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Analysis of Deep Subsurface Microbial Communities by Functional Genes andGenomics

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Links Between Geological Processes, Microbial Activities&Evolution of Life

Part of the book series: Modern Approaches in Solid Earth Sciences ((MASE,volume 4))

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References

  • Abulencia CB, Wyborski DL, Garcia JA, Podar M, Chen W, Chang SH, Chang HW, Watson, D, Brodie EL, Hazen TC, Keller M (2006). Environmental whole-genome amplification to access microbial populations in contaminated sediments. Appl Environ Microbiol 72:3291–3301

    Google Scholar 

  • Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402

    Article  Google Scholar 

  • Amend JP, Teske A (2005) Expanding frontiers in deep subsurface microbiology. Palaeogeogr Palaeoclimatol Palaeoecol 219:131–155

    Article  Google Scholar 

  • Bahr M, Crump BC, Klepac-Ceraj V, Teske A, Sogin ML, Hobbie JE (2005) Molecular characterization of sulfate-reducing bacteria in a New England salt marsh. Environ Microbiol 7:1175–1185

    Article  Google Scholar 

  • Banning N, Brock F, Fry JC, Parkes RJ, Hornibrook ERC, Weightman AJ (2005) Investigation of the methanogen population structure and activity in a brackish lake sediment. Environ Microbiol 7:947–960

    Google Scholar 

  • Biddle JF (2006) Microbial populations and processes in deeply buried marine sediments. PhD thesis, Pennsylvania State University

    Google Scholar 

  • Biddle JF, Fitz-Gibbon S, Schuster S, Brenchley JE, House CH(2008) Metagenomic signatures of the Peru Margin subseafloor biosphere. Proc Natl Acad Sci USA, in press

    Google Scholar 

  • Biddle JF, House CH, Brenchley JE (2005a) Enrichment and cultivation of microorganisms from sediment from the slope of the Peru Trench(ODP site 1230). In: JØrgensen, BB, D’Hondt, SL, Miller, DJ (eds) Proc. ODP, Sci. Results, 201 [Online]. Available from World Wide Web: <http://www-odp.tamu.edu/publications201_SR/107107.htm≫ [Cited2007-04-25]

    Google Scholar 

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

    Article  Google Scholar 

  • Biddle JF, Lipp JS, Lever MA, Lloyd KG, Sôrensen KB, Anderson R, Fredricks HF, Elvert M, Kelly TJ, Schrag DP, Sogin ML, Brenchley JE, Teske A, House CH, Hinrichs KU (2006) Heterotrophic Archaea dominate sedimentary subsurface ecosystems off Peru. Proc Natl Acad Sci USA 103:3846–3851

    Article  Google Scholar 

  • Bidle KA, Kastner M, Bartlett DH (1999) A phylogenetic analysis of microbial communities associated with methane hydrate containing marine fluids and sediments in the Cascadia Margin (ODP Site 892B). FEMS Microbiol Lett 177:101–108

    Article  Google Scholar 

  • Boetius A, Ravenschlag K, Schubert C, Rickert D, Widdel F, Gieseke A, Amann R, Jôrgensen BB, Witte U, Pfannkuche O (2000) A marine microbial consortium apparently mediating anaerobic oxidation of methane. Nature 407:623–626

    Article  Google Scholar 

  • Boone DR, Mah RA. (2001) Genus I. Methanosarcina. In: Boone DR, Castenholz, RW (eds) Bergey’s manual of systematic bacteriology. 2nd Edition. Volume 1. The Archaea and the deeply branching and phototrophic bacteria. New York: Springer, New York, pp269–276

    Google Scholar 

  • Böttcher ME, Ferdelman TG, Jôrgensen BB, Blake RE, Surkov AV, Claypool GE (2006) Sulfur isotope fractionation by the deep biosphere within sediments of the eastern equatorial Pacific and Peru Margin. In: Jôrgensen BB, D’Hondt SL, Miller DJ (eds) Proc ODP, Sci Results, 201 [Online]. Available from World Wide Web: ≪http:p//www-odp.tamu.edu/publications/201_SR/109/109.htm≫.[Cited 2006-06-25]

    Google Scholar 

  • Braker G, Zhou J, Wu L, Devol AH, Tiedje JM (2000) Nitrite reductase genes (nirK and nirS) as functional markers to investigate diversity of denitrifying bacteria in Pacific Northwest marine sediment communities. Appl Environ Microbiol 66:2096–2104

