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Proc Natl Acad Sci U S A. 2016 Dec 6;113(49):E7927-E7936. Epub 2016 Nov 21.

An oligotrophic deep-subsurface community dependent on syntrophy is dominated by sulfur-driven autotrophic denitrifiers.

Author information

Department of Geosciences, Princeton University, Princeton, NJ 08544;
Department of Biology, New Mexico Institute of Mining and Technology, Socorro, NM 87801.
Department of Microbial, Biochemical, and Food Biotechnology, University of the Free State, Bloemfontein 9301, South Africa.
Department of Geosciences, Princeton University, Princeton, NJ 08544.
High Throughput Sequencing and Microarray Facility, Lewis-Sigler Institute for Integrative Genomics, Princeton University, NJ 08544.
Proteomics and Mass Spectrometry Core, Department of Molecular Biology, Princeton University, NJ 08544.
Atmospheric and Oceanic Sciences, Princeton University, Princeton, NJ 08544.
Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544.
Climate and Environmental Physics, Physics Institute, University of Bern, 3012 Bern, Switzerland.
School of Geography and Earth Sciences, McMaster University, Hamilton, ON, Canada L8S 4K1.
Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139.
Department of Earth and Atmospheric Sciences, University of Alberta, Edmonton, AB, Canada T6G 2E3.
Department of Earth Sciences, University of Toronto, Toronto, ON, Canada M5S 3B1.


Subsurface lithoautotrophic microbial ecosystems (SLiMEs) under oligotrophic conditions are typically supported by H2 Methanogens and sulfate reducers, and the respective energy processes, are thought to be the dominant players and have been the research foci. Recent investigations showed that, in some deep, fluid-filled fractures in the Witwatersrand Basin, South Africa, methanogens contribute <5% of the total DNA and appear to produce sufficient CH4 to support the rest of the diverse community. This paradoxical situation reflects our lack of knowledge about the in situ metabolic diversity and the overall ecological trophic structure of SLiMEs. Here, we show the active metabolic processes and interactions in one of these communities by combining metatranscriptomic assemblies, metaproteomic and stable isotopic data, and thermodynamic modeling. Dominating the active community are four autotrophic β-proteobacterial genera that are capable of oxidizing sulfur by denitrification, a process that was previously unnoticed in the deep subsurface. They co-occur with sulfate reducers, anaerobic methane oxidizers, and methanogens, which each comprise <5% of the total community. Syntrophic interactions between these microbial groups remove thermodynamic bottlenecks and enable diverse metabolic reactions to occur under the oligotrophic conditions that dominate in the subsurface. The dominance of sulfur oxidizers is explained by the availability of electron donors and acceptors to these microorganisms and the ability of sulfur-oxidizing denitrifiers to gain energy through concomitant S and H2 oxidation. We demonstrate that SLiMEs support taxonomically and metabolically diverse microorganisms, which, through developing syntrophic partnerships, overcome thermodynamic barriers imposed by the environmental conditions in the deep subsurface.


active subsurface environment; inverted biomass pyramid; metabolic interactions; sulfur-driven autotrophic denitrifiers; syntrophy

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