples were taken and the changes in gene expression measured. This work will be the basis to evaluate selected broodstock for improved performance on diets containing different sources of nutrients.

Poultry byproduct meal replaces fishmeal in hybrid striped bass diets. A major success toward replacing fishmeal and reducing costs in hybrid striped bass production was achieved by ARS scientists at the HKD Stuttgart National Aquaculture Research Center, Stuttgart, AR when hybrid striped bass were observed to grow equally well on test diets in which poultry byproduct meal (PBM) or fishmeal was the major protein source. Fishmeal is an expensive ingredient in aquaculture feeds because natural supplies are limited and it is in high demand. Because potential replacements for fishmeal are often deficient in essential nutrients and availability of amino acids, several animal byproducts were evaluated by feeding them to hybrid striped bass. The Ideal Protein Model was used to estimate which amino acids were most limiting in PBM. Minimal supplementation of two amino acids in the test diets ameliorated potential deficiencies when PBM totally replaced fishmeal.

Hormone found useful to optimize culture conditions. Insulin-like growth factor-I (IGF-I) is an indicator of optimum culture conditions. It appears that IGF-I levels in the blood can be used, after a shorter period of treatment than previously thought, to identify diets and culture conditions that optimize growth. IGF-I is a hormone produced in the liver and is thought to be the most important regulator of fish growth. ARS scientists at the HKD Stuttgart National  Aquaculture Research Center, Stuttgart, AR used plasma (blood) concentrations of IGF-I to help identify optimum temperature and minimum dietary tryptophan (amino acid) levels for sunshine bass.  Stress and withholding feed also resulted in a decrease of IGF-I.  

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.

Recirculation system in place. While rainbow trout production is based on single use water strategies, effluents discharge standards and limited freshwater supplies suggest that efforts to increase production will have to employ water recirculation technologies.  ARS scientist at the National Center for Cool and Cold Water Aquaculture at Leetown, WV, completed a 34-tank recirculation system for to rear rainbow trout that will be included in the facility's selective breeding program.  The recirculating aquaculture system uses biological and mechanical filtration to remove ammonia and suspended solids.  Additionally, carbon dioxide is stripped and dissolved oxygen levels increased prior to returning the water to the culture tanks.  This system has enabled the NCCCWA to maintain its genetic stock, while conserving water resources.  Additionally, this system allows evaluation of the various genetic strains of rainbow trout under different culture environments and to determine if alternative selection criteria are required for each type of culture environment.

Alternative live feed not successful. Threadfin shad stocked as a forage fish did not substitute for formulated feed in multiple-batch catfish production ponds when feed application was restricted. Formulated feed represents the largest component of variable costs, and improved feed management could result in lower feed expenditures for channel catfish production. ARS scientists at the Aquaculture Systems Research Unit, Pine Bluff, AR determined if channel catfish feeding frequency could be reduced to once every three days, compared with daily in ponds co-stocked with threadfin shad as a forage species. The presence of threadfin shad did not substitute for feed when feed was offered every third day. Feeding channel catfish every third day resulted in significantly lower yield and significantly smaller fish, but did not affect feed conversion ratio compared with daily feeding. Thus, additional grow-out time would be needed for fish to attain market size in ponds where threadfin shad was stocked to substitute for formulated feed.

Stocking rates measured for stocker catfish. Stocker channel catfish growth and yield were related linearly to stocking rate over the range of 3,500 to 5,500 fish/acre in single-batch culture. There is increasing interest in using stocker channel catfish (Ictalurus punctatus) instead of fingerlings in grow out ponds. There is little data available on the effect of stocking rate on stocker catfish growth during grow-out. ARS scientists at the Aquaculture Systems Research Unit, Pine Bluff, AR quantified the effect of stocking rate on production characteristics of stocker channel catfish in single-batch culture. Net yield increased linearly with stocking rate and averaged 4,591, 4,802, and 5,533 lb/ac for the 3,500, 4,500, and 5,500 fish/ac stocking rates, respectively. Average fish weight at harvest decreased linearly as stocking rate increased. 

Farmers can select the appropriate stocking rate to ensure that harvested fish meet processing plant fish size requirements

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. 