    Article  Google Scholar 

  • Braker G, Ayala-del-Río HL, Devol AH, Fesefeldt A, Tiedje JM (2001) Community structure of denitrifiers, bacteria, and archaea along redox gradients in Pacific Northwest marine sediments by terminal restriction fragment length polymorphism analysis of amplified ntrite reductase (nirS) and 16S rRNA genes. Appl Environ Microbiol 67:1893–1901

    Article  Google Scholar 

  • Bruns A, Hoffelner H, Overmann J (2003a) A novel approach for high throughput cultivation assays and the isolation of planktonic bacteria. FEMS Microbiol Ecol 45:161–171

    Article  Google Scholar 

  • Bruns A, N¨bel U, Cypionka H, Overmann J (2003b) Effect of signal compounds and incubation conditions on the culturability of freshwater bacterioplankton. Appl Environ Microbiol 69:1980–1989

    Article  Google Scholar 

  • Bustin SA (2000) Absolute quantification of mRNA using real-time reverse transcription polymerase chain reaction assays. J Mol Endocrinol 25:169–193

    Article  Google Scholar 

  • Cho JC, Vergin KL, Morris RM, Giovannoni SJ (2004). Lentisphaera araneosa gen. nov., sp. nov, a transparent exopolymer producing marine bacterium, and the description of a novel bacterial phylum, Lentisphaerae. Environ Microbiol 6:611–621

    Article  Google Scholar 

  • Connon SA, Giovannoni SJ (2002) High-throughput methods for culturingmicro-organisms in very-low-nutrient media yield diverse new marine isolates. Appl Environ Microbiol 68: 3878–3885

    Article  Google Scholar 

  • Coolen MJL, Cypionka H, Sass AM, Sass H, Overmann J (2002) Ongoing modification of Mediterranean sapropels mediated by prokaryotes. Science 296:2407–2410

    Article  Google Scholar 

  • Dhillon A, Teske A, Dillon J, Stahl DA, Sogin ML (2003) Molecular characterization of sulfate-reducing bacteria in the Guaymas Basin. Appl Environ Microbiol 69:2765–2772

    Article  Google Scholar 

  • Dhillon A, Goswami S, Riley M, Teske A, Sogin ML (2005a). Domain evolution and functional diversification of sulfite reductases. Astrobiology 5:18–29

    Article  Google Scholar 

  • Dhillon A, Lever MA, Lloyd KG, Albert DB, Sogin ML, Teske A (2005b) Methanogen Diversity Evidenced by Molecular Characterization of Methyl Coenzyme M Reductase A (mcrA) Genes in Hydrothermal Sediments of the Guaymas Basin. Appl Environ Microbiol 71:4592–4601

    Article  Google Scholar 

  • D’Hondt SL, Jôrgensen BB, Miller DJ, and the Shipboard Scientific Party (2003) Proceedings of the ocean drilling program, Initial Reports 201 [CD-ROM]. Available from: Ocean Drilling Program, Texas A&M University, College Station TX 77845-9547,USA

    Google Scholar 

  • D’Hondt S, Jôrgensen BB, Miller DJ, Batzke A, Blake R, Cragg BA, Cypionka H, Dickens GR, Ferdelman T, Hinrichs KU, Holm NG, Mitterer R, Spivack A, Wang G, Bekins B, EngelenB, Ford K, Gettemy G, Rutherford SD, Sass H, Skilbeck CG, Aiello IW, Guèrin G, House C, Inagaki F, Meister P, Naehr T, Niitsuma S, Parkes RJ, Schippers A, Smith DC, Teske A, WiegelJ,Padilla CN, Acosta JLS (2004) Distributions of microbial activities in deep subseafloor sediments. Science 306:2216–2221

    Article  Google Scholar 

  • Didyk BM, Simoneit BR (1989) Hydrothermal oil of Guaymas Basin and implications for petroleum formation mechanisms. Nature 342:65–69

    Article  Google Scholar 

  • Edwards RA, Rodriguez-Brito B, Wegley L, Haynes M, Breitbart M, Peterson D, Saar M, Alexander S, Alexander EC, Rohwer F (2006) Using pyrosequencing to shed light on deep mine microbial ecology under extreme hydrogeologic conditions. BMC Genomics 7:57

