Multi-Regional Study on the Microbial Community Structure, Core Microbiome and Functional Characteristics in Deep Fracture Waters

The deep terrestrial subsurface is the largest reservoir of Earth's freshwater resources as well as the largest habitat for prokaryotic life. However, the deep-subsurface microbiome, especially its spatial distribution across countries/continents, is still poorly understood. In this study, we compiled and compared 30 16S rRNA gene amplicon libraries from three deep fractured aquifers in different parts of the world (depth range of tens of meters to 2.4 km below surface) to understand the spatial distribution and functions of deep-subsurface microbial community, and to test for the presence of core taxa. The results revealed spatially heterogenous microbial community composition at both the local and the global scales, even at the phylum level. Environmental filtering was identified as an important driver of the microbial community structure of deep groundwaters. Despite the spatial heterogeneity, the three aquifers share a core microbiome at the genus level. Only one family, <i>Comamonadaceae</i>, was present in all the 30 samples analyzed. Several other families were also prevalent, including <i>Hydrogenophilaceae</i>, <i>Omnitrophaceae</i>, <i>BSV26 (Candidatus Kryptonia)</i>, and an unclassified <i>Thermodesulfovibrionia</i>. FAPROTAX functional prediction indicated that chemoheterotrophic functions predominate, and the core microbial genera, together with the dominant genera, collectively govern the functional characteristics. Taken together, our findings provide new insights into the spatial heterogeneity and functional potential of deep-subsurface ecosystems across the globe.