Genetic Evidence of Subseafloor Microbial Communities

Developments in Marine Geology

Volumn 7, Issue , 2014, Pages 85-125

  Teske, Andreas ^a   Biddle, Jennifer F ^b   Lever, Mark A ^c  

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

^b UNIVERSITY OF DELAWARE   (United States)

^c ETH ZURICH   (Switzerland)

Author keywords

16S rRNA gene; Archaea; Bacteria; Deep biosphere; Eukarya; Functinoal genes; Metagenomics; Ocean crust; Review; Sediment; Subseafloor

Indexed keywords

EUKARYOTA;

EID: 84919465490     PISSN: 15725480     EISSN: None     Source Type: Book Series    
DOI: 10.1016/B978-0-444-62617-2.00004-9     Document Type: Chapter

References (212)

1. Amann R., Ludwig W., Schleifer K.H. β-Subunit of ATP-synthase: a useful marker for studying the phylogenetic relationship of Eubacteria. Journal of General Microbiology 1988, 134:2815-2821.
2. Bagwell C.E., Liu X., Wu L., Zhou J. Effects of legacy nuclear waste on the compositional diversity and distributions of sulfate-reducing bacteria in a terrestrial subsurface aquifer. FEMS Microbiology Ecology 2005, 55:424-431.
3. Bahr M., Crump B., Klepac-Ceraj V., Teske A., Sogin M., Hobbie J. Molecular characterization of sulfate-reducing bacteria in a New England salt marsh. Environmental Microbiology 2005, 7:1175-1185.
4. Baker B.J., Dick G.J. Omic approaches in microbial ecology: charting the unknown. ASM News 2013, 9:353-360.
5. Barns S.M., Delwiche C.F., Palmer J.D., Pace N.R. Perspectives on archaeal diversity, thermophily and monophyly from environmental rRNA sequences. Proceedings of the National Academy of Sciences USA 1996, 93:9188-9193.
6. Batzke A., Engelen B., Sass H., Cypionka H. Phylogenetic and physiological diversity of cultured deep-biosphere bacteria from equatorial Pacific Ocean and Peru margin sediments. Geomicrobiology Journal 2007, 24:261-273.
7. Biddle J.F., Cardman Z., Mendlovitz H., Albert D.B., Lloyd K.G., Boetius A., Teske A. Anaerobic oxidation of methane at different temperature regimes in Guaymas Basin hydrothermal sediments. ISME J 2012, 6:1018-1031.
8. Biddle J.F., House C.H., Brenchley J.E. Enrichment and cultivation of microorganisms from sediment from the slope of the Peru Trench (ODP site 1230). Proc. ODP, sci. results 2005, Vol. 201. [Online]. Available from World Wide Web:. http://www-odp.tamu.edu/publications201_SR/107107.htm, B.B. Jørgensen, S.L. D'Hondt, D.J. Miller (Eds.).
9. Biddle J.F., House C.H., Brenchley J.E. Microbial stratification in deeply-buried marine sediment reflects changes in sulfate/methane profiles. Geobiology 2005, 3:287-295.
10. Biddle J.F., Lipp J.S., Lever M.A., Lloyd K.G., Sørensen K.B., Anderson R., et al. Heterotrophic archaea dominate sedimentary subsurface ecosystems off Peru. Proceedings of the National Academy of Sciences USA 2006, 103:3846-3851.
11. Biddle J.F., Fitz-Gibbon S., Schuster S.C., Brenchley J.E., House C.H. Metagenomic signatures of the Peru Margin subseafloor biosphere show a genetically distinct environment. Proceedings of the National Academy of Sciences USA 2008, 105:10583-10588.
12. Biddle J.F., White J.R., Teske A., House C.H. Metagenomics of the subsurface Brazos-Trinity Basin (IODP Site 1320): comparison with other sediment and pyrosequenced metagenomes. The ISME Journal 2011, 5:1038-1047.
13. Binga E.K., Lasken R.S., Neufeld J.D. Something from (almost) nothing: the impact of multiple displacement amplification on microbial ecology. The ISME Journal 2008, 2:233-241.
14. Blazejak A., Schippers A. High abundance of JS-1- and chloroflexi-related bacteria in deeply buried marine sediments revealed by quantitative, real-time PCR. FEMS Microbiology Ecology 2010, 72:198-207.
15. Blazejak A., Schippers A. Real-time quantification and diversity analysis of the functional genes aprA and dsrA of sulfate-reducing prokaryotes in marine sediments of the Peru continental Margin and the Black Sea. Front Microbiology 2012, 2:253. 10.3389/jmicb.2011.00253.
16. Boetius A., Ravenschlag K., Schubert C.J., Rickert D., Widdel F., Gieseke A., et al. A marine microbial consortium apparently mediating anaerobic oxidation of methane. Nature 2000, 407:623-626.
17. Borrel G., O'Toole P.W., Harris H.M.B., Peyret P., Brugere J.-F., Gribaldo S. Phylogenomic data support a seventh order of methylotrophic methanogens and provide insights into the evolution of methanogenesis. Genome Biology and Evolution 2013, 5:1769-1780.
18. Böttcher M.E., Ferdelman T.G., Jørgensen B.B., Blake R.E., Surkov A.V., Claypool G.E. 6. Sulfur isotope fractionation by the deep biosphere within sediments of the Eastern Equatorial Pacific and Peru Margin. Proc. ODP, sci. res 2006, Vol. 201:1-45. ODP, College Station, TX. B.B. Jørgensen, S.L. D'Hondt, D.J. Miller (Eds.).
19. Briggs B.R., Pohlmann J.W., Torres M., Riedel M., Brodie E.L., Colwell F.S. Macroscopic biofilms in fracture-dominated sediment that anaerobically oxidize methane. Applied Environmental Microbiology 2011, 77:6780-6787.
20. Brochier-Armanet C., Boussau B., Gribaldo S., Forterre P. Mesophilic crenarchaeota: proposal for a third archaeal phylum, the thaumarchaeota. Nature Reviews Microbiology 2008, 6:245-252.
21. Bult C.J., White O., Olsen G.J., Zhou L., Fleischmann R.D., Sutton G.G., et al. Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii. Science 1996, 273:1058-1073.
22. Campbell B.J., Cary S.C. Abundance of reverse tricarboxylic acid cycle genes in free-living microorganisms at deep-sea hydrothermal vents. Applied Environmental Microbiology 2004, 70:6282-6289.
23. Cappenberg T.E. Inter-relations between sulfate-reducing and methane-producing bacteria in bottom deposits of a fresh-water lake. 2.Inhibition experiments. Antonie Van Leeuwenhoek 1974, 56:1247-1258.
