Life History, Biogeography, and Functional Parallelism in the Wild Salmo salar Intestinal Microbiome

Atlantic salmon are an anadromous salmonid species with an extensive wild distribution in the northern hemisphere. Atlantic salmon are also an important aquaculture species globally. Commensal microbiota that colonise and cohabit the bodies of vertebrate organisms are known to play crucial roles in host development, health, and nutrition. We employ 16S amplicon profiling and shotgun metagenomic sequencing to explore gut microbiome taxomomic diversity and functional parallelism between S. salar populations at different geographic scales and life cycle stages. Metagenomes are derived from four juvenile freshwater populations (Canada, Ireland) as well as from marine adults at feeding grounds off Sisimiut, West Greenland. Taxonomic comparisons between sites and life cycles stages establish local patterns of bacterial recruitment and longitudinal microbiome stability. Functional parallelism between fresh water metagenomes, as well as between fresh and salt-water metagenomes, is explored. Selection regimes between housekeeping (e.g. DNA repair, transcriptional machinery) and candidate gene (chitinases, peptidases) loci are compared at a nucleotide level. Our data indicate: key bacterial species that comprise the S. salar intestinal microbiome; key ecological services provided by the S. salar microbiome to the species in terms of nutritional health; a biogeoghapic baseline for microbiome functional variability to support future fishery management practices.