Dataset Information

A comparison of neutral and immune genetic variation in Atlantic salmon, Salmo salar L. in Chilean aquaculture facilities.

ABSTRACT: Genetic diversity was assessed in samples of cultured Atlantic salmon, Salmo salar L., obtained from facilities in Chile between 2005 and 2010, a period of time during which the infectious pathogens Infectious Salmon Anemia (ISA) virus, Caligus rogercresseyi (sea lice), and Piscirickettsia salmonis (salmon rickettsial syndrome) were common. Two panels of microsatellite markers were utilized: one with microsatellites with no known gene associations (neutral) and one featuring microsatellites linked to putative immune-related genes (immune-related). Allelic richness and gene diversity across samples were significantly greater in neutral loci as compared to immune-related loci. Both diversity measures were homogeneous among samples for immune-related loci and heterogeneous among samples for neutral loci. Immune-related loci were identified as F(ST) outliers in pairwise comparisons of samples at a 10-fold higher frequency than neutral loci. These results indicate that neutral and immune-related portions of the Atlantic salmon genome may have differed in response to the gauntlet of pathogens and that monitoring of specific, well characterized immune-related loci as well as neutral loci in cultured species could be useful when disease control and prevention is a goal.

SUBMITTER: Portnoy DS

PROVIDER: S-EPMC4053429 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature

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A comparison of neutral and immune genetic variation in Atlantic salmon, Salmo salar L. in Chilean aquaculture facilities.

Portnoy David S DS Hollenbeck Christopher M CM Vidal R Rodrigo RR Gold John R JR

PloS one 20140611 6

Genetic diversity was assessed in samples of cultured Atlantic salmon, Salmo salar L., obtained from facilities in Chile between 2005 and 2010, a period of time during which the infectious pathogens Infectious Salmon Anemia (ISA) virus, Caligus rogercresseyi (sea lice), and Piscirickettsia salmonis (salmon rickettsial syndrome) were common. Two panels of microsatellite markers were utilized: one with microsatellites with no known gene associations (neutral) and one featuring microsatellites link ...[more]

PMID: 24918941

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Project description:UnlabelledReliance on fishmeal as a primary protein source is among the chief economic and environmental concerns in aquaculture today. Fishmeal-based feeds often require harvest from wild fish stocks, placing pressure on natural ecosystems and causing price instability. Alternative diet formulations without the use of fishmeal provide a potential solution to this challenge. Although the impact of alternative diets on fish performance, intestinal inflammation, palatability, and gut microbiota has been a topic of recent interest, less is known about how alternative feeds impact the aquaculture environment as a whole. The recent focus on recirculating aquaculture systems (RAS) and the closed-containment approach to raising food fish highlights the need to maintain stable environmental and microbiological conditions within a farm environment. Microbial stability in RAS biofilters is particularly important, given its role in nutrient processing and water quality in these closed systems. If and how the impacts of alternative feeds on microbial communities in fish translate into changes to the biofilters are not known. We tested the influence of a fishmeal-free diet on the microbial communities in RAS water, biofilters, and salmon microbiomes using high-throughput 16S rRNA gene V6 hypervariable region amplicon sequencing. We grew Atlantic salmon (Salmo salar) to market size in six replicate RAS tanks, three with traditional fishmeal diets and three with alternative-protein, fishmeal-free diets. We sampled intestines and gills from market-ready adult fish, water, and biofilter medium in each corresponding RAS unit. Our results provide data on how fish diet influences the RAS environment and corroborate previous findings that diet has a clear influence on the microbiome structure of the salmon intestine, particularly within the order Lactobacillales (lactic acid bacteria). We conclude that the strong stability of taxa likely involved in water quality processing regardless of diet (e.g., Nitrospira) may further alleviate concerns regarding the use of alternative feeds in RAS operations.ImportanceThe growth of the aquaculture industry has outpaced terrestrial livestock production and wild-capture fisheries for over 2 decades, currently producing nearly 50% of all seafood consumed globally. As wild-capture fisheries continue to decline, aquaculture's role in food production will grow, and it will produce an estimated 62% of all seafood consumed in 2020. A significant environmental concern of the industry is the reliance on fishmeal as a primary feed ingredient, as its production still requires harvest from wild fisheries. Our study adds to the growing body of literature on the feasibility of alternative, fishmeal-free diets. Specifically, we asked how fishmeal-free diets influence microbial communities in recirculating salmon farms. Unlike previous studies, we extended our investigation beyond the microbiome of the fish itself and asked how alterative diets influence microbial communities in water and critical biofilter habitats. We found no evidence for adverse effects of alternative diets on any microbial habitat within the farm.

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Dataset Information

A comparison of neutral and immune genetic variation in Atlantic salmon, Salmo salar L. in Chilean aquaculture facilities.

Publications

A comparison of neutral and immune genetic variation in Atlantic salmon, Salmo salar L. in Chilean aquaculture facilities.

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