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Takamiya H, Kouduka M, Suzuki Y. The Deep Rocky Biosphere: New Geomicrobiological Insights and Prospects. Front Microbiol 2021; 12:785743. [PMID: 34917063 PMCID: PMC8670094 DOI: 10.3389/fmicb.2021.785743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 11/08/2021] [Indexed: 12/02/2022] Open
Abstract
Rocks that react with liquid water are widespread but spatiotemporally limited throughout the solar system, except for Earth. Rock-forming minerals with high iron content and accessory minerals with high amounts of radioactive elements are essential to support rock-hosted microbial life by supplying organics, molecular hydrogen, and/or oxidants. Recent technological advances have broadened our understanding of the rocky biosphere, where microbial inhabitation appears to be difficult without nutrient and energy inputs from minerals. In particular, microbial proliferation in igneous rock basements has been revealed using innovative geomicrobiological techniques. These recent findings have dramatically changed our perspective on the nature and the extent of microbial life in the rocky biosphere, microbial interactions with minerals, and the influence of external factors on habitability. This study aimed to gather information from scientific and/or technological innovations, such as omics-based and single-cell level characterizations, targeting deep rocky habitats of organisms with minimal dependence on photosynthesis. By synthesizing pieces of rock-hosted life, we can explore the evo-phylogeny and ecophysiology of microbial life on Earth and the life’s potential on other planetary bodies.
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Affiliation(s)
- Hinako Takamiya
- Department of Earth and Planetary Science, The University of Tokyo, Bunkyo, Japan
| | - Mariko Kouduka
- Department of Earth and Planetary Science, The University of Tokyo, Bunkyo, Japan
| | - Yohey Suzuki
- Department of Earth and Planetary Science, The University of Tokyo, Bunkyo, Japan
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Escudero C, Oggerin M, Amils R. The deep continental subsurface: the dark biosphere. Int Microbiol 2018; 21:3-14. [DOI: 10.1007/s10123-018-0009-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 05/08/2018] [Accepted: 05/09/2018] [Indexed: 11/28/2022]
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Ino K, Hernsdorf AW, Konno U, Kouduka M, Yanagawa K, Kato S, Sunamura M, Hirota A, Togo YS, Ito K, Fukuda A, Iwatsuki T, Mizuno T, Komatsu DD, Tsunogai U, Ishimura T, Amano Y, Thomas BC, Banfield JF, Suzuki Y. Ecological and genomic profiling of anaerobic methane-oxidizing archaea in a deep granitic environment. ISME JOURNAL 2017; 12:31-47. [PMID: 28885627 DOI: 10.1038/ismej.2017.140] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Revised: 07/06/2017] [Accepted: 07/25/2017] [Indexed: 01/14/2023]
Abstract
Recent single-gene-based surveys of deep continental aquifers demonstrated the widespread occurrence of archaea related to Candidatus Methanoperedens nitroreducens (ANME-2d) known to mediate anaerobic oxidation of methane (AOM). However, it is unclear whether ANME-2d mediates AOM in the deep continental biosphere. In this study, we found the dominance of ANME-2d in groundwater enriched in sulfate and methane from a 300-m deep underground borehole in granitic rock. A near-complete genome of one representative species of the ANME-2d obtained from the underground borehole has most of functional genes required for AOM and assimilatory sulfate reduction. The genome of the subsurface ANME-2d is different from those of other members of ANME-2d by lacking functional genes encoding nitrate and nitrite reductases and multiheme cytochromes. In addition, the subsurface ANME-2d genome contains a membrane-bound NiFe hydrogenase gene putatively involved in respiratory H2 oxidation, which is different from those of other methanotrophic archaea. Short-term incubation of microbial cells collected from the granitic groundwater with 13C-labeled methane also demonstrates that AOM is linked to microbial sulfate reduction. Given the prominence of granitic continental crust and sulfate and methane in terrestrial subsurface fluids, we conclude that AOM may be widespread in the deep continental biosphere.