Biosecure aquaculture production. Recirulating aquaculture systems offer higher biosecurity than other systems of production. Internal disinfection processes should control and reduce risk of amplification of pathogens and other microbial populations.  Scientists at the Conservation Fund's Freshwater Institute in Shepherdstown, WV are working to evaluate the applicability of advanced oxidation processes for controlling and mitigating microbial populations and certain water quality parameters within intensive fish farming systems.  Research determined the ozone dose required to inactivate total heterotrophic and total coliform bacterial populations using a side-stream of water flow from an operating high-density aquaculture recirculating system. The study results are significant in that it identified conditions required to achieve nearly complete ozone disinfection of the recirculating flow, i.e., maintaining a dissolved ozone concentration of 0.1-0.2 mg/L at the outlet of a contact basin that provides 8 to 16 min of hydraulic residence time. This finding is importance for biosecure production and ensuring product quality.

Settling tank design important for solids removal. Dual-drain circular culture tanks can rapidly and effectively concentrate settleable biosolids into a relatively small bottom-center drain flow, which can then be treated using a relatively small settling device.  Scientists at the Conservation Fund's Freshwater Institute in Shepherdstown, WV evaluated two settling tank designs, a radial flow settler and a more conventional swirl separator, that were both operated at a surface loading rate of 0.00086 m3/s of flow per square meter of settling area (i.e., 1.3 gpm/ft2).  Results indicate a highly significant difference (P < 0.001) in mean TSS removal efficiency of the swirl separator and radial-flow settler, (± se) 37.1 ± 3.3% and 77.9 ± 1.6%, respectively.  These findings will help fish farmers improve recirculating system water quality, increase the particle removal efficiency from recirculating systems containing large `Cornell-type' dual-drain circular culture tanks, and decrease the solids loading on the recirculating system’s more costly and complex microscreen drum filter.

Fine sand fluidized biofilters achieve desired control. Biofilters are used to remove ammonia and nitrite from recirculating aquaculture systems and the steady-state removal efficiency of the biofilter controls the concentrations of ammonia and nitrite that accumulate within the recirculating system.  Scientists at the Conservation Fund’s Freshwater Institute in Shepherdstown, WV completed an evaluation of sand bed expansion and long-term nitrification within a full-scale fluidized-sand CycloBio(tm) biofilter.  The finest (D10 0.18 mm) sand tested within the full-scale fluidized-sand CycloBio(tm) biofilter, which expanded approximately 60% (i.e., the clean sand expansion) at a hydraulic loading rate of 0.77 cm/s (11 gpm/ft2), maintained a mean 92.2±0.7% total ammonia nitrogen(TAN) removal efficiency and a mean nitrite nitrogen concentration of 0.06±0.00 mg/L when makeup water flow rates ranged from 4-8% of total recirculating flow.  The results show that exceptionally low TAN and nitrite nitrogen concentrations, similar to that obtained in a single-pass system, can be achieved within large commercial recirculating salmonid systems that use fine sand fluidized-sand biofilters.

Integrated pest management of burrowing shrimp. Burrowing shrimp are serious pests on west coast oyster culture farms and formerly used chemical methods for controlling these shrimp are being phased out by legislation.   The Forage Seed and Cereal Research Unit, Corvallis, OR recruited a new research ecologist who entered on duty in May, 2004 and established laboratory and field operation capabilities that interface with the ARS oyster genetics program at Newport, OR.  This accomplishment integrated an ARS research team with other state and federal collaborators at the Hatfield Marine Science Center in Newport, OR with a mission to develop sustainable approaches to enhance west coast shellfish production. New integrated pest management strategies to control burrowing shrimp will permit continued and profitable production of oysters on west coast aquaculture farms.

Reduced costs to protect ponds from birds. A modified technique was devised to non-lethally exclude fish-eating birds from aquaculture ponds. Using two privately owned, commercial catfish farms within a few miles of the largest roosting colony of double-crested cormorants, ARS scientists at the HKD Stuttgart National Aquaculture Research Center, Stuttgart, AR  evaluated the effectiveness of modifying a low-cost, physical barrier system for deterring cormorants.  The modification limited the materials, setup time, and overall cost significantly and yielded similar significant results for limiting cormorant access to aquaculture ponds by 4 to 10 fold, prevented other fish-eating birds from landing at similar rates to complete exclusion at some ponds, and limited the duration cormorants stayed on ponds.  The modification involved changing a previously researched technique using a simple barrier of twine, flagging and t-posts.  This economical, nonlethal method is used by the industry.

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An alternative to saline water for shrimp culture. ARS scientists at the Aquaculture Systems Research Unit, Pine Bluff, AR amended the ionic composition of freshwater to achieve successful production of the Pacific white shrimp Litopenaeus vannamei in inland ponds. Culture of the Pacific white shrimp in inland ponds filled with low-salinity ground water is attracting attention as a means for farmers to diversify production and increase profits. However, the availability of low-salinity ground water may not necessarily be a requirement for channel catfish farmers considering shrimp culture as an alternative. L. vannamei was produced successfully in freshwater amended with potassium, magnesium, sulfate, sodium, and chloride ions. Shrimp yield was 3,078 lb/acre and individuals averaged 19.3 g each for the125-d study. Inland culture of marine shrimp could expand to areas that lack saline ground water.