24. Castro H., Ogram A., Reddy K.R. Phylogenetic characterization of methanogenic assemblages in eutrophic and oligotrophic areas of the Florida Everglades. Applied Environmental Microbiology 2004, 70:6559-6568.
25. Colwell F.S., Boyd S., Delwiche M.E., Reed D.W., Phelps T.J., Newby D.T. Estimates of biogenic methane production rates in deep marine sediments at Hydrate Ridge, Cascadia Margin. Applied Environmental Microbiology 2008, 74:3444-3452.
26. Cord-Ruwisch R., Seitz H.-J., Conrad R. The capacity of hydrogenotrophic anaerobic bacteria to compete for traces of hydrogen depends on the redox potential of the terminal electron acceptor. Archives of Microbiology 1988, 149:350-357.
27. Dean F.B., Hosono S., Fang L., Wu X., Faruqi A.F., Bray-Ward P., et al. Comprehensive human genome amplification using multiple displacement amplification. Proceedings of the National Academy of Sciences USA 2002, 99:5261-5266.
28. D'Hondt S., Rutherford S., Spivack A.J. Metabolic activity of subsurface life in deep-sea sediments. Science 2002, 295:2067-2070.
29. Proc. ODP, init. repts 2003, Vol. 201:479-493. Ocean Drilling Program, College Station, TX. 10.2973/odp.proc.ir.201.2003. S.L. D'Hondt, B.B. Jørgensen, D.J. Miller (Eds.).
30. D'Hondt S., Jørgensen B.B., Miller D.J., Batzke A., Blake R., Cragg B.A., et al. Distribution of microbial activities in deep subseafloor sediments. Science 2004, 306:2216-2221.
31. D'Hondt S., Spivack A.J., Pockalny R., Ferdelman T.G., Fischer J.P., Kallmeyer J., et al. Subseafloor sedimentary life in the South Pacific Gyre. Proceedings of the National Academy of Sciences USA 2009, 106:11651-11656.
32. DeLong E.F. Archaea in coastal marine environments. Proc Natl Acad Sci USA 1992, 89:5685-5689.
33. Dhillon A., Teske A., Dillon J., Stahl D.A., Sogin M.L. Molecular characterization of sulfate-reducing bacteria in the Guaymas Basin. Applied Environmental Microbiology 2003, 69:2765-2772.
34. Dhillon A., Lever M., Lloyd K.G., Albert D.B., Sogin M.L., Teske A. Methanogen diversity evidenced by molecular characterization of methyl coenzyme M reductase A (mcrA) genes in hydrothermal sediments of the Guaymas Basin. Applied Environmental Microbiology 2005, 71:4592-4601.
35. Durbin A.M., Teske A. Sediment-associated microdiversity within the marine group I crenarchaeota. Environmental Microbiology Reports 2010, 2:693-703.
36. Durbin A.M., Teske A. Microbial diversity and stratification of South Pacific abyssal marine sediments. Environmental Microbiology 2011, 13:3219-3234.
37. Durbin A.M., Teske A. Archaea in organic-lean and organic-rich marine subsurface sediments: an environmental gradient reflected in distinct phylogenetic lineages. Frontiers in Microbiology 2012, 3:168. 10.3389/fmicb.2012.00168.
38. Edgcomb V.P., Beaudoin D., Gast R., Biddle J.F., Teske A. Marine subsurface eukaryotes: the fungal majority. Environmental Microbiology 2011, 13:172-183.
39. Edgcomb V.P., Biddle J.F. Microbial eukaryotes in the marine subsurface. Anoxia: evidence for eukaryote survival and paleontological strategies, cellular origin, life in extreme habitats and astrobiology 2011, Vol. 21. 10.1007/978-94-007-1896-8_25. A.V. Altenbach (Ed.).
40. Elsahed M.S., Senko J.M., Najar F.Z., Kenton S.M., Roe B.A., Dewers T.A., et al. Bacterial diversity and sulfur cycling in a mesophilic sulfide-rich spring. Applied Environmental Microbiology 2003, 69:5609-5621.
41. Elsaied H., Naganuma T. Phylogenetic diversity of ribulose-1,5-bisphosphate carboxylase/oxygenase large-subunit genes from deep-sea microorganisms. Applied Environmental Microbiology 2001, 67:1751-1765.
42. Engelhardt T., Sahlberg M., Cypionka H., Engelen B. Biogeography of Rhizobium radiobacter and distribution of associated temperate phages in deep subseafloor sediments. The ISME Journal 2013, 7:199-209.
43. Expedition 329 Scientists South Pacific Gyre subseafloor life. IODP Preliminary Report 2011, 329. 10.2204/iodp.pr.329.2011.
44. Proc. IODP 2006, Vol. 308. Integrated Ocean Drilling Program Management International, Inc, College Station TX. 10.2204/iodp.proc.308.101.2006. P.B. Flemings, J.H. Behrmann, C.M. John, the Expedition 308 Scientists (Eds.).
45. Forschner S.R., Sheffer R., Rowley D.C., Smith D.C. Microbial diversity in cenozoic sediments from the Lomonosov Ridge in the central Arctic Ocean. Environmental Microbiology 2009, 11:630-639.
46. Fox G.E., Stackebrandt E., Hespell R.B., Gibson J., Maniloff J., Dyer T.A., et al. Science 1980, 209:457-463.
47. Franklin M.J., Wiebe W.J., Whitman W.B. Populations of methanogenic bacteria in a Georgia salt marsh. Applied Environmental Microbiology 1988, 54:1151-1157.
48. Frias-Lopez J., Shi Y., Tyson G.W., Coleman M.L., Schuster S.C., Chisholm S.W., et al. Microbial community gene expression in ocean surface waters. Proceedings of the National Academy of Sciences USA 2008, 105:3805-3810.
49. Friedrich M.W. Phylogenetic analysis reveals multiple lateral transfers of adenosine-5'-phosphosulfate reductase genes among sulfate-reducing microorganisms. Journal of Bacteriology 2002, 184:278-289.
50. Fry J.C., Parkes R.J., Cragg B.A., Weightman A.J., Webster G. Prokaryotic biodiversity and activity in the deep subseafloor biosphere. FEMS Microbiology Ecology 2008, 66:181-196.
51. Fuerst J.A., Sagulenko E. Beyond the bacterium: planctomycetes challenge our concepts of microbial structure and function. Nature Reviews Microbiology 2011, 9:403-413.
52. Futagami T., Morono Y., Terada T., Kaksonen A.H., Inagaki F. Dehalogenation activities and distribution of reductive dehalogenase homologous genes in marine subsurface sediments. Applied Environmental Microbiology 2009, 75:6905-6909.
