Parental thermal environment controls the offspring phenotype in Brook charr (Salvelinus fontinalis): insights from a transcriptomic study.

Brook charr is a cold-water species which is highly sensitive to increased water temperatures, such as those associated with climate change. Environmental variation can potentially induce phenotypic changes that are inherited across generations, for instance, via epigenetic mechanisms. Here, we tested whether parental thermal regimes (intergenerational plasticity) and offspring-rearing temperatures (within-generational plasticity) modify the brain transcriptome of Brook charr progeny (fry stage). Parents were exposed to either cold or warm temperatures during final gonad maturation and their progeny were reared at 5 or 8 °C during the first stages of development. Illumina Novaseq6000 was used to sequence the brain transcriptome at the yolk sac resorption stage. The number of differentially expressed genes was very low when comparing fry reared at different temperatures (79 differentially expressed genes). In contrast, 9,050 differentially expressed genes were significantly differentially expressed between fry issued from parents exposed to either cold or warm temperatures. There was a significant downregulation of processes related to neural and synaptic activity in fry originating from the warm parental group vs fry from the cold parental one. We also observed significant upregulation of DNA methylation genes and of the most salient processes associated with compensation to warming, such as metabolism, cellular response to stress, and adaptive immunity.

Transgenerational effects on body size and survival in Brook charr (Salvelinus fontinalis).

Higher temperatures are now observed in several ecosystems and act as new selective agents that shape traits and fitness of individuals. Transgenerational effects may be important in modulating adaptation of future generations and buffering negative impacts of temperature changes. The potential for these effects may be important in freshwater fish species, as temperature is a key abiotic component of their environment. Yet, still, relatively few studies have assessed the presence and importance of transgenerational effects under natural conditions. The purpose of this study was to test how parental thermal conditions influenced offspring growth and survival following stocking in Brook charr (Salvelinus fontinalis). To do so, part of the breeders were exposed to a "cold" treatment while others were exposed to a "warm" treatment during the final steps of gonad maturation (constant 2°C difference between treatments along the seasonal temperature decrease). The impact on offspring of a selection treatment targeting production traits of interest (absence of sexual maturation at 1+, combined with increased growth) in breeders was also evaluated. After 7-8 months of growth in captivity, offspring were stocked in natural lakes. Their growth and survival were assessed about a year later. Offspring from "cold" breeders showed lower survival than those from "warm" breeders and the selection treatment had no effect on survival. However, the selection treatment was linked to lower Fulton's condition index, which, in turn, was positively correlated to survival in lakes. This study highlights the importance of working in ecological/industrial context to fully assess the different impacts of transgenerational effects on traits and survival. Our results also have important implications for stocking practices used to support the sport fishing industry.

A first glimpse of larval ecology of halibut species in the Gulf of St. Lawrence, Canada.

Knowledge of the larval ecology of winter-spawning fish from the Estuary and Gulf of St. Lawrence, Canada, remains scarce due to the seasonal ice cover that prevents ichthyoplankton sampling using conventional methods. Two winter-spawning species, Atlantic halibut (AH, Hippoglossus hippoglossus) and Greenland halibut (GH, Reinhardtius hippoglossoides), support the most important groundfish fisheries of this area. In March 2020, the authors captured 10 halibut larvae ranging in size from 5 to 14 mm during an opportunistic survey in the GSL onboard an icebreaking vessel. Of these, eight were AH and two GH. Judging by their very small size, the larvae were only a few days old, suggesting that the spawning grounds are close to the capture sites. This effort constitutes a first step in validating the putative spawning areas for these two important GSL stocks. This knowledge is important for the conservation and sustainable management of these fisheries.

Growth regulation in brook charr Salvelinus fontinalis.

