Functional gene surveys from ocean drilling expeditions - a review and perspective

FEMS Microbiology Ecology

Volumn 84, Issue 1, 2013, Pages 1-23

  Lever, Mark A ^a  

^a AARHUS UNIVERSITY   (Denmark)

Author keywords

Contamination; Deep biosphere; dsrAB; fhs; mcrA; rdhA

Indexed keywords

METHANE; SULFATE;

DATA PROCESSING; GENE; METABOLISM; METHANE; METHANOGENESIS; NUTRIENT CYCLING; OCEAN DRILLING PROGRAM; REACTION KINETICS; SEAFLOOR;

ARCHAEAL GENE; ARCHAEON; BACTERIAL GENE; BACTERIUM; CLASSIFICATION; GENETICS; METABOLISM; MICROBIOLOGY; PHYLOGENY; SEA; SEDIMENT; SHORT SURVEY; TRAVEL;

ARCHAEA; BACTERIA; EXPEDITIONS; GENES, ARCHAEAL; GENES, BACTERIAL; GEOLOGIC SEDIMENTS; METHANE; OCEANS AND SEAS; PHYLOGENY; SULFATES;

EID: 84874738788     PISSN: 01686496     EISSN: 15746941     Source Type: Journal    
DOI: 10.1111/1574-6941.12051     Document Type: Short Survey

References (204)

1. Amann R & Fuchs BM (2008) Single-cell identification in microbial communities by improved fluorescence in situ hybridization techniques. Nat Rev Microbiol 6: 339-348.
2. Amann R, Ludwig W & Schleifer KH (1988) β-Subunit of ATP-synthase: a useful marker for studying the phylogenetic relationship of Eubacteria. J Gen Microbiol 134: 2815-2821.
3. Amend JP & Shock EL (2001) Energetics of overall metabolic reactions of thermophilic and hyperthermophilic archaea and bacteria. FEMS Microbiol Rev 25: 175-243.
4. Bagwell CE, Liu X, Wu L & Zhou J (2005) Effects of legacy nuclear waste on the compositional diversity and distributions of sulfate-reducing bacteria in a terrestrial subsurface aquifer. FEMS Microbiol Ecol 55: 424-431.
5. Bahr M, Crump B, Klepac-Ceraj V, Teske A, Sogin M & Hobbie J (2005) Molecular characterization of sulfate-reducing bacteria in a New England salt marsh. Environ Microbiol 7: 1175-1185.
6. Barnes RO & Goldberg ED (1976) Methane production and consumption in anoxic sediments. Geology 4: 297-300.
7. Behrens S, Lösekann T, Pett-Ridge J, Weber PK, Ng W-O, Stevenson BS, Hutcheon ID, Relman DA & Spormann AM (2008) Linking microbial phylogeny to metabolic activity at the single-cell level by using enhanced element labeling-catalyzed reporter deposition fluorescence in situ hybridization (EL-FISH) and NanoSIMS. Appl Environ Microbiol 72: 3143-3150.
8. Bell DC, Thomas WK, Murtagh K & Glover WR (2010) DNA sequencing with TEM. Microsc Microanal 16: 1768-1769.
9. Biddle JF, Lipp JS, Lever MA et al. (2006) Heterotrophic archaea dominate sedimentary subsurface ecosystems off Peru. Proc Natl Acad Sci USA 103: 3846-3851.
10. Biddle JF, Fitz-Gibbon S, Schuster SC, Brenchley JE & House CH (2008) Metagenomic signatures of the Peru Margin subseafloor biosphere show a genetically distinct environment. Proc Natl Acad Sci USA 105: 10583-10588.
11. Biddle JF, Cardman Z, Mendlovitz H, Albert DB, Lloyd KG, Boetius A & Teske A (2012) Anaerobic oxidation of methane at different temperature regimes in Guaymas Basin hydrothermal sediments. ISME J 6: 1018-1031.
12. Blair CC, D'Hondt S, Spivack AJ & KiSGSley RH (2007) Radiolytic hydrogen and microbial respiration in subsurface sediments. Astrobiology 7: 951-970.
13. Boetius A, Ravenschlag K, Schubert CJ, 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.
14. Böttcher ME, Ferdelman TG, Jørgensen BB, Blake RE, Surkov AV & Claypool GE (2006) 6. Sulfur isotope fractionation by the deep biosphere within sediments of the Eastern Equatorial Pacific and Peru Margin. Proc ODP, Sci Res 201 (Jørgensen BB, D'Hondt SL & Miller DJ, eds), pp. 1-21. ODP, College Station, TX.
15. Braker G, Fesefeldt A & Witzel KP (1998) Development of PCR primer systems for amplification of nitrite reductase genes (nirK and nirS) to detect denitrifying bacteria in environmental samples. Appl Environ Microbiol 64: 3769-3775.
16. Campbell BJ & Cary SC (2004) Abundance of reverse tricarboxylic acid cycle genes in free-living microorganisms at deep-sea hydrothermal vents. Appl Environ Microbiol 70: 6282-6289.
17. Cappenberg TE (1974) Inter-relations between sulfate-reducing and methane-producing bacteria in bottom deposits of a fresh-water lake. 2. Inhibition experiments. Antonie Van Leeuwenhoek 56: 1247-1258.
18. Castro H, Ogram A & Reddy KR (2004) Phylogenetic characterization of methanogenic assemblages in eutrophic and oligotrophic areas of the Florida Everglades. Appl Environ Microbiol 70: 6559-6568.
19. Clarke J, Wu H-C, Jayasinghe L, Patel A, Reid S & Bayley H (2009) Continuous base identification for single-molecule nanopore DNA sequencing. Nat Nanotechnol 4: 265-270.
