메뉴 건너뛰기




Volumn 85, Issue 2, 2013, Pages 324-337

Dissecting the deep biosphere: Retrieving authentic microbial communities from packer-isolated deep crystalline bedrock fracture zones

Author keywords

Archaea; Deep terrestrial fracture zones; Microbial communities; Packer method; Sulfate reducing bacteria

Indexed keywords

GROUND WATER; RNA 16S; SULFATE;

EID: 84880134305     PISSN: 01686496     EISSN: 15746941     Source Type: Journal    
DOI: 10.1111/1574-6941.12126     Document Type: Article
Times cited : (44)

References (56)
  • 3
    • 2342565752 scopus 로고    scopus 로고
    • Phylogenetic composition of Arctic Ocean archaeal assemblages and comparison with antarctic assemblages
    • Bano N, Ruffin S, Ransom B & Hollibaugh JT (2004) Phylogenetic composition of Arctic Ocean archaeal assemblages and comparison with antarctic assemblages. Appl Environ Microb 70: 781-789.
    • (2004) Appl Environ Microb , vol.70 , pp. 781-789
    • Bano, N.1    Ruffin, S.2    Ransom, B.3    Hollibaugh, J.T.4
  • 4
    • 34848876011 scopus 로고    scopus 로고
    • Geomicrobiology in cave environments: past, current and future perspectives
    • Barton HA & Northup DE (2007) Geomicrobiology in cave environments: past, current and future perspectives. J Cave Karst Stud 69: 163-178.
    • (2007) J Cave Karst Stud , vol.69 , pp. 163-178
    • Barton, H.A.1    Northup, D.E.2
  • 5
    • 48749117805 scopus 로고    scopus 로고
    • Metagenomic signatures of the Peru Margin subseafloor biosphere show a genetically distinct environment
    • Biddle JF, Fitz-Gibbon S, Schuster SC, Brenchley JE & House CH (2008) Metagenomic signatures of the Peru Margin subseafloor biosphere show a genetically distinct environment. P Natl Acad Sci USA 105: 10583-10588.
    • (2008) P Natl Acad Sci USA , vol.105 , pp. 10583-10588
    • Biddle, J.F.1    Fitz-Gibbon, S.2    Schuster, S.C.3    Brenchley, J.E.4    House, C.H.5
  • 7
    • 36949017757 scopus 로고    scopus 로고
    • Arthrobacter subterraneus sp. nov., isolated from deep subsurface water of the South Coast of Korea
    • Chang HW, Bae JW, Nam YD et al. (2007) Arthrobacter subterraneus sp. nov., isolated from deep subsurface water of the South Coast of Korea. J Microbiol Biotechnol 11: 1875-1879.
    • (2007) J Microbiol Biotechnol , vol.11 , pp. 1875-1879
    • Chang, H.W.1    Bae, J.W.2    Nam, Y.D.3
  • 8
    • 53749096964 scopus 로고    scopus 로고
    • Environmental genomics reveals a single-species ecosystem deep within Earth
    • Chivian D, Brodie EL, Alm EJ et al. (2008) Environmental genomics reveals a single-species ecosystem deep within Earth. Science 322: 275-278.
    • (2008) Science , vol.322 , pp. 275-278
    • Chivian, D.1    Brodie, E.L.2    Alm, E.J.3
  • 9
    • 79957856836 scopus 로고    scopus 로고
    • Capture of planktonic microbial diversity in fractures by long-term monitoring of flowing drill holes, Evander Basin, South Africa
    • Davidson MM, Silver BJ, Onstott TC et al. (2011) Capture of planktonic microbial diversity in fractures by long-term monitoring of flowing drill holes, Evander Basin, South Africa. Geomicrobiol J 28: 275-300.
    • (2011) Geomicrobiol J , vol.28 , pp. 275-300
    • Davidson, M.M.1    Silver, B.J.2    Onstott, T.C.3
  • 10
    • 85023819181 scopus 로고    scopus 로고
    • Geomicrobiological processes and biodiversity in the deep terrestrial subsurface
    • Fredrickson JK & Balkwill DL (2006) Geomicrobiological processes and biodiversity in the deep terrestrial subsurface. Geomicrobiol J 23: 345-356.
