COSC-2 microbiology 16S
Scientific drilling expeditions offer a unique opportunity to characterize the microbial communities in the subsurface that have been long-term isolated from the surface. With subsurface microbial biomass being low in general, biological contamination from the drilling fluid, sample processing, or molecular work is a major concern. To address this, characterization of the contaminant populations in the drilling fluid and negative extraction controls are of great importance to assess the nature of the sequencing data. Here, rock cores down to 2250 m depth, groundwater-bearing fractures, and the drilling fluid were sampled for DNA to characterize the microbial communities using a genomic approach. However, even after removing potential contaminant populations present in the drilling fluid, notorious contaminants were abundant and mainly affiliated with the bacterial order Burkholderiales. These contaminant microorganisms likely originated from the reagents used for isolating DNA despite stringent quality standards during the molecular work. The detection of strictly anaerobic sulfate reducers such as Candidatus Desulforudis audaxviator suggested the presence of autochthonous deep biosphere taxa in the sequenced libraries, yet these clades represented only a minor fraction of the sequence data (< 0.1 %), thereby limiting ecological interpretations. The described methods and findings could support experimental design for future microbiological studies in conjunction with drilling operations.