20. Colwell FS, Boyd S, Delwiche ME, Reed DW, Phelps TJ & Newby DT (2008) Estimates of biogenic methane production rates in deep marine sediments at Hydrate Ridge, Cascadia Margin. Appl Environ Microbiol 74: 3444-3452.
21. Connell L, Barrett A, Templeton A & Staudigel H (2009) Fungal diversity associated with an active deep sea volcano: Vailulu'u Seamount, Samoa. Geomicrobiol J 26: 597-605.
22. Cord-Ruwisch R, Seitz H-J & Conrad R (1988) The capacity of hydrogenotrophic anaerobic bacteria to compete for traces of hydrogen depends on the redox potential of the terminal electron acceptor. Arch Microbiol 149: 350-357.
23. Corinaldesi C, Danovaro R & Dell'Anno A (2005) Simultaneous recovery of extracellular and intracellular DNA suitable for molecular studies from marine sediments. Appl Environ Microbiol 71: 46-50.
24. Corinaldesi C, Barucca M, Luna GM & Dell'Anno A (2011) Preservation, origin and genetic imprint of extracellular DNA in permanently anoxic deep-sea sediments. Mol Ecol 20: 642-654.
25. Cowen JP, Giovannoni SJ, Kenig F, Johnson HP, Butterfield D, Rappé MS, Hutnak M & Lam P (2003) Fluids from aging ocean crust that support microbial life. Science 299: 120-123.
26. Cowen JP, Copson DA, Jolly J, Hsieh C-C, Lin H-T, Glazer BT & Whest CG (2012) Advanced instrument system for real-time and time-series microbial geochemical sampling of the deep (basaltic) crustal biosphere. Deep Sea Res I 61: 43-56.
27. Dang H, Luan X, Zhao J & Li J (2009) Diverse and novel nifH and nifH-like gene sequences in the deep-sea methane seep sediments of the Ohkotsk Sea. Appl Environ Microbiol 75: 2238-2245.
28. 2 from geothermal water. Antonie Van Leeuwenhoek 54: 165-178.
29. Delmont TO, Robe P, Cecillon S, Clark IM, Constancias F, Simonet P, Hirsch PR & Vogel TM (2011) Assessing the soil metagenome for studies of microbial diversity. Appl Environ Microbiol 77: 1315-1324.
30. 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.
31. Dhillon A, Lever M, Lloyd KG, Albert DB, Sogin ML & Teske A (2005) 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.
32. D'Hondt S, Rutherford S & Spivack AJ (2002) Metabolic activity of subsurface life in deep-sea sediments. Science 295: 2067-2070.
33. D'Hondt S, Jørgensen BB, Miller DJ et al. (2004) Distribution of microbial activities in deep subseafloor sediments. Science 306: 2216-2221.
34. D'Hondt S, Spivack AJ, Pockalny R et al. (2009) Subseafloor sedimentary life in the South Pacific Gyre. Proc Natl Acad Sci USA 106: 11651-11656.
35. Edgcomb VP, Beaudoin D, Gast R, Biddle JF & Teske A (2010) Marine subsurface eukaryotes: the fungal majority. Environ Microbiol 13: 172-183.
36. Edwards KJ, McCollom TM, Konishi H & Buseck PR (2003) Seafloor bioalteration of sulfide minerals: results from in situ incubation studies. Geochim Cosmochim Acta 67: 2843-2856.
37. Eid J, Fehr A, Gray J et al. (2009) Real-time DNA sequencing from single polymerase molecules. Science 323: 133-138.
38. Elsahed MS, Senko JM, Nazar FZ, Kenton SM, Roe BA, Dewers TA, Spear JR & Krumholz LR (2003) Bacterial diversity and sulfur cycling in a mesophilic sulfide-rich spring. Appl Environ Microbiol 69: 5609-5621.
39. Elsaied H & Naganuma T (2001) Phylogenetic diversity of ribulose-1, 5-bisphosphate carboxylase/oxygenase large-subunit genes from deep-sea microorganisms. Appl Environ Microbiol 67: 1751-1765.
40. Engelen B, Ziegelmüller K, Wolf L et al. (2008) Fluids from the oceanic crust support microbial activity within the deep biosphere. Geomicrobiol J 25: 56-66.
41. Engelhardt T, Sahlberg M, Cypionka H & Engelen B (2012) Biogeography of Rhizobium radiobacter and distribution of associated temperate phages in deep subseafloor sediments. ISME J 199-209. doi: 10.1038/ismej.2012.92.
42. Expedition 329 Scientists (2011) South Pacific Gyre subseafloor life. IODP Prel Rept 329: 1-108. doi: 10.2204/iodp.pr.329.2011.
43. Franklin MJ, Wiebe WJ & Whitman WB (1998) Populations of methanogenic bacteria in a Georgia salt marsh. Appl Environ Microbiol 54: 1151-1157.
44. Frias-Lopez J, Shi Y, Tyson GW, Coleman ML, Schuster SC, Chisholm SW & DeLong EF (2008) Microbial community gene expression in ocean surface waters. Proc Natl Acad Sci USA 105: 3805-3810.
45. Friedrich M (2005) Methyl-coenzyme M reductase genes: unique functional markers for methanogenic and anaerobic methane-oxidizing Archaea. Methods Enzymol 26: 428-442.
46. Futagami T, Morono Y, Terada T, Kaksonen AH & Inagaki F (2009) Dehalogenation activities and distribution of reductive dehalogenase homologous genes in marine subsurface sediments. Appl Environ Microbiol 75: 6905-6909.
