Microbial diversity with dominance of 16S rRNA gene sequences with high GC contents at 74 and 98°C subsurface crude oil deposits in Japan

FEMS Microbiology Ecology

Volumn 76, Issue 2, 2011, Pages 220-235

  Yamane, Kunio ^a   Hattori, Yoshiyuki ^b   Ohtagaki, Hiroshi ^b   Fujiwara, Kazuhiro ^b  

^a NATIONAL FOOD RESEARCH INSTITUTE   (Japan)

^b Chugai Technos Co Ltd   (Japan)

Author keywords

Anaerobic ecosystem; Petroleum microorganisms; Subsurface; Thermal adaptation

Indexed keywords

ARCHAEAL RNA; BACTERIAL RNA; PETROLEUM; RNA 16S; WATER;

ANOXIC CONDITIONS; CRUDE OIL; GENETIC ANALYSIS; HIGH TEMPERATURE; MICROBIAL COMMUNITY; OIL WELL; POLYMERASE CHAIN REACTION; PROKARYOTE; SUBTERRANEAN ENVIRONMENT;

ARCHAEBACTERIUM; ARTICLE; BACTERIUM; BIOTA; CHEMISTRY; CLASSIFICATION; COMPARATIVE STUDY; DNA BASE COMPOSITION; GENE LIBRARY; GENETICS; JAPAN; MICROBIOLOGY; PHYLOGENY;

ARCHAEA; BACTERIA; BASE COMPOSITION; BIOTA; GENE LIBRARY; JAPAN; PETROLEUM; PHYLOGENY; RNA, ARCHAEAL; RNA, BACTERIAL; RNA, RIBOSOMAL, 16S; WATER; WATER MICROBIOLOGY;

JAPAN;

ARCHAEA; ARCHAEOGLOBUS FULGIDUS; BACTERIA (MICROORGANISMS); FERVIDOBACTERIUM PENNIVORANS; METHANOTHERMOBACTER THERMAUTOTROPHICUS; THERMACETOGENIUM PHAEUM; THERMODESULFOBACTERIUM COMMUNE; THERMOTOGA; THERMOTOGA HYPOGEA; THERMOTOGA PETROPHILA;

EID: 79953781171     PISSN: 01686496     EISSN: 15746941     Source Type: Journal    
DOI: 10.1111/j.1574-6941.2011.01044.x     Document Type: Article

References (51)

1. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W & Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search program. Nucleic Acids Res 25: 3389-3402.
2. Boivin-Jahns V, Ruimy R, Bianchi A, Daumas S & Christen R (1996) Bacterial diversity in a deep-subsurface clay environment. Appl Environ Microb 62: 3405-3412.
3. Bonch-Osmolovskaya EA, Miroshnichenko ML, Lebedinsky AV et al. (2003) Radioisotopic, cultured-based, and oligonucleotide microchip analyses of thermophilic microbial communities in a continental high-temperature petroleum reservoir. Appl Environ Microb 69: 6143-6151.
4. Chen S & Dong X (2005) Proteiniphilum acetatigenes gen. nov., sp. nov., from a UASB reactor treating brewery waste water. Int J Syst Evol Micr 55: 2257-2261.
5. Childers SE, Vargas M & Noll KM (1992) Improved methods for cultivation of the extremely thermophilic bacterium Thermotoga neapolitana. Appl Environ Microb 58: 3949-3953.
6. Dahle H & Birkeland N-K (2006) Thermovirga lienii gen. nov. sp. nov., a novel moderately thermophilic, anaerobic, amino-acid-degrading bacterium isolated from a North Sea oil well. Int J Syst Evol Micr 56: 1539-1545.
7. Dahle H, Garshol F, Madsen M & Birkeland N-K (2008) Microbial community structure analysis of produced water from a high-temperature North Sea oil-field. Antonie van Leeuwenhoek 93: 37-49.
8. Eller C, Crabill MR & Bryant MP (1971) Anaerobic roll tube media for nonselective enumeration and isolation of bacteria in human feces. Appl Microbiol 22: 522-529.
9. Fardeau M-L, Ollivier B, Patel BKC, Dwivedi P, Ragot M & Garcia J-L (1995) Isolation and characterization of a thermophilic sulfate-reducing bacterium, Desulfotomaculum thermosapovorans sp. nov. Int J Syst Bacteriol 45: 218-221.
10. Fardeau M-L, Ollivier B, Patel BKC, Magot M, Thomas P, Rimbault A, Rocchiccioli F & Garcia J-L (1997) Thermotoga hypogea sp. nov., a xylanolytic, thermophilic bacterium from an oil-producing well. Int J Syst Bacteriol 47: 1013-1019.
11. Fardeau M-L, Salinas MB, L'Haridon S, Jeanthon C, Verhé F, Cayol J-L, Patel BKC, Garcia J-L & Olivier B (2004) Isolation from oil reservoirs of novel thermophilic anaerobes phylogenetically related to Thermoanaerobacter subterraneus: reassignment of T. subterraneus, Thermoanaerobacter yonseiensis, Thermoanaerobacter tengcongensis, and Cartoxydibrachium pacificum to Caldanaerobacter subterraneus gen. nov., sp. nov., comb. nov. as four novel subspecies. Int J Syst Evol Micr 54: 467-474.
12. Friedrich AB & Antranikian G (1996) Keratin degradation by Fervidobacterium pennavorans, a novel thermophilic anaerobic species of the order Thermotogales. Appl Environ Microb 62: 2875-2882.
13. Grassia GS, McLean KM, Glenat P, Bauld J & Sheehy AJ (1996) A systematic survey for thermophilic fermentative bacteria and archaea in high temperature petroleum reservoirs. FEMS Microbiol Ecol 21: 47-58.
14. Gray ND, Miskin IP, Kornilova O, Curtis TP & Head IM (2002) Occurrence and activity of Archaea in aerated activated sludge wastewater treatment plants. Environ Microbiol 4: 158-168.
15. Hattori S, Kamagata Y, Hanada S & Shoun H (2000) Thermacetogenium phaeum gen. nov., sp. nov., a strictly anaerobic, thermophilic, syntrophic acetate-oxidizing bacterium. Int J Syst Evol Micr 50: 1601-1609.
16. Hugenholtz P, Goebel BM & Pace NR (1998) Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. J Bacteriol 180: 4765-4774.
17. Imachi H, Sekiguchi Y, Kamagata Y, Loy A, Qiu A-L, Hugenholtz P, Kimura N, Wagner M, Ohashi A & Harada H (2006) Non-sulfate-reducing, syntrophic bacteria affiliated with Desulfotomaculum cluster I are widely distributed in methanogenic environments. Appl Environ Microb 72: 2080-2091.
18. Johnson MR, Conners SB, Montero CI, Chou CJ, Shockley KR & Kelly KM (2006) The Thermotoga maritima phenotype is impacted by syntrophic interaction with Methanococcus jannaschii in hyperthermophilic coculture. Appl Environ Microb 72: 811-818.
19. Juteau P, Côté V, Duckett MF, Beaudet R, Lepine F, Villemur R & Bisaillon JG (2005) Cryptanaerobacter phenolicus gen. nov., sp. nov., an anaerobe that transforms phenol into benzoate via 4-hydroxybenzoate. Int J Syst Evol Micr 55: 245-250.
20. Kemp PF & Aller JY (2004) Bacterial diversity in aquatic and other environments: what 16S rDNA libraries can tell us. FEMS Microbiol Ecol 47: 161-171.
21. Kim W & Whitman WB (1999) Isolation of acetate auxotrophs of methane-producing archaeon Methanococcus maripaludis by random insertional mutagenesis. Genetics 152: 1429-1437.
22. Kimura H, Sugihara M, Kato K & Hanada S (2006) Selective phylogenetic analysis targeted at 16S rRNA genes of thermophiles and hyperthermophiles in deep-subsurface geothermal environments. Appl Environ Microb 72: 21-27.
23. Kimura H, Ishibashi J, Masuda H, Kato K & Hanada S (2007) Selective phylogenetic analysis targeting 16S rRNA genes of hyperthermophilic Archaea in the deep-subsurface hot biosphere. Appl Environ Microb 73: 2110-2117.
24. Lepage E, Marguet E, Geslin C, Matte-Tailliez O, Zillig W, Forterre P & Tailliez P (2004) Molecular diversity of new Thermococcales isolates from a single area of hydrothermal deep-sea vents as revealed by randomly amplified polymorphic DNA fingerprinting and 16S rRNA gene sequence analysis. Appl Environ Microb 70: 1277-1286.
