The deep continental subsurface: the dark biosphere

The deep continental subsurface: the dark biosphere Although information from devoted geomicrobiological drilling studies is limited, it is clear that the results obtained so far call for a systematic exploration of the deep continental subsurface, similar to what has been accomplished in recent years by the Ocean Drilling Initiatives. In addition to devoted drillings from the surface, much of the continental subsurface data has been obtained using different subterranean “windows,” each with their correspondent limitations. In general, the number and diversity of microorganisms decrease with depth, and the abundance of Bacteria is superior to Archaea. Within Bacteria, the most commonly detected phyla correspond to Proteobacteria, Actinobacteria, Bacteroidetes, and Firmicutes. Within Archaea, methanogens are recurrently detected in most analyzed subsurface samples. One of the most controversial topics in the study of subsurface environments is whether the available energy source is endogenous or partly dependent on products photosynthetically generated in the subsurface. More information, at better depth resolution, is needed to build up the catalog of deep subsurface microbiota and the biologically available electron acceptors and donors. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png International Microbiology Springer Journals

The deep continental subsurface: the dark biosphere

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Publisher
Springer Journals
Copyright
Copyright © 2018 by Springer International Publishing AG, part of Springer Nature
Subject
Life Sciences; Microbiology; Medical Microbiology; Microbial Ecology; Applied Microbiology; Eukaryotic Microbiology
ISSN
1139-6709
eISSN
1618-1905
DOI
10.1007/s10123-018-0009-y
Publisher site
See Article on Publisher Site

Abstract

Although information from devoted geomicrobiological drilling studies is limited, it is clear that the results obtained so far call for a systematic exploration of the deep continental subsurface, similar to what has been accomplished in recent years by the Ocean Drilling Initiatives. In addition to devoted drillings from the surface, much of the continental subsurface data has been obtained using different subterranean “windows,” each with their correspondent limitations. In general, the number and diversity of microorganisms decrease with depth, and the abundance of Bacteria is superior to Archaea. Within Bacteria, the most commonly detected phyla correspond to Proteobacteria, Actinobacteria, Bacteroidetes, and Firmicutes. Within Archaea, methanogens are recurrently detected in most analyzed subsurface samples. One of the most controversial topics in the study of subsurface environments is whether the available energy source is endogenous or partly dependent on products photosynthetically generated in the subsurface. More information, at better depth resolution, is needed to build up the catalog of deep subsurface microbiota and the biologically available electron acceptors and donors.