    Article  Google Scholar 

  • Finn RD, Mistry J, Schuster-Bockler B, Griffiths-Jones S, Hollich V, Lassmann T, Moxon S, Marshall M, Khanna A, Durbin R, Eddy SR, Sonnhammer ELL, Bateman A (2006) Pfam: clans, web tools and services. Nucleic Acids Res. 34:D247–D251

    Article  Google Scholar 

  • Friedrich MW (2002) Phylogenetic analysis reveals multiple lateral transfers of adenosine-5-phosphosulfate reductase genes among sulfate-reducing microorganisms. J Bacteriol 184:278–289

    Article  Google Scholar 

  • Friedrich MW (2005) Methyl-coenzyme M reductase genes: unique functional markers for methanogenic and anaerobic methane-oxidizing archaea. Methods Enzymol 397:428–442

    Article  Google Scholar 

  • Fry JC, Webster G, Cragg BA, Weightman AJ, Parkes JR (2006) Analysis of DGGE profiles to explore the relationship between prokaryotic community composition and biogeochemical processes in deep sub-seafloor sediments from the Peru Margin. FEMS Microbiol Ecol 58:86–98

    Article  Google Scholar 

  • Garrity GM, Holt JG (2001) The roadmap to the manual. In:Boone RD, Casteholz RW (eds) Bergey’s manual of systematic bacteriology. Volume 1: the Archaea and the deeply branching and phototrophic bacteria. Springer; New York, Berlin, Heidelberg, pp119–166

    Google Scholar 

  • Hallam SJ, Girguis PR, Preston CM, Richardson PM, DeLong EF (2003) Identification of methyl coenzyme M reductase A (mcrA) genes associated with methane-oxidizing archaea. Appl Environ Microbiol 69:5483–5491

    Article  Google Scholar 

  • Hallam SJ, Putman N, Preston CM, Detter JC, Rokhsar D, Richardson PNM, DeLong EF (2004) Reverse methanogenesis: testing the hypothesis with environmental genomics. Science 305:1457–1462

    Article  Google Scholar 

  • Hôjberg O, Binnerup SJ, Sôrensen J (1997) Growth of silicone-immobolized bacteria on polycarbonate membrane filters, a technique to study microcolony formation under anaerobic conditions. Appl Environ Microbiol 63:2920–2924

    Google Scholar 

  • Hutchinson CA, Smith HO, Pfannkoch C, Venter JC (2005) Cell-free cloning using Φ 29 DNA polymerase. Proc Natl Acad USA 102:17332–17336

    Article  Google Scholar 

  • Inagaki F, Suzuki M, Takai K, Oida H, Sakamoto T, Aoki K, Nealson KH, 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  Google Scholar 

  • Inagaki F, Tsunogai U, Suzuki M, Kosaka A, Machiyama H, Takai K, Nunoura T, Nealson K, Horikoshi K (2004) Characterization of C1-metabolizing prokaryotic communities in methane seep habitats at the Kuroshima Knoll, Southern Ryukyu Arc, by analyzing pmoA, mmoX, mxaF, mcrA, and 16S rRNA genes. Appl Environ Microbiol 70:7445–7455

    Article  Google Scholar 

  • Inagaki F, Nunoura T, Nakagawa S, Teske A, Lever MA, Lauer A, Suzuki M, Takai K, Delwiche M, Colwell FS, Nealson KH, Horikoshi K, D’Hondt SL, Jôrgensen 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  Google Scholar 

  • Jôrgensen BB, D’Hondt SL (2006) A starving majority deep beneath the seafloor. Science 314:932–934

    Article  Google Scholar 

  • Kaeberlein T, Lewis K, Epstein SS (2002) Isolating “uncultivable” microorganisms in pure culture in a simulated natural environment. Science 296:1127–1129

    Article  Google Scholar 

  • Kalyuzhnaya MG, Zabinsky R, Bowerman S, Baker DR, Lidstrom ME, Chistoserdova L (2006) Fluorescence in situ hybridization-flow cytometry-cell sorting-based method for separation and enrichment of type I and type II methanotroph populations. Appl Environ Microbiol 72:4293–4301