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Affiliation(s)
- Kohei Ino
- Department of Earth and Planetary Science, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Alex W Hernsdorf
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Uta Konno
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, Japan
| | - Mariko Kouduka
- Department of Earth and Planetary Science, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Katsunori Yanagawa
- Graduate School of Environmental Engineering, The University of Kitakyushu, Kitakyushu, Fukuoka, Japan
| | - Shingo Kato
- Ore Genesis Research Unit, Project Team for Development of New-generation Research Protocol for Submarine Resources, JAMSTEC (Japan Agency for Marine-Earth Science and Technology), Yokosuka City, Kanagawa, Japan
| | - Michinari Sunamura
- Department of Earth and Planetary Science, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Akinari Hirota
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, Japan
| | - Yoko S Togo
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, Japan
| | - Kazumasa Ito
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, Japan
| | - Akari Fukuda
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, Japan.,Japan Atomic Energy Agency, Naka-gun, Ibaraki, Japan
| | | | | | - Daisuke D Komatsu
- Graduate School of Environmental Studies, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, Japan
| | - Urumu Tsunogai
- Graduate School of Environmental Studies, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, Japan
| | - Toyoho Ishimura
- National Institute of Technology, Ibaraki College, Hitachinaka-shi, Ibaraki, Japan
| | - Yuki Amano
- Japan Atomic Energy Agency, Naka-gun, Ibaraki, Japan
| | - Brian C Thomas
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Jillian F Banfield
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA.,Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Yohey Suzuki
- Department of Earth and Planetary Science, Graduate School of Science, The University of Tokyo, Tokyo, Japan
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Ino K, Konno U, Kouduka M, Hirota A, Togo YS, Fukuda A, Komatsu D, Tsunogai U, Tanabe AS, Yamamoto S, Iwatsuki T, Mizuno T, Ito K, Suzuki Y. Deep microbial life in high-quality granitic groundwater from geochemically and geographically distinct underground boreholes. ENVIRONMENTAL MICROBIOLOGY REPORTS 2016; 8:285-294. [PMID: 26743638 DOI: 10.1111/1758-2229.12379] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2015] [Revised: 12/30/2015] [Accepted: 12/30/2015] [Indexed: 06/05/2023]
Abstract
Deep granitic aquifer is one of the largest, but least understood, microbial habitats. To avoid contamination from the surface biosphere, underground drilling was conducted for 300 m deep granitic rocks at the Mizunami underground research laboratory (URL), Japan. Slightly alkaline groundwater was characterized by low concentrations of dissolved organic matter and sulfate and the presence of > 100 nM H2 . The initial biomass was the highest (∼10(5) cells ml(-1) ) with the dominance of Hydrogenophaga spp., whereas the phylum Nitrospirae became predominant after 3 years with decreasing biomass (∼10(4) cells ml(-1) ). One week incubation of groundwater microbes after 3 years with (13) C-labelled bicarbonate and 1% H2 and subsequent single-cell imaging with nanometer-scale secondary ion mass spectrometry demonstrated that microbial cells were metabolically active. Pyrosequencing of microbial communities in groundwater retrieved at 3-4 years after drilling at the Mizunami URL and at 14 and 25 years after the drilling at the Grimsel Test Site, Switzerland, revealed the occurrence of common Nitrospirae lineages at the geographically distinct sites. As the close relatives of the Nitrospirae lineages were exclusively detected from deep groundwaters and terrestrial hot springs, it suggests that these bacteria are indigenous and potentially adapted to the deep terrestrial subsurface.
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Affiliation(s)
- Kohei Ino
- Graduate School of Science, The University of Tokyo, 7-3-1 Hongo Bunkyo-ku, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Uta Konno
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology, Higashi 1-1-1, Tsukuba, Ibaraki, 305-8567, Japan
| | - Mariko Kouduka
- Graduate School of Science, The University of Tokyo, 7-3-1 Hongo Bunkyo-ku, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Akinari Hirota
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology, Higashi 1-1-1, Tsukuba, Ibaraki, 305-8567, Japan
| | - Yoko S Togo
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology, Higashi 1-1-1, Tsukuba, Ibaraki, 305-8567, Japan
| | - Akari Fukuda
- Japan Atomic Energy Agency, 1-64 Yamanouchi, Akiyo-cho, Mizunami, Gifu, 509-6132, Japan
| | - Daisuke Komatsu
- Graduate School of Environmental Studies, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8601, Japan
| | - Urumu Tsunogai
- Graduate School of Environmental Studies, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8601, Japan
| | - Akihumi S Tanabe
- Graduate School of Global Environmental Studies, Kyoto University, Yoshida-nihonmatsu-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Satoshi Yamamoto
