Microbial communities in the deep subsurface of arid and humid ecosystems

Microorganisms inhabiting the pore space of sedimentary and igneous rocks in the subsurface encounter various challenges, including anoxic, xeric and oligotrophic conditions. In igneous systems, nutrient limitation might be the most limiting factor for microbial life since these initial inorganic settings depend on the input of biomass from the surface through fluid transport along tectonic fractures. Despite growing interest in these extreme habitats, little is known about interactions and processes between the biosphere and the geosphere beneath arid landscapes, where surface water input is limited. This study investigates the deep biosphere of arid and humid ecosystems. Using 16S rRNA amplicon and shotgun metagenomic sequencing, microbial communities in up to 55 m deep subsurface granite rocks could be characterized. We identified an abundant and potentially active deep biosphere community adapted to humid and arid conditions. The overall community was characterized by heterotrophic bacteria, including taxa assigned to the genera Pseudarthrobacter, Janthinobacterium and Pseudomonas. However, lower abundances of taxa affiliated with common chemolithoautrophs, e.g. Thiobacillus, Sulfuriverula and Sulfuricurvum, were only observed in the arid subsurface, indicating an increased need for adaption to low organic conditions and the use of alternative electron donors in the desert deep biosphere. Functional analysis revealed that sulfur and carbon monoxide are the most likely inorganic electron donors, while little evidence for hydrogenotrophy or iron cycling was detected in both climates. These findings expand the current understanding of microbial life in the subsurface of granite rocks and show a clear connection between surface conditions and deep biosphere ecosystems. Observation from this study helps to further deduce the extent and functional capacity of microbial communities in the terrestrial deep biosphere and their role within global biogeochemical processes.