• Tohru Kobayashi
  • Ken Takai

Prokaryotes in Deep Biosphere

The prokaryotes in deep biosphere are estimated to constitute 10–33% of total living biomass in the Earth (Parkes et al. 2000; Whitman et al. 1998). Quite a few bacterial and archaeal genera and species have been isolated and described from the terrestrial and oceanic subsurface environments. For example, the following isolates are representative of the taxonomically described prokaryotes obtained from the subsurface environments: a Fe (III)- and Mn (IV)-reducing anaerobe, Bacillus infernus, was isolated from 2,700 m below the land surface (mbls) of Tarlorsville Triassic Basin in Virginia (Boone et al. 1995); a chemolithoautotrophic methanogen, Methanobacterium subterraneum, and a sulfate-reducing bacterium, Desulfovibrio aespoeensis, were isolated from deep granitic groundwater at depths of ∼420 m (Kotelnikova et al. 1998) and 600 m (Motamedi and Pedersen 1998), respectively; a thermophilic bacterium, Thermus scotoductus (Kieft et al. 1999; Moller and...


Alkaline Protease Extracellular Enzyme Activity Methane Hydrate Alginate Lyase Deep Biosphere 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


  1. Arnosti C (1995) Measurement of depth- and site-related differences in polysaccharide hydrolysis rates in marine sediments. Geochim Cosmochim Acta 59:4247–4257CrossRefGoogle Scholar
  2. Arnosti C (1996) A new method for measuring polysaccharide hydrolysis rates in marine environments. Org Geochem 25:105–115CrossRefGoogle Scholar
  3. Bale SJ, Goodman K, Rochelle PA, Marchesi JR, Fry JC, Weightman AJ, Parkes RJ (1997) Desulfovibrio profundus sp. nov., a novel barophilic sulfate-reducing bacterium from deep sediment layers in the Japan sea. Int J Syst Bacteriol 47:515–521PubMedCrossRefGoogle Scholar
  4. Batzke A, Engelen B, Sass H, Cypionka H (2007) Phylogenetic and physiological diversity of cultured deep-biopshere bacteria from Equatorial Pacific Ocean and Peru Margin sediments. Geomicrobiol J 24:261–273CrossRefGoogle Scholar
  5. Biddle JF, House CH, Brenchley JE (2005) Microbial stratification in deeply buried marine sediment reflects changes in sulfate/methane profiles. Geobiology 3:287–295CrossRefGoogle Scholar
  6. Biddle JF, Lipp JS, Lever MA, Lloyd KG, Sorensen KB, Anderson R, Fredricks HF, Elvert M, Kelly TJ, Schrag DP, Sogin ML, Brenchley JE, Teske A, House CH, Hinrichs K-U (2006) Heterotrophic archaea dominate sedimentary subsurface ecosystems off Peru. Proc Natl Acad Sci USA 103:3486–3851CrossRefGoogle Scholar
  7. Boone DR, Liu Y, Zhao ZJ, Balkwill DL, Drake GR, Stevens TO, Aldrich HC (1995) Bacillus infernus sp. nov., an Fe(III)- and Mn(IV)-reducing anaerobe from the deep terrestrial subsurface. Int J Syst Bacteriol 45:441–448PubMedCrossRefGoogle Scholar
  8. Boschker HTS, Cappenberg TE (1998) Patterns of extracellular enzyme activities in littoral sediments of Lake Gooimeer, The Netherland. FEMS Microbiol Ecol 25:79–86CrossRefGoogle Scholar
  9. Cragg BA, Parkes RJ, Fry JC, Weightman AJ, Rochelle PA, Maxwell JR (1996) Bacterial populations and process in sediments containing gas hydrates (ODP Leg 146: Cascadia, Margin). Earth Planet Sci Lett 139:497–507CrossRefGoogle Scholar