    Article  Google Scholar 

  • Klein M, Friedrich M, Roger AJ, Hugenholtz P, Fishbain S, Abicht H, Blackall LL, Stahl DA, Wagner M (2001) Multiple lateral transfers of dissimilatory sulfite reductase genes between major lineages of sulfate-reducing prokaryotes. J Bacteriol 183:6028–6035

    Article  Google Scholar 

  • Klenk HP, Clayton RA, Tomb JF, White O, etal (1997) The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus. Nature 390:364–370

    Article  Google Scholar 

  • Kondo R, Nedwell DB, Purdy KJ, de Queiroz Silva S (2004) Detection and enumeration of sulphate-reducing bacteria in estuarine sediments by competitive PCR. Geomicrobiol 21:145–157

    Article  Google Scholar 

  • Köpke B, Wilms R, Engelen B, Cypionka H, Sass H (2005) Microbial diversity in coastal subsurface sediments: a cultivation approach using various electron acceptors and substrate gradients. Appl Environ Microbiolm 71:7819–7830

    Google Scholar 

  • Kormas AK, Smith DC, Edgcomb V, Teske A (2003) Molecular analysis of deep subsurface microbial communities in Nankai Trough sediments (ODP Leg 190, Site 1176). FEMS Microbiol Ecol 45:115–125

    Article  Google Scholar 

  • Krause L, Diaz NN, Bartels D, Edwards RA, Puhler A, Rohwer F, Meyer F, Stoye J (2006) Finding novel genes in bacterial communities isolated from the environment. Bioinformatics 22:281–289

    Article  Google Scholar 

  • Kumar S, Tamura K, Nei M (2004) MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform 5:150–163

    Article  Google Scholar 

  • Laue H, Friedrich MW, Ruff J, Cook A (2001) Dissimilatory sulfite reductase (desulfoviridin) of the taurine-degrading, non-sulfdate-reducing bacterium Bilophila wadsworthia RZATAU contains a fused dsrB-dsrD subunit. J Bacteriol 183:1717–1733

    Article  Google Scholar 

  • Lee Y, Wagner I, Brice ME, Kevbrin VV, Mills G, Romanek CS, Wiegel J (2005) Thermosediminibacter oceani gen. nov., sp. nov. and Thermosediminibacter litoriperuensis sp. nov., new anaerobic thermophilic bacteria isolated from Peru Margin. Extremophiles 9:375–383

    Article  Google Scholar 

  • Lever M, Teske A (2007) Vertical distribution of methanogens and active Archaea in subsurface sediments of the Peru Trench as evaluated from functional genes and 16S rRNA profiles. Abstract at 2007 ASLO Meeting, Santa Fe,NM.

    Google Scholar 

  • Liu X, Bagwell CE, Wu L, Devol AH, Zhou J (2003) Molecular diversity of sulfate-reducing bacteria from two different continental margin habitats. Appl Environ Microbiol 69:6073–6081

    Article  Google Scholar 

  • Lloyd KG, Lapham L, Teske A (2006) An anaerobic methane-oxidizing community of ANME-1 Archaea in hypersaline Gulf of Mexico sediments. Appl Environ Microbiol 72:7218–7230

    Google Scholar 

  • Luton PE, Wayne JM, Sharp RJ, Riley PW (2002) The mcrA gene as an alternative to 16S rRNA in the phylogenetic analysis of methanogen populations in landfill. Microbiology 148:3521–3530

    Google Scholar 

  • Martens-Habbena W, Sass H (2006) Sensitive determination of microbial growth by nucleuic acid staining in aqueous suspension. Appl Environ Microbiol 72:87–95

    Article  Google Scholar 

  • Miller TL (2001) Genus II. Methanobrevibacter. In: Boone DR, Castenholz R. (eds) Bergey’s Manual of Systematic Bacteriology. 2nd Edition. Volume 1. The Archaea and the deeply branching and phototrophic bacteria. New York:Springer, New York, pp219–226

    Google Scholar 

  • Neretin LN, Schippers A, Pernthaler A, Hamann K, Amann R, Jôrgensen BB (2003) Quantification of dissimilatory (bi)sulphite reductase gene expression in Desulfo-bacterium autotrophicum using real-time RT-PCR. Environ Microbiol 5:660-671

    Article  Google Scholar 

  • Newberry CJ, Webster G, 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

    Article  Google Scholar 

  • Niemann H, Lösekann T, de Beer D, Elvert M, Nadalig T, Knittel K, Amann R, Sauter EJ, Schl¨ter M, Klages M, Foucher JP, Boetius A (2006) Novel microbial communities of the Haakon Mosby mud volcano and their role as a methane sink. Nature 443:854–858