- Graduate School of Global Environmental Studies, Kyoto University, Yoshida-nihonmatsu-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Teruki Iwatsuki
- Japan Atomic Energy Agency, 1-64 Yamanouchi, Akiyo-cho, Mizunami, Gifu, 509-6132, Japan
| | - Takashi Mizuno
- Japan Atomic Energy Agency, 1-64 Yamanouchi, Akiyo-cho, Mizunami, Gifu, 509-6132, Japan
| | - Kazumasa Ito
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology, Higashi 1-1-1, Tsukuba, Ibaraki, 305-8567, Japan
| | - Yohey Suzuki
- Graduate School of Science, The University of Tokyo, 7-3-1 Hongo Bunkyo-ku, Bunkyo-ku, Tokyo, 113-0033, Japan
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Suzuki Y, Mukai H, Ishimura T, Yokoyama TD, Sakata S, Hirata T, Iwatsuki T, Mizuno T. Formation and Geological Sequestration of Uranium Nanoparticles in Deep Granitic Aquifer. Sci Rep 2016; 6:22701. [PMID: 26948389 PMCID: PMC4780221 DOI: 10.1038/srep22701] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 02/22/2016] [Indexed: 11/09/2022] Open
Abstract
The stimulation of bacterial activities that convert hexavalent uranium, U(VI), to tetravalent uranium, U(IV), appears to be feasible for cost-effective remediation of contaminated aquifers. However, U(VI) reduction typically results in the precipitation of U(IV) particles less than 5 nanometers in diameter, except for environmental conditions enriched with iron. Because these tiny particles are mobile and susceptible to oxidative dissolution after the termination of nutrient injection, in situ bioremediation remains to be impractical. Here we show that U(IV) nanoparticles of coffinite (U(SiO4)1-x(OH)4x) formed in fracture-filling calcium carbonate in a granitic aquifer. In situ U-Pb isotope dating demonstrates that U(IV) nanoparticles have been sequestered in the calcium carbonate for at least 1 million years. As the microbiologically induced precipitation of calcium carbonate in aquifer systems worldwide is extremely common, we anticipate simultaneous stimulation of microbial activities for precipitation reactions of calcium carbonate and U(IV) nanoparticles, which leads to long-term sequestration of uranium and other radionuclides in contaminated aquifers and deep geological repositories.
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Affiliation(s)
- Yohey Suzuki
- Graduate School of Science, The University of Tokyo, 7-3-1 Hongo Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hiroki Mukai
- Graduate School of Science, The University of Tokyo, 7-3-1 Hongo Bunkyo-ku, Tokyo 113-0033, Japan
| | - Toyoho Ishimura
- National Institute of Technology, Ibaraki College, 866 Nakane, Hitachinaka-shi, Ibaraki 312-8508, Japan
| | - Takaomi D Yokoyama
- Graduate School of Science, The University of Tokyo, 7-3-1 Hongo Bunkyo-ku, Tokyo 113-0033, Japan
| | - Shuhei Sakata
- Division of Earth &Planetary Sciences, Kyoto University, Kitashirakawa Oiwakesho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Takafumi Hirata
- Division of Earth &Planetary Sciences, Kyoto University, Kitashirakawa Oiwakesho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Teruki Iwatsuki
- Japan Atomic Energy Agency (JAEA), 1-64 Yamanouchi, Akeyo-cho, Mizunami, Gifu 509-6132, Japan
| | - Takashi Mizuno
- Japan Atomic Energy Agency (JAEA), 1-64 Yamanouchi, Akeyo-cho, Mizunami, Gifu 509-6132, Japan
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A Post-Genomic View of the Ecophysiology, Catabolism and Biotechnological Relevance of Sulphate-Reducing Prokaryotes. Adv Microb Physiol 2015. [PMID: 26210106 DOI: 10.1016/bs.ampbs.2015.05.002] [Citation(s) in RCA: 173] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Dissimilatory sulphate reduction is the unifying and defining trait of sulphate-reducing prokaryotes (SRP). In their predominant habitats, sulphate-rich marine sediments, SRP have long been recognized to be major players in the carbon and sulphur cycles. Other, more recently appreciated, ecophysiological roles include activity in the deep biosphere, symbiotic relations, syntrophic associations, human microbiome/health and long-distance electron transfer. SRP include a high diversity of organisms, with large nutritional versatility and broad metabolic capacities, including anaerobic degradation of aromatic compounds and hydrocarbons. Elucidation of novel catabolic capacities as well as progress in the understanding of metabolic and regulatory networks, energy metabolism, evolutionary processes and adaptation to changing environmental conditions has greatly benefited from genomics, functional OMICS approaches and advances in genetic accessibility and biochemical studies. Important biotechnological roles of SRP range from (i) wastewater and off gas treatment, (ii) bioremediation of metals and hydrocarbons and (iii) bioelectrochemistry, to undesired impacts such as (iv) souring in oil reservoirs and other environments, and (v) corrosion of iron and concrete. Here we review recent advances in our understanding of SRPs focusing mainly on works published after 2000. The wealth of publications in this period, covering many diverse areas, is a testimony to the large environmental, biogeochemical and technological relevance of these organisms and how much the field has progressed in these years, although many important questions and applications remain to be explored.
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