Shifts in sediment bacterial communities reflect changes in depositional environments in a fluviatile context.

Sediments are complex heterogeneous matrices allowing to some extent the recording of past environmental conditions by integrating sediment characteristics, contamination and the microbial community assembly. In aquatic environments, abiotic environmental filtering is considered the primary deterministic mechanism shaping microbial communities in sediments. However, the number and relative contributions of geochemical and physical factors associated with biotic parameters (reservoir of microorganisms) complicate our understanding of community assembly dynamics. In this study, the sampling of a sedimentary archive in a site alternately subjected to contrasting inputs from the Eure and the Seine Rivers allowed us to study the response of microbial communities to changes in depositional environment over time. The coupling of the quantification and sequencing of the gene encoding the 16S rRNA with analyses of grain size, organic matter and major and trace metal contents demonstrated that microbial communities reflected contrasting sedimentary inputs over time. Total organic carbon (TOC) was the main factor influencing microbial biomass, while the quantity and quality of organic matter (R400, RC/TOC), major elements (i.e. Al, Fe, Ti) and trace metals (i.e. Zn, Pb, Cu, Cr, Ni, As, Co, Ag, Sb) shaped the structure of the microbial community. Besides the effect of geochemical factors, a specific microbial signature was associated with the contrasting sedimentary sources, highlighting the importance of the microbial reservoir in the assembly of microbial communities. Indeed, the main genera identified in the facies influenced by the Eure River were affiliated with the phyla Desulfobacterota (Syntrophus, Syntrophorhabdus, Smithella, Desulfatiglans), Firmicutes (Clostridium_sensu_stricto_1), Proteobacteria (Crenothrix), Verrucomicrobiota (Luteolibacter), while the contributions of the Seine River were characterised by some halophilic genera Salirhabdus (Firmicutes), Haliangium (Myxococcota) and SCGC-AB-539-J10 (Chloroflexi). This study sheds light on the overall processes determining the assembly of microbial communities in sediments and the importance of associating geochemical factors with reservoirs of microorganisms inherited from sediment sources.

Decoupled responses of the copepod Eurytemora affinis transcriptome and its microbiota to dissolved copper exposure.

Chemical contamination is a common threat to biota thriving in estuarine and coastal ecosystems. Of particular importance is that trace metals tend to accumulate and exert deleterious effects on small invertebrates such as zooplankton, which are essential trophic links between phytoplankton and higher-level consumers in aquatic food webs. Beyond the direct effects of the contamination, we hypothesized that metal exposure could also affect the zooplankton microbiota, which in turn might further impair host fitness. To assess this assumption, copepods (Eurytemora affinis) were sampled in the oligo-mesohaline zone of the Seine estuary and exposed to dissolved copper (25 µg.L-1) over a 72-hour time period. The copepod response to copper treatment was assessed by determining transcriptomic changes in E. affinis and the alteration of its microbiota. Unexpectedly, very few genes were differentially expressed in the copper-treated copepods compared to the controls for both male and female samples, while a clear dichotomy between sex was highlighted with 80% of the genes showing sex-biased expression. In contrast, copper increased the taxonomic diversity of the microbiota and resulted in substantial compositional changes at both the phyla and genus levels. Phylogenetic reconstruction of the microbiota further suggested that copper mitigated the phylogenetic relatedness of taxa at the basal tree structure of the phylogeny, whereas it strengthened it at the terminal branches. Increased terminal phylogenetic clustering in the copper-treated copepods coincided with higher proportions of bacterial genera previously identified as copper resistant (e.g., Pseudomonas, Acinetobacter, Alkanindiges, Colwellia) and a higher relative abundance of the copAox gene encoding a periplasmic inducible multi-copper oxidase. The enrichment in micro-organisms likely to perform copper sequestration and/or enzymatic transformation processes, underlines the need to consider the microbial component during evaluation of the vulnerability of zooplankton to metallic stress.