47. Gagen EM, Denman SE, Padmanabha J, Zadbuke S, Jassim RA, Morrison M & McSweeney CS (2010) Functional gene analysis suggests different acetogen populations in the bovine rumen and Tammar Wallaby forestomach. Appl Environ Microbiol 76: 7785-7795.
48. Gilbert JA & Dupont CL (2011) Microbial metagenomics: beyond the genome. Ann Rev Mar Sci 3: 347-371.
49. Grossart H-P, Frindte K, Dziallas C, Eckert W & Tang KW (2012) Microbial methane production in oxygenated water column of an oligotrophic lake. Proc Natl Acad Sci USA 49: 19657-19661.
50. Hales BA, Edwards C, Ritchie DA, Hall D, Pickup RW & Saunders JR (1996) Isolation and identification of methanogen-specific DNA from blanket bog peat by PCR amplification and sequence analysis. Appl Environ Microbiol 62: 668-675.
51. Hallam SJ, Putnam N, Preston CM, Detter JC, Rokhsar D, Richardson PM & DeLong EF (2004) Reverse methanogenesis: testing the hypothesis with environmental genomics. Science 305: 1457-1462.
52. Harrison BK, Zhang H, Berelson W & Orphan VJ (2009) Variations in archaeal and bacterial diversity associated with the sulfate-methane transition zone in continental margin sediments (Santa Barbara Basin, California). Appl Environ Microbiol 75: 1487-1499.
53. Heiss-Blanquet S, Benoit Y, Maréchaux C & Monot F (2005) Assessing the role of alkane hydroxylase genotypes in environmental samples by competitive PCR. J Appl Microbiol 99: 1392-1403.
54. Heuer VB, Pohlman JW, Torres ME, Elvert M & Hinrichs K-U (2009) The stable carbon isotope biogeochemistry of acetate and other dissolved carbon species in deep subseafloor sediments at the northern Cascadia Margin. Geochim Cosmochim Acta 73: 3323-3336.
55. Hoehler TM, Alperin MJ, Albert DB & Martens CS (1998) Thermodynamic control on hydrogen concentrations in anoxic sediments. Geochim Cosmochim Acta 62: 1745-1756.
56. Holmkvist L, Ferdelman TG & Jørgensen BB (2011) A cryptic sulfur cycle driven by iron in the methane zone of marine sediment (Aarhus Bay, Denmark). Geochim Cosmochim Acta 75: 3581-3599.
57. Hölscher T, Krajmalnik-Brown R, Ritalahti KM, von Wintzingerode F, Görisch H, Löffler FE & Adrian L (2004) Multiple nonidentical reductive-dehalogenase-homologous genes are common in Dehalococcoides. Appl Environ Microbiol 70: 5290-5297.
58. Hoshino T & Inagaki F (2012) Molecular quantification of environmental DNA using microfluidics and digital PCR. Syst Appl Microbiol 35: 390-395.
59. Hoshino T & Schramm A (2010) Detection of denitrification genes by in situ rolling circle amplification-fluorescence to link metabolic potential with identity inside bacterial cells. Environ Microbiol 12: 2508-2517.
60. Huber R, Rossnagel P, Woese CR, Rachel R, Langworth TA & Stetter KO (1996) Formation of ammonium from nitrate during chemolithoautotrophic growth of the extremely thermophilic bacterium Ammonifex degensii gen. nov. sp. nov. Syst Appl Microbiol 19: 40-49.
61. 2 fixation in microbial communities of hydrothermal vents of the Logatchev field. FEMS Microbiol Ecol 73: 526-537.
62. Imachi H, Aoi K, Tasumi E et al. (2011) Cultivation of methanogenic community from subseafloor sediments using a continuous-flow bioreactor. ISME J 5: 1913-1925.
63. 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.
64. Inagaki F, Nunoura T, Nakagawa S et al. (2006a) 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.
65. Inagaki F, Kuypers MMM, Tsunogai U et al. (2006b) Microbial community in a sediment-hosted CO2 lake of the southern Okinawa Trough hydrothermal system. Proc Natl Acad Sci USA 103: 14164-14169.
66. Inagaki F, Hinrichs K-U, Kubo Y & the Expedition 337 Project Team (2010) Deep coalbed biosphere off Shimokita: microbial processes and hydrocarbon system associated with deeply buried coalbed in the ocean. IODP Sci Prosp 337: 1-51. doi: 10.2204/iodp.sp.337.2010.
67. Ivarsson M (2012) Subseafloor basalts as fungal habitats. Biogeosciences 9: 3625-3635.
68. Ivarsson M, Bengtson S, Belivanova V, Stampanoni M, Marone F & Tehler A (2012) Fossilized fungi in subseafloor Eocene basalts. Geology 40: 163-166.
69. Jannasch HW, Wheat CG, Plant J, Kastner M & Stakes D (2004) Continuous chemical monitoring with osmotically pumped water samplers: OsmoSampler design and applications. Limnol Oceanogr Meth 2: 102-113.
70. Jeng Y-H & Doi RH (1974) Messenger ribonucleic acid of dormant spores of Bacillus subtilis. J Bacteriol 119: 514-521.
71. Jiang L, Zheng Y, Peng X, Zhou H, Zhang C, Xiao X & Wang F (2009) Vertical distribution and diversity of sulfate-reducing prokaryotes in the Pearl River estuarine sediments, Southern China. FEMS Microbiol Ecol 70: 249-262.
72. Jørgensen BB (1982) Mineralization of organic matter in the sea bed - the role of sulphate reduction. Nature 296: 643-645.
73. Jørgensen BB, D'Hondt SL & Miller DJ (2006) 1. Leg 201 synthesis: controls on microbial communities in deeply buried sediments. Proc ODP, Sci Res 201 (Jørgensen BB, D'Hondt SL & Miller DJ, eds), pp. 1-81. ODP, College Station, TX.
