Teleost fishes represent an invaluable repertoire of host species to study the factors shaping animal-associated microbiomes. Several studies have shown that the phylogenetic structure of 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 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 to environmental physicochemistry and bacterioplankton community structure. These results suggest that the variable skin mucus community is a relevant target to develop 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. Especially, 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 fishes 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 different implications: (1) the skin mucus microbiome should be used, rather than the gut, to investigate bacterial biomarkers of ecosystem perturbance in the wild; (2) the gut microbiome is better suited for studies on the drivers of phylosymbiosis, or the co-evolution of fish and their symbionts.

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Microbial symbionts inhabiting the honeybee gut (i.e., gut microbiota) are essential for food digestion, immunity, and gut protection of their host. The taxonomic composition of the gut microbiota is dynamic throughout the honeybee life cycle and the foraging season. However, it remains unclear how drastic changes occurring in winter, such as food shortage and cold weather, impact gut microbiota dynamics. The objective of this study was to characterize the gut microbiota of the honeybee during the overwintering period in a northern temperate climate in Canada. The microbiota of nine honeybee colonies was characterized by metataxonomy of 16S rDNA between September 2017 and June 2018. Overall, the results showed that microbiota taxonomic composition experienced major compositional shifts in fall and spring. From September to November, Enterobacteriaceae decreased, while Neisseriaceae increased. From April to June, Orbaceae increased, whereas Rhizobiaceae nearly disappeared. Bacterial diversity of the gut microbiota decreased drastically before and after overwintering, but it remained stable during winter. We conclude that the honeybee gut microbiota is likely to be impacted by the important meteorological and dietary changes that take place before and after the overwintering period. Laboratory trials are needed to determine how the observed variations affect the honeybee health.

The Amazon River basin sustains dramatic hydrochemical gradients defined by three water types: white, clear and black waters. Black waters contain important loads of allochthonous humic dissolved organic carbon (DOC), mostly coming from bacteria-mediated lignin degradation, a process that remains understudied. Here, we identified the main bacterial taxa and functions associated with contrasting Amazonian water types, and shed light on their potential implication in the lignin degradation process. We performed an extensive field bacterioplankton sampling campaign from the three Amazonian water types, and combined our observations to a meta-analysis of 90 Amazonian basin shotgun metagenomes used to build a tailored functional inference database. We showed that the overall quality of DOC is a major driver of bacterioplankton structure, transcriptional activity and functional repertory. We also showed that among the taxa mostly associated to differences between water types, Polynucleobacter sinensis particularly stood out, as its abundance and transcriptional activity was strongly correlated to black water environments, and specially to humic DOC concentration. Screening the reference genome of this bacteria, we found genes coding for enzymes implicated in all the main lignin degradation steps, suggesting that this bacteria may play key roles in the carbon cycle processes within the Amazon basin.