Analysis of deep subsurface microbial communities by functional genes and genomics

Modern Approaches in Solid Earth Sciences

Volumn 4, Issue , 2008, Pages 159-176

  Teske, Andreas ^a   Biddle, Jennifer F ^b  

^a University of North Carolina at Chapel Hill   (United States)

^b NONE

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84979889776     PISSN: 18761682     EISSN: None     Source Type: Book Series    
DOI: None     Document Type: Chapter

References (110)

1. 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.
2. 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.
3. Amend JP, Teske A (2005) Expanding frontiers in deep subsurface microbiology. Palaeogeogr Palaeoclimatol Palaeoecol 219:131–155.
4. 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.
5. 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.
6. Biddle JF (2006) Microbial populations and processes in deeply buried marine sediments. PhD thesis, Pennsylvania State University
7. 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
8. 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: [Cited 2007-04-25]
9. Biddle JF, House CH, Brenchley JE (2005b) Microbial stratification in deeply-buried marine sediment reflects changes in sulfate/methane profiles. Geobiology 3:287–295.
10. Biddle JF, Lipp JS, Lever MA, Lloyd KG, Sørensen 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.
11. 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.
12. Boetius A, Ravenschlag K, Schubert C, Rickert D, Widdel F, Gieseke A, Amann R, Jørgensen BB, Witte U, Pfannkuche O (2000) A marine microbial consortium apparently mediating anaerobic oxidation of methane. Nature 407:623–626.
13. 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, pp 269–276
14. Böttcher ME, Ferdelman TG, Jørgensen 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: Jørgensen BB, D’Hondt SL, Miller DJ (eds) Proc ODP, Sci Results, 201 [Online]. Available from World Wide Web: .[Cited 2006-06-25]
15. 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.
16. Braker G, Ayala-del-Rìo 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.
17. 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.
18. Bruns A, Nübel 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.
19. Bustin SA (2000) Absolute quantification of mRNA using real-time reverse transcription polymerase chain reaction assays. J Mol Endocrinol 25:169–193.
20. 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.
21. Connon SA, Giovannoni SJ (2002) High-throughput methods for culturing micro-organisms in very-low-nutrient media yield diverse new marine isolates. Appl Environ Microbiol 68: 3878–3885.
22. Coolen MJL, Cypionka H, Sass AM, Sass H, Overmann J (2002) Ongoing modification ofMediterranean sapropels mediated by prokaryotes. Science 296:2407–2410.
23. Dhillon A, Teske A, Dillon J, Stahl DA, Sogin ML (2003) Molecular characterization of sulfatereducing bacteria in the Guaymas Basin. Appl Environ Microbiol 69:2765–2772.
24. Dhillon A, Goswami S, Riley M, Teske A, Sogin ML (2005a). Domain evolution and functional diversification of sulfite reductases. Astrobiology 5:18–29.
25. 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.
26. D’Hondt SL, Jørgensen 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
27. D’Hondt S, Jørgensen 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, Engelen B, 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, Wiegel J, Padilla CN, Acosta JLS (2004) Distributions of microbial activities in deep subseafloor sediments. Science 306:2216–2221.
28. Didyk BM, Simoneit BR (1989) Hydrothermal oil of Guaymas Basin and implications for petroleum formation mechanisms. Nature 342:65–69.
29. 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.
30. 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.
31. Friedrich MW (2002) Phylogenetic analysis reveals multiple lateral transfers of adenosine-5_- phosphosulfate reductase genes among sulfate-reducing microorganisms. J Bacteriol 184: 278–289.
32. Friedrich MW (2005) Methyl-coenzyme M reductase genes: unique functional markers for methanogenic and anaerobic methane-oxidizing archaea. Methods Enzymol 397:428–442.
33. 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.
34. 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, pp 119–166.
35. 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.
36. 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.
37. Højberg O, Binnerup SJ, Sørensen 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.
38. Hutchinson CA, Smith HO, Pfannkoch C, Venter JC (2005) Cell-free cloning using _ 29. DNA polymerase. Proc Natl Acad USA 102:17332–17336.
39. 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.
40. 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.
41. 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, 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.
42. Jørgensen BB, D’Hondt SL (2006) A starving majority deep beneath the seafloor. Science 314:932–934.
43. Kaeberlein T, Lewis K, Epstein SS (2002) Isolating “uncultivable” microorganisms in pure culture in a simulated natural environment. Science 296:1127–1129.
44. 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.
45. 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.
46. Klenk HP, Clayton RA, Tomb JF, White O, et al (1997) The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus. Nature 390:364–370.
47. 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.
48. 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 Microbiol 71:7819–7830.
49. 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.
50. 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.
51. Kumar S, Tamura K, Nei M (2004) MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform 5:150–163.
