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

Amill, Flora; Gauthier, Jeff; Rautio, Milla; Derome, Nicolas

doi:10.1128/spectrum.02943-23

Cited by 2 publications

(1 citation statement)

References 171 publications

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“…The tapbt gene, located adjacent to the daxx gene in the MHC region on chromosome 14 and showing selection signatures in both populations, showed low expression in most tissues in the healthy fish. This gene was, though, moderately expressed in the gill (Figure 4), which acts as a gateway for potential pathogens, highlighting its potential role in the immune response (Amill et al, 2024). It is reported that tapbt expression is upregulated in a rainbow trout monocyte/macrophage cell line in response to viral infection (Sever et al, 2014).…”

Section: Srp011583) Of European Atlantic Salmon (Materials and Methods)mentioning

confidence: 98%

Parallel selection in domesticated Atlantic salmon from divergent founders including parallel selection on WGD-derived homeologous regions

Buso,

Diblasi,

Manousi

et al. 2024

Preprint

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Aquaculture has a considerably shorter history compared to the domestication of plants and animals. Among aquatic species, those that have undergone whole genome duplication events (WGD) seem to have been particularly successful, suggesting that the genetic redundancy created by WGD is important for domestication, possibly similar to plant domestication. Atlantic salmon (Salmo salar), which has experienced a lineage specific WGD, has undergone independent domestications across different phylogeographical lineages since the 1960s, exemplifying rapid domestication through intensive breeding. This provides an opportunity to understand the potential and constraints acting on adaptation. Here, we examined the genomic responses to the domestication of Atlantic salmon, including the impacts of WGD, by comparing the whole genome sequence data of aquaculture and wild populations from two lineages: the Eastern and Western Atlantic (Western Norway and North America). Our analysis revealed shared selective sweeps on identical SNPs in major histocompatibility complex (MHC) genes across distinct aquaculture populations compared to their wild counterparts. This SNP level parallelism suggests that a combination of long-term balancing selection and recent human-induced selection has significantly shaped the evolutionary trajectory of MHC genes. In addition, we observed selective sweeps on gene pairs in the homeologous regions originating from WGD, highlighting WGD's role in maintaining genomic variation and potentially reducing pleiotropy through sub-functionalization. This unique type of "parallel" selection contributes to adapting to the intensive artificial conditions of aquaculture. These findings provide valuable insights into the genetic mechanisms of domestication and adaptive responses in Atlantic salmon, suggesting that the salmonid whole genome duplication has underpinned their successful rapid domestication. Our research emphasizes the importance of maintaining genetic diversity to support sustainable aquaculture practices.

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Section: Srp011583) Of European Atlantic Salmon (Materials and Methods)mentioning

confidence: 98%

Parallel selection in domesticated Atlantic salmon from divergent founders including parallel selection on WGD-derived homeologous regions

Buso,

Diblasi,

Manousi

et al. 2024

Preprint

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Hatchery type influences the gill microbiome of Atlantic farmed salmon (Salmo salar) after transfer to sea

Katchkin-Stewart,

Boerlage,

Barr

et al. 2024

Preprint

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Background Salmon aquaculture involves freshwater and seawater phases. Recently there has been an increase in multifactorial gill health challenges during the seawater phase which has led to an urgent need to understand the gill microbiome. There is a lack of understanding on what drives the composition of the gill microbiome, and the influence the freshwater stage has on its long-term composition. We characterise the gill microbiome from seven cohorts of Atlantic salmon raised in six different freshwater operational systems - recirculating aquaculture system (RAS), flowthrough (FT) and loch-based system, prior to and after transfer to seven seawater farms, over two different input seasons, S0 (2018) and S1 (2019). Results Using the V1-V2 region of the 16S rRNA gene, we produced amplicon libraries absent of host contamination. We show that hatchery system influenced the gill microbiome (PERMAOVA R2 = 0.226, P < 0.001). Loch and FT systems were more similar to each other than the three RAS systems, which clustered together. On transfer to sea, the gill microbiomes of all fish changed and became more similar irrespective of initial hatchery system, seawater farm location or season of input. Even though the gill microbiome among seawater farm locations was different between locations (PERMAOVA R2 = 0.528, P < 0.001), a clustering of the gill microbiomes by hatchery system of origin was still observed soon after transfer (PERMAOVA R = 0.164, P < 0.001). Core microbiomes were found between all salmon, hatcheries and seawater groups at a genus level, and at ASV level among FT and loch systems; and again among all seawater farms. The gill microbiome and surrounding water at each hatchery had more shared ASVs than seawater farms. Conclusion We show that hatchery system, loch, FT or RAS, significantly impacts the gill microbiome. On transfer to sea, the microbiomes change and become more similar. After transfer, the individual sites to which the fish are transferred become a significant driver, while a signature from the hatchery operation system remains. Future gill disease mitigation methods that target enhancing the gill microbiome may be most effective in the freshwater stage, as there were more shared ASVs between water and gill at hatchery, compared to at sea.

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

Cited by 2 publications

References 171 publications

Parallel selection in domesticated Atlantic salmon from divergent founders including parallel selection on WGD-derived homeologous regions

Parallel selection in domesticated Atlantic salmon from divergent founders including parallel selection on WGD-derived homeologous regions

Hatchery type influences the gill microbiome of Atlantic farmed salmon (Salmo salar) after transfer to sea

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