Fish Skin and Gut Microbiomes Show Contrasting Signatures of Host Species and Habitat

Abstract

Teleost fish represent an invaluable repertoire of host species to study the factors shaping animal-associated microbiomes. Several studies have shown that the phylogenetic structure of the fish gut microbiome is driven by species-specific (e.g., host ancestry, genotype, or diet) and habitat-specific (e.g., hydrochemical parameters and bacterioplankton composition) factors. However, our understanding of other host-associated microbial niches, such as the skin mucus microbiome, remains limited. The goal of our study was to explore simultaneously the phylogenetic structure of the fish skin mucus and gut microbiome and compare the effect of species- and habitat-specific drivers on the structure of microbial communities in both tissues. We sampled 114 wild fish from 6 populations of 3 ecologically and phylogenetically contrasting Amazonian teleost species. Water samples were collected at each site, and 10 physicochemical parameters were characterized. The skin mucus, gut, and water microbial communities were characterized using a metabarcoding approach targeting the V3-V4 regions of the 16S rRNA. Our results showed a significant distinction between the phylogenetic profile and diversity of the microbiome from each microbial niche. Skin mucus and bacterioplankton communities were significantly closer in composition than gut and free-living communities. Species-specific factors mostly modulated gut bacterial communities, while the skin mucus microbiome was predominantly associated with environmental physicochemistry and bacterioplankton community structure. These results suggest that the variable skin mucus community is a relevant target for the development of microbial biomarkers of environmental status, while the more conserved gut microbiome is better suited to study long-term host-microbe interactions over evolutionary time scales.IMPORTANCE Whether host-associated microbiomes are mostly shaped by species-specific or environmental factors is still unresolved. In particular, it is unknown to what extent microbial communities from two different host tissues from the same host respond to these factors. Our study is one of the first to focus on the microbiome of teleost fish to shed a light on this topic as we investigate how the phylogenetic structure of microbial communities from two distinct fish tissues are shaped by species- and habitat-specific factors. Our study showed that in contrast to the teleost gut microbiome, skin mucus communities are highly environment dependent. This result has various implications: (i) the skin mucus microbiome should be used, rather than the gut, to investigate bacterial biomarkers of ecosystem perturbance in the wild, and (ii) the gut microbiome is better suited for studies of the drivers of phylosymbiosis, or the coevolution of fish and their symbionts.

Keywords: Amazon; fish; gut; habitat; host; microbiome; phylosymbiosis; skin; species; teleost.

FIG 1

The phylogenetic structure of the skin mucus community is closer to bacterioplankton than to the gut community. Stacked bar plots display the relative abundance of the 12 most abundant classes in all sample types collected. Box plots of Faith’s phylogenetic alpha diversity index were added below the bar plots for each sample type. (a to d) These analyses were performed on the 4 sampling sites from which we have bacterioplankton samples with adequate sequencing depth (>5,000 sequences): Catalão (a), MPWS2_3 (b), BWS2 (c), and WWS2 (d). All specimens from each species were pooled for these analyses.

FIG 2

The gut and skin mucus have unique community structures, as shown for the three species sampled. (a to c) Principal-component analyses show the clustering of gut versus skin communities for flag cichlids (a), black piranhas (b), and pacus (c). Results of PERMANOVA tests between groups are indicated on the top left corner of each PCA plot. (d to f) LEfSe analyses highlight the phyla and classes that are significantly more abundant in one of the two tissues considered for flag cichlids (d), black piranhas (e), and pacus (f). (g to i) Heatmaps produced with metagenomeSeq show that samples cluster according to the relative abundance of the 100 most abundant ASVs for flag cichlids (g), black piranhas (h), and pacus (i). (j to l) Bar plots produced with metagenomeSeq highlight the 10 discriminant ASVs with the highest LDA score for each tissue for flag cichlids (j), black piranhas (k), and pacus (l).

FIG 3

Host species has a more important impact on the structure of gut communities than of skin mucus communities. The assessment of host species impact was based on PERMANOVA F and P values, and the total percentage of variance is explained by the 2 first axes of PCA plots. The PCAs show the clustering of bacterial communities according to the host fish species at each sampling site. PERMANOVAs with 10,000 permutations tested the significance of the “host species” factor at each site. At least two species were found at every site, and all three species were found at the sites Catalão and MPWS2_3.

FIG 4

Overall, skin mucus communities are more associated with habitat-specific factors than gut communities. The figure shows the clustering of nodes (i.e., samples) according to the pattern of Spearman correlations when all samples (for communities of the same tissue) are compared to one another. Nodes sharing and edge (link) have a Spearman correlation of >0.5 with a P value of <0.05 (with Bonferroni correction). The color of the node indicates the host species, while the shape indicates the sampling site of the sample.

FIG 5

Interaction networks show high connectivity between skin communities, environmental bacterioplankton, and hydrochemical parameters. Nodes sharing an edge (link) have a Spearman correlation of >0.5 with a P value of <0.05 (with Bonferroni correction). The color of the node indicates the type of sample: blue nodes represent bacterioplankton taxa, orange nodes are hydrochemical parameters, and gray nodes are host fish taxa. No significant correlations were detected between gut taxa and environmental hydrochemical parameters for black piranha and flag cichlid samples. The numbers under each network indicate the number and percentage of ASVs implicated in significant interactions in each community.