74. Kalisky T & Quake SR (2011) Single-cell genomics. Nat Methods 8: 311-314.
75. Kaneko R, Hayashi T, Tanahashi M & Naganuma T (2007) Phylogenetic diversity and distribution of dissimilatory sulfite reductase genes from deep-sea sediment cores. Mar Biotechnol 9: 429-436.
76. Kendall MM, Liu Y, Sieprawska-Lupa M, Stetter KO, Whitman WB & Boone DR (2006) Methanococcus aeolicus sp. nov., a mesophilic, methanogenic archaeon from shallow and deep marine sediments. Int J Syst Evol Microbiol 56: 1525-1529.
77. Kiene RP, Oremland RS, Catena A, Miller LG & Capone DG (1986) Metabolism of reduced methylated sulfur compounds in anaerobic sediments and by a pure culture of an estuarine methanogen. Appl Environ Microbiol 52: 1037-1045.
78. King GM, Klug MJ & Lovley DR (1983) Metabolism of acetate, methanol, and methylated amines in intertidal sediments of Lowes Cove, Maine. Appl Environ Microbiol 45: 1848-1853.
79. 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.
80. Knittel K & Boetius A (2009) Anaerobic oxidation of methane: progress with an unknown process. Ann Rev Microbiol 63: 311-334.
81. 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 J 21: 145-157.
82. Kormas KA, Smith DC, Edgcomb V & Teske A (2003) Molecular analyses of deep subsurface microbial communities in Nankai Trough sediments (ODP Leg 190, Site 1176). FEMS Microbiol Ecol 45: 115-125.
83. Krajmalnik-Brown R, Hölscher T, Thomson IN, Saunders FM, Ritalahti KM & Löffler FE (2004) Genetic identification of a putative vinyl chloride reductase in Dehalococcoides sp. strain BAV1. Appl Environ Microbiol 70: 6347-6351.
84. Kubota K, Imachi H, Kawakami S, Nakamura K, Harada H & Ohashi A (2008) Evaluation of enzymatic cell treatments for application of CARD-FISH to methanogens. J Microbiol Meth 72: 54-59.
85. Lai X, Cao L, Tan H, Fang S, Huang Y & Zhou S (2007) Fungal communities from methane hydrate-bearing deep-sea marine sediments in South China Sea. ISME J 1: 756-762.
86. Lanoil BD, Sassen R, La Duc MT, Sweet ST & Nealson KH (2001) Bacteria and Archaea physically associated with Gulf of Mexico gas hydrates. Appl Environ Microbiol 67: 5143-5153.
87. Leaphart AB, Friez MJ & Lovell CR (2003) Formyltetrahydrofolate synthetase sequences from salt marsh plant roots reveal a diversity of acetogenic Bacteria and other bacterial functional groups. Appl Environ Microbiol 69: 693-696.
88. Leloup J, Fossing H, Kohls K, Holmkvist L, Borowski C & Jørgensen BB (2009) Sulfate-reducing bacteria in marine sediment (Aarhus Bay, Denmark): abundance and diversity related to geochemical zonation. Environ Microbiol 11: 1278-1291.
89. Lever MA (2012) Acetogenesis in the energy-starved deep biosphere - a paradox? Front Microbiol 2: 284.
90. Lever MA, Alperin MJ, Engelen B, Inagaki F, Nakagawa S, Steinsbu BO & Teske A (2006) Trends in basalt and sediment core contamination during IODP Expedition 301. Geomicrobiol J 23: 517-530.
91. Lever MA, Heuer VB, Morono Y, Masui N, Schmidt F, Alperin MJ, Inagaki F, Hinrichs K-U & Teske A (2010) Acetogenesis in deep subseafloor sediments of the Juan de Fuca Ridge Flank: a synthesis of geochemical, thermodynamic, and gene-based evidence. Geomicrobiol J 27: 183-211.
92. Liang Y, van Nostrand JD, Deng Y, He Z, Wu L, Zhang X, Li G & Zhou J (2011) Functional gene diversity of soil microbial communities from five oil-contaminated fields in China. ISME J 5: 403-413.
93. Lin YS, Heuer VB, Ferdelman TG & Hinrichs K-U (2010) Microbial conversion of inorganic carbon to dimethyl sulfide in anoxic lake sediment (Plußsee, Germany). Biogeosciences 7: 2433-2444.
94. 2-dependent anaerobic Ο-demethylation activity in subsurface sediments and by an isolated bacterium. Appl Environ Microbiol 59: 1325-1331.
95. Liu Y & Whitman WB (2008) Metabolic, phylogenetic, and ecological diversity of the methanogenic Archaea. Ann NY Acad Sci 1125: 171-189.
96. Liu Z, Lozupone C, Hamady M, Bushman FD & Knight R (2007) Short pyrosequencing reads suffice for accurate microbial community analysis. Nucleic Acids Res 35: e120.
97. Lloyd KG, Alperin MJ & Teske A (2011) Environmental evidence for net methane production and oxidation in putative Anaerobic MEthanotrophic (ANME) archaea. Environ Microbiol 13: 2548-2564.
98. Lomstein BA, Langerhuus AT, D'Hondt S, Jørgensen BB & Spivack AJ (2012) Endospore abundance, microbial growth and necromass turnover in deep sub-seafloor sediment. Nature 484: 101-104.
99. Lovley DR & Goodwin S (1988) Hydrogen concentrations as an indicator of the terminal electron-accepting reactions in aquatic sediments. Geochim Cosmochim Acta 52: 2993-3003.
