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Extremophiles Handbook

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References

  • Arnosti C (1995) Measurement of depth- and site-related differences in polysaccharide hydrolysis rates in marine sediments. Geochim Cosmochim Acta 59:4247–4257

    Article  CAS  Google Scholar 

  • Arnosti C (1996) A new method for measuring polysaccharide hydrolysis rates in marine environments. Org Geochem 25:105–115

    Article  CAS  Google Scholar 

  • 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 47:515–521

    Article  PubMed  CAS  Google Scholar 

  • 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 24:261–273

    Article  CAS  Google Scholar 

  • Biddle JF, House CH, Brenchley JE (2005) Microbial stratification in deeply buried marine sediment reflects changes in sulfate/methane profiles. Geobiology 3:287–295

    Article  CAS  Google Scholar 

  • 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 103:3486–3851

    Article  Google Scholar 

  • 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 45:441–448

    Article  PubMed  CAS  Google Scholar 

  • Boschker HTS, Cappenberg TE (1998) Patterns of extracellular enzyme activities in littoral sediments of Lake Gooimeer, The Netherland. FEMS Microbiol Ecol 25:79–86

    Article  CAS  Google Scholar 

  • 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 139:497–507

    Article  CAS  Google Scholar 

  • D’Hondt S, Rutherfold S, Spivack AJ (2002) Metabolic activity of subsurface life in deep-sea sediments. Science 295:2067–2070

    Article  PubMed  Google Scholar 

  • 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 306:2216–2221

    Article  PubMed  Google Scholar 

  • 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 73:949–959

    Article  PubMed  CAS  Google Scholar 

  • Fabiano M, Danovaro R (1998) Enzymatic activity, bacterial distribution, and organic matter composition in sediments of the Ross Sea (Antarctica). Appl Environ Microbiol 64:3838–3845

    PubMed  CAS  Google Scholar 

  • Fry JC, Parkes RJ, Cragg BA, Weightman AJ, Webster G (2008) Prokaryotic biodiversity and activity in the deep subseafloor biosphere. FEMS Microbiol Ecol 66:181–196

    Article  PubMed  CAS  Google Scholar 

  • 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 55:1113–1121

    Article  PubMed  CAS  Google Scholar 

  • 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 78:105–108

    Article  CAS  Google Scholar 

  • 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 55:467–472

    Article  PubMed  CAS  Google Scholar 

  • 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 60–79

    Chapter  Google Scholar 

  • Hoppe HG (2003) Phosphatase activity in the sea. Hydrobiologia 493:187–200

    Article  CAS  Google Scholar 

  • Horikoshi K (1971) Production of alkaline enzymes by alkaliphilic microorganisms part I. Alkaline protease produced by Bacillus no. 221. Biosci Biotechnol Biochem 35:1407–1414

    CAS  Google Scholar 

  • Horikoshi K (1999) Alkaliphiles: some applications of their products for biotechnology. Microbiol Mol Biol Rev 63:735–750

    PubMed  CAS  Google Scholar 

  • 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 69:7224–7235

    Article  PubMed  CAS  Google Scholar 

  • 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 103:2815–2820

    Article  PubMed  CAS  Google Scholar 

  • 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 6:233–243

    Article  PubMed  CAS  Google Scholar 

  • 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 35:498–507

    Article  PubMed  CAS  Google Scholar 

  • 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 164:91–97

    Article  PubMed  CAS  Google Scholar 

  • 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 56:1525–1529

    Article  PubMed  CAS  Google Scholar 

  • 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 65:1214–1221

    PubMed  CAS  Google Scholar 

  • 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 43:473–481

    Article  PubMed  CAS  Google Scholar 

  • 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 75:71–80

    Article  PubMed  CAS  Google Scholar 

  • 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 12:519–527

    Article  PubMed  CAS  Google Scholar 

  • 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 54:2297–2300

    Article  PubMed  CAS  Google Scholar 

  • 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 48:357–367

    Article  PubMed  Google Scholar 

  • Meyer-Reil LA (1990) Microorganisms in marine sediments: considerations concerning activity measurements. Arch Hydrobiol Beih Ergeb limnol 34:1–6

    Google Scholar 

  • 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 81:65–72

    Article  Google Scholar 

  • 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 69:3311–3316

    Article  Google Scholar 

  • 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 265:237–243

    Article  PubMed  CAS  Google Scholar 

  • 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 35:210–214

    Article  PubMed  CAS  Google Scholar 

  • 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 48:311–315

    Article  PubMed  Google Scholar 

  • Nakanishi T, Yamamoto T (1974) Action and specificity of a Streptomyces alkaliphilic proteinase. Biosci Biotechnol Biochem 38:2391–2397

