Microbial communities of deep marine subsurface sediments: Molecular and cultivation surveys

Geomicrobiology Journal

Volumn 23, Issue 6, 2006, Pages 357-368

  Teske, Andreas P ^a  

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

Author keywords

Deep subsurface; Functional genes; Marine sediments; Microbial diversity; Ribosomal RNA

Indexed keywords

EID: 85023884574     PISSN: 01490451     EISSN: 15210529     Source Type: Journal    
DOI: 10.1080/01490450600875613     Document Type: Article

References (94)

1. Bale SJ, Goodman K, Rochelle PA, Marchesi JR, Fry JC, Weightman AJ, Parkes RJ. 1997. Desulfovobrio profundus sp. nov., a novel barophilic sulphatereducing bacterium from deep sediment layers in the Japan Sea. Int J Syst Bact 47:515–521.
2. Barnes SP, Bradbrook SD, Cragg BA, Marchesi JR, Weightman AJ, Fry JC, Parkes RJ. 1998. Isolation of sulphate reducing bacteria from deep sediment layers of the Pacific Ocean. Geomicrobiology J 15:67–83.
3. Barns SM, Delwiche CF, Palmer JD, Pace NR. 1996. Perspectives on archaeal diversity, thermophily and monophyly from environmental rRNA sequences. Proc Natl Acad Sci USA 93:9188–9193.
4. 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, B.B., D’Hondt, S.L., Miller, D.J. (Eds.), Proc ODP, Sci Results, 201 [Online]. Available from World Wide Web: [Cited 2005–10–10].
5. Biddle JF, House CH, Brenchley JE. 2005b. Microbial stratification in deeplyburied marine sediments reflect changes in sulfate/methane profiles. Geobiology 3:287:295.
6. Biddle JF, Lipp JS, Lever M, Lloyd KG, Sørensen KB, Anderson R, Fredricks HF, Elvert M, Kelly TJ, Schrag DP, Sogin ML, Brenchley JE, Teske A, House CH, Hinrich KU. 2006. Heterotrophic Archaea dominate sedimentary subsurface ecosystems off Peru, Proc Natl Acad Sci 103:3846–3851.
7. 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.
8. Braun M, Mayer F, Gottschalk G. 1981. Clostridium aceticum (Wieringa), a microorganism producing acetic acid from molecular hydrogen and carbon dioxide. Arch Microbiol 128:288–293.
9. Cano RJ, Borucki MK. 1995. Revival and identification of bacterial spores in 25 to 40 million year–old Dominican amber. Science 268:1060–1064.
10. Chandler DP, Brockman FJ, Bailey TJ, Fredrickson JK. 1998. Phylogenetic diversity of Archaea and Bacteria in a deep subsurface paleosol. Microb Ecol 36:37–50.
11. Colwell FS, Stormberg GJ, Phelps TJ, Birnbaum SA, McKinley J, Rawson SA, Veverla C, Goodwin S, Long PE, Russell BF, Garland T, Thompson D, Skinner P, Grover S. 1992. Innovative techniques for collection of saturated and unsaturated subsurface basalts and sediments for microbiological characterization. J Microbiol Meth 15:279–292.
12. Coolen MJL, Cypionka H, Sass AM, Sass H, Overmann J. 2002. Ongoing modification of Mediterranean sapropels mediated by prokaryotes. Science 296:2407–2410.
13. DeLong EF. 1992. Archaea in coastal marine environments. Proc Natl Acad Sci USA 89:5685–5689.
14. Delong EF. 1998. Everything in moderation: Archaea as “non–extremophiles.” Curr Opin Gen and Develop 8:649–654.
15. DeLong EF, Wu KY, Prezelin BB, Jovine RVM. 1994. High abundance of archaea in Antarctic marine picoplankton. Nature 371:695–697.
16. D’Hondt S, Rutherford S, Spivack AJ. 2002. Metabolic activity of subsurface life in deep–sea sediments. Science 295:2067–2070.
17. D’ Hondt SL, Jørgensen BB, Miller DJ, 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.
18. D’Hondt S, Jørgensen BB, Miller DJ, Batzke A, Blake R, Cragg BA, Cypionka H, Dickens GR, Ferdelman T, Hinrichs K-U, Holm NG, Mitterer R, Spivack A, Wang G, Bekins B, Engelen B, Ford K, Gettemy G, Rutherford SD, Sass H, Skilbeck CG, 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.
19. Fuhrman JA, McCallum, Davis AA. 1992. Novel archaebacterial group from marine plankton. Nature 356:148–149.
20. Fuhrman JA, Ouverney CC. 1998. Marine microbial diversity studied via 16S RNA sequences: cloning results from coastal waters and counting of native archaea with fluorescent single cell probes. Aquatic Ecology 32:3–15.
