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Methyl-compound use and slow growth characterize microbial life in 2-km-deep subseafloor coal and shale beds

Trembath-Reichert, Elizabeth and Morono, Yuki and Ijiri, Akira and Hoshino, Tatsuhiko and Dawson, Katherine S. and Inagaki, Fumio and Orphan, Victoria J. (2017) Methyl-compound use and slow growth characterize microbial life in 2-km-deep subseafloor coal and shale beds. Proceedings of the National Academy of Sciences of the United States of America, 114 (44). E9206-E9215. ISSN 0027-8424. PMCID PMC5676895. http://resolver.caltech.edu/CaltechAUTHORS:20171005-093343465

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Abstract

The past decade of scientific ocean drilling has revealed seemingly ubiquitous, slow-growing microbial life within a range of deep biosphere habitats. Integrated Ocean Drilling Program Expedition 337 expanded these studies by successfully coring Miocene-aged coal beds 2 km below the seafloor hypothesized to be “hot spots” for microbial life. To characterize the activity of coal-associated microorganisms from this site, a series of stable isotope probing (SIP) experiments were conducted using intact pieces of coal and overlying shale incubated at in situ temperatures (45 °C). The 30-month SIP incubations were amended with deuterated water as a passive tracer for growth and different combinations of ^(13)C- or ^(15)N-labeled methanol, methylamine, and ammonium added at low (micromolar) concentrations to investigate methylotrophy in the deep subseafloor biosphere. Although the cell densities were low (50–2,000 cells per cubic centimeter), bulk geochemical measurements and single-cell–targeted nanometer-scale secondary ion mass spectrometry demonstrated active metabolism of methylated substrates by the thermally adapted microbial assemblage, with differing substrate utilization profiles between coal and shale incubations. The conversion of labeled methylamine and methanol was predominantly through heterotrophic processes, with only minor stimulation of methanogenesis. These findings were consistent with in situ and incubation 16S rRNA gene surveys. Microbial growth estimates in the incubations ranged from several months to over 100 y, representing some of the slowest direct measurements of environmental microbial biosynthesis rates. Collectively, these data highlight a small, but viable, deep coal bed biosphere characterized by extremely slow-growing heterotrophs that can utilize a diverse range of carbon and nitrogen substrates.