Fish growth can be modulated through genetic selection. However, it is not known whether growth regulatory mechanisms modulated by genetic selection can provide information about phenotypic growth variations among families or populations. Following a five-generation breeding program that selected for the absence of early sexual maturity and increased growth in brook charr we aimed to understand how the genetic selection process modifies the growth regulatory pathway of brook charr at the molecular level. To achieve this, we studied the regulation of growth traits at three different levels: 1) between lines-one under selection, the other not, 2) among-families expressing differences in average growth phenotypes, which we termed family performance, and 3) among individuals within families that expressed extreme growth phenotypes, which we termed slow- and fast-growing. At age 1+, individuals from four of the highest performing and four of the lowest performing families in terms of growth were sampled in both the control and selected lines. The gene expression levels of three reference and ten target genes were analyzed by real-time PCR. Results showed that better growth performance (in terms of weight and length at age) in the selected line was associated with an upregulation in the expression of genes involved in the growth hormone (GH)/insulin growth factor-1 (IGF-1) axis, including the igf-1 receptor in pituitary; the gh-1 receptor and igf-1 in liver; and ghr and igf-1r in white muscle. When looking at gene expression within families, family performance and individual phenotypes were associated with upregulations of the leptin receptor and neuropeptid Y-genes related to appetite regulation-in the slower-growing phenotypes. However, other genes related to appetite (ghrelin, somatostatin) or involved in muscle growth (myosin heavy chain, myogenin) were not differentially expressed. This study highlights how transcriptomics may improve our understanding of the roles of different key endocrine steps that regulate physiological performance. Large variations in growth still exist in the selected line, indicating that the full genetic selection potential has not been reached.

Thermal regime during parental sexual maturation, but not during offspring rearing, modulates DNA methylation in brook charr (Salvelinus fontinalis).

Epigenetic inheritance can result in plastic responses to changing environments being faithfully transmitted to offspring. However, it remains unclear how epigenetic mechanisms such as DNA methylation can contribute to multigenerational acclimation and adaptation to environmental stressors. Brook charr (Salvelinus fontinalis), an economically important salmonid, is highly sensitive to thermal stress and is of conservation concern in the context of climate change. We studied the effects of temperature during parental sexual maturation and offspring rearing on whole-genome DNA methylation in brook charr juveniles (fry). Parents were split between warm and cold temperatures during sexual maturation, mated in controlled breeding designs, then offspring from each family were split between warm (8°C) and cold (5°C) rearing environments. Using whole-genome bisulfite sequencing, we found 188 differentially methylated regions (DMRs) due to parental maturation temperature after controlling for family structure. By contrast, offspring rearing temperature had a negligible effect on offspring methylation. Stable intergenerational inheritance of DNA methylation and minimal plasticity in progeny could result in the transmission of acclimatory epigenetic states to offspring, priming them for a warming environment. Our findings have implications pertaining to the role of intergenerational epigenetic inheritance in response to ongoing climate change.

Evaluation of different extractions for the metabolite identification of malachite green in brook trout and shrimp.

Applications of mass spectrometry-based metabolomics in food science have developed fast in the last decade. Sample preparation and data processing are critical in non-target/metabolomic workflows but there is currently no standardized protocol for the development of these methods. The impact of data processing parameters or the inclusion of a different matrix is not often taken into account during the selection of an extraction. Thus, this study aimed to investigate the impact of different extractions, e.g., QuEChERS, and data processing on the determination of malachite green metabolites in two different organisms, brook trout and shrimp. The results obtained confirm the need for a harmonized approach for the validation of non-target workflows, as depending on the comparison criteria, the matrix, the mode of ionization or data processing, a different extraction could be chosen. This study also identified for the first time des-methylated leucomalachite green as another metabolite in the two organisms.

Chromosome-level assembly reveals a putative Y-autosomal fusion in the sex determination system of the Greenland Halibut (Reinhardtius hippoglossoides).

Despite the commercial importance of Greenland Halibut (Reinhardtius hippoglossoides), important gaps still persist in our knowledge of this species, including its reproductive biology and sex determination mechanism. Here, we combined single-molecule sequencing of long reads (Pacific Sciences) with chromatin conformation capture sequencing (Hi-C) data to assemble the first chromosome-level reference genome for this species. The high-quality assembly encompassed more than 598 Megabases (Mb) assigned to 1594 scaffolds (scaffold N50 = 25 Mb) with 96% of its total length distributed among 24 chromosomes. Investigation of the syntenic relationship with other economically important flatfish species revealed a high conservation of synteny blocks among members of this phylogenetic clade. Sex determination analysis revealed that similar to other teleost fishes, flatfishes also exhibit a high level of plasticity and turnover in sex determination mechanisms. A low-coverage whole-genome sequence analysis of 198 individuals revealed that Greenland Halibut possesses a male heterogametic XY system and several putative candidate genes implied in the sex determination of this species. Our study also suggests for the first time in flatfishes that a putative Y-autosomal fusion could be associated with a reduction of recombination typical of the early steps of sex chromosome evolution.

Application of non-target analysis to study the thermal transformation of malachite and leucomalachite green in brook trout and shrimp.