100. Loy A, Duller S & Wagner M (2008) Evolution and ecology of microbes dissimilating sulfur compounds: insights from siroheme sulfite reductases. Microbial Sulfur Metabolism (Dahl C & Friedrich CG, eds), pp. 46-59. Springer, Berlin, Germany.
101. Loy A, Duller S, Baranyi C, Mussmann M, Ott J, Sharon I, Béjà O, Le Paslier D, Dahl C & Wagner M (2009) Reverse dissimilatory sulfite reductase as phylogenetic marker for a subgroup of sulfur-oxidizing prokaryotes. Environ Microbiol 11: 289-299.
102. Lu Z, Deng Y, Van Nostrand JD et al. (2011) Microbial gene functions enriched in the deepwater horizon deep-sea oil plume. ISME J 6: 451-460.
103. Ludwig W, Strunk O, Westram R et al. (2004) ARB: a software environment for sequence data. Nucleic Acids Res 32: 1363-1371.
104. Lueders T & Friedrich M (2003) Evaluation of PCR amplification bias by terminal restriction fragment length polymorphism analysis of small-subunit rRNA and mcrA genes by using defined template mixtures of methanogenic pure cultures and soil DNA extracts. Appl Environ Microbiol 69: 320-326.
105. Lueders T, Chin KJ, Conrad R & Friedrich M (2001) 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. Environ Microbiol 3: 194-204.
106. Luton PE, Wayne JM, Sharp RJ & Riley PW (2001) The mcrA gene as an alternative to 16S rRNA in the phylogenetic analysis of methanogen populations in landfill. Microbiology 148: 3521-3530.
107. Martens CS & Berner RA (1977) Interstitial water chemistry of anoxic long island sound sediments. 1. Dissolved gases. Limnol Oceanogr 22: 10-25.
108. Mason OU, Di Meo-Savoie CA, Van Nostrand JD, Zhou J, Fisk MR & Giovannoni SJ (2009) Prokaryotic diversity, distribution, and insights into their role in biogeochemical cycling in marine basalts. ISME J 3: 231-242.
109. Mason OU, Hazen TC, Borglin S et al. (2012) Metagenome, metatranscriptome and single-cell sequencing reveal microbial response to deepwater horizon oil spill. ISME J 6: 1715-1727.
110. Masui N, Morono Y & Inagaki F (2008) Microbiological assessment of circulation mud fluids during the first operation of riser drilling by the deep-earth research vessel Chikyu. Geomicrobiol J 25: 274-282.
111. Matsuki T, Watanabe K, Fujimoto J, Takada T & Tanaka R (2004) Use of 16S rRNA gene-targeted group-specific primers for real-time PCR analyses of predominant Bacteria in human feces. Appl Environ Microbiol 70: 7220-7228.
112. McDonald IR, Bodrossy L, Chen Y & Murrell JC (2008) Molecular ecology techniques for the study of aerobic methanotrophs. Appl Environ Microbiol 74: 1305-1315.
113. Mende DR, Waller AS, Sunagawa S, Järvelin AI, Chan MM, Arumugam M, Raes J & Bork P (2012) Assessment of metagenomic assembly using simulated next generation sequencing data. PLoS ONE 7: e31386.
114. Meyer B & Kuever J (2007) Phylogeny of the alpha and beta subunits of the dissimilatory adenosine-5′-phosphosulfate (APS) reductase from sulfate-reducing prokaryotes - origin and evolution of the dissimilatory sulfate-reduction pathway. Microbiology 153: 2026-2044.
115. Michaelis W, Seifert R, Nauhaus K et al. (2002) Microbial reefs in the Black Sea fueled by anaerobic oxidation of methane. Science 297: 1013-1015.
116. Mikucki JA, Liu Y, Delwiche M, Colwell FS & Boone DR (2003) Isolation of a methanogen from deep marine sediments that contain methane hydrates, and description of Methanoculleus submarinus sp. nov. Appl Environ Microbiol 69: 3311-3316.
117. Miller TL & Wolin MJ (1986) Methanogens in human and animal intestinal tracts. Syst Appl Microbiol 7: 223-229.
118. Mitterer RM (2006) 12. Data report: D/L ratios and concentrations of selected amino acids in interstitial waters, Equatorial Pacific and Peru Margin, ODP Leg 201, in Controls on microbial communities in deeply buried sediments, Eastern Equatorial Pacific and Peru Margin sites 1225-1231. Proc. ODP Scient. Res. 201 (Jørgensen BB, D'Hondt SL & Miller DJ, eds), pp. 1-7. ODP, College Station, TX.
119. Mohan SB, Schmid M, Jetten M & Cole J (2004) Detection and widespread distribution of the nrfA gene encoding nitrite reduction to ammonia, a short circuit in the biological nitrogen cycle that competes with denitrification. FEMS Microbiol Ecol 49: 433-443.
120. Mori K & Harayama S (2011) Methanobacterium petrolearium sp. nov. and Methanobacterium ferruginis sp. nov., mesophilic methanogens isolated from salty environments. Int J Syst Evol Microbiol 61: 138-143.
121. Morono Y, Terada T, Nishizawa M, Ito M, Hillion F, Takahata N, Sano Y & Inagaki F (2011) Carbon and nitrogen assimilation in deep subseafloor microbial cells. Proc Natl Acad Sci USA 108: 18295-18300.
122. Nakagawa S, Inagaki F, Suzuki Y et al. (2006) Microbial community in black rust exposed to hot ridge flank crustal fluids. Appl Environ Microbiol 72: 6789-6799.
123. Neufeld JD, Vohra J, Dumont MG, Lueders T, Manefiled M, Friedrich MW & Murrell JC (2007) DNA stable-isotope probing. Nat Protoc 2: 860-866.