21. Gest H, Mandelstam J. 1987. Longevity of microorganisms in natural environments. Microbiol Sci 4:69–71.
22. Graber KK, Pollard E, Jonasson B, Schulte E. 2002. Overview of Ocean Drilling Program engineering tools and hardware. ODP Tech. Note, 31 [Online]. Available from World Wide Web: . [Cited 2005–10–10]
23. Hales BA, Edwards C, Ritchie DA, Hall G, 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.
24. Harvey RW, George LH, Smith RL, LeBlanc DR. 1989. Transport of microspheres and indigenous bacteria through a sandy aquifer. Results of natural–and forced–gradient tracer experiments. Environ Sci Technol 23:51–56.
25. Hinrichs K-U, Hayes JM, Sylva SP, Brewer PG, DeLong EF. 1999. Methane–consuming archaebacteria in marine sediments. Nature 398:802–805.
26. House C, Cragg BA, Teske A. 2003. Drilling Contamination Tests on ODP Leg 201 Using Chemical and Particulate Tracers. Proc ODP, Init. Repts., 201 [CD–ROM]. Available from: Ocean Drilling Program, Texas A&M University, College Station TX 77845–9547, USA.
27. Huber JA, Butterfield DA, Baross JA. 2002. Temporal changes in archaeal diversity and chemistry in a mid–ocean ridge subseafloor habitat. Appl Environ Microbiol 68:1585–1594.
28. Hugenholtz P. 2002. Exploring prokaryotic diversity in the genomic era. .
29. Hugenholtz P, Goebel BM, Pace NR. 1998. Impact of culture–independent studies on the emerging phylogenetic view of bacterial diversity. J Bacteriol 180:4765–4774.
30. Inagaki F, Sakihama Y, Inoue A, Kato C, Horikoshi K. 2002. Molecular phylogenetic analyses of reverse–transcribed bacterial rRNA obtained from deep–sea cold seep sediments. Environ Microbiol 4:277–286
31. 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.
32. Inagaki F, Nunoura T, Nakagawa S, Teske A, Lever M, 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. unidentified prokaryotes in deeply buried marine sediments. Submitted to PNAS.
33. Inagaki F, Takai K, Komatsu T, Kanamatsu T, Fujiioka K, Horikoshi K. 2001. Archaeology of Archaea: geomicrobiological record of Pleistocene thermal events concealed in a deep–sea subseafloor environment. Extremophiles 5:385–392.
34. Inagaki F, Okada H, Tsapin AI, Nealson KH. 2005. The Paleome:Asedimentary genetic record of past microbial communities. Astrobiology 5:141–153.
35. Isaksen MF, Bak F, Jørgensen BB. 1994. Thermophilic sulfate–reducing bacteria in cold marine sediment. FEMS Microbiol Ecol 14:1–8.
36. Juck DF, Whissell G, Steven B, Pollard W, McKay CP, Greer CW, Whyte LG. 2005. Utilization of fluorescent microspheres and a green fluorescent protein–marked strain for assessment of microbiological contamination of permafrost and ground ice core samples from the Canadian High Arctic. Appl Environ Microbiol 71:1035–1041.
37. Karner MB, DeLong EF, Karl DM. 2001. Archaeal dominance in the mesopelagic zone of the Pacific Ocean. Nature 409:507–510.
38. 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.
39. Knittel K, Lösekann T, Boetius A, Kort R, Amann R. 2005. Diversity and distribution of methanotrophic archaea at cold seeps. Appl Environ Microbiol 71:467–479.
40. Knoblauch C, Jørgensen BB, Harder J. 1999. Community size and specific sulfate reduction rates of psychrophilic sulfate–reducing bacteria in arctic marine sediments: evidence for high activity at low temperature. Appl Environ Microbiol 65:4230–4233.
41. Könneke M, Bernhard AE, de la Torre JR, Walker CB, Waterbury JB, Stahl DA. 2005. Isolation of an autotrophic ammonia–oxidizing marine archaeon. Nature 437:543–546.
42. 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.
43. Lee Y, Wagner I, Brice M-E, 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, in press (Published online in August 2005: DOI: 10.1007/s00792-005-0453-4.)
44. Lever M, Teske A. 2005. Deep marine subsurface microbial communities of the Peru Trench: Sulfate reducers, Methanogens, and Unknowns (Abstract # 558). Astrobiology 5:259.
45. 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.
