Characterization of gill bacterial microbiota in wild Arctic char (Salvelinus alpinus) across lakes, rivers, and bays in the Canadian Arctic ecosystems

Abstract

Teleost gill mucus has a highly diverse microbiota, which plays an essential role in the host's fitness and is greatly influenced by the environment. Arctic char (Salvelinus alpinus), a salmonid well adapted to northern conditions, faces multiple stressors in the Arctic, including water chemistry modifications, that could negatively impact the gill microbiota dynamics related to the host's health. In the context of increasing environmental disturbances, we aimed to characterize the taxonomic distribution of transcriptionally active taxa within the bacterial gill microbiota of Arctic char in the Canadian Arctic in order to identify active bacterial composition that correlates with environmental factors. For this purpose, a total of 140 adult anadromous individuals were collected from rivers, lakes, and bays belonging to five Inuit communities located in four distinct hydrologic basins in the Canadian Arctic (Nunavut and Nunavik) during spring (May) and autumn (August). Various environmental factors were collected, including latitudes, water and air temperatures, oxygen concentration, pH, dissolved organic carbon (DOC), salinity, and chlorophyll-a concentration. The taxonomic distribution of transcriptionally active taxa within the gill microbiota was quantified by 16S rRNA gene transcripts sequencing. The results showed differential bacterial activity between the different geographical locations, explained by latitude, salinity, and, to a lesser extent, air temperature. Network analysis allowed the detection of a potential dysbiosis signature (i.e., bacterial imbalance) in fish gill microbiota from Duquet Lake in the Hudson Strait and the system Five Mile Inlet connected to the Hudson Bay, both showing the lowest alpha diversity and connectivity between taxa.IMPORTANCEThis paper aims to decipher the complex relationship between Arctic char (Salvelinus alpinus) and its symbiotic microbial consortium in gills. This salmonid is widespread in the Canadian Arctic and is the main protein and polyunsaturated fatty acids source for Inuit people. The influence of environmental parameters on gill microbiota in wild populations remains poorly understood. However, assessing the Arctic char's active gill bacterial community is essential to look for potential pathogens or dysbiosis that could threaten wild populations. Here, we concluded that Arctic char gill microbiota was mainly influenced by latitude and air temperature, the latter being correlated with water temperature. In addition, a dysbiosis signature detected in gill microbiota was potentially associated with poor fish health status recorded in these disturbed environments. With those results, we hypothesized that rapid climate change and increasing anthropic activities in the Arctic might profoundly disturb Arctic char gill microbiota, affecting their survival.

Keywords: 16S rRNA gene transcripts; Arctic char; Canadian Arctic; bacterial activity; fish; gill microbiota; microbial ecology.

Fig 1

Maps of the fishing sites with the location of the main Inuit communities in Kativik, Nunavik: Hudson Strait (Salluit), Ungava Bay (Kangiqsualujjuaq), and Hudson Bay (Akulivik and Inukjuak) and in Kikmeot, Nunavut: Cambridge Bay (Ekaluktutiak) (A). Fishing sites in Ekaluktutiak were CBL5 (n = 7), the three connected lakes Greiner (n = 25), first (n = 12), second (n = 12), and the bay (n = 7) (B). In Akulivik, the three rivers Chukotat (n = 3), Saparuajuiit (n = 3), and Korak (n = 7) were sampled (C). In Salluit, Duquet Lake (n = 24) was the only fishing site (D), and in Inukjuak, the fishing site was Five Mile Inlet (n = 25) (E). Fish coming from Koroc (n = 5) and George (n = 10) rivers in Kangiqsualujjuaq were also used for this project (F). A total of 140 anadromous Arctic char were caught in freshwater (FW) and saltwater (SW) sites across the Canadian Arctic. Maps were created using the “leaflet” package on RStudio and manually modified in Inkscape.

Fig 2

Relative activity of the 50 most abundant transcripts (ASVs) at family rank found in the microbiota of the Arctic char’s gills across the five different communities Ekaluktutiak (EK), Salluit (SA), Akulivik (AK), Inukjuak (IN), and Kangiqsualujjuaq (KG). The relative activity of ASVs in the microbiota was highly heterogeneous between sites, with different species predominating.

Fig 3

Heatmap of ASVs’ relative activity in the gills’ microbiota of Arctic char in five different communities in the Arctic. The visualization was performed with METAGENassist. In blue are transcripts with low abundance (active ASVs), and in red are transcripts with high abundance (active ASVs). The y-axis represents all community samples, and the x-axis represents all the 307 ASVs obtained after filtration. Ekaluktutiak (EK) samples were represented in green, Salluit (SA) in pink, Akulivik (AK) in red, Inukjuak (IN) in blue, and Kangiqsualujjuaq (KG) in turquoise. A pattern of an active ASV group in Ekaluktutiak showed a potentially important difference in bacterial activity in Arctic char gill microbiota between this site and the four other groups.

Fig 4

Alpha diversity. Boxplot of the Pielou index (A), the Chao1 index (B), and the species richness with Faith’s diversity index (C) across the five communities Ekaluktutiak (EK), Salluit (SA), Akulivik (AK), Inukjuak (IN), and Kangiqsualujjuaq(KG). One star indicates a significative P-value <0.05; two stars indicate a P-value <0.01, and three stars indicate a P-value <0.001. Sites from Salluit and Inukjuak showed the lowest bacterial alpha diversity in richness and evenness.

Fig 5

Beta diversity. Principal coordinates analysis of the samples from the five different communities in the Arctic: Ekaluktutiak (green), Salluit (pink), Akulivik (orange), Inukjuak (blue), and Kangiqsualujjuaq (turquoise). The weighted UniFrac distances were used to construct PCoA, and a multivariate analysis of variance with 9,999 permutations was performed to obtain the P-value. Relative ASV activity in Ekaluktutiak (axis 1) and Salluit (axis 2) significantly differed from the three other groups.

Fig 6

Beta diversity. NMDS on weighted UniFrac distances with environmental independent parameters fitted. The environmental parameters were represented across the samples from the five different communities in the Arctic: Ekaluktutiak (green), Salluit (pink), Akulivik (orange), Inukjuak (blue), and Kangiqsualujjuaq (turquoise). Latitude and air temperature were significantly correlated to the bacterial relative activity in Arctic char gill microbiota.

Fig 7

Microbial interaction networks at the five different geographic sites: Ekaluktutiak (green), Akulivik (orange), Salluit (pink), Kangiqsualujjuaq (turquoise), and Inukjuak (blue). Spearman’s correlations between the different ASVs at a genus rank, with a score <−0.4 (red edges) and >0.4 (green edges) and with a P-value adjusted with false discovery rate <0.05, were represented in the networks. The correlation score scales with the thickness of the edge. Each node is a genus; its size varies with its activity, and its color changes with its phylum. Ekaluktutiak was the most connected network, showing a resilient pattern, while Salluit and Inukjuak showed the lowest number of interactions.