    Article  Google Scholar 

  • Nunoura T, Oida H, Toki T, Ashi J, Takai K, Horikoshu K (2006) Quantification of mcrA by quantitative fluorescent PCR in sediments from methane seep of the Nankai Trough. FEMS Microbiol Ecol 57:149–157

    Article  Google Scholar 

  • Orphan VJ, House CH, Hinrichs KU, McKeegan KD, DeLong EF (2001) Methane-consuming archaea revealed by directly coupled isotopic and phylogenetic analysis. Science 293:484–487

    Article  Google Scholar 

  • Orphan VJ, House CH, Hinrichs KU, McKeegan KD, DeLong EF (2002) Multiple groups mediate methane oxidation in anoxic cold seep sediments. Proc Natl Acad Sci USA 99: 7663–7668

    Article  Google Scholar 

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

    Article  Google Scholar 

  • Parkes RJ, Webster G, Cragg BA, Weightman AJ, Newberry CJ, Ferdelman TG, Kallmeyer J, Jôrgensen BB, Aiello IW, Fry JC (2005) Deep sub-seafloor prokaryotes stimulated at interfaces over geological time. Nature 436:390–394

    Article  Google Scholar 

  • Parkes RJ, Cragg BA, Banning N, Brock F, Webster G, Fry JC, Hornibrook E, Pancost RD, Kelly S, Knab N, Jôrgensen BB, Rinna J, Weightman AJ (2007) Biogeochemistry and biodiversity of methane cycling in subsurface marine sediments (Skagerrak, Denmark). Environ Microbiol 9:1146–1161

    Article  Google Scholar 

  • Patel GB (2001) Genus I. Methanosaeta. In: Boone DR, Castenholz RW (eds) Bergey’s manual of systematic bacteriology. 2nd Edition. Volume 1. The Archaea and the deeply branching and phototrophic bacteria. New York: Springer, New York, pp289–294

    Google Scholar 

  • Pearson A, Seewald JS, Eglinton TI (2005) Bacterial incorporation of relict carbon in the hydrothermal environment of Guaymas Basin. Geochim Cosmochim Acta 69:5477–5486

    Article  Google Scholar 

  • Raghunathan A, Ferguson HR, Bornarth CJ, Song W, Driscoll M, Lasken RS (2005) Genomic amplification from a single bacterium. Appl Environ Microbiol 71:3342–3347

    Article  Google Scholar 

  • Rappé MS, Connon SA, Vergin KL, Giovannoni SJ (2002) Cultivation of the ubiquitous SAR11 marine bacterioplankton clade. Nature 418:630–633

    Article  Google Scholar 

  • Reed DW, Fujita Y, Delwiche ME, Blackwelder DB, Sheridan PP, Uchida T, Colwell FS (2002) Microbial communities from methane hydrate-bearing deep marine sediments in a forearc basin. Appl Environ Microbiol 68:3759–3770

    Article  Google Scholar 

  • Schippers A, Neretin LN (2006) Quantification of microbial communities in near-surface and deeply buried marine sediments on the Peru continental margin using real-time PCR. Environ Microbiol 8:1251–1260

    Article  Google Scholar 

  • Schippers A, Neretin LN, Kallmeyer J, Ferdelman TG, Cragg BA, Parkes JR, Jôrgensen BB (2005) Prokaryotic cells of the deep sub-seafloor biosphere identified as living bacteria. Nature 433:861–864

    Article  Google Scholar 

  • Shipboard Scientific Party (2003a) Site 1228. In: D’Hondt SL, Jôrgensen BB, Miller DJ, etal (eds) Proceedings of the ocean drilling program, Initial reports 201. Ocean Drilling Program, Texas &M University, College Station, Tex. [CD-ROM], pp1–72

    Google Scholar 

  • Shipboard Scientific Party (2003b) Site 1229. In: D’Hondt SL, Jôrgensen BB, Miller DJ, etal (eds) Proceedings of the ocean drilling program, Initial reports 201. Ocean Drilling Program, Texas &M University, College Station, Tex. [CD-ROM], pp1–78

