Taxonomic and Metabolic Profiling for Microbial Communities in Opalinus Clay Rocks from Deep Subsurface Biosphere

Background: Microorganisms in deep terrestrial subsurface harbor unique metabolic traits due to insufficient sunlight, oxygen and organic carbons. Previous studies reported that in the porewaters from boreholes of Opalinus clay rocks under a deep geological repository (DGR), autotrophoic H2-oxidizing sulfate-reducing bacteria (SRB)—Peptococcaceae, Desulfatialea and Desulfobulbaceae—together with other heterotrophic and fermentative bacteria were able to alleviate the H2 pressure accumulated from the process during anoxic corrosion of steel containers for nuclear wastes. Objective and Method: What remains elusive is whether these microorganisms are porewater- or rock-origin. Thus, we re-analyzed the above-mentioned porewater communities based on the amplicon sequence variant (ASV) instead of operational taxonomic unit clustering. In addition, two cores of Opalinus rocks were collected in November of 2019. The extracted DNA/RNA from these rock samples will be subjected to 16S amplicon sequencing, metagenome and metatransctriptome to investigate microbial diversity and metabolisms; microbial colonization will also be examined via scanning electron microscopy. Result: Our principal coordinates analysis indicated that the community structure of original porewaters between different boreholes were significantly distinct in the same DGR site. Moreover, the chao1 diversity index suggested that some rare biosphere may thrive in the H2-spiked communities. The differential analysis further showed that up to 213 ASVs were significantly enriched in the H2-injected porewater communities, mainly belonging to Proteobacteria, Firmicutes, Desulfobacterota, and Bacteroidota. This ASV-resolute analysis indicated that bacteria involved in this microbial loop is more complex than previously appreciated. Besides, the preliminary results showed the DNA content of newly collected Opalinus rocks was extremely low based on Qubit quantification (0.57 ± 0.07 to 0.61 ± 0.04 ng/g of clay), whereas the total RNA was not quantifiable via Qubit. Despite this, the V4 region of 16S rRNA gene was able to be amplified, indicating the presence of microorganisms with low biomass. In future, 16S amplicon sequences from rocks will be analyzed together with porewater communities. The DNA will be applied to multiple displacement amplification prior to metagenome sequencing. The understanding of microbial ecology in deep subsurface not only benefits nuclear wastes management but also underpins the notion of evolutionary and astrobiology.