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Abstract:
Scientific drilling expeditions offer a unique op-
portunity to characterize microbial communities in the sub-
surface that have long been isolated from the surface. With
subsurface microbial biomass being low in general, biologi-
cal contamination from the drilling fluid, sample processing,
or molecular work is a major concern. To address this, char-
acterization of the contaminant populations in the drilling
fluid and negative extraction controls are essential for assess-
ing and evaluating such 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 broad genomic approach.
However, even after removing potential contaminant popu-
lations 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 Candi-
datus Desulforudis audaxviator suggested the presence of au-
tochthonous deep biosphere taxa in the sequenced libraries,
yet these clades represented only a minor fraction of the se-
quence counts (< 0.1 %), hindering further ecological inter-
pretations. The described methods and findings emphasize
the importance of sequencing extraction controls and can
support experimental design for future microbiological stud-
ies in conjunction with continental drilling operations.
