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All hydrocarbon (HC) reservoirs leak to some extent. When small quantities of HCs escape offshore reservoirs and migrate through overlying organic-poor marine sediments towards the surface, these HCs are often completely metabolized by microorganisms before reaching the sediment–water interface. However, these low and often unnoticed upward HC fluxes still influence the geochemistry of surrounding sediments and potentially stimulate metabolic activity by microbial populations in shallow subseafloor environments. In this study, we examined how localized HC seepage affects microbial sulfate reduction in organic-poor sediments from the SW Barents Sea, focusing on three sampling areas overlying known HC deposits and two pristine seabed reference areas. The analysis of 50 gravity cores revealed significant variability in the predicted sulfate depletion depth, ranging from 3 to 12 m below the seafloor. We observed nearly linear pore water sulfate and alkalinity profiles, alongside low rates of sulfate reduction (pmol cm3 d−1). Metagenomic and metatranscriptomic data indicated metabolic potential and activity towards sulfate reduction and anaerobic oxidation of methane (AOM). Expression of functional marker genes (aprAB, dsrAB, mcrA) revealed metabolic activities by sulfate-reducing Desulfobacterota and methanotrophic ANME-1 archaea sustained by HC traces in the sediment. Furthermore, in concomitance to AOM processes, we found that archaea amongst the classes Lokiarchaeia and Thorarchaeia were expressing genes involved in sulfur reduction (hydB, hydG). Overall, our study demonstrates that the gradient in pore water geochemistry, the rates of sulfate reduction processes, and the genetic features of microbial populations actively involved in sulfate-driven AOM processes are all affected by low and often unnoticed upward HC fluxes. This slight HC seepage resulted in sulfate depletion at shallower depths compared to what would be expected at a comparable non-affected site and produced concomitant biogeochemical signatures in the shallow subsurface that enable the inference of deeply buried reservoirs.

Abstract Background Alterations to the gut microbiome have been linked to multiple chronic diseases. However, the drivers of such changes remain largely unknown. The oral cavity acts as a major route of exposure to exogenous factors including pathogens, and processes therein may affect the communities in the subsequent compartments of the gastrointestinal tract. Here, we perform strain-resolved, integrated meta-genomic, transcriptomic, and proteomic analyses of paired saliva and stool samples collected from 35 individuals from eight families with multiple cases of type 1 diabetes mellitus (T1DM). Results We identified distinct oral microbiota mostly reflecting competition between streptococcal species. More specifically, we found a decreased abundance of the commensal Streptococcus salivarius in the oral cavity of T1DM individuals, which is linked to its apparent competition with the pathobiont Streptococcus mutans. The decrease in S. salivarius in the oral cavity was also associated with its decrease in the gut as well as higher abundances in facultative anaerobes including Enterobacteria. In addition, we found evidence of gut inflammation in T1DM as reflected in the expression profiles of the Enterobacteria as well as in the human gut proteome. Finally, we were able to follow transmitted strain-variants from the oral cavity to the gut at the individual omic levels, highlighting not only the transfer, but also the activity of the transmitted taxa along the gastrointestinal tract. Conclusions Alterations of the oral microbiome in the context of T1DM impact the microbial communities in the lower gut, in particular through the reduction of “mouth-to-gut” transfer of Streptococcus salivarius. Our results indicate that the observed oral-cavity-driven gut microbiome changes may contribute towards the inflammatory processes involved in T1DM. Through the integration of multi-omic analyses, we resolve strain-variant “mouth-to-gut” transfer in a disease context. Video Abstract