    • (2006) Geomicrobiol J , vol.23 , pp. 345-356
    • Fredrickson, J.K.1    Balkwill, D.L.2
  • 11
    • 77955417023 scopus 로고    scopus 로고
    • Geomicrobiological properties of ultra-deep granitic groundwater from Mizunami Underground Research Laboratory (MIU), Central Japan
    • Fukuda A, Hagiwara H, Ishimura T, Koudoka M, Ioka S, Amano Y, Tsunogai U, Suzuki Y & Mizuno T (2010) Geomicrobiological properties of ultra-deep granitic groundwater from Mizunami Underground Research Laboratory (MIU), Central Japan. Microb Ecol 60: 214-225.
    • (2010) Microb Ecol , vol.60 , pp. 214-225
    • Fukuda, A.1    Hagiwara, H.2    Ishimura, T.3    Koudoka, M.4    Ioka, S.5    Amano, Y.6    Tsunogai, U.7    Suzuki, Y.8    Mizuno, T.9
  • 13
    • 53749085723 scopus 로고    scopus 로고
    • The distribution of microbial taxa in the subsurface water of the Kalahari Shield, South Africa
    • Gihring TM, Moser DP, Lin L-H et al. (2006) The distribution of microbial taxa in the subsurface water of the Kalahari Shield, South Africa. Geomicrobiol J 23: 415-430.
    • (2006) Geomicrobiol J , vol.23 , pp. 415-430
    • Gihring, T.M.1    Moser, D.P.2    Lin, L.-H.3
  • 14
    • 2542508293 scopus 로고    scopus 로고
    • Diversity and structure of the methanogenic community in anoxic rice paddy soil microcosms as examined by cultivation and direct 16s rRNA gene sequence retrieval
    • Grosskopf R, Janssen PH & Liesack W (1998) Diversity and structure of the methanogenic community in anoxic rice paddy soil microcosms as examined by cultivation and direct 16s rRNA gene sequence retrieval. Appl Environ Microbiol 64: 960-969.
    • (1998) Appl Environ Microbiol , vol.64 , pp. 960-969
    • Grosskopf, R.1    Janssen, P.H.2    Liesack, W.3
  • 15
    • 0242578620 scopus 로고    scopus 로고
    • A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood
    • Guindon S & Gascuel O (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52: 696-704.
    • (2003) Syst Biol , vol.52 , pp. 696-704
    • Guindon, S.1    Gascuel, O.2
  • 16
    • 0036201950 scopus 로고    scopus 로고
    • Distribution of culturable microorganisms in Fennoscandian Shield groundwater
    • Haveman SA & Pedersen K (2002) Distribution of culturable microorganisms in Fennoscandian Shield groundwater. FEMS Microbiol Ecol 39: 129-137.
    • (2002) FEMS Microbiol Ecol , vol.39 , pp. 129-137
    • Haveman, S.A.1    Pedersen, K.2
  • 17
    • 0033389854 scopus 로고    scopus 로고
    • Distribution and metabolic diversity of microorganisms in deep igneous rock aquifers of Finland
    • Haveman SA, Pedersen K & Ruotsalainen P (1999) Distribution and metabolic diversity of microorganisms in deep igneous rock aquifers of Finland. Geomicrobiol J 16: 277-294.
    • (1999) Geomicrobiol J , vol.16 , pp. 277-294
    • Haveman, S.A.1    Pedersen, K.2    Ruotsalainen, P.3
  • 18
    • 84979942164 scopus 로고    scopus 로고
    • Spatial distribution of the subseafloor life: diversity and biogeography
    • Dilek Y, Furnes H & Muehlenbachs K, eds. Springer, Netherlands.
    • Inagaki F & Nakagawa S (2008) Spatial distribution of the subseafloor life: diversity and biogeography. Links Between Geological Processes, Microbial Activities & Evolution of Life (Dilek Y, Furnes H & Muehlenbachs K, eds), pp. 135-158. Springer, Netherlands.
