Physiological and evolutionary potential of microorganisms from the Canterbury Basin subseafloor, a metagenomic...

Subseafloor sediments represent a large reservoir of organic matter and are inhabited by microbial groups of the three domains of life. Besides impacting the planetary geochemical cycles, the subsurface biosphere remains poorly understood, notably questions related to possible metabolic pathways and selective advantages that may be deployed by buried microorganisms (sporulation, response to stress, dormancy). In order to better understand physiological potentials and possible lifestyles of subseafloor microbial communities, we analyzed two metagenomes from subseafloor sediments collected at 31 mbsf (meters below the sea floor) and 136 mbsf in the Canterbury Basin. Metagenomic phylogenetic and functional diversities were very similar. Phylogenetic diversity was mostly represented by Chloroflexi, Firmicutes and Proteobacteria for Bacteria and by Thaumarchaeota and Euryarchaeota for Archaea. Predicted anaerobic metabolisms encompassed fermentation, methanogenesis and utilization of fatty acids, aromatic and halogenated substrates. Potential processes that may confer selective advantages for subsurface microorganisms included sporulation, detoxication equipment or osmolyte accumulation. Annotation of genomic fragments described the metabolic versatility of Chloroflexi, Miscellaneous Crenarchaeotic Group and Euryarchaeota and showed frequent recombination events within subsurface taxa. This study confirmed that the subseafloor habitat is unique compared to other habitats at the (meta)-genomic level and described physiological potential of still uncultured groups.