124. Newberry CJ, Webster G, Cragg BA, Parkes RJ, 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.
125. Newton RJ, VandeWalle JL, Borchardt MA, Gorelick MH & McLellan SL (2011) Lachnospiraceae and Bacteriodales alternative fecal indicators reveal chronic human sewage contamination in an urban harbor. Appl Environ Microbiol 77: 6972-6981.
126. Nunoura T, Inagaki F, Delwiche ME, Colwell FS & Takai K (2008) Subseafloor microbial communities in methane hydrate-bearing sediment at two distinct locations (ODP Leg 204) in the Cascadia Margin. Microbes Environ 23: 317-325.
127. Nunoura T, Soffientino B, Blazejak A, Kakuta J, Oida H, Schippers A & Takai K (2009) Subseafloor microbial communities associated with rapid turbidite deposition in the Gulf of Mexico continental slope (IODP Expedition 308). FEMS Microbiol Ecol 69: 410-424.
128. Ogram A, Sayler GS, Gustin D & Lewis RJ (1988) DNA adsorption to soils and sediments. Environ Sci Technol 22: 982-984.
129. Orcutt BN, Bach W, Becker K, Fisher AT, Hentscher M, Toner BM, Wheat CG & Edwards KJ (2010a) Colonization of subsurface microbial observatories deployed in young ocean crust. ISME J 5: 692-703.
130. Orcutt B, Wheat CG & Edwards KJ (2010b) Subseafloor ocean crust microbial observatories: development of FLOCS (FLow-through Osmo Colonization System) and evaluation of borehole construction materials. Geomicrobiol J 27: 143-157.
131. Orcutt B, Lapham L & Girguis P (2011) Introducing MIMOSA - a microbial methane observatory for seafloor analysis. Geophys Res Abstr 13: 2368.
132. Oremland RS & Polcin S (1982) Methanogenesis and sulfate reduction: competitive and noncompetitive substrates in estuarine sediments. Appl Environ Microbiol 44: 1270-1276.
133. Parameswaran P, Jalili R, Tao L, Shokralla S, Gharizadeh B, Ronaghi M & Fire AZ (2007) A pyrosequencing-tailored nucleotide barcode design unveils opportunities for large-scale sample multiplexing. Nucleic Acids Res 35: 2-9.
134. 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.
135. 2 formation for the deep biosphere and subsequent thermogenic activity. Geology 39: 219-222.
136. Parkes RJ, Brock F, Banning N, Hornibrook ERC, Roussel EG, Weightman AJ & Fry JC (2012) Changes in methanogenic substrate utilization and communities with depth in a salt-marsh, creek sediment in southern England. Estuar Coast Shelf Sci 96: 170-178.
137. Pawlowski J, Christen R, Lecroq B, Bachar D, Shahbazkia HR, Amaral-Zettler L & Guillou L (2011) Eukaryotic richness in the abyss: insights from pyrotag sequencing. PLoS ONE 6: e18169.
138. Pereyra LP, Hiibel SR, Prieto Riquelme MV, Reardon KF & Pruden A (2010) Detection and quantification of functional genes of cellulose-degrading, fermentative, and sulfate-reducing bacteria and methagenic archaea. Appl Environ Microbiol 76: 2192-2202.
139. Pernthaler A & Amann R (2004) Simultaneous fluorescence in situ hybridization of mRNA in environmental Bacteria. Appl Environ Microbiol 70: 5426-5433.
140. Pester M, Bittner N, Pinsurang D, Wagner M & Loy A (2010) A 'rare biosphere' microorganism contributes to sulfate reduction in a peatland. ISME J 4: 1591-1602.
141. Pietramellara G, Ascher J, Borgogni F, Ceccherini MT, Guerri G & Nannipieri P (2009) Extracellular DNA in soil and sediment: fate and ecological relevance. Biol Fertil Soils 45: 219-235.
142. Pignatelli M & Moya A (2011) Evaluating the fidelity of de novo short read metagenomic assembly using simulated data. PLoS ONE 6: e19984.
143. Pilloni G, Granitsiotis MS, Engel M & Lueders T (2012) Testing the limits of 454 pyrotag sequencing: reproducibility, quantitative assessment and comparison to T-RFLP fingerprinting of aquifer microbes. PLoS ONE 7: e40467.
144. Pinto AJ & Raskin L (2012) PCR biases distort bacterial and archaeal community structure in pyrosequencing datasets. PLoS ONE 7: e43093.
145. Poretsky RS, Bano N, Buchan A, LeCleir G, Kleinkemper J, Pickering M, Pate WM, Moran MA & Hollibaugh JT (2005) Analysis of microbial gene transcripts in environmental samples. Environ Microbiol 72: 4121-4126.
146. Preston CM, Harris A, Ryan JP et al. (2011) Underwater application of quantitative PCR on an ocean mooring. PLoS ONE 6: e22522.
147. Raghukumar C, Damare SR & Singh P (2010) A review on deep-sea fungi: occurrence, diversity and adaptations. Bot Mar 53: 479-492.
148. Rappé MS & Giovannoni SJ (2003) The uncultured microbial majority. Annu Rev Microbiol 57: 369-394.
149. Rauhut R & Klug G (1999) mRNA degradation in bacteria. FEMS Microbiol Rev 23: 353-370.
150. Reed AJ, Lutz RA & Vetriani C (2006) Vertical distribution and diversity of bacteria and archaea in sulfide and methane-rich cold seep sediments located at the base of the Florida Escarpment. Extremophiles 10: 199-211.