  10. D’Hondt S, Rutherfold S, Spivack AJ (2002) Metabolic activity of subsurface life in deep-sea sediments. Science 295:2067–2070PubMedCrossRefGoogle Scholar
  11. D’Hondt S, Jørgensen BB, Miller DJ, Batzke A, Blake R, Cragg BA, Cypionka H, Dickens GR, Ferdelman T, Hinrichs K-U, Holm NG, Mitterer R, Spivack A, Wang G, Bekins B, Engelen B, Ford K, Gettemy G, Rutherford SD, Sass H, Skilbeck CG, Ailleo IW, Guerin G, House CH, Inagaki F, Meister P, Naehr T, Niitsuma S, Parkes RJ, Schippers A, Smith DC, Teske A, Wiegel J, Padilla CN, Acosta JLS (2004) Distribution of microbial activities in deep subseafloor sediments. Science 306:2216–2221PubMedCrossRefGoogle Scholar
  12. da Cunha CD, Rosado AS, Sebastián GV, Seldin L, von der Weid I (2006) Oil biodegradation by Bacillus strains isolated from the rock of an oil reservoir located in a deep-water production basin in Brazil. Appl Microbiol Biotechnol 73:949–959PubMedCrossRefGoogle Scholar
  13. Fabiano M, Danovaro R (1998) Enzymatic activity, bacterial distribution, and organic matter composition in sediments of the Ross Sea (Antarctica). Appl Environ Microbiol 64:3838–3845PubMedGoogle Scholar
  14. Fry JC, Parkes RJ, Cragg BA, Weightman AJ, Webster G (2008) Prokaryotic biodiversity and activity in the deep subseafloor biosphere. FEMS Microbiol Ecol 66:181–196PubMedCrossRefGoogle Scholar
  15. Grabowski A, Tindall BJ, Bardin V, Blanchet D, Jeanthon C (2005) Petrimonas sulfuriphila gen nov., sp. nov., a mesophilic fermentative bacterium isolated from a biodegraded oil reservoir. Int J Syst Evol Microbiol 55:1113–1121PubMedCrossRefGoogle Scholar
  16. Hakamada Y, Kobayashi T, Hitomi J, Kawai S, Ito S (1994) Molecular cloning and nucleotide sequence of the gene for an alkaline protease from the alkaliphilic Bacillus sp. KSM-K16. J Ferment Bioeng 78:105–108CrossRefGoogle Scholar
  17. Hirayama H, Takai K, Inagaki F, Nealson KH, Horikoshi K (2005) Thiobacter subterraneus gen. nov., sp nov., an obligately chemolithoautotrophic, thermophilic, sulfur-oxidizing bacterium from a subsurface hot aquifer. Int J Syst Evol Microbiol 55:467–472PubMedCrossRefGoogle Scholar
  18. Hoppe HG (1991) Microbial extracellular enzyme activity: a new key parameter in aquatic ecology. In: Chrøst J (ed) Microbial enzymes in aquatic environments. Springer, New York, pp 60–79CrossRefGoogle Scholar
  19. Hoppe HG (2003) Phosphatase activity in the sea. Hydrobiologia 493:187–200CrossRefGoogle Scholar
  20. Horikoshi K (1971) Production of alkaline enzymes by alkaliphilic microorganisms part I. Alkaline protease produced by Bacillus no. 221. Biosci Biotechnol Biochem 35:1407–1414Google Scholar
  21. Horikoshi K (1999) Alkaliphiles: some applications of their products for biotechnology. Microbiol Mol Biol Rev 63:735–750PubMedGoogle Scholar
  22. Inagaki F, Suzuki M, Takai K, Oida H, Sakamoto T, Aoki K, Nealson K, Horikoshi K (2003) Microbial communities associated with geological horizons in coastal subseafloor sediments from the Sea of Okhotsk. Appl Environ Microbiol 69:7224–7235PubMedCrossRefGoogle Scholar
