Links between host genetics, metabolism, gut microbiome and amoebic gill disease (AGD) in Atlantic Salmon

Background: Rapidly spreading parasitic infections like amoebic gill disease (AGD) are increasingly problematic for Atlantic salmon reared in aquaculture facilities and potentially pose a risk to wild fish species in surrounding waters. Currently, it is not known whether susceptibility to AGD differs between wild and farmed salmon. Wild Atlantic salmon populations are declining and this emerging disease could represent an additional threat to their long-term viability. A better understanding of how AGD affects fish health is therefore relevant for the accurate assessment of the associated risk, both to farming and to the well-being of wild populations. In this study, we assessed the impact of natural exposure to AGD on wild, hybrid and farmed post-smolt Atlantic salmon reared in a sea farm together under common garden conditions. Results: Wild fish showed substantially higher mortality levels (64%) than farmed fish (25%), with intermediate levels for hybrid fish (39%) suggesting that AGD susceptibility has an additive genetic basis. Metabolic rate measures representing physiological performance were similar among the genetic groups but were significantly lower in AGD-symptomatic fish than healthy fish. Gut microbial diversity was significantly lower in infected fish. We observed major shifts in gut microbial community composition in response to AGD infections. In symptomatic fish the relative abundance of key taxa Aliivibrio, Marinomonas and Pseudoalteromonas declined, whereas the abundance of Polaribacter and Vibrio increased compared to healthy fish. Conclusions: Our results highlight the stress AGD imposes on fish physiology and suggest that low metabolic-rate fish phenotypes may be associated with better infection outcomes. We consider the role increased AGD outbreak events and a warmer future may have in driving secondary bacterial infections and in reducing performance in farmed and wild fish

Warming winters threaten peripheral Arctic charr populations of Europe

As the global climate warms, the fate of lacustrine fish is of huge concern, especially given their sensitivity as ectotherms to changes in water temperature. The Arctic charr (Salvelinus alpinus L.) is a salmonid with a Holarctic distribution, with peripheral populations persisting at temperate latitudes, where it is found only in sufficiently cold, deep lakes. Thus, warmer temperatures in these habitats particularly during early life stages could have catastrophic consequences on population dynamics. Here, we combined lake temperature observations, a 1-D hydrodynamic model, and a multi-decadal climate reanalysis to show coherence in warming winter water temperatures in four European charr lakes near the southernmost limit of the species’ distribution. Current maximum and mean winter temperatures are on average ~ 1 °C warmer compared to early the 1980s, and temperatures of 8.5 °C, adverse for high charr egg survival, have frequently been exceeded in recent winters. Simulations of winter lake temperatures toward century-end showed that these warming trends will continue, with further increases of 3–4 °C projected. An additional 324 total accumulated degree-days during winter is projected on average across lakes, which could impair egg quality and viability. We suggest that the perpetuating winter warming trends shown here will imperil the future status of these lakes as charr refugia and generally do not augur well for the fate of coldwater-adapted lake fish in a warming climate

Where the Lake Meets the Sea: Strong Reproductive Isolation Is Associated with Adaptive Divergence between Lake Resident and Anadromous Three-Spined Sticklebacks

Contact zones between divergent forms of the same species are often characterised by high levels of phenotypic diversity over small geographic distances. What processes are involved in generating such high phenotypic diversity? One possibility is that introgression and recombination between divergent forms in contact zones results in greater phenotypic and genetic polymorphism. Alternatively, strong reproductive isolation between forms may maintain distinct phenotypes, preventing homogenisation by gene flow. Contact zones between divergent freshwater-resident and anadromous stickleback (Gasterosteus aculeatus L.) forms are numerous and common throughout the species distribution, offering an opportunity to examine these contrasting hypotheses in greater detail. This study reports on an interesting new contact zone located in a tidally influenced lake catchment in western Ireland, characterised by high polymorphism for lateral plate phenotypes. Using neutral and QTL-linked microsatellite markers, we tested whether the high diversity observed in this contact zone arose as a result of introgression or reproductive isolation between divergent forms: we found strong support for the latter hypothesis. Three phenotypic and genetic clusters were identified, consistent with two divergent resident forms and a distinct anadromous completely plated population that migrates in and out of the system. Given the strong neutral differentiation detected between all three morphotypes (mean F-ST = 0.12), we hypothesised that divergent selection between forms maintains reproductive isolation. We found a correlation between neutral genetic and adaptive genetic differentiation that support this. While strong associations between QTL linked markers and phenotypes were also observed in this wild population, our results support the suggestion that such associations may be more complex in some Atlantic populations compared to those in the Pacific. These findings provide an important foundation for future work investigating the dynamics of gene flow and adaptive divergence in this newly discovered stickleback contact zone