53. Futagami T., Morono Y., Terada T., Kaksonen A.H., Inagaki F. Distribution of dehalogenation activity in subseafloor sediments of the Nankai Trough subduction zone. Philosophical Transactions of the Royal Society B 2013, 368:20120249.
54. Gagen E.J., Denman S.E., Padmanabha J., Zadbuke S., Jassim R.A., Morrison M., et al. Functional gene analysis suggests different acetogen populations in the bovine rumen and Tammar Wallaby forestomach. Applied Environmental Microbiology 2010, 76:7785-7795.
55. Gagen E.J., Huber H., Meador T., Hinrichs K.-U., Thomm M. A novel cultivation-based approach for understanding the miscellaneous crenarchaeotic group (MCG) archaea from sedimentary ecosystems. Applied Environmental Microbiology 2013, 79:6400-6406.
56. Guy L., Ettema T.J. The archaeal 'TACK' superphylum and the origin of eukaryotes. Trends in Microbiology 2011, 19:580-587.
57. Hales B.A., Edwards C., Ritchie D.A., Hall D., Pickup R.W., Saunders J.R. Isolation and identification of methanogen-specific DNA from blanket bog peat by PCR amplification and sequence analysis. Applied Environmental Microbiology 1996, 62:668-675.
58. Hallam S.J., Putnam N., Preston C.M., Detter J.C., Rokhsar D., Richardson P.M., et al. Reverse methanogenesis: testing the hypothesis with environmental genomics. Science 2004, 305:1457-1462.
59. Harrison B.K., Zhang H., Berelson W., Orphan V.J. Variations in archaeal and bacterial diversity associated with the sulfate-methane transition zone in continental margin sediments (Santa Barbara Basin, California). Applied Environmental Microbiology 2009, 75:1487-1499.
60. Heuer V.B., Pohlman J.W., Torres M.E., Elvert M., Hinrichs K.-U. The stable carbon isotope biogeochemistry of acetate and other dissolved carbon species in deep subseafloor sediments at the northern Cascadia Margin. Geochim Cosmochim Acta 2009, 73:3323-3336.
61. Hinrichs K.-U., Inagaki F. Downsizing the deep biosphere. Science 2012, 338:204-205.
62. Hoehler T.M., Alperin M.J., Albert D.B., Martens C.S. Thermodynamic control on hydrogen concentrations in anoxic sediments. Geochim Cosmochim Acta 1998, 62:1745-1756.
63. Hoshino T., Morono Y., Terada T., Imachi H., Ferdelman T.G., Inagaki F. Comparative study of subseafloor microbial community structures in deeply buried coral fossils and sediment matrices from the Challenger Mound in the Porcupine Seabight. Frontiers in Microbiology 2011, 2:231. 10.3389/fmicb.2011.00231.
64. House C.H., Cragg B.A., Teske A., Leg 201 Scientific Party 2. Drilling contamination tests during ODP Leg 201 using chemical and particulate tracers. Proc Ocean Drilling Prog Init Rept 2003, 201:1-18.
65. Huber R., Rossnagel P., Woese C.R., Rachel R., Langworth T.A., Stetter K.O. Formation of ammonium from nitrate during chemolithoautotrophic growth of the extremely thermophilic bacterium Ammonifex degensii gen. nov. sp. nov. Systematic and Applied Microbiology 1996, 19:40-49.
66. Huber H., Hohn M.J., Rachel R., Fuchs T., Wimmer V.C., Stetter K.O. A new phylum of archaea represented by a nanosized hyperthermophilic symbiont. Nature 2002, 417:63-67.
67. Hug L.A., Castelle C.J., Wrighton K.C., Thomas B.C., Sharon I., Frischkorn K.R., et al. Community genomic analyses constrain the distribution of metabolic traits across the Chloroflexi phylum and indicate roles in sediment carbon cycling. Microbiome 2013, 1:22. 10.1186/2049-2618-1-22.
68. 2 fixation in microbial communities of hydrothermal vents of the Logatchev field. FEMS Microbiology Ecology 2010, 73:526-537.
69. Hugenholtz P., Pitulle C., Hershberger K.L., Pace N.R. Novel division level bacterial diversity in a Yellowstone hot spring. Journal of Bacteriology 1998, 180:366-376.
70. Hugenholtz P. Exploring prokaryotic diversity in the genomic era. Genome Biology 2002, 3:1-8.
71. Imachi H., Aoi K., Tasumi E., Saito Y., Yamanaka Y., Saito Y., et al. Cultivation of methanogenic community from subseafloor sediments using a continuous-flow bioreactor. ISME Journal 2011, 5:1913-1925.
72. Imachi H., Sakai S., Lipp J.S., Miyzaki M., Saito Y., Yamanaka Y., et al. Pelolinea submarina gen.nov., sp. nov., an anaerobic, filamentous bacterium of the phylum Chloroflexi isolated from subseafloor sediment. International Journal of Systematic and Evolutionary Microbiology 2014, 64:812-818.
73. Inagaki F., Takai K., Komatsu T., Kanamatsu T., Fujiioka K., Horikoshi K. Archaeology of archaea: geomicrobiological record of pleistocene thermal events concealed in a deep-sea subseafloor environment. Extremophiles 2001, 5:385-392.
74. Inagaki F., Suzuki M., Takai K., Oida H., Sakamoto T., Aoki K., et al. Microbial communities associated with geological horizons in coastal subseafloor sediments from the Sea of Okhotsk. Applied Environmental Microbiology 2003, 69:7224-7235.
75. Inagaki F., Nunoura T., Nakagawa S., Teske A., Lever M.A., Lauer A., et al. Biogeographical distribution and diversity of microbes in methane hydrate-bearing deep marine sediments on the Pacific Ocean Margin. Proceedings of the National Academy of Sciences USA 2006, 103:2815-2820.
76. Inagaki F., Hinrichs K.-U., Kubo Y., the Expedition 337 Scientists Deep coalbed biosphere off shimokita: microbial processes and hydrocarbon system associated with deeply buried coalbed in the ocean. IODP Preliminary Report 2012, 337. 10.2204/iodp.pr.337.2012.
77. Jiang L., Zheng Y., Peng X., Zhou H., Zhang C., Xiao X., et al. Vertical distribution and diversity of sulfate-reducing prokaryotes in the Pearl River estuarine sediments, Southern China. FEMS Microbiology Ecology 2009, 70:249-262.
78. Jørgensen B.B. Mineralization of organic matter in the sea bed - the role of sulphate reduction. Nature 1982, 296:643-645.