151. Regeard C, Maillard J & Holliger C (2004) Development of degenerate and specific PCR primers for the detection and isolation of known and putative chloroethene reductive dehalogenase genes. J Microbiol Meth 56: 107-118.
152. Roh SW, Abell GCJ, Kim K-H, Nam Y-D & Bae J-W (2010) Comparing microarrays and next-generation sequencing technologies for microbial ecology research. Trends Biotechnol 28: 291-299.
153. Rotthauwe JH, Witzel KP & Liesack W (1997) The ammonia monooxygenase structural gene amoA as a functional marker: molecular fine-scale analysis of natural ammonia-oxidizing populations. Appl Environ Microbiol 63: 4704-4712.
154. Roussel EG, Sauvadet A-L, Chaduteau C, Fouquet Y, Charlou J-L, Prieur D & Cambon Bonavita M-A (2009a) Archaeal communities associated with shallow to deep subseafloor sediments of New Caledonia Basin. Environ Microbiol 11: 2446-2462.
155. Roussel EG, Sauvadet A-L, Allard J, Chaduteau C, Richard P, Cambon Bonavita M-A & Chaumillon E (2009b) Archaeal methane cycling communities associated with gassy subsurface sediments of Marennes-Oléron Bay (France). Geomicrobiol J 26: 31-43.
156. Sakai S, Imachi H, Hanada S, Ohashi A, Harada H & Kamagata Y (2008) 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. Int J Syst Evol Microbiol 58: 929-936.
157. Santelli CM, Banerjee N, Bach W & Edwards KJ (2010) Tapping the subsurface ocean crust biosphere: low biomass and drilling-related contamination calls for improved quality controls. Geomicrobiol J 27: 158-169.
158. Schadt EE, Turner S & Kasarskis A (2010) A window into third-generation sequencing. Hum Mol Genet 19: R227-R240.
159. 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.
160. Schippers A, Neretin LN, Kallmeyer J, Ferdelman TG, Cragg BA, Parkes RJ & Jørgensen BB (2005) Prokaryotic cells of the deep sub-seafloor biosphere identified as living bacteria. Nature 433: 861-864.
161. Schippers A, Kock D, Höft C, Köweker G & Siegert M (2012) Quantification of microbial communities in subsurface marine sediments of the Black Sea and off Namibia. Front Microbiol 3: 16.
162. Schrum HN, Spivack AJ, Kastner M & D'Hondt S (2009) Sulfate-reducing ammonium oxidation: a thermodynamically feasible metabolic pathway in subseafloor sediment. Geology 37: 939-942.
163. Segev E, Smith Y & Ben-Yehuda S (2012) RNA dynamics in aging bacterial spores. Cell 148: 139-149.
164. Shlimon AG, Friedrich MW, Niemann H, Ramsing NB & Finster K (2004) Methanobacterium aarhusense sp. nov., a novel methanogen isolated from a marine sediment (Aarhus Bay, Denmark). Int J Syst Evol Microbiol 54: 759-763.
165. Singh N, Kendall MM, Liu Y & Boone DR (2005) 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. Int J Syst Evol Microbiol 55: 2531-2538.
166. Smith DC, Spivack AJ, Fisk MR, Haveman SA & Staudigel H (2000) Tracer-based estimates of drilling-induced microbial contamination of deep sea crust. Geomicrobiol J 17: 207-219.
167. Smith CJ, Nedwell DB, Dong LF & Osborn AM (2007) Diversity and abundance of nitrate reductase genes (narG and napA), nitrite reductase genes (nirS and nrfA), and their transcripts in estuarine sediments. Appl Environ Microbiol 73: 3612-3622.
168. Sowers KR & Ferry JG (1983) Isolation and characterization of a methylotrophic methanogen, Methanococcoides methylutens gen. nov., sp. nov. Appl Environ Microbiol 45: 684-690.
169. Springer E, Sachs MS, Woese CR & Boone DR (1995) Partial gene sequences for the A subunit of methyl-coenzyme M reductase (mcrI) as a phylogenetic tool for the family Methanosarcinaceae. Int J Syst Bacteriol 45: 554-559.
170. Stepanauskas R & Sieracki ME (2007) Matching phylogeny and metabolism in the uncultured marine bacteria, one cell at a time. P Natl Acad Sci USA 104: 9052-9057.
171. 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.
172. Süss J, Herrmann K, Seidel M, Cypionka H, Engelen B & Sass H (2008) Two distinct Photobacterium populations thrive in ancient Mediterranean sapropels. Microbial Ecol 55: 371-383.
173. 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.
174. Teske AP (2006) Microbial communities of deep marine subsurface sediments: molecular and cultivation surveys. Geomicrobiol J 23: 357-368.
175. Teske A & Sørensen KB (2008) Uncultured archaea in deep marine subsurface sediments: have we caught them all? ISME J 2: 3-18.
176. Teske A, Hinrichs K-U, Edgcomb V, Gomez AD, Kysela D, Sylva SP, Sogin ML & Jannasch HW (2002) Microbial diversity of hydrothermal sediments in the Guaymas Basin: evidence for anaerobic methanotrophic communities. Appl Environ Microbiol 68: 1994-2007.
177. 2. Curr Opin Microbiol 14: 292-299.
178. 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.
179. Ufnar JA, Wang SY, Christiansen JM, Yampara-Iquise H, Carson CA & Ellender RD (2006) Detection of the nifH gene of Methanobrevibacter smithii: a potential tool to identify sewage pollution in recreational waters. J Appl Microbiol 101: 44-52.
180. Wagner A, Adrian L, Kleinsteuber S, Andreesen JR & Lechner U (2009) Transcription analysis of genes encoding homologues of reductive dehalogenases in "Dehalococcoides" sp. Strain CBDB1 by using terminal restriction fragment length polymorphism and quantitative PCR. Appl Environ Microbiol 75: 1876-1884.
