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Itävaara M, Salavirta H, Marjamaa K, Ruskeeniemi T. Geomicrobiology and Metagenomics of Terrestrial Deep Subsurface Microbiomes. ADVANCES IN APPLIED MICROBIOLOGY 2016; 94:1-77. [PMID: 26917241 DOI: 10.1016/bs.aambs.2015.12.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Fractures in the deep subsurface of Earth's crust are inhabited by diverse microbial communities that participate in biogeochemical cycles of the Earth. Life on Earth, which arose c. 3.5-4.0 billion years ago, reaches down at least 5 km in the crust. Deep mines, caves, and boreholes have provided scientists with opportunities to sample deep subsurface microbiomes and to obtain information on the species diversity and functions. A wide variety of bacteria, archaea, eukaryotes, and viruses are now known to reside in the crust, but their functions are still largely unknown. The crust at different depths has varying geological composition and hosts endemic microbiomes accordingly. The diversity is driven by geological formations and gases evolving from deeper depths. Cooperation among different species is still mostly unexplored, but viruses are known to restrict density of bacterial and archaeal populations. Due to the complex growth requirements of the deep subsurface microbiomes, the new knowledge about their diversity and functions is mostly obtained by molecular methods, eg, meta'omics'. Geomicrobiology is a multidisciplinary research area combining disciplines from geology, mineralogy, geochemistry, and microbiology. Geomicrobiology is concerned with the interaction of microorganisms and geological processes. At the surface of mineralogical or rock surfaces, geomicrobial processes occur mainly under aerobic conditions. In the deep subsurface, however, the environmental conditions are reducing and anaerobic. The present chapter describes the world of microbiomes in deep terrestrial geological environments as well as metagenomic and metatranscriptomic methods suitable for studies of these enigmatic communities.
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Affiliation(s)
- M Itävaara
- VTT Technical Research Centre of Finland Ltd, Espoo, Finland
| | - H Salavirta
- VTT Technical Research Centre of Finland Ltd, Espoo, Finland
| | - K Marjamaa
- VTT Technical Research Centre of Finland Ltd, Espoo, Finland
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Wilkins MJ, Daly RA, Mouser PJ, Trexler R, Sharma S, Cole DR, Wrighton KC, Biddle JF, Denis EH, Fredrickson JK, Kieft TL, Onstott TC, Peterson L, Pfiffner SM, Phelps TJ, Schrenk MO. Trends and future challenges in sampling the deep terrestrial biosphere. Front Microbiol 2014; 5:481. [PMID: 25309520 PMCID: PMC4162470 DOI: 10.3389/fmicb.2014.00481] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Accepted: 08/27/2014] [Indexed: 11/28/2022] Open
Abstract
Research in the deep terrestrial biosphere is driven by interest in novel biodiversity and metabolisms, biogeochemical cycling, and the impact of human activities on this ecosystem. As this interest continues to grow, it is important to ensure that when subsurface investigations are proposed, materials recovered from the subsurface are sampled and preserved in an appropriate manner to limit contamination and ensure preservation of accurate microbial, geochemical, and mineralogical signatures. On February 20th, 2014, a workshop on "Trends and Future Challenges in Sampling The Deep Subsurface" was coordinated in Columbus, Ohio by The Ohio State University and West Virginia University faculty, and sponsored by The Ohio State University and the Sloan Foundation's Deep Carbon Observatory. The workshop aims were to identify and develop best practices for the collection, preservation, and analysis of terrestrial deep rock samples. This document summarizes the information shared during this workshop.
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Affiliation(s)
- Michael J. Wilkins
- School of Earth Sciences, The Ohio State UniversityColumbus, OH, USA
- Department of Microbiology, The Ohio State UniversityColumbus, OH, USA
| | - Rebecca A. Daly
- Department of Microbiology, The Ohio State UniversityColumbus, OH, USA
| | - Paula J. Mouser
- Department of Engineering, The Ohio State UniversityColumbus, OH, USA
| | - Ryan Trexler
- Department of Engineering, The Ohio State UniversityColumbus, OH, USA
| | - Shihka Sharma
- Department of Geology and Geography, West Virginia UniversityMorgantown, WV, USA
| | - David R. Cole
- School of Earth Sciences, The Ohio State UniversityColumbus, OH, USA
| | - Kelly C. Wrighton
- Department of Microbiology, The Ohio State UniversityColumbus, OH, USA
| | - Jennifer F. Biddle
- College of Earth, Ocean, and Environment, University of DelawareLewes, DE, USA
| | | | - Jim K. Fredrickson
- Biological Sciences Division, Pacific Northwest National LaboratoryRichland, WA, USA
| | | | | | | | - Susan M. Pfiffner
- Center for Environmental Biotechnology, University of TennesseeKnoxville, TN, USA
| | - Tommy J. Phelps
- Center for Environmental Biotechnology, University of TennesseeKnoxville, TN, USA
| | - Matthew O. Schrenk
- Department of Geological Sciences, Michigan State UniversityEast Lansing, MI, USA
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