79. Jørgensen B.B., D'Hondt S.L., Miller D.J. Leg 201 synthesis: controls on microbial communities in deeply buried sediments. Proc. ODP, sci. res 2006, Vol. 201:1-45. ODP, College Station, TX. B.B. Jørgensen, S.L. D'Hondt, D.J. Miller (Eds.).
80. Jurgens G., Glöckner F.O., Amann R., Saano A., Montonen L., Likolammi M., et al. Identification of novel archaea in bacterioplankton of a boreal forest lake by phylogenetic analysis and fluorescent in situ hybridization. FEMS Microbiology Ecology 2000, 34:45-56.
81. Kallmeyer J., Pockalny R., Adhikari R.R., Smith D.C., D'Hondt S. Global distribution of microbial abundance and biomass in subseafloor sediment. Proceedings of the National Academy of Sciences USA 2012, 109:16213-16216.
82. Kaneko R., Hayashi T., Tanahashi M., Naganuma T. Phylogenetic diversity and distribution of dissimilatory sulfite reductase genes from deep-sea sediment cores. Marine Biotechnology 2007, 9:429-436.
83. Kawai M., Futagami T., Toyoda A., Takaki Y., Nishi S., Hori S., et al. High frequency of phylogenetically diverse reductive dehalogenase-homologius genes in deep subsurface sedmentary metagenomes. Frontiers in Microbiology 2014, 5:80. 10.3389/fmic.201400080.
84. Kellermann M., Wegener G., Elvert M., Yoshinaga M.Y., Lin Yu-S., Holler T., et al. Autotrophy as a predominant mode of carbon fixation in anaerobic methane-oxidizing microbial communities. Proceedings of the National Academy of Sciences USA 2012, 109:19321-19326.
85. Kendall M.M., Liu Y., Sieprawska-Lupa M., Stetter K.O., Whitman W.B., Boone D.R. Methanococcus aeolicus sp. nov., a mesophilic, methanogenic archaeon from shallow and deep marine sediments. International Journal of Systematic and Evolutionary Microbiology 2006, 56:1525-1529.
86. Kirkpatrick J., Oakley B., Fuchsman C., Srinivasan S., Staley J.T., Murray J.W. Diversity and distribution of Planktomycetes and related bacteria in the suboxic zone of the Black Sea. Applied Environmental Microbiology 2006, 72:3079-3083.
87. Klein M., Friedrich M., Roger A.J., Hugenholtz P., Fishbain S., Abicht H., et al. Multiple lateral transfers of dissimilatory sulfite reductase genes between major lineages of sulfate-reducing prokaryotes. Journal of Bacteriology 2001, 183:6028-6035.
88. Kondo R., Nedwell D.B., Purdy K.J., de Queiroz Silva S. Detection and enumeration of sulphate-reducing bacteria in estuarine sediments by competitive PCR. Geomicrobiology Journal 2004, 21:145-157.
89. Kormas A.K., Smith D.C., Edgcomb V., Teske A. Molecular analysis of deep subsurface microbial communities in Nankai Trough sediments (ODP Leg 190, Site 1176). FEMS Microbiology Ecology 2003, 45:115-125.
90. Kubo K., Lloyd K.G., Biddle J.F., Amann R., Teske A., Knittel K. Archaea of the miscellaneous crenarchaeotal group (MCG) are abundant, diverse and widespread in marine sediments. The ISME Journal 2012, 6:1949-1965.
91. Knittel K., Boetius A. Anaerobic oxidation of methane: progress with an unknown process. Annual Review of Microbiology 2009, 63:311-334.
92. Kragelund C., Levantesi C., Borger A., Thelen K., Eikelboom D., Tandoi V., et al. Identity, abundance and ecosphysiology of filamentous Chloroflexi species present in activated sludge treatment plants. FEMS Microbiology Ecology 2007, 59:671-682.
93. Krajmalnik-Brown R., Hölscher T., Thomson I.N., Saunders F.M., Ritalahti K.M., Löffler F.E. Genetic identification of a putative vinyl chloride reductase in Dehalococcoides sp. strain BAV1. Applied Environmental Microbiology 2004, 70:6347-6351.
94. Lanoil B.D., Sassen R., La Duc M.T., Sweet S.T., Nealson K.H. Bacteria and archaea physically associated with Gulf of Mexico gas hydrates. Applied Environmental Microbiology 2001, 67:5143-5153.
95. Leaphart A.B., Friez M.J., Lovell C.R. Formyltetrahydrofolate synthetase sequences from salt marsh plant roots reveal a diversity of acetogenic bacteria and other bacterial functional groups. Applied Environmental Microbiology 2003, 69:693-696.
96. Leloup J., Fossing H., Kohls K., Holmkvist L., Borowski C., Jørgensen B.B. Sulfate-reducing bacteria in marine sediment (Aarhus Bay, Denmark): abundance and diversity related to geochemical zonation. Environmental Microbiology 2009, 11:1278-1291.
97. Leloup J., Loy A., Knab N.J., Borowski C., Wagner M., Jørgensen B.B. Diversity and abundance of sulfate-reducing microorganisms in the sulfate and methane zones of a marine sediment, Black Sea. Environ Microbiol 2007, 9:131-142.
98. Lever M.A., Alperin M.J., Engelen B., Inagaki F., Nakagawa S., Steinsbu B., et al. Trends in basalt and sediment core contamination during IODP Expedition 301. Geomicrobiology Journal 2006, 23:517-530.
99. Lever, M.A. (2008). Anaerobic carbon cycling pathways in the subseafloor investigated via functional genes, chemical gradients, stable carbon isotopes, and thermodynamic calculations. (PhD thesis) The University of North Carolina at Chapel Hill, Dept. of Marine Sciences.
100. Lever M.A. Acetogenesis in the energy-starved deep biosphere - a paradox?. Frontiers in Microbiology 2012, 2:1-18.
101. Lever M.A. Functional gene surveys from ocean drilling expeditions - a review and perspective. FEMS Microbiol Rev 2013, 84:1-23.
102. Lever M.A., Heuer V.B., Morono Y., Masui N., Schmidt F., Alperin M.J., et al. Acetogenesis in deep subseafloor sediments of the Juan de Fuca Ridge Flank: a synthesis of geochemical, thermodynamic, and gene-based evidence. Geomicrobiology Journal 2010, 27:183-211.
103. Lever M.A., Rouxel O., Alt J.C., Shimizu N., Ono S., Coggon R.M., et al. Evidence for microbial carbon and sulfur cycling in deeply buried Ridge Flank Basalt. Science 2013, 339:1305-1308.
104. Li P.-Y., Xie B.B., Zhang X.Y., Qin Q-L., Dang H.Y., Wang X.M., et al. Genetic structure of three fosmid-fragments encoding 16S rRNA genes of the miscellaneous crenarchaeotic group (MCG): implications for physiology and evolution of marine sedimentary archaea. Environmental Microbiology 2012, 14:467-479.