The fate of malachite green and its main metabolite leucomalachite green during thermal treatment was examined in seafood (brook trout and white shrimp) using non-target analysis. Samples were extracted using QuEChERS and analyzed using liquid chromatography coupled with quadruple time of flight mass spectrometry. Malachite green levels were reduced in meat during boiling (∼40%), microwaving (64%), and canning (96%). Only microwaving was successful in significantly decreasing leucomalachite green levels in brook trout. The reduction percentages of the two target analytes were not significantly different in shrimp (mean fat content = 0.8 ± 0.3%) and in brook trout (mean fat content = 3.5 ± 1.7%), suggesting that a higher fat content may not affect the reduction of the more lipophilic leucomalachite green in these two matrices. Three transformation products were tentatively identified in the cooked tissues, resulting from the cleavage of the conjugated structure or through demethylation. Further research is needed to determine possible adverse health effects. The findings of this study show how non-target analysis can complement targeted methodologies in identifying and evaluating risks to human health.

Under ice spills of conventional crude oil and diluted bitumen: Physiological resilience of the blue mussel and transgenerational effects.

Spillages at sea of diluted bitumen (dilbit) from oil sands have received little attention until now. To our best knowledge, there are no reports on the impact of a severe exposure to dilbit on the Blue mussel (Mytilus edulis). In this study, adult Blue mussels were exposed to one conventional crude oil (Heidrun) and two dilbits (Cold Lake Blend and Access Western Blend) for a period of 7 days in an ice-covered environment and then maintained for three months until the spawning season. The exposed mussels were monitored for aromatic hydrocarbon bioaccumulation, physiological energetic budget, cellular stress, byssus production and gametogenesis. In spring, spawning was induced to characterize breeding success. Bioaccumulation of polycyclic aromatic hydrocarbons (PAHs) was detected after three days of exposure, with higher concentrations of PAHs associated to the conventional oil (5.49 ± 0.12 µg·g-1 d.w.) compared to both dilbits (0.91 ± 0.02 µg·g-1; 0.51 ± 0.03 µg·g-1 d.w.). Despite a fast depuration rate and a good resilience of the exposed mussels, significant negative effects were observed at the cellular, physiological and fitness levels, especially in offspring. Our results suggest a higher toxicity of the diluted bitumen compared to the conventional crude despite the lower bioaccumulation of total PAHs. Dilbit treatments caused evident negative transgenerational effects on unexposed F1 generation.

Population genomics and history of speciation reveal fishery management gaps in two related redfish species (Sebastes mentella and Sebastes fasciatus).

Understanding the processes shaping population structure and reproductive isolation of marine organisms can improve their management and conservation. Using genomic markers combined with estimation of individual ancestries, assignment tests, spatial ecology, and demographic modeling, we (i) characterized the contemporary population structure, (ii) assessed the influence of space, fishing depth, and sampling years on contemporary distribution, and (iii) reconstructed the speciation history of two cryptic redfish species, Sebastes mentella and S. fasciatus. We genotyped 860 individuals in the Northwest Atlantic Ocean using 24,603 filtered single nucleotide polymorphisms (SNPs). Our results confirmed the clear genetic distinctiveness of the two species and identified three ecotypes within S. mentella and five populations in S. fasciatus. Multivariate analyses highlighted the influence of spatial distribution and depth on the overall genomic variation, while demographic modeling revealed that secondary contact models best explained inter- and intragenomic divergence. These species, ecotypes, and populations can be considered as a rare and wide continuum of genomic divergence in the marine environment. This acquired knowledge pertaining to the evolutionary processes driving population divergence and reproductive isolation will help optimizing the assessment of demographic units and possibly to refine fishery management units.

Harmful or harmless: Biological effects of marennine on marine organisms.

Marennine is a water-soluble blue-green pigment produced by the marine diatom Haslea ostrearia. The diatom and its pigment are well known from oyster farming areas as the source of the greening of oyster gills, a natural process increasing their market value in Western France. Blooms of blue Haslea are also present outside oyster ponds and hence marine organisms can be exposed, periodically and locally, to significant amounts of marennine in natural environments. Due to its demonstrated antibacterial activities against marine pathogenic bacteria (e.g. Vibrio) and possible prophylactic effects toward bivalve larvae, marennine is of special interest for the aquaculture industry, especially bivalve hatcheries. The present study aimed to provide new insights into the effects of marennine on a large spectrum of marine organisms belonging to different phyla, including species of aquaculture interest and organisms frequently employed in standardised ecotoxicological assays. Different active solutions containing marennine were tested: partially purified Extracellular Marennine (EMn), and concentrated solutions of marennine present in H. ostrearia culture supernatant; the Blue Water (BW) and a new process called Concentrated Supernatant (CS). Biological effects were meanwhile demonstrated in invertebrate species for the three marennine-based solutions at the highest concentrations tested (e.g., decrease of fertilization success, delay of embryonic developmental stages or larval mortality). Exposure to low concentrations did not impact larval survival or development and even tended to enhance larval physiological state. Furthermore, no effects of marennine were observed on the fish gill cell line tested. Marennine could be viewed as a Jekyll and Hyde molecule, which possibly affects the earliest stages of development of some organisms but with no direct impacts on adults. Our results emphasize the need to determine dosages that optimize beneficial effects and critical concentrations not to be exceeded before considering the use of marennine in bivalve or fish hatcheries.