    • (2008) Links Between Geological Processes, Microbial Activities & Evolution of Life , pp. 135-158
    • Inagaki, F.1    Nakagawa, S.2
  • 20
    • 80955177493 scopus 로고    scopus 로고
    • Characterization of bacterial diversity down to a depth of 1500 m in the Outokumpu deep drill hole, Fennoscandian Shield
    • Itävaara M, Nyyssönen M, Kapanen A, Nousiainen A, Ahonen L & Kukkonen I (2011b) Characterization of bacterial diversity down to a depth of 1500 m in the Outokumpu deep drill hole, Fennoscandian Shield. FEMS Microbiol Ecol 77: 295-309.
    • (2011) FEMS Microbiol Ecol , vol.77 , pp. 295-309
    • Itävaara, M.1    Nyyssönen, M.2    Kapanen, A.3    Nousiainen, A.4    Ahonen, L.5    Kukkonen, I.6
  • 22
    • 84876308246 scopus 로고    scopus 로고
    • Characterisation and isotopic evolution of saline waters of the Outokumpu Deep Drill Hole, Finland - implications for water origin and deep terrestrial biosphere
    • Kietäväinen R, Ahonen L, Kukkonen I, Hendriksson N, Nyyssönen M & Itävaara M (2013) Characterisation and isotopic evolution of saline waters of the Outokumpu Deep Drill Hole, Finland - implications for water origin and deep terrestrial biosphere. Appl Geochem 32: 37-51.
    • (2013) Appl Geochem , vol.32 , pp. 37-51
    • Kietäväinen, R.1    Ahonen, L.2    Kukkonen, I.3    Hendriksson, N.4    Nyyssönen, M.5    Itävaara, M.6
  • 23
    • 84871808499 scopus 로고    scopus 로고
    • Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies
    • Klindworth A, Pruesse E, Schweer T, Peplies J, Quast C, Horn M & Glöckner FO (2013) Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nucleic Acids Res 41: e1.
    • (2013) Nucleic Acids Res , vol.41
    • Klindworth, A.1    Pruesse, E.2    Schweer, T.3    Peplies, J.4    Quast, C.5    Horn, M.6    Glöckner, F.O.7
  • 24
    • 84866440384 scopus 로고    scopus 로고
    • Ed Outokumpu Deep Drilling Project 2003-2010. Geological Survey of Finland, Special Paper
    • Kukkonen IT (Ed) (2011) Outokumpu Deep Drilling Project 2003-2010. Geological Survey of Finland, Special Paper, 51, 252 pp.
    • (2011) , vol.51 , pp. 252
    • Kukkonen, I.T.1
  • 25
    • 80053316188 scopus 로고    scopus 로고
    • Geothermal studies of the Outokumpu Deep Drill Hole, Finland: vertical variation in heat flow and palaeoclimatic implications
    • Kukkonen IT, Rath V, Kivekäs L, Safanda J & Cermak V (2011) Geothermal studies of the Outokumpu Deep Drill Hole, Finland: vertical variation in heat flow and palaeoclimatic implications. Phys Earth Planet Inter 188: 9-25.
    • (2011) Phys Earth Planet Inter , vol.188 , pp. 9-25
    • Kukkonen, I.T.1    Rath, V.2    Kivekäs, L.3    Safanda, J.4    Cermak, V.5
  • 27
    • 0001857117 scopus 로고
    • 16S/23S rRNA sequencing
    • 1st edn (Stackebrandt E & Goodfellow M, eds) John Wiley and Sons, New York, NY.
    • Lane DJ (1991) 16S/23S rRNA sequencing. Nucleic Acid Techniques in Bacterial Systematics, 1st edn (Stackebrandt E & Goodfellow M, eds), pp. 115-175. John Wiley and Sons, New York, NY.