105. Lin Y.-S., Biddle J.F., Lipp J.S., Orcutt B., Holler T., Teske A., et al. Effect of storage conditions on archaeal and bacterial communities in subsurface marine sediments. Geomicrobiology Journal 2010, 27:261-272.
106. Lipp J.S., Morono Y., Inagaki F., Hinrichs K.-U. Significant contribution of archaea to extant biomass in marine subsurface sediments. Nature 2008, 454:991-994.
107. Liu Y., Whitman W.B. Metabolic, phylogenetic, and ecological diversity of the methanogenic Archaea. Annals of the New York Academy of Sciences 2008, 1125:171-189.
108. Lloyd K.G., Alperin M., Teske A. Environmental evidence for net methane production and oxidation in putative anaerobic methanotrophic (ANME) archaea. Environmental Microbiology 2011, 13:2548-2564.
109. Lloyd K.G., Lapham L., Teske A. An anaerobic methane-oxidizing community of ANME-1 archaea in hypersaline Gulf of Mexico sediments. Applied Environmental Microbiology 2006, 72:7218-7230.
110. Lloyd K.G., Albert D., Biddle J.F., Chanton L., Pizarro O., Teske A. Spatial structure and activity of sedimentary microbial communities underlying a Beggiatoa spp. mat in a Gulf of Mexico hydrocarbon seep. PLoS One 2010, 5(1):e8738. 10.1371/journal.pone.0008738.
111. Lloyd K.G., Schreiber L., Petersen D.G., Kjeldsen K.U., Lever M.A., Steen A.D., et al. Predominant archaea in marine sediments degrade detrital proteins. Nature 2013, 496:215-218.
112. Lonergan D.J., Jenter H.L., Coates J.D., Phillips E.J.P., Schmidt T.M., Lovley D.E. Phylogenetic analysis of dissimilatory Fe(III)-reducing bacteria. Journal of Bacteriology 1996, 178:2402-2408.
113. López-García P., Moreira D., Lopez-Lopez A., Rodriguez-Valera F. A novel haloarchaeal-related lineage is widely distributed in deep oceanic regions. Environmental Microbiology 2001, 3:72-78.
114. Lovley D.R., Goodwin S. Hydrogen concentrations as an indicator of the terminal electron-accepting reactions in aquatic sediments. Geochim Cosmochim Acta 1988, 52:2993-3003.
115. Loy A., Duller S., Wagner M. Evolution and ecology of microbes dissimilating sulfur compounds: insights from siroheme sulfite reductases. Microbial sulfur metabolism 2008, 46-59. Springer, Berlin. C. Dahl, C.G. Friedrich (Eds.).
116. Loy A., Duller S., Baranyi C., Mussmann M., Ott J., Sharon I., et al. Reverse dissimilatory sulfite reductase as phylogenetic marker for a subgroup of sulfur-oxidizing prokaryotes. Environmental Microbiology 2009, 11:289-299.
117. Ludwig W., Strunk O., Westram R., Richter L., Meier H., Yadhukumar A., et al. ARB: a software environment for sequence data. Nucleic Acids Research 2004, 32:1363-1371.
118. Lueders T., Chin K.J., Conrad R., Friedrich M. Molecular analyses of methyl-coenzyme M reductase α-subunit (mcrA) genes in rice field soil and enrichment cultures reveal the methanogenic phenotype of a novel archaeal lineage. Environmental Microbiology 2001, 3:194-204.
119. Luton P.E., Wayne J.M., Sharp R.J., Riley P.W. The mcrA gene as an alternative to 16S rRNA in the phylogenetic analysis of methanogen populations in landfill. Microbiology 2001, 148:3521-3530.
120. Martino A.J., Rhodes M.E., Biddle J.F., Brandt L.D., Tomsho L.P., House C.H. Novel degenerate PCR method for whole-genome amplification applied to Peru Margin (ODP Leg 201) subsurface samples. Frontiers in Microbiology 2012, 3:17. 10.3389/fmicb.2012.00017.
121. Masui N., Morono Y., Inagaki F. Microbiological assessment of circulation mud fluids during the first operation of riser drilling by the deep-earth research vessel Chikyu. Geomicrobiology Journal 2008, 25:274-282.
122. Meng J., Wang F., Zheng Y., Peng X., Zhou H., Xiao X. An uncultivated crenarchaeota contains functional bacteriochlorophyll a synthase. The ISME Journal 2009, 3:106-116.
123. Meng J., Xu J., Qin D., He Y., Xiao X., Wang F. Genetic and functional properties of uncultivated MCG archaea assessed by metagenomic expression analysis. The ISME Journal 2014, 8:650-659.
124. Michaelis W., Seifert R., Nauhaus K., Treude T., Thiel V., Blumenberg M., et al. Microbial reefs in the Black Sea fueled by anaerobic oxidation of methane. Science 2002, 297:1013-1015.
125. Miller T.L., Wolin M.J. Methanogens in human and animal intestinal tracts. Systematic and Applied Microbiology 1986, 7:223-229.
126. Mills H.J., Reese B.K., Shepard A.K., Riedinger N., Dowd S.E., Morono Y., et al. Characterization of metabolically active bacterial populations in subseafloor nankai trough sediments above, within, and below the sulfate-methane transition zone. Frontiers in Microbiology 2012, 3:113. 10.3389/fmicb.2012.00113.
127. Mills H.J., Reese B.K., Peter C.S. Characterization of microbial population shifts during sample storage. Frontiers in Microbiology 2012, 3:49. 10.3389/fmicb.2012.00049.
128. Moe W.M., Yan J., Fernanda Nobre M., da Costa M.S., Rainey F.A. Dehalogenimonas lykanthroporepellens gen. nov., sp. nov., a reductively dehalogenating bacterium isolated from chlorinated solvent-contaminated groundwater. International Journal of Systematic and Evolutionary Microbiology 2009, 59:2692-2697.
129. Morono Y., Terada T., Nishizawa M., Ito M., Hillion F., Takahata N., et al. Carbon and nitrogen assimilation in deep subseafloor microbial cells. Proceedings of the National Academy of Sciences USA 2011, 108:18295-18300.
130. Nakagawa S., Inagaki F., Suzuki Y., Steinsbu B.O., Lever M.A., Takai K., et al. Microbial community in black rust exposed to hot ridge flank crustal fluids. Applied Environmental Microbiology 2006, 72:6789-6799. Integrated Ocean Drilling Program Expedition 301 Scientists.