  23. Inagaki F, Nunoura T, Nakagawa S, Teske A, Lever A, Lauer A, Suzuki M, Takai K, Delwiche M, Colwell FS, Nealson KH, Horikoshi K, D’Hondt S, Jørgensen BB (2006) Biogeographical distribution and diversity of microbes in methane hydrate-bearing deep marine sediments on the Pacific Ocean Margin. Proc Natl Acad Sci USA 103:2815–2820PubMedCrossRefGoogle Scholar
  24. Jang HJ, Kim BC, Pyun YR, Kim YS (2002a) A novel subtilisin-like serine protease from Thermoanaerobacter yonseiensis KB-1: its cloning, expression, and biochemical properties. Extremophiles 6:233–243PubMedCrossRefGoogle Scholar
  25. Jang HJ, Lee CH, Lee W, Kim YS (2002b) Two flexible loops in subtilisin-like thermophilic protease, thermicin, from Thermoanaerobacter yonseiensis. J Biochem Mol Biol 35:498–507PubMedCrossRefGoogle Scholar
  26. Jeanthon C, Reysenbach AL, L’Haridon S, Gambacorta A, Pace NR, Glénat P, Prieur D (1995) Thermotoga subterranean sp. nov., a new thermophilic bacterium isolated from a continental oil reservoir. Arch Microbiol 164:91–97PubMedCrossRefGoogle Scholar
  27. Kendall MM, Liu Y, Sieprawska-Lupa M, Stetter KO, Whitman WB, Boone DR (2006) Methanococcus aeolicus sp. nov., a mesophilic, methanogenic archaeon from shallow and deep marine sediments. Int J Syst Evol Microbiol 56:1525–1529PubMedCrossRefGoogle Scholar
  28. Kieft TL, Fredrickson JK, Onstott TC, Gorby YA, Kostandarithes HM, Bailey TJ, Kennedy DW, Li SW, Plymale AE, Spadoni CM, Gray MS (1999) Dissimilatory reduction of Fe(III) and other electron acceptors by a Thermus isolate. Appl Environ Microbiol 65:1214–1221PubMedGoogle Scholar
  29. Kobayashi T, Hakamada Y, Adachi S, Hitomi J, Yoshimatsu T, Koike K, Kawai S, Ito S (1995) Purification and properties of an alkaline protease from alkaliphilic Bacillus sp. KSM-K16. Appl Microbiol Biotechnol 43:473–481PubMedCrossRefGoogle Scholar
  30. Kobayashi T, Lu J, Li Z, Hung VS, Kurata A, Hatada Y, Takai K, Ito S, Horikoshi K (2007) Extremely high alkaline protease from a deep-subsurface bacterium, Alkaliphilus transvaalensis. Appl Microbiol Biotechnol 75:71–80PubMedCrossRefGoogle Scholar
  31. Kobayashi T, Koide O, Mori K, Shimamura S, Matsuura T, Miura T, Takaki Y, Morono Y, Nunoura T, Imachi H, Inagaki F, Takai K, Horikoshi K (2008) Phylogenetic and enzymatic diversity of deep suseafloor aerobic microorganisms in organics- and methane-rich sediments off Shimokita Peninsula. Extremophiles 12:519–527PubMedCrossRefGoogle Scholar
  32. Kodama Y, Watanabe K (2004) Sulfuricurvum kujiense gen. nov., sp nov., a facultatively anaerobic, chemolithoautotrophic, sulfur-oxidizing bacterium isolated from an underground crude-oil storage cavity. Int J Syst Evol Microbiol 54:2297–2300PubMedCrossRefGoogle Scholar
  33. Kotelnikova S, Macario AJL, Pedersen K (1998) Methanobacterium subterraneum sp. nov., a new alkaliphilic, eurythermic and halotolerant methanogen isolated from deep granitic groundwater. Int J Syst Bacteriol 48:357–367PubMedCrossRefGoogle Scholar
  34. Meyer-Reil LA (1990) Microorganisms in marine sediments: considerations concerning activity measurements. Arch Hydrobiol Beih Ergeb limnol 34:1–6Google Scholar
