Abstract
Recent single-gene-based surveys of deep continental aquifers demonstrated the widespread occurrence of archaea related to Candidatus Methanoperedens nitroreducens (ANME-2d) known to mediate anaerobic oxidation of methane (AOM). However, it is unclear whether ANME-2d mediates AOM in the deep continental biosphere. In this study, we found the dominance of ANME-2d in groundwater enriched in sulfate and methane from a 300-m deep underground borehole in granitic rock. A near-complete genome of one representative species of the ANME-2d obtained from the underground borehole has most of functional genes required for AOM and assimilatory sulfate reduction. The genome of the subsurface ANME-2d is different from those of other members of ANME-2d by lacking functional genes encoding nitrate and nitrite reductases and multiheme cytochromes. In addition, the subsurface ANME-2d genome contains a membrane-bound NiFe hydrogenase gene putatively involved in respiratory H2 oxidation, which is different from those of other methanotrophic archaea. Short-term incubation of microbial cells collected from the granitic groundwater with 13C-labeled methane also demonstrates that AOM is linked to microbial sulfate reduction. Given the prominence of granitic continental crust and sulfate and methane in terrestrial subsurface fluids, we conclude that AOM may be widespread in the deep continental biosphere.
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Acknowledgements
We thank the members of the Geological Isolation Research Group of AIST and Crystalline Environment Research Group of JAEA. We also thank Y Nakamura and T Tonooka for their technical assistant. Comments from three anonymous reviewers and discussions with SE McGlynn for ANME genomes substantially improved our manuscript. Main part of this research project has been conducted as the regulatory supporting research funded by the Secretariat of Nuclear Regulation Authority (Secretariat of NRA), Japan. This work was partly supported by JSPS KAKENHI Grant Number JP26287133. As part of ‘The project for validating assessment methodology in geological disposal system’, this study was funded by the Ministry of Economy, Trade and Industry of Japan.
Author contributions
Drilling, hydraulic tests and geochemical analyses were performed by KI, UK, MK, AH, YT, KI, AF, TI, TM, DK, UT and YS. Microbial community analyses were conducted by KI, UT, MK, KY, AH, AF and YS. Multivariate function analyses were performed by KI and MS. Thermodynamic calculation was performed by YS. KI, TI and YS performed stable isotope labeling experiments. Metagenomic analysis was performed by AWH, YA, SK, BCT, JFB and YS. KI, AWH, BCT, JFB and YS wrote the manuscript with contributions of all co-authors.
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Ino, K., Hernsdorf, A., Konno, U. et al. Ecological and genomic profiling of anaerobic methane-oxidizing archaea in a deep granitic environment. ISME J 12, 31–47 (2018). https://doi.org/10.1038/ismej.2017.140
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DOI: https://doi.org/10.1038/ismej.2017.140
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