Anadromous Arctic Char Microbiomes: Bioprospecting in the High Arctic

Abstract

Northern populations of Arctic char ( Salvelinus alpinus ) can be anadromous, migrating annually from the ocean to freshwater lakes and rivers in order to escape sub-zero temperatures. Such seasonal behavior demands that these fish and their associated microbiomes adapt to changes in salinity, temperature, and other environmental challenges. We characterized the microbial community composition of anadromous S. alpinus , netted by Inuit fishermen at freshwater and seawater fishing sites in the high Arctic, both under ice and in open water. Bacterial profiles were generated by DNA extraction and high-throughput sequencing of PCR-amplified 16S ribosomal RNA genes. Results showed that microbial communities on the skin and intestine of Arctic char were statistically different when sampled from freshwater or saline water sites. This association was tested using hierarchical Ward's linkage clustering, showing eight distinct clusters in each of the skin and intestinal microbiomes, with the clusters reflecting sampling location between fresh and saline environments, confirming a salinity-linked turnover. This analysis also provided evidence for a core composition of skin and intestinal bacteria, with the phyla Proteobacteria, Firmicutes, and Cyanobacteria presenting as major phyla within the skin-associated microbiomes. The intestine-associated microbiome was characterized by unidentified genera from families Fusobacteriaceae, Comamonadaceae, Pseudomonadaceae, and Vibrionaceae. The salinity-linked turnover was further tested through ordinations that showed samples grouping based on environment for both skin- and intestine-associated microbiomes. This finding implies that core microbiomes between fresh and saline conditions could be used to assist in regulating optimal fish health in aquaculture practices. Furthermore, identified taxa from known psychrophiles and with nitrogen cycling properties suggest that there is additional potential for biotechnological applications for fish farm and waste management practices.

Distinct intestinal microbial communities of two sympatric anadromous Arctic salmonids and the effects of migration and feeding

“…In all, fish were netted at five different sites within the Kitikmeot region of Nunavut, Canada by Inuit fishers from the hamlet of Gjoa Haven (Table 1). Collection and processing of fish samples have been described in detail (Hamilton et al, 2019;Element et al, 2020) but briefly, morphometric data was collected, parasites were noted, otoliths for age interpretation were processed (Casselman, 2015;Casselman et al, 2019), and tissue samples including skeletal muscle and intestines were dissected from the fish on-site using sterile technique (tissue was excised with fillet knives, scalpels and tweezers that were soaked in ethanol and flamed). Tissue samples were placed in sterile sample bags and immediately frozen in an on-site freezer at -20°C for shipment to the laboratory with frozen cold packs, and stored at -20 °C until further processing.…”

“…S10 in Element et al, 2020). The use of NTCs and replicate samples, as well as removal of contaminant OTUs and rarefaction of this OTU table have been described in more detail previously (Hamilton et al, 2019;Element et al, 2020). Sequences have been deposited at the European Bioinformatics Institute (EBI) database under accession numbers PRJEB29173 and PRJEB31040.…”

“…Statistical analyses have been described previously in detail with citations (Hamilton et al, 2019;Element et al, 2020). Concisely, these included univariate diversity metrics Chao1 and Shannon diversity measures, and stepwise model selection with R (ver.…”

“…It is possible that the internal microbiota of these two salmonids are similar since habitat and behavior appear to be primary drivers of bacterial community composition. For example, in Arctic char, gut bacterial communities change when the fish migrate seasonally between different habitats (Hamilton et al, 2019;Element et al, 2020), although habitat alone does not explain most variation in community composition. Other variables that could play a role in defining the gut microbial community include genetics and diet.…”

“…Rather, mechanical avoidance of non-epithelial material with scalpel and tweezers (ethanol and flame sterilized) meant that both adherent and non-adherent microbes present in the lumen were theoretically included in the sample, but with a prioritization of those adherent and proximal to the epithelium. The three intestinal tissue subsamples were subsequently pooled and subjected to DNA extraction using commercial kits (Hamilton et al, 2019;Element et al, 2020). A pre-amplification step targeting the bacterial 16S rRNA V1-V9 region, followed by the amplification of the V4-V5 region, with a subsequent agarose gel purification step, allowed the recovery of a final amplification products with a relatively modest amount of contamination from salmonid mitochondrial DNA.…”