    • (1991) Nucleic Acid Techniques in Bacterial Systematics , pp. 115-175
    • Lane, D.J.1
  • 28
    • 33750332574 scopus 로고    scopus 로고
    • Long-term sustainability of a high-energy low-diversity crustal biome
    • Lin LH, Wang PL, Rumble D et al. (2006) Long-term sustainability of a high-energy low-diversity crustal biome. Science 314: 479-482.
    • (2006) Science , vol.314 , pp. 479-482
    • Lin, L.H.1    Wang, P.L.2    Rumble, D.3
  • 29
    • 62049085009 scopus 로고    scopus 로고
    • Abundance and community structure of sulfate reducing prokaryotes in a paddy soil of southern China under different fertilization regimes
    • Liu XZ, Zhang LM, Prosser JI & He JZ (2009) Abundance and community structure of sulfate reducing prokaryotes in a paddy soil of southern China under different fertilization regimes. Soil Biol Biochem 41: 687-694.
    • (2009) Soil Biol Biochem , vol.41 , pp. 687-694
    • Liu, X.Z.1    Zhang, L.M.2    Prosser, J.I.3    He, J.Z.4
  • 30
    • 0029540914 scopus 로고
    • Deep subsurface microbial processes
    • Lovley DR & Chappelle FH (1995) Deep subsurface microbial processes. Rev Geophys 33: 365-381.
    • (1995) Rev Geophys , vol.33 , pp. 365-381
    • Lovley, D.R.1    Chappelle, F.H.2
  • 31
    • 0347723719 scopus 로고    scopus 로고
    • Temporal shifts in the geochemistry and microbial community structure of an ultradeep mine drill hole following isolation
    • Moser DP, Onstott TC, Fredrickson JK et al. (2003) Temporal shifts in the geochemistry and microbial community structure of an ultradeep mine drill hole following isolation. Geomicrobiol J 20: 517-548.
    • (2003) Geomicrobiol J , vol.20 , pp. 517-548
    • Moser, D.P.1    Onstott, T.C.2    Fredrickson, J.K.3
  • 32
    • 43849095105 scopus 로고    scopus 로고
    • The ecology and biotechnology of sulphate-reducing bacteria
    • Muyzer G & Stams AJM (2008) The ecology and biotechnology of sulphate-reducing bacteria. Nat Rev Microbiol 6: 441-454.
    • (2008) Nat Rev Microbiol , vol.6 , pp. 441-454
    • Muyzer, G.1    Stams, A.J.M.2
  • 33
    • 0027460328 scopus 로고
    • Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16s rRNA
    • Muyzer G, De Waal EC & Uitterlinden AG (1993) Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16s rRNA. Appl Environ Microbiol 59: 695-700.
    • (1993) Appl Environ Microbiol , vol.59 , pp. 695-700
    • Muyzer, G.1    De Waal, E.C.2    Uitterlinden, A.G.3
  • 34
    • 0034799674 scopus 로고    scopus 로고
    • Geomicrobiology of caves: a review
    • Northup DE & Lavoie KH (2001) Geomicrobiology of caves: a review. Geomicrobiol J 18: 199-222.
    • (2001) Geomicrobiol J , vol.18 , pp. 199-222
    • Northup, D.E.1    Lavoie, K.H.2
  • 35
    • 84866457734 scopus 로고    scopus 로고
    • 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 (2012) Methanogenic and sulphate-reducing microbial communities in deep groundwater of crystalline rock fractures in Olkiluoto, Finland. Geomicrobiol J 29: 863-878.
    • (2012) Geomicrobiol J , vol.29 , pp. 863-878
    • Nyyssönen, M.1    Bomberg, M.2    Kapanen, A.3    Nousiainen, A.4    Pitkänen, P.5    Itävaara, M.6
  • 36
    • 0032462770 scopus 로고    scopus 로고
    • Observations pertaining to the origin and ecology of microorganisms recovered from the deep subsurface of Taylorsville Basin, Virginia
    • Onstott TC, Phelps TJ, Colwell FS et al. (1998) Observations pertaining to the origin and ecology of microorganisms recovered from the deep subsurface of Taylorsville Basin, Virginia. Geomicrobiol J 15: 353-385.