  35. Meyer-Reil LA, Köster M (1992) Microbial life in pelagic sediments: the impact of environmental parameters on enzymatic degradation of organic material. Mar Ecol Prog Ser 81:65–72CrossRefGoogle Scholar
  36. Mikuchi JA, Liu Y, Delwiche M, Colwell FS, Boone DR (2003) Isolation of a methanogen from deep marine sediments that contain methane hydrates, and description of Methanoculleus submarines sp. nov. Appl Environ Microbiol 69:3311–3316CrossRefGoogle Scholar
  37. Moller C, van Heerden E (2006) Isolation of a soluble and membrane-associated Fe(III) reductase from the thermophile, Thermus scotoductus (SA-01). FEMS Microbiol Lett 265:237–243PubMedCrossRefGoogle Scholar
  38. Morihara K, Oka T, Tsuzuki H (1969) Comparison of alpha-chymotrypsin and subtilisin BPN’: size and specificity of the active site. Biochem Biophys Res Commun 35:210–214PubMedCrossRefGoogle Scholar
  39. Motamedi M, Pedersen K (1998) Desulfovibrio aespoeensis sp. nov., a mesophilic sulfate-reducing bacterium from deep groundwater at Äspö hard rock laboratory, Sweden. Int J Syst Bacteriol 48:311–315PubMedCrossRefGoogle Scholar
  40. Nakanishi T, Yamamoto T (1974) Action and specificity of a Streptomyces alkaliphilic proteinase. Biosci Biotechnol Biochem 38:2391–2397Google Scholar
  41. Nunoura T, Soffientino B, Blazejak A, Kakuta J, Oida H, Schippers A, Takai K (2009) Subseafloor microbial communities associated with rapid turbidite deposition in the Gulf of Mexico continental slope (IODP Expedition 308). FEMS Microbiol Ecol 69:410–424PubMedCrossRefGoogle Scholar
  42. Ogawa A, Sumitomo N, Okuda M, Saeki K, Kawai S, Kobayashi T, Ito S (2003) Nucleotide and deduced amino acid sequences of a high-molecular-mass subtilisin from alkaliphilic Bacillus isolate. Biochim Biophys Acta 1624:109–114PubMedCrossRefGoogle Scholar
  43. Okuda M, Sumitomo N, Takimura Y, Ogawa A, Saeki K, Kawai S, Kobayashi T, Ito S (2004) A new subtilisin family: nucleotide and deduced amino acid sequences of new high-molecular-mass alkaline proteases from Bacillus spp. Extremophiles 8:229–235PubMedCrossRefGoogle Scholar
  44. Parkes RJ, Cragg BA, Bale SJ, Getliff JM, Goodman K, Rochelle PA, Fry JC, Weightman AJ, Harvey SM (1994) Deep bacterial biosphere in Pacific Ocean sediments. Nature 371:410–413CrossRefGoogle Scholar
  45. Parkes RJ, Cragg BA, Wellsbury P (2000) Recent studies on bacterial populations and progresses in subseafloor sediments: a review. Hydrogeol J 8:11–28CrossRefGoogle Scholar
  46. Parkes RJ, Webster G, Cragg BA, Weightman AJ, Newberry CJ, Ferdelman TG, Kallmeyer J, Jørgensen BB, Aiello IW, Fry JC (2005) Deep sub-seafloor prokaryotes stimulated at interfaces over geological time. Nature 436:390–394PubMedCrossRefGoogle Scholar
  47. Poremba K (1995) Hydrolytic enzymatic activity in deep-sea sediments. FEMS Microbiol Ecol 16:213–222CrossRefGoogle Scholar
  48. Poremba K, Hoppe H-G (1995) Spatial variation of benthic microbial production and hydrolytic enzymatic activity down the continental slope of the Celtic Sea. Mar Ecol Prog Ser 118:237–245CrossRefGoogle Scholar