131. Newberry C.J., Webster G., Weightman A.J., Fry J.C. Diversity of prokaryotes and methanogenesis in deep subsurface sediments from the Nankai Trough, ocean drilling program Leg 190. Environmental Microbiology 2004, 6:274-287.
132. Nunoura T., Inagaki F., Delwiche M.E., Colwell F.S., Takai K. Subseafloor microbial communities in methane-hydrate bearing sediments at two distinct locations (ODP Leg 204) in the Cascadia Margin. Microbe Environments 2008, 23:317-325.
133. Nunoura T., Soffientino B., Blazejak A., Kakuta J., Oida H., Schippers A., et al. Subseafloor microbial communities associated with rapid turbidite deposition in the Gulf of Mexico continental slope (IODP Expedition 308). FEMS Microbiology Ecology 2009, 69:410-424.
134. Nunoura T., Takai Y., Kakuta J., Nishi S., Sugahara J., Kazama H., et al. Insights into the evolution of archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group. Nucleic Acids Research 2011, 39:3204-3223.
135. Orcutt B.N., Bach W., Becker K., Fisher A.T., Hentscher M., Toner B.M., et al. Colonization of subsurface microbial observatories deployed in young ocean crust. The ISME Journal 2010, 5:692-703.
136. Orcutt B.N., Sylvan J.B., Knab N.J., Edwards K.J. Microbial ecology of the dark ocean above, at, and below the seafloor. Microbiology and Molecular Biology Reviews 2011, 75:361-422.
137. Orsi W., Biddle J.F., Edgcomb V. Deep sequencing of subseafloor eukaryotic rRNA reveals active fungi across marine subsurface provinces. PloS One 2013, 8:e56335. 10.1371/journal/pne.0056335.
138. Orsi W., Edgcomb V., Christman G.D., Biddle J.F. Gene expression in the deep biosphere. Nature 2013, 499:205-208.
139. Pace N.R. A molecular view of microbial diversity and the biosphere. Science 1997, 276:734-740.
140. Parkes R.J., Webster G., Cragg B.A., Weightman A.J., Newberry C.J., Ferdelman T.G., et al. Deep sub-seafloor prokaryotes stimulated at interfaces over geological time. Nature 2005, 436:390-394.
141. Parkes R.J., Sellek G., Webster G., Martin D., Anders E., Weightman A.J., et al. Culturable prokaryotic diversity of deep, gas hydrate sediments: first use of a continuous high-pressure, anaerobic, enrichment and isolation system for subseafloor sediments (DeepIsoBUG). Environmental Microbiology 2009, 11:3140-3153.
142. Parkes R.J., Brock F., Banning N., Hornibrook E.R.C., Rousel E.G., Weightman A.J., et al. Changes in methanogenic substrate utilization and communities with depth in a salt-marsh, creek sediment in southern England. Estuarine Coastal and Shelf Science 2012, 96:170-178.
143. Pereyra L.P., Hiibel S.R., Prieto Riquelme M.V., Reardon K.F., Pruden A. Detection and quantification of functional genes of cellulose-degrading, fermentative, and sulfate-reducing bacteria and methagenic archaea. Applied Environmental Microbiology 2010, 76:2192-2202.
144. Pester M., Bittner N., Pinsurang D., Wagner M., Loy A. A 'rare biosphere' microorganism contributes to sulfate reduction in a peatland. ISME Journal 2010, 4:1591-1602.
145. Pester M., Schleper C., Wagner M. The Thaumarchaeota: an emerging view of their phylogeny and ecophysiology. Current Opinion in Microbiology 2011, 14:300-306.
146. Rabus R., Hansen T.A., Widdel F. Dissimilatory sulfate- and sulfur-reducing prokaryotes. Chapter 1.22. The prokaryotes 2006, Vol. 2:659-768. 3rd ed. M. Dworkin, K.-H. Schleifer (Eds.).
147. Rappé M.S., Giovannoni S.J. The uncultured microbial majority. Annual Review of Microbiology 2003, 57:369-394.
148. Reed D.W., Fujita Y., Delwiche D.E., Blackwelder D.B., Sheridan P.P., Uchida T., Colwell F.S. Microbial communities from methane hydrate-bearing deep marine sediments in a Forearch Basin. Appl Environ Microbiol 2002, 68:3759-3770.
149. Rinke C., Schwientek P., Sczyrba A., Ivanova N.N., Anderson I.J., Cheng J-F., et al. Insights into the phylogeny and coding potential of microbial dark matter. Nature 2013, 499:431-437.
150. Rochelle P.A., Cragg B.A., Fry J.C., Parkes R.J., Weightman A.J. Effect of sample handling on estimation of bacterial diversity in marine sediments by 16S rRNA gene sequence analysis. FEMS Microbiology Ecology 1994, 19:215-226.
151. Ronaghi M., Uhlen M., Nyren P. A sequencing method based on real-time pyrophosphate. Science 1998, 281:363-365.
152. Roy H., Kallmeyer J., Adhikari R.R., Pockalny R., Jørgensen B.B., D'Hondt S. Aerobic microbial respiration in 86-million-year-old deep-sea red clay. Science 2012, 336:922-925.
153. Roussel E.G., Bonavita M.-A.C., Querellou J., Cragg B.A., Webster G., Prieur D., et al. Extending the sub-sea-floor biosphere. Science 2008, 320:1046.
154. Roussel E.G., Sauvadet A.-L., Chaduteau C., Fouquet Y., Charlou J.-L., Prieur D., et al. Archaeal communities associated with shallow to deep subseafloor sediments of New Caledonia Basin. Environmental Microbiology 2009, 11:2446-2462.
155. Rey R.E., Harris J.K., Wilcox J., Spear J.R., Miller S.R., Bebout B.M., et al. Unexpected diversity and complexity of the Guerrero Negro hypersaline microbial mat. Applied Environmental Microbiology 2006, 72:3685-3695.
156. Sakai S., Imachi H., Hanada S., Ohashi A., Harada H., Kamagata Y. Methanocella paludicola gen. nov., sp. nov., a methane-producing archaeon, the first isolate of the lineage 'Rice Cluster I', and proposal of the new archaeal order Methanocellales ord. nov. International Journal of Systematic and Evolutionary Microbiology 2008, 58:929-936.
157. Santelli C.M., Banerjee N., Bach W., Edwards K.J. Tapping the subsurface ocean crust biosphere: low biomass and drilling-related contamination calls for improved quality controls. Geomicrobiology Journal 2010, 27:158-169.
158. Scheller S., Goenrich M., Boecher R., Thauer R., Jaun B. The key nickel enzyme of methanogenesis catalyzes the anaerobic oxidation of methane. Nature 2010, 465:606-609.