Journal

International Microbiology – Springer Journals

Published: May 30, 2018

References

  • Energetics of chemolithoautotrophy in the hydrothermal system of Vulcano Island, southern Italy
    Amend, JP; Rogers, KL; Shock, EL; Gurrieri, S; Inguaggiato, S
  • Expanding frontiers in deep subsurface microbiology
    Amend, JP; Teske, A
  • Characterization by culture and molecular analysis of the microbial diversity of a deep subsurface gas storage aquifer
    Basso, O; Lascourreges, J-F; Borgne, F; Goff, C; Magot, M
  • The presence of sulphate reducing bacteria in oil field waters
    Bastin, ES; Greer, FE; Merritt, C; Moulton, G
  • Evaluation of molecular techniques in characterization of deep terrestrial biosphere
    Bomberg, M; Nyyssönen, M; Nousiainen, A; Hultman, J; Paulin, L; Auvinen, P; Itävaara, M
  • Nematoda from the terrestrial deep subsurface of South Africa
    Borgonie, G; García-Moyano, A; Litthauer, D; Bert, W; Bester, A; Heerden, E; Möller, C; Erasmus, M; Onstott, T
  • Impact disruption and recovery of the deep subsurface biosphere
    Cockell, CS; Voytek, MA; Gronstal, AL; Finster, K; Kirshtein, JD; Howard, K; Reitner, J; Gohn, GS; Sanford, WE; Horton Jr, JW
  • Submarine thermal springs on the Galapagos Rift
    Corliss, JB; Dymond, J; Gordon, LI; Edmond, JM; Herzen, RP; Ballard, RD; Green, K; Williams, D; Bainbridge, A; Crane, K
  • Environmental genomics reveals a single-species ecosystem deep within Earth
    Chivian, D; Brodie, EL; Alm, EJ; Culley, DE; Dehal, PS; DeSantis, TZ; Gihring, TM; Lapidus, A; Lin, L-H; Lowry, SR
  • Metabolic activity of subsurface life in deep-sea sediments
    D’Hondt, S; Rutherford, S; Spivack, AJ
  • Voyages of the adventure and beagle, volume III–journal and remarks, 1832–1836
    Darwin, C
  • An archaeal iron-oxidizing extreme acidophile important in acid mine drainage
    Edwards, KJ; Bond, PL; Gihring, TM; Banfield, JF
  • Electrical transport along bacterial nanowires from Shewanella oneidensis MR-1
    El-Naggar, MY; Wanger, G; Leung, KM; Yuzvinsky, TD; Southam, G; Yang, J; Lau, WM; Nealson, KH; Gorby, YA
  • Active microbial biofilms in deep poor porous continental subsurface rocks
    Escudero, C; Vera, M; Oggerin, M; Amils, R
  • Bacteriophage lytic to Desulfovibrio aespoeensis isolated from deep groundwater
    Eydal, HS; Jägevall, S; Hermansson, M; Pedersen, K
  • Geomicrobial processes and biodiversity in the deep terrestrial subsurface
    Fredrickson, JK; Balkwill, DL
  • Pore-size constraints on the activity and survival of subsurface bacteria in a late cretaceous shale-sandstone sequence, northwestern New Mexico
    Fredrickson, JK; McKinley, JP; Bjornstad, BN; Long, PE; Ringelberg, DB; White, DC; Krumholz, LR; Suflita, JM; Colwell, FS; Lehman, RM; Phelps, TJ; Onstott, TC
  • Population structure of microbial communities associated with two deep, anaerobic, alkaline aquifers
    Fry, NK; Fredrickson, JK; Fishbain, S; Wagner, M; Stahl, DA
  • Microbial ecology of the terrestrial subsurface
    Ghiorse, WC; Wilson, JT
  • The distribution of microbial taxa in the subsurface water of the Kalahari Shield, South Africa
    Gihring, T; Moser, D; Lin, L-H; Davidson, M; Onstott, T; Morgan, L; Milleson, M; Kieft, T; Trimarco, E; Balkwill, D
  • The deep, hot biosphere
    Gold, T
  • Contamination assessment in microbiological sampling of the Eyreville core, Chesapeake Bay impact structure
    Gronstal, AL; Voytek, MA; Kirshtein, JD; Nicole, M; Lowit, MD; Cockell, CS
  • Biological energy requirements as quantitative boundary conditions for life in the subsurface
    Hoehler, TM
  • Quantification of target molecules needed to detect microorganisms by fluorescence in situ hybridization (FISH) and catalyzed reporter deposition-FISH
    Hoshino, T; Yilmaz, LS; Noguera, DR; Daims, H; Wagner, M
  • Deep microbial life in high-quality granitic groundwater from geochemically and geographically distinct underground boreholes
    Ino, K; Konno, U; Kouduka, M; Hirota, A; Togo, YS; Fukuda, A; Komatsu, D; Tsunogai, U; Tanabe, AS; Yamamoto, S
  • Special paper - geological survey of Finland, vol 51. Finland
    Itävaara, M; Nyyssönen, M; Bomberg, M; Kapanen, A; Nousiainen, A; Ahonen, L; Hultman, J; Paulin, L; Auvinen, P; Kukkonen, IT
  • Hydrochemical disturbances measured in groundwater during the construction and operation of a large-scale underground facility in deep crystalline rock in Japan
    Iwatsuki, T; Hagiwara, H; Ohmori, K; Munemoto, T; Onoe, H
