Paleomic analysis of endolithic microbial communities

The terrestrial subsurface is home to a significant proportion of the Earth´s microbial biomass. Our understanding about terrestrial subsurface microbiomes is almost exclusively derived from groundwater and porous sediments and rocks. The contribution of macroscopically dense consolidated rock is largely ignored and receives much less attention due to a supposed lack of microbial habitats. In this study, we investigated interbedded limestone and mudstone from the vadose zone and deep aquitards and could recover sufficient genomic DNA for downstream metagenomic analysis independent of porosity. Based on the extracted DNA, we estimated between 2.81 and 4.25 × 105 cells × g-1 rock from the different lithologies and depths. Analyzing DNA damage patterns revealed paleome signatures, genetic records of past microbial communities, for three out of seven studied cores. All paleome signatures were obtained from the vadose zone. DNA obtained from deep aquitards isolated from surface input was not affected by DNA decay. Our findings indicate that not flow but water saturation might be controlling microbial survival. Decoding the taxonomy and functional potential revealed that paleome communities were driven by chemolithotrophy, carried out by taxa such Cand. Rokubacteria, through potentially available sulfur and nitrogen compounds. High abundances of taxa such as Acidobacteria highlight that genome-encoded metabolic flexibility is in addition advantageous in subsurface environments. Mixed carbonate-siliciclastic bedrocks might represent paleome archives that could be exploited for learning more about the geological and biological past and present of subsurface environments.