Sex-Specific Co-expression Networks and Sex-Biased Gene Expression in the Salmonid Brook Charr Salvelinus fontinalis.

Networks of co-expressed genes produce complex phenotypes associated with functional novelty. Sex differences in gene expression levels or in the structure of gene co-expression networks can cause sexual dimorphism and may resolve sexually antagonistic selection. Here we used RNA-sequencing in the salmonid Brook Charr Salvelinus fontinalis to characterize sex-specific co-expression networks in the liver of 47 female and 53 male offspring. In both networks, modules were characterized for functional enrichment, hub gene identification, and associations with 15 growth, reproduction, and stress-related phenotypes. Modules were then evaluated for preservation in the opposite sex, and in the congener Arctic Charr Salvelinus alpinus Overall, more transcripts were assigned to a module in the female network than in the male network, which coincided with higher inter-individual gene expression and phenotype variation in the females. Most modules were preserved between sexes and species, including those involved in conserved cellular processes (e.g., translation, immune pathways). However, two sex-specific male modules were identified, and these may contribute to sexual dimorphism. To compare with the network analysis, differentially expressed transcripts were identified between the sexes, revealing a total of 16% of expressed transcripts as sex-biased. For both sexes, there was no overrepresentation of sex-biased genes or sex-specific modules on the putative sex chromosome. Sex-biased transcripts were also not overrepresented in sex-specific modules, and in fact highly male-biased transcripts were enriched in preserved modules. Comparative network analysis and differential expression analyses identified different aspects of sex differences in gene expression, and both provided new insights on the genes underlying sexual dimorphism in the salmonid Brook Charr.

Sex Chromosome Evolution, Heterochiasmy, and Physiological QTL in the Salmonid Brook Charr Salvelinus fontinalis.

Whole-genome duplication (WGD) can have large impacts on genome evolution, and much remains unknown about these impacts. This includes the mechanisms of coping with a duplicated sex determination system and whether this has an impact on increasing the diversity of sex determination mechanisms. Other impacts include sexual conflict, where alleles having different optimums in each sex can result in sequestration of genes into nonrecombining sex chromosomes. Sex chromosome development itself may involve sex-specific recombination rate (i.e., heterochiasmy), which is also poorly understood. The family Salmonidae is a model system for these phenomena, having undergone autotetraploidization and subsequent rediploidization in most of the genome at the base of the lineage. The salmonid master sex determining gene is known, and many species have nonhomologous sex chromosomes, putatively due to transposition of this gene. In this study, we identify the sex chromosome of Brook Charr Salvelinus fontinalis and compare sex chromosome identities across the lineage (eight species and four genera). Although nonhomology is frequent, homologous sex chromosomes and other consistencies are present in distantly related species, indicating probable convergence on specific sex and neo-sex chromosomes. We also characterize strong heterochiasmy with 2.7-fold more crossovers in maternal than paternal haplotypes with paternal crossovers biased to chromosome ends. When considering only rediploidized chromosomes, the overall heterochiasmy trend remains, although with only 1.9-fold more recombination in the female than the male. Y chromosome crossovers are restricted to a single end of the chromosome, and this chromosome contains a large interspecific inversion, although its status between males and females remains unknown. Finally, we identify quantitative trait loci (QTL) for 21 unique growth, reproductive, and stress-related phenotypes to improve knowledge of the genetic architecture of these traits important to aquaculture and evolution.

Draft genome of the American Eel (Anguilla rostrata).

