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Active sulfur cycling in the terrestrial deep subsurface


The deep terrestrial subsurface remains an environment where there is limited understanding of the extant microbial metabolisms. At Olkiluoto, Finland, a deep geological repository is under construction for the final storage of spent nuclear fuel. It is therefore critical to evaluate the potential impact microbial metabolism, including sulfide generation, could have upon the safety of the repository. We investigated a deep groundwater where sulfate is present, but groundwater geochemistry suggests limited microbial sulfate-reducing activity. Examination of the microbial community at the genome-level revealed microorganisms with the metabolic capacity for both oxidative and reductive sulfur transformations. Deltaproteobacteria are shown to have the genetic capacity for sulfate reduction and possibly sulfur disproportionation, while Rhizobiaceae, Rhodocyclaceae, Sideroxydans, and Sulfurimonas oxidize reduced sulfur compounds. Further examination of the proteome confirmed an active sulfur cycle, serving for microbial energy generation and growth. Our results reveal that this sulfide-poor groundwater harbors an active microbial community of sulfate-reducing and sulfide-oxidizing bacteria, together mediating a sulfur cycle that remained undetected by geochemical monitoring alone. The ability of sulfide-oxidizing bacteria to limit the accumulation of sulfide was further demonstrated in groundwater incubations and highlights a potential sink for sulfide that could be beneficial for geological repository safety.

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Fig. 1: Operational taxonomic units (OTUs) identified by 16S rRNA gene amplicon sequencing.
Fig. 2: Metabolic analysis of metagenome-assembled genomes (MAGs) and single amplified genomes (SAGs) uncovered from Olkiluoto groundwater.
Fig. 3: Sulfur cycling in Olkiluoto groundwater.
Fig. 4: Enrichment of sulfide-oxidizing bacteria from Olkiluoto groundwater.

Data availability

16S rRNA gene amplicon data are available at the National Centre for Biotechnology Information (NCBI) Sequence Read Archive (SRA) under BioProject PRJNA472445. Metagenomic data were deposited at the NCBI SRA; accession numbers PRJNA404452, PRJNA404453, PRJNA444021, and PRJNA472439. MAGs are available under accessions SAMN12221356–SAMN12221381. SAGs are available at the JGI Genome Portal, GOLD Study ID’s Ga0214289 and Gs0127568.


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The authors would like to thank Maarit Yli-Kaila and Raila Viitala for their support and assistance conducting field work, Louise Balmer and Guillaume Sommer for their help collecting samples, and Petteri Pitkänen for valuable discussions. This research was funded by a grant from Posiva Oy to RBL (2015-06-17). Additional funding for metagenomic sequencing was provided by The Census of Deep Life within the Deep Carbon Observatory and the U.S. Department of Energy Joint Genome Institute (JGI). The work conducted by the JGI, a DOE Office of Science User Facility, is supported under contract no. DE-AC02-05CH11231. The metagenomic computations were performed on resources provided by SNIC through Uppsala Multidisciplinary Center for Advanced Computational Science (UPPMAX).

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Bell, E., Lamminmäki, T., Alneberg, J. et al. Active sulfur cycling in the terrestrial deep subsurface. ISME J 14, 1260–1272 (2020).

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