159. Schippers A., Neretin L.N. Quantification of microbial communities in near-surface and deeply buried marine sediments on the Peru continental margin using real-time PCR. Environmental Microbiology 2006, 8:1251-1260.
160. Schippers A., Kock D., Höft C., Köweker G., Siegert M. Quantification of microbial communities in subsurface sediments of the Black Sea and off Namibia. Frontiers in Microbiology 2012, 3:16. 10.3389/fmicb.2012.00016.
161. Schleper C., Jurgens G., Jonuscheit M. Genomic studies of uncultivated archaea. Nature Reviews Microbiology 2005, 3:479-488.
162. Seyler L.M., McGuinness L.M., Kerkhof L.J. Crenarchaeal heterotrophy in salt marsh sediments. ISME J 2014, 8:1534-1543.
163. Shima S., Krüger M., Weinert T., Demmer U., Kahnt J., Thauer R.K., et al. Structure of a methylcoenzyme M reductase from Black Sea mats that oxidize methane anaerobically. Nature 2012, 481:98-101.
164. Singh N., Kendall M.M., Liu Y., Boone D.R. Isolation and characterization of methylotrophic methanogens from anoxic marine sediments in Skan Bay, Alaska: description of Methanococcoides alaskense sp. nov., and emended description of Methanosarcina baltica. International Journal of Systematic and Evolutionary Microbiology 2005, 55:2531-2538.
165. Smith D.C., Spivack A.J., Fisk M.R., Haveman S.A., Staudigel H. Tracer-based estimates of drilling-induced microbial contamination of deep sea crust. Geomicrobiology Journal 2000, 17:207-219.
166. Sogin M.L., Morrison H.G., Huber J.A., Welch D.M., Huse S.M., Neal P.R., et al. Microbial diversity in the deep sea and the underexplored "rare biosphere". Proceedings of the National Academy of Sciences USA 2006, 103:12115-12120.
167. Sørensen K.B., Lauer A., Teske A. Archaeal phylotypes in a metal-rich and low-activity deep subsurface sediment of the Peru Basin, ODP Leg 201, Site 1231. Geobiology 2004, 2:151-161.
168. Sørensen K.B., Teske A. Stratified communities of active archaea in deep marine subsurface sediments. Applied Environmental Microbiology 2006, 72:4596-4603.
169. Sowers K.R., Ferry J.G. Isolation and characterization of a methylotrophic methanogen, Methanococcoides methylutens gen. nov., sp. nov. Applied Environmental Microbiology 1983, 45:684-690.
170. Springer E., Sachs M.S., Woese C.R., Boone D.R. Partial gene sequences for the A subunit of methyl-coenzyme M reductase (mcrI) as a phylogenetic tool for the family Methanosarcinaceae. International Journal of Systematic Bacteriology 1995, 45:554-559.
171. Suess J., Engelen B., Cypionka H., Sass H. Quantitative analysis of bacterial communities from mediterranean sapropels based on cultivation-dependent methods. FEMS Microbiology Ecology 2004, 51:109-121.
172. Stepanauskas R. Single cell genomics: an individual look at microbes. Current Opinion in Microbiology 2012, 15:613-620.
173. Suess J., Schubert K., Sass H., Cypionka H., Overmann J., Engelen B. Widespread distribution and high abundance of Rhizobium radiobacter within mediterranean subsurface sediments. Environmental Microbiology 2006, 8:1753-1763.
174. Swofford D.L. PAUP*. Phylogenetic analysis using parsimony (and other methods), version 4 2000, Sinauer Associates, Sunderland, Massachusetts.
175. Takai K., Horikoshi K. Genetic diversity of archaea in deep-sea hydrothermal vent environments. Genetics 1999, 152:1284-1297.
176. Takai K., Moser D.P., DeFlaun M., Onstott T.C., Fredrickson J.K. Archaeal diversity in waters from deep South African gold mines. Applied Environmental Microbiology 2001, 67:5750-5760.
177. Teske A., Hinrichs K.-U., Edgcomb V., Gomez A.D., Kysela D., Sylva S.P., et al. Microbial diversity of hydrothermal sediments in the guaymas basin: evidence for anaerobic methanotrophic communities. Applied Environmental Microbiology 2002, 68:1994-2007.
178. Teske A.P. Microbial communities of deep marine subsurface sediments: molecular and cultivation surveys. Geomicrobiology Journal 2006, 23:357-368.
179. Teske A., Sørensen K.B. Uncultured archaea in deep marine subsurface sediments: have we caught them all?. The ISME Journal 2008, 2:3-18.
180. 2. Current Opinion in Microbiology 2011, 14:292-299.
181. Thomsen T.R., Finster K., Ramsing N.B. Biogeochemical and molecular signatures of anaerobic methane oxidation in a marine sediment. Applied Environmental Microbiology 2001, 67:1646-1656.
182. Ufnar J.A., Wang S.Y., Christiansen J.M., Yampara-Iquise H., Carson C.A., Ellender R.D. Detection of the nifH gene of Methanobrevibacter smithii: a potential tool to identify sewage pollution in recreational waters. Journal of Applied Microbiol 2006, 101:44-52.
183. Vetriani C., Jannasch H.W., MacGregor B.J., Stahl D.A., Reysenbach A.L. Population structure and phylogenetic characterization of marine benthic archaea in deep-sea sediments. Applied Environmental Microbiology 1999, 65:4375-4384.
184. Wagner M., Horn M. The Planctomycetes, Verrucomicrobia, Chlamydiae and sister phyla comprise a superphylum with biotechnological and medical relevance. Current Opinion in Biotechnology 2006, 17:241-249.
185. Wagner M., Roger A.J., Flax J.L., Brusseau G.A., Stahl D.A. Phylogeny of dissimilatory sulfite reductases supports an early origin of sulfate reduction. J Bacteriol 1998, 180:2975-2982.
186. Ward J.M., Smith P.H., Boone D.R. Emended description of strain PS ( = OGC 70 = ATCC 33273 = DSM 1537), the type strain of Methanococcus voltae. International Journal of Systematic Bacteriology 1989, 39:493-494.
187. Wasmund K., Schreiber L., Lloyd K.G., Petersen D.G., Schramm A., Stepanauskas R., et al. Genome sequencing of a single cell of the widely distributed marine subsurface Dehalococcoidia, phylum Chloroflexi. The ISME Journal 2014, 8:383-397.
188. Webster G., Newberry C.J., Fry J.C., Weightman A.J. Assessment of bacterial community structure in the deep sub-seafloor biosphere by 16S rDNA-based techniques: a cautionary tale. Journal of Microbiological Methods 2003, 55:155-164.