  49. Ravot G, Magot M, Fardeau ML, Patel BKC, Thomas P, Garcia JL, Olliver B (1999) Fusibacter paucivorans gen. nov., sp. nov., an anaerobic, thiosulfate-reducing bacterium from an oil-producing well. Int J Syst Bacteriol 49:1141–1147PubMedCrossRefGoogle Scholar
  50. Saeki K, Okuda M, Hatada Y, Kobayashi T, Ito S, Takami H, Horikoshi K (2000) Novel oxidatively stable subtilisin-like serine proteases from alkaliphilic Bacillus spp.: enzymatic properties, sequences, and evolutionary relationships. Biochem Biophys Res Commun 279:313–319PubMedCrossRefGoogle Scholar
  51. Saeki K, Hitomi J, Okuda M, Hatada Y, Kageyama Y, Takaiwa M, Kubota H, Hagihara H, Kobayashi T, Kawai S, Ito S (2002) A novel species of alkaliphilic Bacillus that produces an oxidatively stable alkaline serine protease. Extremophiles 6:65–72PubMedCrossRefGoogle Scholar
  52. Saeki K, Magallones MV, Takimura Y, Hatada Y, Kobayashi T, Kawai S, Ito S (2003) Nucleotide and deduced amino acid sequences of a new subtilisin from an alkaliphilic Bacillus isolate. Curr Microbiol 47:337–340PubMedCrossRefGoogle Scholar
  53. Salinas MB, Fardeau ML, Thomas P, Cayol JL, Patel BKC, Olliver B (2004) Mahella australiensis gen. nov., sp. nov., a moderately thermophilic anaerobic bacterium isolated from an Australian oil well. Int J Syst Evol Microbiol 54:2169–2173PubMedCrossRefGoogle Scholar
  54. Schmidt BF, Woodhouse L, Adams RM, Ward T, Mainzer SE, Lad PJ (1995) Alkaliphilic Bacillus sp. strain LG12 has a series of serine protease genes. Appl Environ Microbiol 61:4490–4493PubMedGoogle Scholar
  55. Siezen RJ, Leunissen JA (1997) Subtilases: the superfamily of subtilisin-like serine proteases. Protein Sci 6:501–523PubMedCrossRefGoogle Scholar
  56. Slobodkin AI, Jeanthon C, L’Haridon S, Nazina T, Miroshinichenko M, Osmolovskaya EB (1999) Dissimilatory reduction of Fe(III) by thermophilic bacteria and archaea in deep subsurface petroleum reservoirs of Western Siberia. Curr Microbiol 39:99–102PubMedCrossRefGoogle Scholar
  57. Soffientino B, Spivack AJ, Smith DC, Roggenstein EB, D’Hondt S (2006) A versatile and sensitive tritium-based radioassay for measuring hydrogenase activity in aquatic sediments. J Microbiol Meth 66:136–146CrossRefGoogle Scholar
  58. Sørensen KB, Teske A (2006) Stratified communities of active archaea in deep marine subsurface sediments. Appl Environ Microbiol 72:4596–4603PubMedCrossRefGoogle Scholar
  59. 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 365:743–745CrossRefGoogle Scholar
  60. Süß J, Engelen B, Cypionka H, Sass H (2004) Quantitative analysis of bacterial communities from Mediterranean sapropels based on cultivation-dependent methods. FEMS Microbiol Ecol 51:109–121PubMedCrossRefGoogle Scholar
  61. Taira A (2005) Shimokita area site survey: Northern Japan Trench seismic survey, northern Honshu, Japan. CDEX Tech Rep vol 2, pp 155. Available from:
  62. Takahata Y, Nishijima M, Hoaki T, Maruyama T (2000) Distibution and physiological characteristics of hyperthermophiles in the Kubiki oil reservoir in Niigata, Japan. Appl Environ Microbiol 66:73–79PubMedCrossRefGoogle Scholar
