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Metagenomic identification of active methanogens and methanotrophs in serpentinite springs of the Voltri Massif, Italy

, , , , , , , ,
1 Department of Biology, University of Utah, Salt Lake City, Utah, United States
2 Department of Earth and Ocean Sciences, University of South Carolina, Columbia, South Carolina, United States
3 Department of Earth Sciences, ETH Zurich, Zurich, Switzerland
4 School of Oceanography, University of Washington, Seattle, WA, United States
5 Department of Earth and Environmental Sciences, Michigan State University, East Lansing, Michigan, United States
DOI
10.7287/peerj.preprints.2315v1
Published
Accepted
Subject Areas
Ecology, Environmental Sciences, Genomics, Marine Biology, Microbiology
Keywords
metagenomics, serpentinization, methanogenesis
Copyright
© 2016 Brazelton et al.
Licence
This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ Preprints) and either DOI or URL of the article must be cited.
Cite this article
Brazelton WJ, Thornton CN, Hyer A, Twing KI, Longino AA, Lang SQ, Lilley MD, Früh-Green GL, Schrenk MO. 2016. Metagenomic identification of active methanogens and methanotrophs in serpentinite springs of the Voltri Massif, Italy. PeerJ Preprints 4:e2315v1

Abstract

The production of hydrogen and methane by geochemical reactions associated with the serpentinization of ultramafic rocks can potentially support subsurface microbial ecosystems independent of the photosynthetic biosphere. Methanogenic and methanotrophic microorganisms are abundant in marine hydrothermal systems heavily influenced by serpentinization, but evidence for methane-cycling archaea and bacteria in continental serpentinite springs has been limited. This report provides metagenomic and experimental evidence for active methanogenesis and methanotrophy by microbial communities in serpentinite springs of the Voltri Massif, Italy. Methanogens belonging to family Methanobacteriaceae and methanotrophic bacteria belonging to family Methylococcaceae were heavily enriched in three ultrabasic springs (pH 12). Metagenomic data also suggest the potential for hydrogen oxidation, hydrogen production, carbon fixation, fermentation, and organic acid metabolism in the ultrabasic springs. The predicted metabolic capabilities are consistent with an active subsurface ecosystem supported by energy and carbon liberated by geochemical reactions within the serpentinite rocks of the Voltri Massif.

Author Comment

This is a submission to PeerJ for review.

Supplemental Information

16S rRNA taxonomy table, bacterial family

DOI: 10.7287/peerj.preprints.2315v1/supp-1

16S rRNA taxonomy table, bacterial sequence

DOI: 10.7287/peerj.preprints.2315v1/supp-2

16S rRNA taxonomy table, archaeal family

DOI: 10.7287/peerj.preprints.2315v1/supp-3

16S rRNA taxonomy table, archaeal sequence

DOI: 10.7287/peerj.preprints.2315v1/supp-4

Metagenome PhyloSift taxonomy table

DOI: 10.7287/peerj.preprints.2315v1/supp-5

Metagenome PhyloSift taxonomy Krona graphs

DOI: 10.7287/peerj.preprints.2315v1/supp-6

Metagenome metabolic pathway abundances

DOI: 10.7287/peerj.preprints.2315v1/supp-7

Metagenome key protein abundances

DOI: 10.7287/peerj.preprints.2315v1/supp-8

Additional Information

Competing Interests

The authors declare that they have no competing interests.

Author Contributions

William J Brazelton conceived and designed the experiments, performed the experiments, analyzed the data, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.

Christopher N Thornton analyzed the data, wrote the paper, reviewed drafts of the paper.

Alex Hyer analyzed the data, reviewed drafts of the paper.

Katrina I Twing conceived and designed the experiments, performed the experiments, analyzed the data, wrote the paper, reviewed drafts of the paper.

August A Longino analyzed the data, reviewed drafts of the paper.

Susan Q Lang conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, reviewed drafts of the paper.

Marvin D Lilley conceived and designed the experiments, performed the experiments, contributed reagents/materials/analysis tools, reviewed drafts of the paper.

Gretchen L Früh-Green conceived and designed the experiments, contributed reagents/materials/analysis tools, wrote the paper, reviewed drafts of the paper.

Matthew O Schrenk conceived and designed the experiments, contributed reagents/materials/analysis tools, wrote the paper, reviewed drafts of the paper.

DNA Deposition

The following information was supplied regarding the deposition of DNA sequences:

VAMPS database (http://vamps.mbl.edu) under the project code DCO_BRZ and sample code Serp_LIG.

MG-RAST under IDs 4545477.3, 4545478.3, 4545479.3, 4545480.3, 4537863.3, 4537864.3, 4537868.3, and 4537869.3.

SRA identifier SRP049438 and BioProject PRJNA265986.

Data Deposition

The following information was supplied regarding data availability:

https://github.com/Brazelton-Lab

Funding

WJB received funding from a NASA Astrobiology Institute Postdoctoral Fellowship and University of Utah start-up funds. Additional funding to the Schrenk lab was provided by the Alfred P. Sloan Foundation’s Deep Carbon Observatory and the NASA Astrobiology Institute (NASA-CAN5 through the Carnegie Institution for Science). SQL and GLFG were funded by SNF Project 200020 14389. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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Metagenomic identification of active methanogens and methanotrophs in serpentinite springs of the Voltri Massif, Italy
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