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Patterns of in situ Mineral Colonization by Microorganisms in a ~60°C Deep Continental Subsurface Aquifer

Mullin, Sean W. and Wanger, Greg and Kruger, Brittany R. and Sackett, Joshua D. and Hamilton-Brehm, Scott D. and Bhartia, Rohit and Amend, Jan P. and Moser, Duane P. and Orphan, Victoria J. (2020) Patterns of in situ Mineral Colonization by Microorganisms in a ~60°C Deep Continental Subsurface Aquifer. Frontiers in Microbiology, 11 . Art. No. 536535. ISSN 1664-302X. PMCID PMC7711152. doi:10.3389/fmicb.2020.536535.

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The microbial ecology of the deep biosphere is difficult to characterize, owing in part to sampling challenges and poorly understood response mechanisms to environmental change. Pre-drilled wells, including oil wells or boreholes, offer convenient access, but sampling is frequently limited to the water alone, which may provide only a partial view of the native diversity. Mineral heterogeneity demonstrably affects colonization by deep biosphere microorganisms, but the connections between the mineral-associated and planktonic communities remain unclear. To understand the substrate effects on microbial colonization and the community response to changes in organic carbon, we conducted an 18-month series of in situ experiments in a warm (57°C), anoxic, fractured carbonate aquifer at 752 m depth using replicate open, screened cartridges containing different solid substrates, with a proteinaceous organic matter perturbation halfway through this series. Samples from these cartridges were analyzed microscopically and by Illumina (iTag) 16S rRNA gene libraries to characterize changes in mineralogy and the diversity of the colonizing microbial community. The substrate-attached and planktonic communities were significantly different in our data, with some taxa (e.g., Candidate Division KB-1) rare or undetectable in the first fraction and abundant in the other. The substrate-attached community composition also varied significantly with mineralogy, such as with two Rhodocyclaceae OTUs, one of which was abundant on carbonate minerals and the other on silicic substrates. Secondary sulfide mineral formation, including iron sulfide framboids, was observed on two sets of incubated carbonates. Notably, microorganisms were attached to the framboids, which were correlated with abundant Sulfurovum and Desulfotomaculum sp. sequences in our analysis. Upon organic matter perturbation, mineral-associated microbial diversity differences were temporarily masked by the dominance of putative heterotrophic taxa in all samples, including OTUs identified as Caulobacter, Methyloversatilis, and Pseudomonas. Subsequent experimental deployments included a methanogen-dominated stage (Methanobacteriales and Methanomicrobiales) 6 months after the perturbation and a return to an assemblage similar to the pre-perturbation community after 9 months. Substrate-associated community differences were again significant within these subsequent phases, however, demonstrating the value of in situ time course experiments to capture a fraction of the microbial assemblage that is frequently difficult to observe in pre-drilled wells.

Item Type:Article
Related URLs:
URLURL TypeDescription CentralArticle
Mullin, Sean W.0000-0002-6225-3279
Hamilton-Brehm, Scott D.0000-0002-7474-207X
Bhartia, Rohit0000-0002-1434-7481
Amend, Jan P.0000-0003-4953-7776
Moser, Duane P.0000-0003-2825-5753
Orphan, Victoria J.0000-0002-5374-6178
Additional Information:© 2020 Mullin, Wanger, Kruger, Sackett, Hamilton-Brehm, Bhartia, Amend, Moser and Orphan. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. Received: 20 February 2020. Accepted: 24 September 2020. Published: 19 November 2020. Samples were obtained under scientific research permit DEVA-2013-SCI-0069, issued to DM from the U.S. National Park Service (NPS), and we thank Terry Fisk, Richard Friese, Josh Hoines, Genne Nelson, and Kevin Wilson of the NPS and Alisa Lembke of the Inyo County Planning Commission for site access. We extend our thanks also to John Healey, Brad Lyles, and Chuck Russell of the Desert Research Institute, John Bredehoeft and Michael King of The Hydronamics Group, LLC for logistical assistance; and Rachel Gates, Stephanie Connon, Haley Sapers, Daan Speth, Erin Bertrand, Ted Present, and Elizabeth Trembath-Reichert for occasional field and lab assistance. Thanks also to Bill Willborn and others from the DOE UGTA program for allowing use of their downhole logging system. This work was supported by the NASA Astrobiology Institute “Life Underground” project (NNA13AA92A) and the Center for Dark Energy Biosphere Investigations (C-DEBI). SM received additional support from an NIH Training Grant. JS was partially supported by a NASA Space Grant Consortium Fellowship. Author Contributions. SM coordinated field experiment set-up and sampling and performed DNA sequencing, sequence analysis, microscopy, and gas chromatography. GW coordinated field sampling, including the design of the in situ suspension line and provided microscopy data. BK, JS, and SH-B performed field sampling. Additionally, BK and JS coordinated retrieval and processing of geochemistry analyses. SH-B performed phase contrast cell counts. DM supervised BK, JS, and SH-B, identified and secured the field site, co-wrote the funding proposal, and organized downhole logging. RB, JA, and VO co-wrote the proposal and supervised field activities. VO helped conceive the experimental design and supervised SM. All authors contributed to the article and approved the submitted version. Data Availability Statement. The datasets generated for this study can be found in the NCBI SRA # PRJNA605066. Conflict of Interest. Two authors declared commercial interests at the time of publication but not during the period of data collection: GW is employed by Oberland Agriscience, Inc., and RB is employed by Photon Systems, Inc. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
Funding AgencyGrant Number
Center for Dark Energy Biosphere InvestigationsUNSPECIFIED
NIH Predoctoral FellowshipUNSPECIFIED
Subject Keywords:microbial ecology, deep biosphere, fractured rock, mineral colonization, microbial succession, carbonate, pyrite, methanogenesis
PubMed Central ID:PMC7711152
Record Number:CaltechAUTHORS:20201224-085808375
Persistent URL:
Official Citation:Mullin SW, Wanger G, Kruger BR, Sackett JD, Hamilton-Brehm SD, Bhartia R, Amend JP, Moser DP and Orphan VJ (2020) Patterns of in situ Mineral Colonization by Microorganisms in a ~60°C Deep Continental Subsurface Aquifer. Front. Microbiol. 11:536535. doi: 10.3389/fmicb.2020.536535
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:107283
Deposited By: George Porter
Deposited On:04 Jan 2021 15:39
Last Modified:16 Nov 2021 19:01

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