Freshwater eels (Anguilla sp.) have large economic, cultural, ecological and aesthetic importance worldwide, but they suffered more than 90% decline in global stocks over the past few decades. Proper genetic resources, such as sequenced, assembled and annotated genomes, are essential to help plan sustainable recoveries by identifying physiological, biochemical and genetic mechanisms that caused the declines or that may lead to recoveries. Here, we present the first sequenced genome of the American eel. This genome contained 305 043 contigs (N50 = 7397) and 79 209 scaffolds (N50 = 86 641) for a total size of 1.41 Gb, which is in the middle of the range of previous estimations for this species. In addition, protein-coding regions, including introns and flanking regions, are very well represented in the genome, as 95.2% of the 458 core eukaryotic genes and 98.8% of the 248 ultra-conserved subset were represented in the assembly and a total of 26 564 genes were annotated for future functional genomics studies. We performed a candidate gene analysis to compare three genes among all three freshwater eel species and, congruent with the phylogenetic relationships, Japanese eel (A. japanica) exhibited the most divergence. Overall, the sequenced genome presented in this study is a crucial addition to the presently available genetic tools to help guide future conservation efforts of freshwater eels.

Regional variation of gene regulation associated with storage lipid metabolism in American glass eels (Anguilla rostrata).

Variation in gene regulation may be involved in the differences observed for life history traits within species. American eel (Anguilla rostrata) is well known to harbor distinct ecotypes within a single panmictic population. We examined the expression of genes involved in the regulation of appetite as well as lipid and glycogen among glass eels migrating to different locations on the Canadian east coast and captured at two different periods of upstream migration. Gene expression levels of three reference and five candidate genes were analyzed by real-time PCR with Taqman probes in recently captured wild glass eels. All gene transcripts were detected in glass eels. Of the five candidate genes, bile salt activated and triacylglycerol lipases were respectively 7.65 and 3.25 times more expressed in glass eels from the St. Lawrence estuary than in those from Nova Scotia, and there was no effect related to the two-week difference in capture date. These two genes explained 82.41% of the dissimilarity between the two rivers. In contrast, glycogen phosphorylase, ghrelin, and leptin receptor genes showed no significant differences in gene transcription. These results confirmed at the molecular level an observation that was recently made at the phenotypic level that glass eels from the St. Lawrence estuary have a greater capacity to use lipid reserves to sustain their metabolic needs. These observations add to the body of evidence supporting the hypothesis that regional phenotypic variation observed in American eel is determined early in life and that part of this variation is likely under genetic control.

Salmonid Chromosome Evolution as Revealed by a Novel Method for Comparing RADseq Linkage Maps.

Whole genome duplication (WGD) can provide material for evolutionary innovation. Family Salmonidae is ideal for studying the effects of WGD as the ancestral salmonid underwent WGD relatively recently, ∼65 Ma, then rediploidized and diversified. Extensive synteny between homologous chromosome arms occurs in extant salmonids, but each species has both conserved and unique chromosome arm fusions and fissions. Assembly of large, outbred eukaryotic genomes can be difficult, but structural rearrangements within such taxa can be investigated using linkage maps. RAD sequencing provides unprecedented ability to generate high-density linkage maps for nonmodel species, but can result in low numbers of homologous markers between species due to phylogenetic distance or differences in library preparation. Here, we generate a high-density linkage map (3,826 markers) for the Salvelinus genera (Brook Charr S. fontinalis), and then identify corresponding chromosome arms among the other available salmonid high-density linkage maps, including six species of Oncorhynchus, and one species for each of Salmo, Coregonus, and the nonduplicated sister group for the salmonids, Northern Pike Esox lucius for identifying post-duplicated homeologs. To facilitate this process, we developed MapComp to identify identical and proximate (i.e. nearby) markers between linkage maps using a reference genome of a related species as an intermediate, increasing the number of comparable markers between linkage maps by 5-fold. This enabled a characterization of the most likely history of retained chromosomal rearrangements post-WGD, and several conserved chromosomal inversions. Analyses of RADseq-based linkage maps from other taxa will also benefit from MapComp, available at: https://github.com/enormandeau/mapcomp/

Regional variation in energy storage strategies in American glass eels from Eastern Canada.

Energy status was analyzed in glass eels captured during two early waves of arrival at the mouths of the Mersey River, Nova Scotia, Canada (MR), and Grande-Rivière-Blanche, Québec, Canada (GRB), and according to their salinity preference (freshwater, brackish, or saltwater). Glass eels captured in the GRB estuary were larger, more pigmented, and exhibited higher whole-body glycogen, phospholipid, and sterol and wax ester contents. Those from MR had a higher condition index and a higher whole-body triacylglycerol content, suggesting different patterns of storage and/or use of energy reserves. Within a river, a delay of two weeks in estuarine arrival was characterized by significantly lower energy reserves. No differences in energy storage were observed according to salinity preference. Thus, the results revealed the occurrence of different energy storage strategies according to glass eel migration distance and duration, but not according to salinity preference.