25. Li H, Yang S-Z, Mu B-Z, Rong Z-F & Zhang J (2006) Molecular analysis of the bacterial community in a continental high-temperature and water-flooded petroleum reservoir. FEMS Microbiol Lett 257: 92-98.
26. Li H, Yang S-Z, Mu B-Z, Rong Z-F & Zhang J (2007) Molecular phylogenetic diversity of the microbial community associated with a high-temperature petroleum reservoir at an offshore oilfield. FEMS Microbiol Ecol 60: 74-84.
27. Luijten ML, de Weert J, Smidt H, Boschker HT, de Vos WM, Schraa G & Stams AJ (2003) Description of Sulfurospirillum halorespirans, sp. nov., an anaerobic, tetrachloroethene-respiring bacterium, and transfer of Dehalospirillum multivorans to genus Sulfurospirillum as Sulfurospirillum multivorans comb. nov. Int J Syst Evol Micr 53: 787-793.
28. Magot M, Ollivier B & Patel BKC (2000) Microbiology of petroleum reservoirs. Antonie van Leeuwenhoek 77: 103-116.
29. Magot M (2005) Indigenous microbial communities in oil fields. Petroleum Microbiology (Ollivier B & Magot M, eds), pp. 21-33. ASM Press, Washington, DC.
30. Maidak BL, Cole JR, Lilburn TG et al. (2000) The RDP (Ribosomal Database Project) continues. Nucleic Acids Res 28: 173-174.
31. Marchesi JR, Sato T, Weightman AT, Martin TA, Fry JC, Hiom SJ & Wade WG (1998) Design and evaluation of useful bacteria-specific PCR primers that amplify genes coding for bacterial 16S rRNA. Appl Environ Microb 64: 795-799.
32. Mochimaru H, Uchiyama H, Yoshioka H, Imachi H, Hoaki T, Tamaki H, Nakamura K, Sekiguchi Y & Komagata Y (2007) Methanogen diversity in deep subsurface gas-associated water at the Minami-Kanto gas field in Japan. Geomicrobiol J 24: 93-100.
33. Muyzer G, Teske A, Wirson CO & Jannasch HW (1995) Phylogenetic relationships of Thiomicrospira species and their identification in deep-sea hydrothermal vent samples by denaturing gradient gel electrophoresis of 16S rDNA fragments. Arch Microbiol 164: 165-172.
34. Nakagawa S, Takai K, Inagaki F, Chiba H, Ishibashi J, Kataoka S, Hirayama H, Nunoura T, Horikoshi K & Sako Y (2005) Variability in microbial community and venting chemistry in a sediment-hosed backarc hydrothermal system: impacts of subseafloor phase-separation. FEMS Microbiol Ecol 54: 141-155.
35. Newberry CJ, Webster G, Cragg BA, Parkes RJ, Weightman AJ & Fry JC (2004) Diversity of prokaryotes and methanogenesis in deep subsurface sediments from the Nankai Trough, Ocean Drilling Program Leg 190. Environ Microbiol 6: 274-287.
36. Oremland RS & Boone DR (1994) Methanolobus taylorii sp. nov., a new methanotrophic, estuarine methanogen. Int J Syst Bacteriol 44: 573-575.
37. Orphan VJ, Taylor LT, Hafenbradl D & Delong EF (2000) Culture-dependent and culture-independent characterization of microbial assemblages associated with high-temperature petroleum reservoirs. Appl Environ Microb 66: 700-711.
38. Pham VD, Hnatow LL, Zhang S, Fallon RD, Jackson SC, Tomb J-F, DeLong EF & Keeler SL (2009) Characterizing microbial diversity in production water from an Alaskan mesothermic petroleum reservoir with two independent molecular methods. Environ Microbiol 11: 176-187.
39. Rule PL & Alexander AD (1986) Gellan gum as a substitute for agar in leptospiral media. J Clin Microbiol 23: 500-504.
40. Saitou N & Nei M (1987) The neighbor-joining method: a method for reconstructing phylogenetic trees. Mol Biol Evol 4: 406-425.
41. Schippers A, Neretin LN, Kallmeyer J, Ferdelman TG, Gragg BA, Parkes RJ & Jørgense BB (2005) Prokaryotic cells of the deep sub-seafloor biosphere identified as living bacteria. Nature 433: 861-864.
42. Smith DR, Doucette-Stamm LA, Deloughery C et al. (1997) Complete genome sequence of Methanobacterium thermoautotrophicumΔH: functional analysis and comparative genomics. J Bacteriol 179: 7135-7155.
43. Stetter KO, Lauerer G, Thomm M & Neuner A (1987) Isolation of extremely thermophilic sulfate reducers: evidence for a novel branch of archaebacteria. Science 236: 822-824.
44. Stetter KO, Huber R, Blöchl E, Kurr M, Eden RD, Fielder M, Cash H & Vance I (1993) Hyperthermophilic archaea are thriving in deep North Sea and Alaskan oil reservoirs. Nature 365: 743-745.
45. Sung Y, Ritalahti KM, Sanford RA, Urbance JW, Flynn SJ, Tiedje JM & Löffler FE (2003) Characterization of two tetrachloroethene-reducing, acetate-oxidizing anaerobic bacteria and their description as Desulfuromonas michiganensis sp. nov. Appl Environ Microb 69: 2964-2974.
46. Suzuki MT & Giovannoni SJ (1996) Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR. Appl Environ Microb 62: 625-630.
47. Takahata Y, Nishijima M, Hoaki T & Maruyama T (2000) Distribution and physiological characteristics of hyperthermophiles in the Kubiki oil reservoir in Niigata, Japan. Appl Environ Microb 66: 73-79.
48. Thompson JD, Gibson TJ, Plewniak F & Higgins DG (1997) The CLUSTAL-X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25: 4876-4882.
49. Weisburg WG, Barns SM, Pelletier DA & Lane DJ (1991) 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 173: 697-703.
50. Yamane K, Maki H, Nakayama T, Nakajima T, Nomura N, Uchiyama H & Kitaoka M (2008) Diversity and similarity of microbial communities in petroleum crude oils produced in Asia. Biosci Biotech Bioch 72: 2831-2839.
51. Zeikus JG, Dawson MA, Thompson TE, Ingvorsen K & Hatchikian EC (1983) Microbial ecology of volcanic sulfidogenesis: isolation and characterization of Thermodesulfobacterium commune gen. nov. and sp. nov. J Gen Microbiol 129: 1159-1169.