Impacts of a record-breaking storm on physical and biogeochemical regimes along a catchment-to-coast continuum.

The impacts of changes in climate are often most readily observed through the effects of extremes in local weather, effects that often propagate through multiple ecosystem levels. Precise effects of any extreme weather event depend not only on the type of event and its timing, but also on the ecosystem affected. Here the cascade of effects following the arrival of an atmospheric river (directed by record-breaking Storm Desmond) across terrestrial, freshwater and coastal zones is quantified, using the Burrishoole system on the Atlantic coast of Ireland as a natural observatory. We used a network of high-frequency in-situ sensors to capture in detail the effects of an unprecedented period of rainfall, high wind speeds and above-average winter air temperatures on catchment and estuarine dynamics. In the main freshwater lake, water clarity decreased and acidity increased during Storm Desmond. Surface heat input, due to a warm and moist above-lake air mass, was rapidly distributed throughout the water column. River discharge into the downstream coastal basin was estimated to be the highest on record (since 1976), increasing the buoyancy flux by an order of magnitude and doubling the water column stratification stability. Entrainment of salt into the outflowing freshwater plume exported resident salt from the inner estuarine basin, resulting in net salt loss. Here, the increased stratification markedly reinforced isolation of the bottom waters, promoting deoxygenation. Measurements of current between the inner estuarine basin and the adjacent coastal waters indicated a 20-fold increase in the volume of seaward flowing low-salinity water, as a result of storm rainfall over the watershed. Storm impacts spanned the full catchment-to-coast continuum and these results provide a glimpse into a potential future for hydrological systems where these severe hydroclimatic events are expected to occur more frequently

Interim Report of the Working Group on Application of Genetics in Fisheries and Mariculture (WGAGFM): ToR b) Review and map decision channels for integrating WGAGFM advice into fisheries assessment and management

It is a scientific aim to integrate genetic monitoring and assessment methods into advice and management. There is, in principle, particular potential to implement advances in salient concepts and technologies into fisheries resource management, governance and policy formulation. The overall aim is to enhance the integration of genetic monitoring and assessment methods into advice and management. The nature and effectiveness of implementation processes, as well as a consideration of strategies to promote such integration within the context of the ICES structure and community and beyond will be considered. As such, the ToR provides an opportunity to review past and current impact of outputs generated via the annual WGAGFM meetings and associated activities.JRC.D.2-Water and Marine Resource

Additional file 1 of Links between host genetics, metabolism, gut microbiome and amoebic gill disease (AGD) in Atlantic salmon