52. 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.
53. 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.
54. 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.
55. ASLO Meeting, Santa Fe, NM. Liu X, Bagwell CE, Wu L, Devol AH, Zhou J (2003) Molecular diversity of sulfate-reducing bacteria from two different continental margin habitats. Appl EnvironMicrobiol 69:6073–6081.
56. 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.
57. 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.
58. Martens-Habbena W, Sass H (2006) Sensitive determination of microbial growth by nucleuic acid staining in aqueous suspension. Appl Environ Microbiol 72:87–95.
59. 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, pp 219–226.
60. Neretin LN, Schippers A, Pernthaler A, Hamann K, Amann R, Jørgensen BB (2003) Quantification of dissimilatory (bi)sulphite reductase gene expression in Desulfo-bacterium autotrophicum using real-time RT-PCR. Environ Microbiol 5:660-671.
61. 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.
62. Niemann H, Lösekann T, de Beer D, Elvert M, Nadalig T, Knittel K, Amann R, Sauter EJ, Schlüter 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.
63. 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.
64. 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.
65. 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.
66. Parkes RJ, Cragg BA, Wellsbury P (2000) Recent studies on bacterial populations and processes in subseafloor sediments: a review. Hydrogeology J. 8:11–28.
67. 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.
68. Parkes RJ, Cragg BA, Banning N, Brock F, Webster G, Fry JC, Hornibrook E, Pancost RD, Kelly S, Knab N, Jørgensen BB, Rinna J, Weightman AJ (2007) Biogeochemistry and biodiversity of methane cycling in subsurface marine sediments (Skagerrak, Denmark). Environ Microbiol 9:1146–1161.
69. 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, pp 289–294.
70. 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.
71. 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.
72. Rappé MS, Connon SA, Vergin KL, Giovannoni SJ (2002) Cultivation of the ubiquitous SAR11 marine bacterioplankton clade. Nature 418:630–633.
73. 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.
74. 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.
75. Schippers A, Neretin LN, Kallmeyer J, Ferdelman TG, Cragg BA, Parkes JR, Jørgensen BB (2005) Prokaryotic cells of the deep sub-seafloor biosphere identified as living bacteria. Nature 433:861–864.
76. Shipboard Scientific Party (2003a) Site 1228. In: D’Hondt SL, Jørgensen BB, Miller DJ, et al (eds) Proceedings of the ocean drilling program, Initial reports 201. Ocean Drilling Program, Texas &M University, College Station, Tex. [CD-ROM], pp 1–72.
77. Shipboard Scientific Party (2003b) Site 1229. In: D’Hondt SL, Jørgensen BB, Miller DJ, et al (eds) Proceedings of the ocean drilling program, Initial reports 201. Ocean Drilling Program, Texas &M University, College Station, Tex. [CD-ROM], pp 1–78.
78. Shipboard Scientific Party (2003c) Site 1230. In: D’Hondt SL, Jørgensen BB, Miller DJ, et al (eds) Proceedings of the Ocean Drilling Program, Initial reports 201. Ocean Drilling Program, Texas &M University, College Station, Tex. [CD-ROM], pp 1–107.
79. 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.
80. Sørensen KB, Teske A (2006) Stratified communities of active archaea in deep marine subsurface sediments. Appl Environ Microbiol 72:4596–4603.
81. Sørensen 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.
82. 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.
83. Stahl DA, Fishbain S, Klein M, Baker BJ,WagnerW(2002) Origins and diversification of sulfaterespiring microorganisms. Antonie Van Leeuwenhoek 81:189–195.
84. 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.
85. 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.
86. Süss 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
87. 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.
88. 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.
89. Teske A (2006) Microbial communities of deep marine subsurface sediments: molecular and cultivation surveys. Geomicrobiol J 23:357–368.
90. 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.
91. Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTALW: 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.
92. 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.
93. 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.
94. 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.
95. 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.
96. 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.
97. 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.
98. 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.
99. 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.
100. 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. J Microbiol Meth 55:155–164.
101. 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.
102. 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.
103. 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.
104. Whitman WB, Coleman DC, Wiebe WJ (1998) Prokaryotes: the unseen majority. Proc Natl Acad Sci USA 95:6578–6583.
105. Wilms R, Köpke B, Sass H, Chang TS, Cypionka H, Engelen B (2006a) Deep biosphererelated bacteria within the subsurface of tidal flat sediments. Environ Microbiol 8: 709–719
106. 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.
107. 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.
108. 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.
109. 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.
110. 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