189. Webster G., Parkes R.J., Fry J.C., Weightman A.J. Widespread occurrence of a novel division of bacteria identified by 16S rRNA gene sequences originally found in deep marine sediments. Applied Environmental Microbiology 2004, 70:5708-5713.
190. Webster G., Parkes R.J., Cragg B.A., Newberry C.J., Weightman A.J., Fry J.C. Prokaryotic community composition and biogeochemical processes in deep subseafloor sediments from the Peru Margin. FEMS Microbiology Ecology 2006, 58:65-85.
191. Webster G., Yarram L., Freese E., öster J.K., Sass J.H., Parkes R.J., et al. Distribution of candidate division JS1 and other bacteria in tidal sediments of the German Wadden Sea using targeted 16S rRNA gene PCR-DGGE. FEMS Microbiology Ecology 2007, 62:78-89.
192. Webster G., Blazejak A., Cragg B.A., Schippers A., Sass H., Rinna J., et al. Subsurface microbiology and biogeochemistry of a deep, cold-water carbonate mound from the Porcupine Seabight (IODP Expedition 307). Environmental Microbiology 2009, 11:239-257.
193. Webster G., Rinna J., Roussel E.G., Fry J.C., Weightman A.J., Parkes R.J. Prokaryotic functional diversity in different biogeochemical depth zones in todal sediments of the Severn Estuary, UK, revealed by stable-isotope probing. FEMS Microbiology Ecology 2010, 72:179-197.
194. Webster G., Sass H., Cragg B.A., Gorra R., Knab N.J., Green C.J., et al. Enrichment and cultivation of prokaryotes associated with the sulphate-methane transition zone of diffusion-controlled sediments of Aarhus Bay, Denmark, under heterotrophic conditions. FEMS Microbiology Ecology 2011, 77:248-263.
195. Whitman W.B., Shieh J., Sohn S., Caras D.S., Premachandran U. Isolation and characterization of 22 mesophilic methanococci. Systematic Applied Microbiology 1986, 7:235-240.
196. Whitman W.B., Bowen T.L., Boone D.R. The methanogenic bacteria. The prokaryotes: an evolving electronic resource for the microbiological community 2006, 3:165-207. Springer, New York, NY. M. Dworkin, S. Falkow, E. Rosenberg, K.-H. Schleifer, E. Stackebrandt (Eds.).
197. Wilms R., Köpke B., Sass H., Chang T.S., Cypionka H., Engelen B. Deep biosphere-related bacteria within the subsurface of tidal flat sediments. Environmental Microbiology 2006, 8:709-719.
198. Woese C.R. Bacterial evolution. Microbiological Review 1987, 51:221-271.
199. Woese C.R., Fox G.E. The phylogenetic structure of the prokaryotic domains. Proceedings of the National Academy of Sciences USA 1977, 74:5088-5090.
200. Woese C.R., Kandler O., Wheelis M.L. Towards a natural system of organisms: proposal for the domains archaea, bacteria and eucarya. Proceedings of the National Academy of Sciences USA 1990, 87:4576-4579.
201. Woese C.R. The universal ancestor. Proceedings of the National Academy of Sciences USA 1998, 95:6854-6859.
202. Yamada T., Sekiguchi Y., Hanada S., Imachi H., Ohashi A., Harada H., et al. Anaerolinea thermolimosa sp. nov., Levilinea saccarolytica gen. nov., sp. nov. and Leptolinea tardivitalis gen. nov., sp. nov., novel filamentous anaerobes, and description of the new classes Anaerolineae classis nov. and Caldineae classis nov. in the bacterial phylum Chloroflexi. International Journal of Systematic and Evolutionary Microbiology 2006, 56:1331-1340.
203. Yamada T., Imachi H., Ohashi A., Harada H., Hanada S., Kamagata Y., et al. Bellilinea caldifistulae gen. nov., sp. nov. and Longilinea arvoryzae gen. nov., sp. nov., strictly anaerobic, filamentous bacteria of the phylum Chloroflexi isolated from methanogenic propionate-degrading consortia. International Journal of Systematic and Evolutionary Microbiology 2007, 57:2299-2306.
204. Yanagawa K., Sunamura M., Lever M.A., Morono Y., Hiruta A., Ishizaki O., et al. Niche separation of methanotrophic archaea (ANME-1 and -2) in methane-seep sediments of the Eastern Japan Sea offshore Joetsu. Geomicrobiology Journal 2011, 28:118-129.
205. Ye G., Wang S., Jiang L., Xiao X., Wang F., Noakes J., et al. Distribution and diversity of bacteria and archaea in marine sediments affected by gas hydrates at Mississippi Canyon in the Gulf of Mexico. Geomicrobiology Journal 2009, 26:370-381.
206. Yoshioka H., Maruyama A., Nakamura T., Higashi Y., Fuse H., Sakata S., et al. Activities and distribution of methanogenic and methane-oxidizing microbes in marine sediments from the Cascadia Margin. Geobiology 2010, 8:223-233.
207. Young J.M., Kuykendall L.D., Martinez-Romero E., Kerr A., Sawada H. A revision of Rhizobium Frank 1889, with an emended description of the genus, and the inclusion of all species of Agrobacterium Conn 1942 and Allorhizobium undicola de Lajudie etal. 1998 as new combinations: Rhizobium radiobacter, R. rhizogenes, R. rubi, R. undicola and R. vitis. International Journal of Systematic and Evolutionary Microbiology 2001, 51:89-103.
208. Zehr P.J., Jenkins B.D., Short S.M., Steward G.F. Nitrogenase gene diversity and microbial community structure: a cross-system comparison. Environmental Microbiology 2003, 5:539-554.
209. Zeikus J.G., Henning D.L. Methanobacterium arboriphilum sp. nov. An obligate anaerobe isolated from wetwood of living trees. Antonie van Leeuwenhoek 1975, 41:543-552.
210. Ziebis W., McManus J., Ferdelman T., Schmidt-Schierhorn F., Bach W., Muratl J., et al. Interstitial fluid chemistry of sediments underlying the North Atlantic Gyre and the influence of subsurface fluid flow. Earth and Planetary Science Letters 2012, 323-324:79-91.
211. Zhang G., Tian J., Jiang N., Guo X., Wang Y., Dong X. Methanogen community in Zoige wetland of Tibetan plateau and phenotypic characterization of a dominant uncultured methanogen cluster ZC-I. Environmental Microbiology 2008, 10:1850-1860.
212. Zverlov V., Klein M., Lücker S., Friedrich M.W., Kellermann J., Stahl D.A., et al. Lateral gene transfer of dissimilatory (bi)sulfite reductase revisited. Journal of Bacteriology 2005, 187:2203-2208.