    Google Scholar 

  • Shipboard Scientific Party (2003c) Site 1230. In: D’Hondt SL, Jôrgensen BB, Miller DJ, etal (eds) Proceedings of the Ocean Drilling Program, Initial reports 201. Ocean Drilling Program, Texas &M University, College Station, Tex. [CD-ROM], pp1–107

    Google Scholar 

  • Sogin ML, Morrison HG, Huber JA, Welch DM, Huse SM, Neal PR, JArrieta JM, Herndl GJ (2006) Microbial diversity in the deep sea and the under explored “rare biosphere”. Proc Natl Acad Sci USA 103:12115–12120

    Article  Google Scholar 

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

    Article  Google Scholar 

  • Sôrensen KB, Lauer A, Teske A (2004) Archaeal phylotypes in a metal-rich, low-activity deep subsurface sediment of the Peru Basin, ODP Leg 201, Site 1231. Geobiology 2:151–161

    Article  Google Scholar 

  • Springer E, Sachs MS, Woese CR, Boone DR (1995) Partial gene sequences for the alpha-subunit of methyl-coenzyme M reductase (MCR1) as a phylogenetic tool for the family Methanosarcinaceae. Int J Syst Bacteriol 45:554–559

    Article  Google Scholar 

  • Stahl DA, Fishbain S, Klein M, Baker BJ, Wagner W (2002) Origins and diversification of sulfate-respiring microorganisms. Antonie Van Leeuwenhoek 81:189–195

    Article  Google Scholar 

  • Stults JR, Snoeyenbos-West O, Methe B, Lovley DR, Chandler DP (2001) Application of the 5 fluorogenic exonuclease assay (TaqMan) for quantitative ribosomal DNA and rRNA analysis in sediments. Appl Environ Microbiol 67:2781–2789

    Article  Google Scholar 

  • S¨ss 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

    Google Scholar 

  • S¨ss J, Schubert K, Sass H, Cypionka H, Overmann J, Engelen B (2006) Widespread distribution and high abundance of Rhizobium radiobacter within Mediterranean subsurface sediments. Environ Microbiol 8:1753–1763

    Article  Google Scholar 

  • Suzuki MT, Taylor LT, DeLong EF (2000) Quantitative analysis of small-subunit rRNA genes in mixed microbial populations via 5-nuclease assays. Appl Environ Microbiol 66:4605–4614

    Article  Google Scholar 

  • Teira E, Reinthaler T, Pernthaler A, Pernthaler J, Herndl GJ (2004) Combining catalyzed reporter deposition-fluorescence in situ hybridization and microautoradiography to detect substrate utilization by bacteria and archaea in the deep ocean. Appl Environ Microbiol 70:4411–4414

    Article  Google Scholar 

  • Teske A (2006) Microbial communities of deep marine subsurface sediments: molecular and cultivation surveys. Geomicrobiol J 23:357–368

    Article  Google Scholar 

  • Thomsen TR, Finster K, Ramsing NB (2001) Biogeochemical and molecular signatures of anaerobic methane oxidation in a marine sediment. Appl Environ Microbiol 67:1646–1656

    Article  Google Scholar 

  • Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignments through sequence weighting, position specific gap penalties and weight matrix choice. Nucl Acids Res 22:4673–4680

    Article  Google Scholar 

  • Toffin L, Bidault A, Pignet P, Tindall BJ, Slobodkin A, Kato C, Prieur D (2004a) Shewanella profunda sp. nov., isolated from deep marine sediment of the Nankai Trough. Int J Syst Evol Microbiol 54:1943–1949

    Article  Google Scholar 

  • Toffin L, Webster G, Weightman AJ, Fry JC, Prieur D (2004b) Molecular monitoring of culturable bacteria from deep-sea sediment of the Nankai Trough, Leg 190 Ocean Drilling Program. FEMS Microbiol Ecol 48:357–367

    Google Scholar 

  • Toffin L, Zink K, Kato C, Pignet P, Bidault A, Bienvenu N, Birrien JL, Prieur D (2005) Marinilactobacillus piezotolerans sp. nov., a novel marine lactic acid bacterium isolated from deep subseafloor sediment of the Nankai Trough. Int J Syst Evol Microbiol 55:345–351

    Article  Google Scholar 

  • Tyson GW, Chapman J, Hugenholtz P, Allen EE, Ram RJ, Richardson PM, Solovyev VV, Rubin EM, Rokhsar DS, Banfield JF (2004) Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428:37–43

