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Journal Article

Continental scientific drilling and microbiology: (extremely) low biomass in bedrock of central Sweden

Authors

Westmeijer,  George
External Organizations;

Escudero,  Cristina
External Organizations;

Bergin,  Claudia
External Organizations;

Turner,  Stephanie
External Organizations;

Ståhle,  Magnus
External Organizations;

Mehrshad,  Maliheh
External Organizations;

Leroy,  Prune
External Organizations;

Buck,  Moritz
External Organizations;

López-Hernández,  Pilar
External Organizations;

/persons/resource/kallm

Kallmeyer,  J.
3.7 Geomicrobiology, 3.0 Geochemistry, Departments, GFZ Publication Database, Deutsches GeoForschungsZentrum;

Amils,  Ricardo
External Organizations;

Bertilsson,  Stefan
External Organizations;

Dopson,  Mark
External Organizations;

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Fulltext (public)

5025109.pdf
(Publisher version), 3MB

Supplementary Material (public)
There is no public supplementary material available
Citation

Westmeijer, G., Escudero, C., Bergin, C., Turner, S., Ståhle, M., Mehrshad, M., Leroy, P., Buck, M., López-Hernández, P., Kallmeyer, J., Amils, R., Bertilsson, S., Dopson, M. (2024): Continental scientific drilling and microbiology: (extremely) low biomass in bedrock of central Sweden. - Biogeosciences, 21, 2, 591-604.
https://doi.org/10.5194/bg-21-591-2024


Cite as: https://gfzpublic.gfz-potsdam.de/pubman/item/item_5025109
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.