  63. Takai K, Moser DP, Onstott TC, Spoelstra N, Pfiffner SM, Dohnalkova A, Fredrickson JK (2001a) Alkaliphilus transvaalensis gen. nov., sp. nov., an extremely alkaliphilic bacterium isolated from a deep South African gold mine. Int J Syst Evol Microbiol 51:1245–1256PubMedGoogle Scholar
  64. Takai K, Komatsu T, Horikoshi K (2001b) Hydrogenobacter subterraneus sp. nov., an extremely thermophilic, heterotrophic bacterium unable to grow on hydrogen gas, from deep subsurface geothermal water. Int J Syst Evol Microbiol 51:1425–1435PubMedGoogle Scholar
  65. Takai K, Kobayashi H, Nealson KH, Horikoshi K (2003) Sulfurihydrogenibium subterraneum gen. nov., sp. nov., from a subsurface hot aquifer. Int J Syst Evol Microbiol 53:823–827PubMedCrossRefGoogle Scholar
  66. Takami H, Akiba T, Horikoshi K (1989) Production of extremely thermostable alkaline protease from Bacillus sp. no. AH-101. Appl Microbiol Biotechnol 30:120–124CrossRefGoogle Scholar
  67. Takami H, Akiba T, Horikoshi K (1992a) Substrate specificity of thermostable alkaline protease from Bacillus sp. No. AH-101. Biosci Biotechnol Biochem 56:333–334PubMedCrossRefGoogle Scholar
  68. Takami H, Kobayashi T, Kobayashi M, Yamamoto M, Nakamura S, Aono R, Horikoshi K (1992b) Molecular cloning, nucleotide sequence, and expression of the structural gene for alkaline serine protease from alkaliphilic Bacillus sp. 221. Biosci Biotechnol Biochem 56:1455–1460PubMedCrossRefGoogle Scholar
  69. Takimura Y, Saito K, Okuda M, Kageyama Y, Saeki K, Ozaki K, Ito S, Kobayashi T (2007) Alkaliphilic Bacillus sp. strain KSM-LD1 contains a record number of subtilisin-like serine protease genes. Appl Microbiol Biotechnol 76:393–405CrossRefGoogle Scholar
  70. Teske A, Sørensen KB (2008) Uncultured archaea in deep marine subsurface sediments: have we caught them all? ISME J 2:3–18PubMedCrossRefGoogle Scholar
  71. Vetter YA, Deming JW (1994) Extracellular enzyme activity in the Arctic Northeast Water Polynya. Mar Ecol Prog Ser 114:23–34CrossRefGoogle Scholar
  72. Wellsbury P, Marther I, Parkes RJ (2002) Ggeomicrobiology of deep, low organic carbon sediments in the Woodlark Basin, Pacific Ocean. FEMS Microbiol Ecol 42:59–70PubMedCrossRefGoogle Scholar
  73. Whitman WB, Coleman DC, Wiebe WJ (1998) Prokaryotes: the unseen majority. Proc Natl Acad Sci USA 95:6578–6583PubMedCrossRefGoogle Scholar
  74. Wobus A, Bleul C, Maassen S, Scheerer C, Schuppler M, Jacobs E, Röske I (2003) Microbial diversity and functional characterization of sediments from reservoirs of different trophic states. FEMS Microbiol Ecol 46:331–334PubMedCrossRefGoogle Scholar
  75. Yamagata Y, Isshiki K, Ichishima E (1995) Subtilisin Sendai from alkaliphilic Bacillus sp.: molecular and enzymatic properties of the enzyme and molecular cloning and characterization of the gene, aprS. Enzyme Microb Technol 17:653–663PubMedCrossRefGoogle Scholar

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© Springer 2011

Authors and Affiliations

  1. 1.Institute of BiogeoscienceJapan Marine-Earth Science and Technology (JAMSTEC)YokosukaJapan
  2. 2.Subground Animalcule Retrieval (SUGAR) ProjectJapan Agency for Marine-Earth Science & TechnologyYokosukaJapan

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