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.

Liquids from fish processing contain valuable nutrients.  Over one million metric tons of fish processing by-products is produced each year from fish harvested in Alaska; however, much of this protein is not utilized and during the manufacturing of fish meal the soluble protein fraction, called stickwater, is often discarded. ARS scientists in the Subarctic Agriculture research Unit, Fairbanks, AK. determined the composition and properties of soluble protein generated during the production of fish meal and chemically and nutritionally characterized the stick water obtained from a commercial fish meal plant. Samples had high protein contents on a dry-basis of which approximately 25 % was connective tissue protein. Proteins in stick water were shown to have chemical and nutrient contents useful for development of food and non-food products. 

Liver separated from waste stream. Viscera, a major part of fish waste, contains substantial quantities of liver, and in Alaska most fish liver is made into fish meal and oil or discarded. Efforts to separate liver from other by-products during fish processing and utilizing them in high value products are lacking. ARS scientists at the Subarctic Agricultural Research Unit, Fairbanks, Alaska and collaborators examined the chemical content of liver protein isolated from six different species of cold water marine fish including Arrowtooth Flounder, Pacific Halibut , Alaska Pollock, Pink Salmon, Flathead Sole and Spiny Head Rock Fish.  Liver protein was of high nutritional quality and ranged from 18 to 7% of the fish weight. Liver protein from the six different species of fish was of similar chemical composition with useful nutrient values that can be exploited for commercialization.

Alaskan fish meal may be better than commercial source.  Replacement of traditional fish meals, which are often imported, with fish meals made from by products of the Alaska fish processing industry, will enhance the Alaskan economy. ARS scientists in the Subarctic Agricultural Research Unit, Fairbanks, AK and collaborators at the University of Alaska found that the nutritional quality of Alaska fish meal for Longfin amberjack was high in two growth trials. The growth and survival of the fish fed the diet containing the Alaska meal was similar to those fed the commercial feed and the liver lipid levels were lower in the Alaska fish meal feed than in those fed the commercial feed. The information will be used to persuade aquatic feed manufacturers to utilize fish waste meals from Alaska in fish diets.

Previously thought harmless alga cause fish kills. An alga, previously thought to be benign, has been associated with a series of fish kills in Mississippi, North Carolina, Texas, and Arkansas.  The causative organism has been identified and cultured by ARS scientists at the Catfish Genetics Unit, Stoneville, MS, in collaboration with NOAA's Harmful Algal Bloom Chemistry Staff who have identified a small molecular weight toxic fraction.  Identification of the mode of action, toxin identity, and resulting management recommendations during toxic bloom episodes is ongoing from this work. This alga is easily controlled by low copper sulfate additions, providing a simple management remedy for commercial fish farmers.

An alga that produces an anatoxin correlated with fish kills. VTC, visceral toxicosis of catfish, has killed 30-40% of brood fish during fall and winter in the four-state region.  This condition  was studied by ARS scientists at the Catfish Genetics Unit, Stoneville, MS in collaboration with scientists from the MSU College of Veterinary Medicine. An alga capable of anatoxin-a production has been correlated with these events.  Ongoing research includes exposure of fish to sub-acute doses to reproduce the fish responses; management alternatives will result from this research.

Natural algicide tested . Currently there are only two algicides, copper sulfate and diuron, registered for managing algae-related off-flavors in pond-raised catfish. Mississippi State scientists at the National Warm Water Aquaculture Center, Stoneville, MS cooperated with ARS scientists at the Natural Products Research Unit, Oxford, Mississippi, to identify and evaluate new algicides for use in managing algae-related off-flavors. One promising compound - a modified anthroquinone - 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. This compound is undergoing patent application.

Conditions established to observe the presence of viruses.  With "normal," single-celled bacteria, viruses lyse the cells when plated at high density and form a clearing called a plaque.  The cyanobacteria producing off-flavor compounds are not single cells, but rather they grow in long filaments that don't allow plaques to form.  ARS scientists at the Food Processing and Sensory Quality Unit, New Orleans, LA established methods to shear the filaments into smaller pieces. The plaque-forming capacity of environmental water samples can now be tested for viruses.. Viruses against cyanobacteria could be used as a strategy to control their growth and production of off-flavors compounds in pond water.  

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