    Article  Google Scholar 

  • Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen JA, Wu D, Paulsen I, Nelson K, Nelson W, Fouts DE, Levy S, Knap AH, Lomas MW, Nealson K, White O, Peterson J, Hoffman J, Parsons R, Baden-Tillson H, Pfannkoch C, Rogers Y-H, Hamilton SO (2004) Environmental genome shotgun sequencing of the sargasso sea. Science 304:66–74

    Article  Google Scholar 

  • Von Mering C, Hugenholtz P, Raes J, Tringe SG, Doerks T, Jensen LJ, Ward N, Bork P (2007) Quantitative phylogenetic assessment of microbial communities in diverse environments. Science 315:1126–1130

    Article  Google Scholar 

  • 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

    Google Scholar 

  • Wagner M, Loy A, Klein M, Lee N, Ramsing NB, Stahl DA, Friedrich MW(2005) Functional marker genes for identification of sulfate-reducing prokaryotes. Environ Microbiol Meth Enzymol 397:469–489

    Google Scholar 

  • Webster G, Newberry CJ, Fry JC, Weightman AJ (2003) Assessment of bacterial community structure in the deep sub-seafloor biosphere by 16S rDNA-based techniques: a cautionary tale. JMicrobiol Meth 55:155–164

    Article  Google Scholar 

  • Webster G, Parkes RJ, JFry JC, Weightman AJ (2004) Widespread occurrence of a novel division of bacteria identified by 16S rRNA gene sequences originally found in deep marine sediments. Appl Environ Microbiol 70:5708–5713

    Article  Google Scholar 

  • Webster G, Parkes RJ, Cragg BA, Newberry CJ, Weightman AJ, Fry JC (2006) Prokaryotic community composition and biogeochemical processes in deep subseafloor sediments from the Peru margin. FEMS Microbiol Ecol 58:65–85

    Article  Google Scholar 

  • Wellsbury P, Goodman K, Barth T, Cragg BA, Barnes SP, Parkes RJ (1997) Deep bacterial biosphere fuelled by increasing organic matter availability during burial and reheating. Nature 388:573–576

    Article  Google Scholar 

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

    Article  Google Scholar 

  • Wilms R, Köpke B, Sass H, Chang TS, Cypionka H, Engelen B (2006a) Deep biosphere-related bacteria within the subsurface of tidal flat sediments. Environ Microbiol 8: 709–719

    Article  Google Scholar 

  • Wilms R, Sass H, Köpke B, Koster H, Cypionka H, Engelen B (2006b) Specific bacterial, archaeal, and eukaryotic communities in tidal-flat sediments along a vertical profile of several meters. Appl Environ Microbiol 72:2756–2764

    Article  Google Scholar 

  • Wilms R, Sass H, Köpke B, Cypionka H, Engelen B (2007) Methane and sulfate profiles within the subsurface of a tidal flat are reflected by the distribution of sulfate-reducing bacteria and methanogenic archaea. FEMS Microbiol Ecol 59:611–621

    Article  Google Scholar 

  • Wu L, Liu X, Schadt CW, Zhou J (2006) Microarray-based analysis of subnanogram quantities of microbial community DNAs by using whole community genome amplification. Appl Environ Microbiol 72:4931–4941

    Article  Google Scholar 

  • Zhang K, Martiny AC, Reppas NB, Barry KW, Malek J, Chisholm S, Church GM (2006) Sequencing genomes from single cells by polymerase cloning. Nat Biotechnol 24:680–686

    Article  Google Scholar 

  • Zverlov V, Klein M, Lucker S, Friedrich MW, Kellermann J, Stahl DA, Loy A, Wagner M (2005) Lateral gene transfer of dissimilatory (bi)sulfite reductase revisited. J Bacteriol 187:2203–2208

    Article  Google Scholar 

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Teske, A., Biddle, J. (2008). Analysis of Deep Subsurface Microbial Communities by Functional Genes andGenomics. In: Dilek, Y., Furnes, H., Muehlenbachs, K. (eds) Links Between Geological Processes, Microbial Activities&Evolution of Life. Modern Approaches in Solid Earth Sciences, vol 4. Springer, Dordrecht. https://doi.org/10.1007/978-1-4020-8306-8_5

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