    CAS  Google Scholar 

  • 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 69:410–424

    Article  PubMed  CAS  Google Scholar 

  • 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 1624:109–114

    Article  PubMed  CAS  Google Scholar 

  • 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 8:229–235

    Article  PubMed  CAS  Google Scholar 

  • 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 371:410–413

    Article  Google Scholar 

  • Parkes RJ, Cragg BA, Wellsbury P (2000) Recent studies on bacterial populations and progresses in subseafloor sediments: a review. Hydrogeol J 8:11–28

    Article  Google Scholar 

  • 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 436:390–394

    Article  PubMed  CAS  Google Scholar 

  • Poremba K (1995) Hydrolytic enzymatic activity in deep-sea sediments. FEMS Microbiol Ecol 16:213–222

    Article  CAS  Google Scholar 

  • 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 118:237–245

    Article  Google Scholar 

  • 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 49:1141–1147

    Article  PubMed  CAS  Google Scholar 

  • 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 279:313–319

    Article  PubMed  CAS  Google Scholar 

  • 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 6:65–72

    Article  PubMed  CAS  Google Scholar 

  • 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 47:337–340

    Article  PubMed  CAS  Google Scholar 

  • 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 54:2169–2173

    Article  PubMed  CAS  Google Scholar 

  • 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 61:4490–4493

    PubMed  CAS  Google Scholar 

  • Siezen RJ, Leunissen JA (1997) Subtilases: the superfamily of subtilisin-like serine proteases. Protein Sci 6:501–523

    Article  PubMed  CAS  Google Scholar 

  • 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 39:99–102

    Article  PubMed  CAS  Google Scholar 

  • 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 66:136–146

    Article  CAS  Google Scholar 

  • Sørensen KB, Teske A (2006) Stratified communities of active archaea in deep marine subsurface sediments. Appl Environ Microbiol 72:4596–4603

    Article  PubMed  Google Scholar 

  • 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

    Article  Google Scholar 

  • 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 51:109–121

    Article  PubMed  Google Scholar 

  • Taira A (2005) Shimokita area site survey: Northern Japan Trench seismic survey, northern Honshu, Japan. CDEX Tech Rep vol 2, pp 155. Available from: http://sio7.jamstec.go.jp/publication/pdf/TechRep/CDEXTRV02.pdf

  • 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 66:73–79

    Article  PubMed  CAS  Google Scholar 

  • 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 51:1245–1256

    PubMed  CAS  Google Scholar 

  • 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 51:1425–1435

    PubMed  CAS  Google Scholar 

  • 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 53:823–827

    Article  PubMed  CAS  Google Scholar 

  • Takami H, Akiba T, Horikoshi K (1989) Production of extremely thermostable alkaline protease from Bacillus sp. no. AH-101. Appl Microbiol Biotechnol 30:120–124

    Article  CAS  Google Scholar 

  • Takami H, Akiba T, Horikoshi K (1992a) Substrate specificity of thermostable alkaline protease from Bacillus sp. No. AH-101. Biosci Biotechnol Biochem 56:333–334

    Article  PubMed  CAS  Google Scholar 

  • 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 56:1455–1460

    Article  PubMed  CAS  Google Scholar 

  • 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 76:393–405

    Article  Google Scholar 

  • Teske A, Sørensen KB (2008) Uncultured archaea in deep marine subsurface sediments: have we caught them all? ISME J 2:3–18

    Article  PubMed  CAS  Google Scholar 

  • Vetter YA, Deming JW (1994) Extracellular enzyme activity in the Arctic Northeast Water Polynya. Mar Ecol Prog Ser 114:23–34

    Article  CAS  Google Scholar 

  • Wellsbury P, Marther I, Parkes RJ (2002) Ggeomicrobiology of deep, low organic carbon sediments in the Woodlark Basin, Pacific Ocean. FEMS Microbiol Ecol 42:59–70

    Article  PubMed  CAS  Google Scholar 

  • Whitman WB, Coleman DC, Wiebe WJ (1998) Prokaryotes: the unseen majority. Proc Natl Acad Sci USA 95:6578–6583

    Article  PubMed  CAS  Google Scholar 

  • 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 46:331–334

    Article  PubMed  CAS  Google Scholar 

  • 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 17:653–663

    Article  PubMed  CAS  Google Scholar 

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Kobayashi, T., Takai, K. (2011). Biochemistry. In: Horikoshi, K. (eds) Extremophiles Handbook. Springer, Tokyo. https://doi.org/10.1007/978-4-431-53898-1_51

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