  • Microbial degradation of organic matter in the deep sea
    Jannasch, HW; Eimhjellen, K; Farmanfarmalan, A
  • Global distribution of microbial abundance and biomass in subseafloor sediment
    Kallmeyer, J; Pockalny, R; Adhikari, RR; Smith, DC; D’Hondt, S
  • Diversity of facultatively anaerobic microscopic mycelial fungi in soils
    Kurakov, A; Lavrent’Ev, R; Nechitailo, TY; Golyshin, P; Zvyagintsev, D
  • Viruses in granitic groundwater from 69 to 450 m depth of the Äspö hard rock laboratory, Sweden
    Kyle, JE; Eydal, HS; Ferris, FG; Pedersen, K
  • Microbiological comparison of core and groundwater samples collected from a fractured basalt aquifer with that of dialysis chambers incubated in situ
    Lehman, RM; O'Connell, SP; Banta, A; Fredrickson, JK; Reysenbach, A-L; Kieft, TL; Colwell, FS
  • Planktonic microbial communities associated with fracture-derived groundwater in a deep gold mine of South Africa
    Lin, L-H; Hall, J; Onstott, T; Gihring, T; Lollar, BS; Boice, E; Pratt, L; Lippmann-Pipke, J; Bellamy, RE
  • Living microörganisms in ancient rocks
    Lipman, CB
  • A metagenomic window into carbon metabolism at 3 km depth in Precambrian continental crust
    Magnabosco, C; Ryan, K; Lau, MC; Kuloyo, O; Lollar, BS; Kieft, TL; Heerden, E; Onstott, TC
  • Dark heterotrophic growth conditions result in an increase in the content of photosystem II units in the filamentous cyanobacterium Anabaena variabilis ATCC 29413
    Mannan, RM; Pakrasi, HB
  • Weighing the deep continental biosphere
    McMahon, S; Parnell, J
  • Energy and carbon metabolisms in a deep terrestrial subsurface fluid microbial community
    Momper, L; Jungbluth, SP; Lee, MD; Amend, JP
  • Major phylum-level differences between porefluid and host rock bacterial communities in the terrestrial deep subsurface
    Momper, L; Reese, BK; Zinke, L; Wanger, G; Osburn, MR; Moser, D; Amend, JP
  • Crystal ball: fluorescence in situ hybridization in the age of super-resolution microscopy
    Moraru, C; Amann, R
  • GeneFISH—an in situ technique for linking gene presence and cell identity in environmental microorganisms
    Moraru, C; Lam, P; Fuchs, BM; Kuypers, MM; Amann, R
  • Is H2 the universal energy source for long-term survival?
    Morita, RY
  • Desulfotomaculum and Methanobacterium spp. dominate a 4- to 5-kilometer-deep fault
    Moser, DP; Gihring, TM; Brockman, FJ; Fredrickson, JK; Balkwill, DL; Dollhopf, ME; Lollar, BS; Pratt, LM; Boice, E; Southam, G
  • Temporal shifts in the geochemistry and microbial community structure of an ultradeep mine borehole following isolation
    Moser, DP; Onstott, T; Fredrickson, JK; Brockman, FJ; Balkwill, DL; Drake, G; Pfiffner, S; White, D; Takai, K; Pratt, L
  • Abundance and viability of the groundwater microbial communities from a borehole in the Tono uranium deposit area, central Japan
    Murakami, Y; Fujita, Y; Naganuma, T; Iwatsuki, T
  • A single-cell view on the ecophysiology of anaerobic phototrophic bacteria
    Musat, N; Halm, H; Winterholler, B; Hoppe, P; Peduzzi, S; Hillion, F; Horreard, F; Amann, R; Jørgensen, BB; Kuypers, MMM
  • Hydrogen-driven subsurface lithoautotrophic microbial ecosystems (SLiMEs): do they exist and why should we care?
    Nealson, KH; Inagaki, F; Takai, K
  • Methanogenic and sulphate-reducing microbial communities in deep groundwater of crystalline rock fractures in Olkiluoto, Finland
    Nyyssönen, M; Bomberg, M; Kapanen, A; Nousiainen, A; Pitkänen, P; Itävaara, M
  • Taxonomically and functionally diverse microbial communities in deep crystalline rocks of the Fennoscandian shield
    Nyyssönen, M; Hultman, J; Ahonen, L; Kukkonen, I; Paulin, L; Laine, P; Itävaara, M; Auvinen, P
  • Indigenous and contaminant microbes in ultradeep mines
    Onstott, T; Moser, DP; Pfiffner, SM; Fredrickson, JK; Brockman, FJ; Phelps, T; White, D; Peacock, A; Balkwill, D; Hoover, R
  • Microbial ecology of the dark ocean above, at, and below the seafloor
    Orcutt, BN; Sylvan, JB; Knab, NJ; Edwards, KJ
  • Microbial life in deep granitic rock
    Pedersen, K
  • Subterranean microorganisms and radioactive waste disposal in Sweden
    Pedersen, K
  • Exploration of deep intraterrestrial microbial life: current perspectives
    Pedersen, K
  • Subterranean microbial populations metabolize hydrogen and acetate under in situ conditions in granitic groundwater at 450 m depth in the Äspö Hard Rock Laboratory, Sweden
    Pedersen, K