    • (1998) Geomicrobiol J , vol.15 , pp. 353-385
    • Onstott, T.C.1    Phelps, T.J.2    Colwell, F.S.3
  • 38
    • 2442551475 scopus 로고    scopus 로고
    • The importance of physical isolation to microbial diversification
    • Papke RT & Ward DM (2004) The importance of physical isolation to microbial diversification. FEMS Microbiol Ecol 48: 293-303.
    • (2004) FEMS Microbiol Ecol , vol.48 , pp. 293-303
    • Papke, R.T.1    Ward, D.M.2
  • 39
    • 0030875389 scopus 로고    scopus 로고
    • Microbial life in deep granitic rock
    • Pedersen K (1997) Microbial life in deep granitic rock. FEMS Microbiol Ecol 20: 399-414.
    • (1997) FEMS Microbiol Ecol , vol.20 , pp. 399-414
    • Pedersen, K.1
  • 40
    • 0029973821 scopus 로고    scopus 로고
    • 16S rRNA gene diversity of attached and unattached bacteria in drill holes along the access tunnel to the Äspö hard rock laboratory
    • Pedersen K, Arlinger J, Ekendahl S & Hallbeck L (1996) 16S rRNA gene diversity of attached and unattached bacteria in drill holes along the access tunnel to the Äspö hard rock laboratory. Sweden FEMS Microbiol Ecol 19: 249-262.
    • (1996) Sweden FEMS Microbiol Ecol , vol.19 , pp. 249-262
    • Pedersen, K.1    Arlinger, J.2    Ekendahl, S.3    Hallbeck, L.4
  • 41
    • 46749101410 scopus 로고    scopus 로고
    • Numbers, biomass and cultivable diversity of microbial populations relate to depth and drill hole-specific conditions in groundwater from depths of 4-450 m in Olkiluoto, Finland
    • Pedersen K, Arlinger J, Eriksson S, Hallbeck A, Hallbeck L & Johansson J (2008) Numbers, biomass and cultivable diversity of microbial populations relate to depth and drill hole-specific conditions in groundwater from depths of 4-450 m in Olkiluoto, Finland. ISME J 2: 760-775.
    • (2008) ISME J , vol.2 , pp. 760-775
    • Pedersen, K.1    Arlinger, J.2    Eriksson, S.3    Hallbeck, A.4    Hallbeck, L.5    Johansson, J.6
  • 45
    • 33747492397 scopus 로고    scopus 로고
    • Molecular characterization of microbial communities in fault-bordered aquifers in the Miocene formation of northernmost Japan
    • Shimizu S, Akiyama M, Ishijima Y, Hama K, Kunimaru T & Naganuma T (2006) Molecular characterization of microbial communities in fault-bordered aquifers in the Miocene formation of northernmost Japan. Geobiology 4: 203-213.
    • (2006) Geobiology , vol.4 , pp. 203-213
    • Shimizu, S.1    Akiyama, M.2    Ishijima, Y.3    Hama, K.4    Kunimaru, T.5    Naganuma, T.6
  • 46
    • 0003341851 scopus 로고
    • Development and application of nucleic acid probes
    • Stackebrandt E & Goodfellow M, eds. John Wiley & Sons Ltd, Chichester, England.
    • Stahl DA & Amann R (1991) Development and application of nucleic acid probes. Nucleic Acid Techniques in Bacterial Systematics (Stackebrandt E & Goodfellow M, eds), pp. 205-248. John Wiley & Sons Ltd, Chichester, England.
    • (1991) Nucleic Acid Techniques in Bacterial Systematics , pp. 205-248
    • Stahl, D.A.1    Amann, R.2
  • 47
    • 0028972702 scopus 로고
    • Lithoautotrophic microbial ecosystems in deep basalt aquifers
    • Stevens TO & McKinley JP (1995) Lithoautotrophic microbial ecosystems in deep basalt aquifers. Science 270: 450-455.