RAD sequencing highlights polygenic discrimination of habitat ecotypes in the panmictic American eel.

The two primary ways that species respond to heterogeneous environments is through local adaptation and phenotypic plasticity. The American eel (Anguilla rostrata) presents a paradox; despite inhabiting drastically different environments [1], the species is panmictic [2, 3]. Spawning takes place only in the southern Sargasso Sea in the Atlantic Ocean [1]. Then, the planktonic larvae (leptocephali) disperse to rearing locations from Cuba to Greenland, and juveniles colonize either freshwater or brackish/saltwater habitats, where they spend 3-25 years before returning to the Sargasso Sea to spawn as a panmictic species. Depending on rearing habitat, individuals exhibit drastically different ecotypes [4-6]. In particular, individuals rearing in freshwater tend to grow slowly and mature older and are more likely to be female in comparison to individuals that rear in brackish/saltwater [4, 6]. The hypothesis that phenotypic plasticity alone can account for all of the differences was not supported by three independent controlled experiments [7-10]. Here, we present a genome-wide association study that demonstrates a polygenic basis that discriminates these habitat-specific ecotypes belonging to the same panmictic population. We found that 331 co-varying loci out of 42,424 initially considered were associated with the divergent ecotypes, allowing a reclassification of 89.6%. These 331 SNPs are associated with 101 genes that represent vascular and morphological development, calcium ion regulation, growth and transcription factors, and olfactory receptors. Our results are consistent with divergent natural selection of phenotypes and/or genotype-dependent habitat choice by individuals that results in these genetic differences between habitats, occurring every generation anew in this panmictic species.

Inter individual variations of the fish skin microbiota: host genetics basis of mutualism?

The commensal microbiota of fish skin is suspected to provide a protection against opportunist infections. The skin of fish harbors a complex and diverse microbiota that closely interacts with the surrounding water microbial communities. Up to now there is no clear evidence as to whether the host regulates the recruitment of environmental bacteria to build a specific skin microbiota. To address this question, we detected Quantitative Trait Loci (QTL) associated with the abundance of specific skin microbiota bacterial strains in brook charr (Salvelinus fontinalis), combining 16S RNA tagged-amplicon 454 pyrosequencing with genetic linkage analysis. Skin microbiota analysis revealed high inter-individual variation among 86 F2 fish progeny based upon the relative abundance of bacterial operational taxonomic units (OTUs). Out of those OTUs, the pathogenic strain Flavobacterium psychrophilum and the non-pathogenic strain Methylobacterium rhodesianum explained the majority of inter-individual distances. Furthermore, a strong negative correlation was found between Flavobacterium and Methylobacterium, suggesting a mutually competitive relationship. Finally, after considering a total of 266 markers, genetic linkage analysis highlighted three major QTL associated with the abundance of Lysobacter, Rheinheimera and Methylobacterium. All these three genera are known for their beneficial antibacterial activity. Overall, our results provide evidence that host genotype may regulate the abundance of specific genera among their surface microbiota. They also indicate that Lysobacter, Rheinheimera and Methylobacterium are potentially important genera in providing protection against pathogens.

Network analysis highlights complex interactions between pathogen, host and commensal microbiota.

Interactions between bacteria and their host represent a full continuum from pathogenicity to mutualism. From an evolutionary perspective, host-bacteria relationships are no longer considered a two-component system but rather a complex network. In this study, we focused on the relationship between brook charr (Salvelinus fontinalis) and bacterial communities developing on skin mucus. We hypothesized that stressful conditions such as those occurring in aquaculture production induce shifts in the bacterial community of healthy fish, thus allowing pathogens to cause infections. The results showed that fish skin mucus microbiota taxonomical structure is highly specific, its diversity being partly influenced by the surrounding water bacterial community. Two types of taxonomic co-variation patterns emerged across 121 contrasted communities' samples: one encompassing four genera well known for their probiotic properties, the other harboring five genera mostly associated with pathogen species. The homeostasis of fish bacterial community was extensively disturbed by induction of physiological stress in that both: 1) the abundance of probiotic-like bacteria decreased after stress exposure; and 2) pathogenic bacteria increased following stress exposure. This study provides further insights regarding the role of mutualistic bacteria as a primary host protection barrier.