46. Marchesi JR, Weightman AJ, Cragg BA, Parkes RJ, Fry JC. 2001. Methanogen and bacterial diversity and distribution in deep gas hydrate sediments from the Cascadia Margin as revealed by 16S rRNA molecular analysis. FEMS Microbiol Ecol 34:221–228.
47. Matsuda N, Agui W, Tougou T, Sakai H, Ogino K, Abe M. 1996. Gram–negative bacteria viable in ultra pure water and effect of temperature on their behaviour. Coll Surf B Biointerfaces 5:279–289.
48. Mauclaire L, Zepp K, Meister P, McKenzie J. 2005. Direct in situ detection of cells in deep–sea sediment cores from the Peru Margin (ODP Leg 201, Site 1229). Geobiology 2: 217–223.
49. Maymó Gatell X, Chien Y-T, Gossett JM, Zinder SH. 1997. Isolation of a bacterium that reductively dechlorinates tetrachloroethene to ethane. Science 276:1568–1571.
50. McKinley JP, Colwell FS. 1996. Application of perfluorocarbon tracers to microbial sampling in subsurface environments using mud-rotary and air–rotary drilling techniques. J Microbiol Meth 26:1–9.
51. Michaelis W, Seifert R, Nauhaus K, Treude T, Thiel V, Blumenberg M, Knittel K, Gieseke A, Peterknecht K, Pape T, Boetius A, Amann R, Jørgensen BB, Widdel F, Peckmann J, Pimenov NV, Gulin MB. 2002. Microbial reefs in the Black Sea fueled by anaerobic oxidation of methane. Science 297:1013–1015.
52. Molin S, Givskov M. 1999. Application of molecular tools for in–situ monitoring of bacterial growth activity. Environ Microbiol 1:383–391.
53. 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.
54. Orphan VJ, House CH, Hinrichs K-U, McKeegan KD DeLong EF. 2001. Methane–consuming archaea revealed by directly coupled isotopic and phylogenetic analysis. Science 293:484–487.
55. Orphan VJ, House CH, Hinrichs K-U, McKeegan KD, DeLong EF. 2002. Multiple groups mediate methane oxidation in anoxic cold seep sediments. Proc Natl Acad Sci USA 99:7663–7668.
56. Ouverney CC, Fuhrman JA. 2000. Marine planktonic archaea take up amino acids. Appl Environ Microbiol 66:4829–4833.
57. Parkes R, Cragg B, Wellsbury P. 2000. Recent studies on bacterial populations and processes in subseafloor sediments: a review. Hydrogeology J 8:11–28.
58. 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.
59. Pearson A, McNichol AP, Benitez–Nelson BC, Hayes JM, Eglinton TI. 2001. Origins of lipid biomarkers in Santa Monica Basin surface sediment: A case study using compound-specific delta C-14 analysis. Geochim. Cosmochim. Acta 65:3123–3137.
60. Percival SL, Knapp JS, Edyvean R, Wales DS. 1998. Biofilm development on stainless steel in mains water. Water Res. 32:243–253.
61. Pernthaler A, Pernthaler J, Amann R. 2002. Fluorescence in situ hybridization and catalyzed reporter deposition for the identification of marine bacteria. Appl Environ Microbol. 68:3094–3101.
62. Rappe MS, Giovannoni SJ. 2003. The uncultured microbial majority. Ann Rev Microbiol 57:369–394.
63. Ravenschlag K, Sahm K, Knoblauch C, Jørgensen BB, Amann R. 2000. Community structure, cellular rRNA content, and activity of sulfate-reducing bacteria in marine arctic sediments. Appl Environ Microbiol 66:3592–3602.
64. 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.
65. Reysenbach A-L, Longnecker K, Kirshtein J. 2000. Novel bacterial and archaeal lineages from an in–situ growth chamber deployed at a mid–atlantic ridge hydrothermal vent. Appl Environ Microbiol 66:3798–3806.
66. Russell, BF, Phelps TJ, Griffin WT, Sargent KA. 1992. Procedures for sampling deep subsurface microbial communities in unconsolidated sediments. Groundwater Monitor Rev. 12:96–104.
67. Schippers, A. Neretin, LN. 2006. Quantificatio 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.
68. 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.
69. Schleper C, Jurgens G, Jonuscheit M. 2005. Genomic studies of uncultivated archaea. Nature Rev Microbiol 3:479–488.
70. Schrenk MO, Kelley DS, Delaney JR, Baross JA. 2003. Incidence and diversity of microorganisms within the walls of an active deep-sea sulfide chimney. Appl Environ Microbiol 69:3580–3592.