    • (1995) Science , vol.270 , pp. 450-455
    • Stevens, T.O.1    McKinley, J.P.2
  • 49
    • 35648967556 scopus 로고    scopus 로고
    • Dethiosulfatibacter aminovorans gen. nov., sp. nov., a novel thiosulfate-reducing bacterium isolated from coastal marine sediment via sulfate-reducing enrichment with Casamino acids
    • Takii S, Hanada S, Tamaki H, Ueno Y, Sekiguchi Y, Ibe A & Matsuura K (2007) Dethiosulfatibacter aminovorans gen. nov., sp. nov., a novel thiosulfate-reducing bacterium isolated from coastal marine sediment via sulfate-reducing enrichment with Casamino acids. Int J Syst Evol Microbiol 57: 2320-2326.
    • (2007) Int J Syst Evol Microbiol , vol.57 , pp. 2320-2326
    • Takii, S.1    Hanada, S.2    Tamaki, H.3    Ueno, Y.4    Sekiguchi, Y.5    Ibe, A.6    Matsuura, K.7
  • 50
    • 85023887078 scopus 로고    scopus 로고
    • In situ enrichment of a diverse community of bacteria from a 4-5 km deep fault zone in South Africa
    • Trimarco E, Balkwill D, Davidson M & Onstott T (2006) In situ enrichment of a diverse community of bacteria from a 4-5 km deep fault zone in South Africa. Geomicrobiol J 23: 463-473.
    • (2006) Geomicrobiol J , vol.23 , pp. 463-473
    • Trimarco, E.1    Balkwill, D.2    Davidson, M.3    Onstott, T.4
  • 51
    • 0032463021 scopus 로고    scopus 로고
    • Phylogeny of dissimilatory sulfite reductases supports an early origin of sulfate respiration
    • Wagner M, Roger AJ, Flax JL, Brusseau GA & Stahl DA (1998) Phylogeny of dissimilatory sulfite reductases supports an early origin of sulfate respiration. J Bacteriol 180: 2975-2982.
    • (1998) J Bacteriol , vol.180 , pp. 2975-2982
    • Wagner, M.1    Roger, A.J.2    Flax, J.L.3    Brusseau, G.A.4    Stahl, D.A.5
  • 52
    • 34548293679 scopus 로고    scopus 로고
    • Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy
    • Wang Q, Garrity GM, Tiedje JM & Cole JR (2007) Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 73: 5261-5267.
    • (2007) Appl Environ Microbiol , vol.73 , pp. 5261-5267
    • Wang, Q.1    Garrity, G.M.2    Tiedje, J.M.3    Cole, J.R.4
  • 53
    • 0035031966 scopus 로고    scopus 로고
    • A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach
    • Whelan S & Goldman N (2001) A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. Mol Biol Evol 18: 691-699.
    • (2001) Mol Biol Evol , vol.18 , pp. 691-699
    • Whelan, S.1    Goldman, N.2
  • 55
    • 34548157781 scopus 로고    scopus 로고
    • Loktanella maricola sp. nov., isolated from seawater of the East Sea in Korea
    • Yoon JH, Kang SJ, Le ST & Oh TK (2007) Loktanella maricola sp. nov., isolated from seawater of the East Sea in Korea. Int J Syst Evol Microbiol 57: 1799-1802.
    • (2007) Int J Syst Evol Microbiol , vol.57 , pp. 1799-1802
    • Yoon, J.H.1    Kang, S.J.2    Le, S.T.3    Oh, T.K.4
  • 56
    • 39749188705 scopus 로고    scopus 로고
    • Hydrogenophaga bisanensis sp. nov., isolated from wastewater of a textile dye works
    • Yoon JH, Kang SJ, Ryu SH, Jeon CO & Oh TK (2008) Hydrogenophaga bisanensis sp. nov., isolated from wastewater of a textile dye works. Int J Syst Evol Microbiol 58: 393-397.
    • (2008) Int J Syst Evol Microbiol , vol.58 , pp. 393-397
    • Yoon, J.H.1    Kang, S.J.2    Ryu, S.H.3    Jeon, C.O.4    Oh, T.K.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.