Microbial community analysis of deeply buried marine sediments of the New Jersey shallow shelf (IODP Expedition 313)

FEMS Microbiology Ecology

Volumn 85, Issue 3, 2013, Pages 578-592

  Breuker, Anja ^a   Stadler, Susanne ^a   Schippers, Axel ^a  

^a FEDERAL INSTITUTE FOR GEOSCIENCES AND NATURAL RESOURCES BGR   (Germany)

Author keywords

Crenarchaeota; Deep biosphere; Euryarchaeota; IODP; Miscellaneous Crenarchaeotal Group; Sediments

Indexed keywords

RNA 16S;

ABUNDANCE; BIOSPHERE; DATA SET; GENE; MANGANESE; MARINE SEDIMENT; MICROBIAL COMMUNITY; ORGANIC CARBON; POLYMERASE CHAIN REACTION; POREWATER; SEAFLOOR; SHALLOW SOIL; SULFATE;

ARCHAEON; ARTICLE; BACTERIUM; BIODIVERSITY; CHLOROFLEXI; CLASSIFICATION; CRENARCHAEOTA; DEEP BIOSPHERE; DELTAPROTEOBACTERIA; EURYARCHAEOTA; GENETICS; IODP; ISOLATION AND PURIFICATION; MICROBIOLOGY; MISCELLANEOUS CRENARCHAEOTAL GROUP; PHYLOGENY; SEA; SEDIMENT; SEDIMENTS; TRAVEL; UNITED STATES;

CRENARCHAEOTA; DEEP BIOSPHERE; EURYARCHAEOTA; IODP; MISCELLANEOUS CRENARCHAEOTAL GROUP; SEDIMENTS;

ARCHAEA; BACTERIA; BIODIVERSITY; CHLOROFLEXI; CRENARCHAEOTA; DELTAPROTEOBACTERIA; EURYARCHAEOTA; EXPEDITIONS; GEOLOGIC SEDIMENTS; NEW JERSEY; OCEANS AND SEAS; PHYLOGENY; RNA, RIBOSOMAL, 16S;

NEW JERSEY; UNITED STATES;

ANAEROLINEAE; ARCHAEA; BACTERIA (MICROORGANISMS); CHLOROFLEXI; CHLOROFLEXI (CLASS); CRENARCHAEOTA; EURYARCHAEOTA; GEOBACTERACEAE; LAKE VICTORIA MARBURGVIRUS;

EID: 84881557283     PISSN: 01686496     EISSN: 15746941     Source Type: Journal    
DOI: 10.1111/1574-6941.12146     Document Type: Article

References (68)