181. Wang Q, Garrity GM, Tiedje JM & Cole JR (2007) Naïve Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 73: 5261-5267.
182. Wang F, Zhou H, Meng J et al. (2008a) GeoChip-based analysis of metabolic diversity of microbial communities at the Juan de Fuca Ridge hydrothermal vent. P Natl Acad Sci USA 106: 4840-4845.
183. Wang G, Spivack AJ, Rutherford S, Manor U & D'Hondt S (2008b) Quantification of co-occurring reaction rates in deep subseafloor sediments. Geochim Cosmochim Acta 72: 3479-3488.
184. Wang J, van Nostrand JD, Wu L, He Z, Li G & Zhou J (2011) Microarray-based evaluation of whole-community genome DNA amplification methods. Appl Environ Microbiol 77: 4241-4245.
185. Wankel SD, Joye SB, Samarkin VA, Shan SR, Friederich G, Melas-Kyriazi J & Girguis PR (2010) New constraints on methane fluxes and rates of anaerobic methane oxidation in a Gulf of Mexico brine pool via in situ mass spectrometry. Deep-Sea Res II 57: 21-23.
186. Wankel SD, Germanovich LN, Lilley MD, Genc G, DiPerna CJ, Bradley AS, Olson EJ & Girguis PR (2011) Influence of subsurface biosphere on geochemical fluxes from diffuse hydrothermal fluids. Nat Geosci 4: 461-468.
187. Ward JM, Smith PH & Boone DR (1989) Emended description of strain PS (=OGC 70 = ATCC 33273 = DSM 1537), the type strain of Methanococcus voltae. Int J Syst Bacteriol 39: 493-494.
188. Webster G, Newberry CJ, Fry JC & Weightman AJ (2003) Assessment of bacterial community structure in the deep sub-seafloor biosphere by 16S rRNA-based techniques: a cautionary tale. J Microbiol Meth 55: 155-164.
189. 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.
190. Webster G, Blazejak A, Cragg BA et al. (2009) Subsurface microbiology and biogeochemistry of a deep, cold-water carbonate mound from the Porcupine Seabight (IODP Expedition 307). Environ Microbiol 11: 239-257.
191. Wegener G, Bausch M, Holler T, Thang NM, Prieto-Mollar X, Kellermann MY, Hinrichs K-U & Boetius A (2012) Assessing sub-seafloor microbial activity by combined stable isotope probing with deuterated water and 13C-bicarbonate. Environ Microbiol 14: 1517-1527.
192. Whitman WB, Shieh J, Sohn S, Caras DS & Premachandran U (1986) Isolation and characterization of 22 mesophilic methanococci. Syst Appl Microbiol 7: 235-240.
193. Whitman WB, Bowen TL & Boone DR (2006) The methanogenic bacteria. The Prokaryotes: An Evolving Electronic Resource for the Microbiological Community, Vol. 3 (Dworkin M, Falkow S, Rosenberg E, Schleifer K-H & Stackebrandt E, eds), pp. 165-207. Springer, New York, NY.
194. Willerslev E, Hansen AJ, Binladen J, Brand TB, Gilbert MTP, Shapiro B, Bunce M, Wiuf C, Gilichinsky DA & Cooper A (2003) Diverse plant and animal genetic records from Holocene and Pleistocene sediments. Science 300: 791-795.
195. Winderl C, Schaefer S & Lueders T (2007) Detection of anaerobic toluene and hydrocarbon degraders in contaminated aquifers using benzylsuccinate synthase (bssA) genes as a functional marker. Environ Microbiol 9: 1035-1046.
196. Wu J & Xi C (2009) Evaluation of different methods for extracting extracellular DNA from the biofilm matrix. Appl Environ Microbiol 75: 5390-5395.
197. 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.
198. Yanagawa K, Sunamura M, Lever MA, Morono Y, Hiruta A, Ishizaki O, Matsumoto R, Urabe T & Inagaki F (2011) Niche separation of methanotrophic Archaea (ANME-1 and -2) in methane-seep sediments of the Eastern Japan Sea offshore Joetsu. Geomicrobiol J 28: 118-129.
199. Ye G, Wang S, Jiang L, Xiao X, Wang F, Noakes J & Zhang C (2009) Distribution and diversity of bacteria and Archaea in marine sediments affected by gas hydrates at Mississippi Canyon in the Gulf of Mexico. Geomicrobiol J 26: 370-381.
200. Yoshioka H, Maruyama A, Nakamura T, Higashi Y, Fuse H, Sakata S & Bartlett DH (2010) Activities and distribution of methanogenic and methane-oxidizing microbes in marine sediments from the Cascadia Margin. Geobiology 8: 223-233.
201. Zehr PJ, Jenkins BD, Short SM & Steward GF (2003) Nitrogenase gene diversity and microbial community structure: a cross-system comparison. Environ Microbiol 5: 539-554.
202. Zeikus JG & Henning DL (1975) Methanobacterium arboriphilum sp. nov. An obligate anaerobe isolated from wetwood of living trees. Antonie Van Leeuwenhoek 41: 543-552.
203. Zhang G, Tian J, Jiang N, Guo X, Wang Y & Dong X (2008) Methanogen community in Zoige wetland of Tibetan plateau and phenotypic characterization of a dominant uncultured methanogen cluster ZC-I. Environ Microbiol 10: 1850-1860.
204. Zhou J, He Z, Van Nostrand JD, Wu L & Deng Y (2010) Applying GeoChip analysis to disparate microbial communities. Microbe 5: 60-65.