  • Comparison between geochemical and biological estimates of subsurface microbial activities
    Phelps, T; Murphy, E; Pfiffner, S; White, D
  • Coupling genetic and chemical microbiome profiling reveals heterogeneity of archaeome and bacteriome in subsurface biofilms that are dominated by the same archaeal species
    Probst, AJ; Birarda, G; Holman, H-YN; DeSantis, TZ; Wanner, G; Andersen, GL; Perras, AK; Meck, S; Völkel, J; Bechtel, HA
  • Tackling the minority: sulfate-reducing bacteria in an archaea-dominated subsurface biofilm
    Probst, AJ; Holman, H-YN; DeSantis, TZ; Andersen, GL; Birarda, G; Bechtel, HA; Piceno, YM; Sonnleitner, M; Venkateswaran, K; Moissl-Eichinger, C
  • “Altiarchaeales”: uncultivated Archaea from the subsurface
    Probst, AJ; Moissl-Eichinger, C
  • Biology of a widespread uncultivated archaeon that contributes to carbon fixation in the subsurface
    Probst, AJ; Weinmaier, T; Raymann, K; Perras, A; Emerson, JB; Rattei, T; Wanner, G; Klingl, A; Berg, IA; Yoshinaga, M
  • Dissecting the deep biosphere: retrieving authentic microbial communities from packer-isolated deep crystalline bedrock fracture zones
    Purkamo, L; Bomberg, M; Nyyssönen, M; Kukkonen, I; Ahonen, L; Kietäväinen, R; Itävaara, M
  • Rapid reactivation of deep subsurface microbes in the presence of C-1 compounds
    Rajala, P; Bomberg, M; Kietäväinen, R; Kukkonen, I; Ahonen, L; Nyyssönen, M; Itävaara, M
  • Feldspars as a source of nutrients for microorganisms
    Rogers, J; Bennett, P; Choi, W
  • Subsurface microbial diversity in deep-granitic-fracture water in Colorado
    Sahl, JW; Schmidt, R; Swanner, ED; Mandernack, KW; Templeton, AS; Kieft, TL; Smith, RL; Sanford, WE; Callaghan, RL; Mitton, JB
  • Microbial lithotrophic oxidation of structural Fe (II) in biotite
    Shelobolina, E; Xu, H; Konishi, H; Kukkadapu, R; Wu, T; Blöthe, M; Roden, E
  • Minerals as energy sources for microorganisms
    Shock, EL
  • Lithoautotrophic microbial ecosystems in deep basalt aquifers
    Stevens, TO; McKinley, JP
  • Microbial diversity in The Cedars, an ultrabasic, ultrareducing, and low salinity serpentinizing ecosystem
    Suzuki, S; Si, I; Wu, A; Cheung, A; Tenney, A; Wanger, G; Kuenen, JG; Nealson, KH
  • Biogeochemical signals from deep microbial life in terrestrial crust
    Suzuki, Y; Konno, U; Fukuda, A; Komatsu, DD; Hirota, A; Watanabe, K; Togo, Y; Morikawa, N; Hagiwara, H; Aosai, D
  • Ralstonia species mediate Fe-oxidation in circumneutral, metal-rich subsurface fluids of Henderson mine, CO
    Swanner, ED; Nell, RM; Templeton, AS
  • Archaeal diversity in waters from deep South African gold mines
    Takai, K; Moser, DP; DeFlaun, M; Onstott, TC; Fredrickson, JK
  • Progress in bioleaching: fundamentals and mechanisms of bacterial metal sulfide oxidation—part A
    Vera, M; Schippers, A; Sand, W
  • Distribution and diversity of halophilic bacteria in a subsurface salt formation
    Vreeland, RH; Piselli Jr, AF; McDonnough, S; Meyers, S
  • Prokaryotes: the unseen majority
    Whitman, WB; Coleman, DC; Wiebe, WJ
  • Evidence and characteristics of a diverse and metabolically active microbial community in deep subsurface clay borehole water
    Wouters, K; Moors, H; Boven, P; Leys, N
  • Microbial metagenomes from three aquifers in the Fennoscandian shield terrestrial deep biosphere reveal metabolic partitioning among populations
    Wu, X; Holmfeldt, K; Hubalek, V; Lundin, D; Åström, M; Bertilsson, S; Dopson, M
  • Potential for hydrogen-oxidizing chemolithoautotrophic and diazotrophic populations to initiate biofilm formation in oligotrophic, deep terrestrial subsurface waters
    Wu, X; Pedersen, K; Edlund, J; Eriksson, L; Åström, M; Andersson, AF; Bertilsson, S; Dopson, M
  • Unique microbial community in drilling fluids from Chinese continental scientific drilling
    Zhang, G; Dong, H; Jiang, H; Xu, Z; Eberl, DD
  • Microbial diversity in ultra-high-pressure rocks and fluids from the Chinese Continental Scientific Drilling Project in China
    Zhang, G; Dong, H; Xu, Z; Zhao, D; Zhang, C
  • Thriving or surviving? Evaluating active microbial guilds in Baltic Sea sediment
    Zinke, LA; Mullis, MM; Bird, JT; Marshall, IP; Jørgensen, BB; Lloyd, KG; Amend, JP; Kiel Reese, B
  • Studies on the bacterial flora of marine bottom sediments
    Zobell, CE
  • Vertical distribution of bacteria in marine sediments
    ZoBell, CE; Anderson, DQ

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