Abstract
The terrestrial deep subsurface is a huge repository of microbial biomass, but in relation to its size and physical heterogeneity, few sites have been investigated in detail. Here, we applied a culture-independent metagenomic approach to characterize the microbial community composition in deep (1500 meters below surface) terrestrial fluids. Samples were collected from a former gold mine in Lead, South Dakota, USA, now Sanford Underground Research Facility (SURF). We reconstructed 74 genomes from metagenomes (MAGs), enabling the identification of common metabolic pathways. Sulfate and nitrate/nitrite reduction were the most common putative energy metabolisms. Complete pathways for autotrophic carbon fixation were found in more than half of the MAGs, with the reductive acetyl-CoA pathway by far the most common. Nearly 40% (29 of 74) of the recovered MAGs belong to bacterial phyla without any cultivated members—microbial dark matter. Three of our MAGs constitute two novel phyla previously only identified in 16 S rRNA gene surveys. The uniqueness of this data set—its physical depth in the terrestrial subsurface, the relative abundance and completeness of microbial dark matter genomes and the overall diversity of this physically deep, dark, community—make it an invaluable addition to our knowledge of deep subsurface microbial ecology.
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Acknowledgements
This work was supported by the NASA Astrobiology Institute under cooperative agreement NNA13AA92A. Many thanks to John Heidelberg and Rohan Sachdeva at USC for use of their servers and help in metagenomic analysis. We would also like to recognize A Murat Eren for his invaluable help in utilizing the Anvi’o interface. We want to thank especially staff and personnel at SURF for access to the deep subsurface and repeated access to samples used in this study. This work was funded by the NASA Astrobiology Institute under cooperative agreement NNA13AA92A.
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Momper, L., Jungbluth, S., Lee, M. et al. Energy and carbon metabolisms in a deep terrestrial subsurface fluid microbial community. ISME J 11, 2319–2333 (2017). https://doi.org/10.1038/ismej.2017.94
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DOI: https://doi.org/10.1038/ismej.2017.94
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