71. Sekiguchi Y, Takahashi H, Kamagata Y, Ohashi A, Harada H. 2001. In Situ Detection, Isolation, and Physiological Properties of a Thin Filamentous Microorganism Abundant in Methanogenic Granular Sludges: A Novel Isolate Affiliated with a Clone Cluster, the Green Non–Sulfur Bacteria, Subdivision I. Appl Environ Microbiol 67:5740–5749.
72. Sekiguchi Y, Yamada T, Hanada S, Ohashi A, Harada H, Kamagata Y. 2003. Anaerolinea thermophila gen. nov., sp. nov. and Caldilinea aerophila gen. nov., sp. nov., novel filamentous thermophiles that represent a previously uncultured lineage of the domain Bacteria at the subphylum level. Int J Syst Evol Microbiol 53:1843–1851.
73. Smith DA, Spivack AJ, Fisk MR, Haveman SA, Staudigel H, Leg 185 Shipboard Scientific Party. 2000a. Methods for Quantifying Potential Microbial Contamination During Deep Ocean Coring. ODP Tech, Note, 28 [Online]. .
74. Smith DA, Spivack AJ, Fisk MR, Haveman SA, Staudigel H, ODP Leg 185 Shipboard Scientific Party. 2000b. Tracer–based estimates of drilling–induced microbial contamination of deep sea crust. Geomicrobiology J 17:207–219.
75. Sørensen, KB, Teske A. 2006. Stratified communities of active archaea in deep marine subsurface sediments. Appl Environ Microbiol 72:4596–4603.
76. 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.
77. 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.
78. Sturt HF, Summons RE, Smith KJ, Elvert M, Hinrichs K-U. 2004. Intact polar lipids in prokaryotes and sediments deciphered by high–performance liquid chromatography/electrospray ionization multistage mass spectrometry—new biomarkers for biogeochemistry and microbial ecology. Rapid Communi Mass Spect 18:617–628.
79. Suess 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.
80. Swofford DL 2000. PAUP. Phylogenetic analysis using parsimony (and other methods), version 4, CD–ROM. Sunderland Massachusetts: Sinauer Associates. Takai K, Horikoshi K. 1999. Genetic diversity of archaea in deep–sea hydrothermal vent environments. Genetics 152:1285–1297.
81. Takai K, Moser DP, DeFlaun M, Onstott TC, Fredrickson JK. 2001. Archaeal diversity in waters from deep South African gold mines. Appl Environ Microbiol 67:5750–5760.
82. Tanner MA, Goebel BM, Dojka MA, Pace NR. 1998. Specific ribosomal DNA sequences from diverse environmental settings correlate with experimental contaminants. Appl Environ Microbiol 64:3110–3113.
83. 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.
84. Teske A, Hinrichs K-U, Edgcomb V, Gomez AdV, 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.
85. Teske A, Dhillon A, Sogin MS. 2003. Genomic Markers of ancient anaerobic microbial pathways: sulfate reduction, methanogenesis, and methane oxidation. Biol Bull 204:186–191.
86. Teske A, Lauer A, Sørensen KB. 2005. Prokaryotes in deep marine subsurface sediments: Phylogenetic diversity of a global extreme habitat (Abstract # 578). Astrobiology 5:268
87. Toffin L, Webster G, Weightman AJ, Fry JC, Prieur D. 2004. Molecular monitoring of culturable bacteria from deep–sea sediment of the Nankai Trough, Leg 190 Ocean Drilling Program. FEMS Microbiol Ecol 48:357–367.
88. Vetriani C, Jannasch HW, MacGregor BJ, Stahl DA, Reysenbach A–L. 1999. Population structure and phylogenetic characterization of marine benthic archaea in deep–sea sediments. Appl Environ Microbiol 65:4375–4384.
89. 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.
90. 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.
91. Webster G, Parkes RJ, Fry JC, Weigthman 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.
92. Whitman WB, Coleman DC, Wiebe WJ. 1998. Prokaryotes: the unseen majority. Proc Natl Acad Sci USA 95:6578–6583.
93. Wuchter C, Schouten S, Boschker HTS, Damst´e JS. 2003. Bicarbonate uptake by marine crenarchaeota. FEMS Microbiol Lett 219:203–207.
94. Zink K-G, Wilkes H, Disko U, Elvert M, Horsfield B. 2003. Intact phospholipids—microbial “life markers” in marine deep sediments. Org Geochem 34: 755–769.