Item Type:Article
Related URLs:
URLURL TypeDescription
https://doi.org/10.1073/pnas.1707525114DOIArticle
http://www.pnas.org/content/114/44/E9206PublisherArticle
http://www.pnas.org/lookup/suppl/doi:10.1073/pnas.1707525114/-/DCSupplementalPublisherSupporting Information
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5676895PubMed CentralArticle
ORCID:
AuthorORCID
Orphan, Victoria J.0000-0002-5374-6178
Additional Information:© 2017 National Academy of Sciences. Freely available online through the PNAS open access option. NAS retains a nonexclusive License to Publish, and these articles are distributed under a CC BY-NC-ND license. Edited by David M. Karl, University of Hawaii, Honolulu, HI, and approved September 6, 2017 (received for review May 5, 2017). Published online before print October 3, 2017. We thank the IODP for providing access and samples from the deep coalbed biosphere off Shimokita during Expedition 337. We thank the crew, drilling team members, laboratory technicians, and scientists on the drilling vessel Chikyu for supporting core sampling and onboard measurements. We also thank S. Fukunaga, S. Hashimoto, and A. Imajo [Japan Agency for Marine-Earth Science and Technology (JAMSTEC)] and T. Terada (Marine Works Japan, Ltd) for assistance in microbiological analyses; Y. Guan, F. Wu, C. Ma, and N. Dalleska (Caltech) for assistance with geochemical analyses; and A. L. Sessions, G. L. Chadwick, K. S. Metcalfe, M. K. Lloyd, and S. Kopf (Caltech) and H. Imachi (JAMSTEC) for feedback and valuable discussions. We appreciate the comments of two reviewers that also improved this manuscript. Funding for this work was provided by the Center for Dark Energy Biosphere (C-DEBI), NASA Astrobiology-Life Underground (NAI-LU; Award NNA13AA92A), the Gordon and Betty Moore Foundation Grant GBMF3780 (to V.J.O.), and Post Expedition Award (to E.T.-R. and V.J.O.), the Japan Society for the Promotion of Science (JSPS) Strategic Fund for Strengthening Leading-Edge Research and Development (F.I. and JAMSTEC), the JSPS Funding Program for Next Generation World-Leading Researchers (NEXT Program, Grant GR102 to F.I.), and JSPS Grants-in-Aid for Science Research (Grant 26251041 to F.I.; Grant 15K14907 to T.H.; and Grants 24687004, 15H05608, 24651018, 2665169, and 16K14817 to Y.M.). E.T.-R. was additionally supported, in part, by a Schlanger Ocean Drilling Fellowship, a C-DEBI travel grant for sample processing at the JAMSTEC Kochi Institute for Core Sample Research, and the Deep Life Cultivation Internship Program from the Deep Carbon Observatory (DCO). This is C-DEBI Grant contribution no. 389 and NAI-LU no. 314. Author contributions: E.T.-R., Y.M., F.I., and V.J.O. designed research; E.T.-R. performed research; Y.M., A.I., and T.H. contributed new reagents/analytic tools; E.T.-R., Y.M., A.I., T.H., K.S.D., and V.J.O. analyzed data; and E.T.-R., Y.M., K.S.D., F.I., and V.J.O. wrote the paper. The authors declare no conflict of interest. This article is a PNAS Direct Submission. Data deposition: Data are available at National Center for Biotechnology Information (NCBI) BioProject, https://www.ncbi.nlm.nih.gov/bioproject/ (PRJNA381552) and NCBI BioSample, https://www.ncbi.nlm.nih.gov/biosample/ (SAMN06676442-48). BioSamples are identified in Dataset S2. Nanometer-scale secondary ion mass spectrometry and geochemical data are available at Biological and Chemical Oceanography Data Management Office (https://www.bco-dmo.org/projects; Project 672592). This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1707525114/-/DCSupplemental.
Funders:
Funding AgencyGrant Number
Center for Dark Energy Biosphere InvestigationsUNSPECIFIED
NASANNA13AA92A
Gordon and Betty Moore FoundationGBMF3780
Post Expedition AwardUNSPECIFIED
Japan Society for the Promotion of Science (JSPS)GR102
Japan Society for the Promotion of Science (JSPS)26251041
Japan Society for the Promotion of Science (JSPS)15K14907
Japan Society for the Promotion of Science (JSPS)24687004
Japan Society for the Promotion of Science (JSPS)15H05608
Japan Society for the Promotion of Science (JSPS)24651018
Japan Society for the Promotion of Science (JSPS)2665169
Japan Society for the Promotion of Science (JSPS)16K14817
Schlanger Ocean Drilling FellowshipUNSPECIFIED
Deep Carbon ObservatoryUNSPECIFIED
Subject Keywords:subseafloor life; coal bed biosphere; NanoSIMS; stable isotope probing; microbial generation time
PubMed Central ID:PMC5676895
Record Number:CaltechAUTHORS:20171005-093343465
Persistent URL:http://resolver.caltech.edu/CaltechAUTHORS:20171005-093343465
Official Citation:Elizabeth Trembath-Reichert, Yuki Morono, Akira Ijiri, Tatsuhiko Hoshino, Katherine S. Dawson, Fumio Inagaki, and Victoria J. Orphan Methyl-compound use and slow growth characterize microbial life in 2-km-deep subseafloor coal and shale beds PNAS 2017 114 (44) E9206-E9215; published ahead of print October 3, 2017, doi:10.1073/pnas.1707525114
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:82111
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:05 Oct 2017 16:50
Last Modified:16 Nov 2017 16:02

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