Additional file 1: Table S1. Overview of the metabolic rate experiment. Sample_Id refers to individual fish. Sampling day refers to the day when fish were caught. Processing day refers to the day fish were dissected. Experiment day equals processing days, only in another format. Temperature refers to the water temperature at the sea pens on each sampling day. Table S2. First round PCR primers used for NGS library preparation. Table S3. Second round PCR primers used for NGS library preparation. Table S4. Mean length, weight and Fulton’s condition factor per genetic origin for 3 points in time (pre sea pen hatchery, date of sea pen transfer and at the termination point of the experiment). Table S5. ANCOVA results of the effect of AGD severity Score on weight adjusted SMR (left), MMR (middle) and AS (right) measures. Significance codes: *** < 0.001; ** < 0.01; * < 0.05. Table S6. Multiple comparisons of means of metabolic rate measures between different AGD severity scores (Tukey post-hoc for weight-adjusted model). Significance codes: ** < 0.01; * < 0.05. Table S7. Permanova results showing differences between gut microbial community compositions of starved and fed fish for two different timepoints T0 and T1 in PC samples. Significance codes: ** < 0.01; * < 0.05. Table S8. Permanova results showing differences between gut microbial community compositions of starved and fed fish for two different timepoints T0 and T1 in MG samples. Significance codes: ** < 0.01; * < 0.05. Table S9. Linear model for Chao1 richness estimates in MG samples calculated by the interaction term of AGD severity score and genetic origin. AGD severity of 0 and farmed origin served as baseline for comparisons. Significance codes: *** < 0.001; ** < 0.01; * < 0.05. Table S10. Permutational analysis of variance (PERMANOVA) results testing the effect of AGD severity score, genetic origin and processing day (day of gut dissection) on pyloric caeca (PC) microbial community composition based on weighted unifrac distance matrices. Table S11. Permanova of pairwise comparisons of PC samples grouped by day of their processing. Distance matrix calculated by weighted UniFrac measure. Permutations used: 9999. Significance codes: *** < 0.001; ** < 0.01; * < 0.05. Table S12. Permutational analysis of variance (PERMANOVA) results testing the effect of AGD severity score, genetic origin and processing day (day of gut dissection) on midgut (MG) microbial community composition based on weighted unifrac distance matrices. Table S13. Permutational analysis of variance (PERMANOVA) testing pairwise comparisons for midgut (MG) samples from different AGD severity groups. Distance matrix calculated by weighted UniFrac measure. Permutations used: 9999. Significance codes: **p < 0.01; *p < 0.05

Additional file 2 of Links between host genetics, metabolism, gut microbiome and amoebic gill disease (AGD) in Atlantic salmon

Additional file 2: Fig. S1. Percent water content of fish from different origins during the sea pen experiments. Data derived from fish of mixed (4th) sentinel pen over the course of the experiment. Significance was determined by pairwise t-testing against fish from farmed origin. F = Farmed, HFF = Hybrid Farmed Female, HWF = Hybrid Wild Female, W = Wild, Significance codes: ***p < 0.001; **p < 0.01. Fig. S2. Stacked bar plot showing the mean relative abundance of gut microbiota on phylum level for recently fed fish, starved fish (48 h feed withdrawal) and environmental control samples (feed and marine water (MW))

shape_analyses_data

Data used for shape analysis used in Ravinet et al (2015) MS. Excel file contains data for shape and measured traits (raw and size corrected). See Ravinet et al (2015) MS for details

bur_plate_loc - Genotypic microsatellite data in GENEPOP format

Genotypic microsatellite data (GENEPOP) format used in Ravinet et al (2015) MS. File contain genotypic data for 14 microsatellite data four for population samples. See original MS for detail

Half a century of genetic interaction between farmed and wild Atlantic salmon: Status of knowledge and unanswered questions

Atlantic salmon (Salmo salar) is one of the best researched fishes, and its aquaculture plays a global role in the blue revolution. However, since the 1970s, tens of millions of farmed salmon have escaped into the wild. We review current knowledge of genetic interactions and identify the unanswered questions. Native salmon populations are typically genetically distinct from each other and potentially locally adapted. Farmed salmon represent a limited number of wild source populations that have been exposed to ≥12 generations of domestication. Consequently, farmed and wild salmon differ in many traits including molecular-genetic polymorphisms, growth, morphology, life history, behaviour, physiology and gene transcription. Field experiments have demonstrated that the offspring of farmed salmon display lower lifetime fitness in the wild than wild salmon and that following introgression, there is a reduced production of genetically wild salmon and, potentially, of total salmon production. It is a formidable task to estimate introgression of farmed salmon in wild populations where they are not exotic. New methods have revealed introgression in half of ~150 Norwegian populations, with point estimates as high as 47%, and an unweighted average of 6.4% across 109 populations. Outside Norway, introgression remains unquantified, and in all regions, biological changes and the mechanisms driving population-specific impacts remain poorly documented. Nevertheless, existing knowledge shows that the long-term consequences of introgression is expected to lead to changes in life-history traits, reduced population productivity and decreased resilience to future challenges. Only a major reduction in the number of escapees and/or sterility of farmed salmon can eliminate further impacts. aquaculture, evolution, fish farming, fitness, genetic, hybri