1. Baker GC, Smith JJ & Cowan DA (2003) Review and re-analysis of domain-specific 16S primers. J Microbiol Methods 55: 541-555.
2. Barns S, Fudyga RE, Jeffries MW & Pace NR (1994) Remarkable archaeal diversity detected in a Yellowstone National Park hot spring environment. P Natl Acad Sci USA 91: 1609-1613.
3. Biddle JF, Lipp JS, Lever M et al. (2006) Heterotrophic Archaea dominate sedimentary subsurface ecosystems off Peru. P Natl Acad Sci USA 103: 3846-3851.
4. Blazejak A & Schippers A (2010) High abundance of JS-1- and Chloroflexi-related Bacteria in deeply buried marine sediments revealed by quantitative, real-time PCR. FEMS Microbiol Ecol 72: 198-207.
5. Blazejak A & Schippers A (2011) Real-time PCR 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 Microbiol 2: 253.
6. Breuker A & Schippers A (2013) Data Report: Total cell counts and qPCR abundance of Archaea and Bacteria in shallow subsurface marine sediments of North Pond: Gravity cores collected on site survey cruise prior to IODP Expedition 336. In: Edwards, K. J., Bach, W., Klaus, A., and the Expedition 336 Scientists (eds.), Proc. IODP, 336: Tokyo (Integrated Ocean Drilling Program Management International, Inc.). http://publications.iodp.org/proceedings/336/336toc.htm.
7. Breuker A, Köweker G, Blazejak A & Schippers A (2011) The deep biosphere in terrestrial sediments in the Chesapeake Bay area, Virginia, USA. Front Microbiol 2: 156.
8. De Long EF (1992) Archaea in coastal marine environments. P Natl Acad Sci USA 80: 5685-5689.
9. D'Hondt SL, Jørgensen BB, Miller DJ et al. (2004) Distributions of microbial activities in deep subseafloor sediments. Science 306: 2216-2221.
10. Durbin AM & Teske A (2010) Sediment-associated microdiversity within the Marine Group I Crenarchaeota. Environ Microbiol Rep 2: 693-703.
11. Durbin AM & Teske A (2011) Microbial diversity and stratification of oligotrophic abyssal South Pacific sediments. Environ Microbiol 13: 3219-3234.
12. Durbin AM & Teske A (2012) Archaea in organic-lean and organic-rich marine subsurface sediments: an environmental gradient reflected in distinct phylogenetic lineages. Front Microbiol 3: 168.
13. Edgcomb VP, Beaudoin D, Gast R, Biddle JF & Teske A (2011) Marine subsurface eukaryotes: the fungal majority. Environ Microbiol 13: 172-183.
14. Engelen B, Ziegelmüller K, Wolf L et al. (2008) Fluids from the oceanic crust support microbial activities within the deep biosphere. Geomicrobiol J 25: 55-66.
15. Engelhardt T, Sahlberg M, Cypionka H & Engelen B (2013) Biogeography of Rhizobium radiobacter and distribution of associated temperate phages in deep subseafloor sediments. ISME J 7: 199-209.
16. Fry JC, Parkes RJ, Cragg BA, Weightman AJ & Webster G (2008) Prokaryotic diversity and activity in the deep subseafloor biosphere. FEMS Microbiol Ecol 66: 181-196.
17. Holmes DE, Finneran KT, O'Neil RA & Lovley DR (2002) Enrichment of members of the family Geobacteraceae associated with stimulation of dissimilatory metal reduction in uranium-contaminated aquifer sediments. Appl Environ Microbiol 68: 2300-2306.
18. House CH, Cragg BA, Teske A & the Leg 201 Scientific Party (2003) Drilling contamination tests during ODP Leg 201 using chemical and particulate tracers. In Proceedings of the Ocean Drilling Program, Initial Reports 201, 1-19 [CD-ROM] (eds D'Hondt SL, Jorgensen BB, Miller DJ et al. ). Available from: Ocean Drilling Program, Texas A & M University, College Station TX 77845-9547, USA.
19. 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.
20. 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.
21. Inagaki F, Nunoura T, Nakagawa S et al. (2006) Biogeographical distribution and diversity of microbes in methane hydrate-bearing deep marine sediments on the Pacific ocean margin. P Natl Acad Sci USA 103: 2815-2820.
22. Kallmeyer J, Pockalny R, Adhikaria RR, Smith DC & D'Hond S (2012) Global distribution of microbial abundance and biomass in subseafloor sediment. P Natl Acad Sci USA 109: 16213-16216.
23. Könnecke M, Bernhard AE, de la Torre R, Walker CB, Waterbury JB & Stahl DA (2005) Isolation of an autotrophic ammonia-oxidizing marine archaeon. Nature 437: 543-546.
24. Kubo K, Lloyd K, Biddle J, Amann R, Teske A & Knittel K (2012) Archaea of the Miscellaneous Crenarchaeotal Group are abundant, diverse and widespread in marine sediments. ISME J 6: 1949-1965.
25. Leloup J, Loy A, Knab NJ, Borowski C, Wagner M & Jorgensen BB (2007) Diversity and abundance of sulfate-reducing microorganisms in the sulfate and methane zones of a marine sediment, Black Sea. Environ Microbiol 9: 131-142.
26. Lipp JS, Morono Y, Inagaki F & Hinrichs KU (2008) Significant contribution of Archaea to extent biomass in marine subsurface sediments. Nature 454: 991-994.
27. Lloyd KG, Schreiber L, Petersen DG et al. (2013) Predominant archaea in marine sediments degrade detrital proteins. Nature 496: 215-218.
28. Logemann J, Graue J, Köster J, Engelen B, Rullkötter J & Cypionka H (2011) A laboratory experiment of intact polar lipid degradation in sandy sediments. Biogeosciences 8: 2547-2560.
29. 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.
30. Lozupone C & Knight R (2005) UniFrac: an new phylogenetic method for comparing microbial communities. Appl Environ Microbiol 71: 8228-8235.
31. Ludwig W, Strunk O, Westram R et al. (2004) ARB: a software environment for sequence data. Nucleic Acids Res 32: 1363-1371.
32. Lunau M, Lemke A, Walther K, Martens-Habbena W & Simon M (2005) An improved method for counting bacteria from sediments and turbid environments by epifluorescence microscopy. Environ Microbiol 7: 961-968.
33. Massana R, DeLong EF & Pedros-Alio C (2000) A few cosmopolitan phylotypes dominate planktonic archaeal assemblages in widely different oceanic provinces. Appl Environ Microbiol 66: 1777-1787.
34. Mountain G, Proust JN, McInroy D, Cotterill C & the Expedition 313 Scientists (2010) Proceedings of the Integrated Ocean Drilling Program, Volume 313.
35. Nadkarni M, Martin FE, Jacques NA & Hunter N (2002) Determination of bacterial load by real-time PCR using a broad range (universal) probe and primer set. Microbiology 148: 257-266.
36. 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.
37. Orsi W, Biddle JF & Edgcomb V (2013) Deep sequencing of subseafloor eukaryotic rRNA reveals active fungi across marine subsurface provinces. PLoS ONE 8: e56335.
38. Parkes RJ, Cragg BA & Wellsbury P (2000) Recent studies on bacterial populations and processes in subseafloor sediments: a review. Hydrogeol J 8: 11-28.
39. Parkes RJ, Webster G, Cragg BA et al. (2005) Deep sub-seafloor prokaryotes stimulated at interfaces over geological time. Nature 436: 390-394.
40. Pruesse E, Quast C, Knittel K, Fuchs B, Ludwig W, Peplies J & Glöckner FO (2007) SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res 35: 7188-7196.
41. Roussel EG, Sauvadet AL, Chaduteau C, Fouquet Y, Charlou JL, Prieur D & Bonavita MAC (2009) Archaeal communities associated with shallow to deep subseafloor sediments of the New Caledonia Basin. Environ Microbiol 11: 2446-2462.
42. 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.
43. 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.
44. Schippers A, Köweker G, Höft C & Teichert B (2010) Quantification of microbial communities in three forearc sediment basins off Sumatra. Geomicrobiol J 27: 170-182.
45. 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.
46. Schloss PD, Westcott S, Ryabin T et al. (2009) Introducing mothur: open-source, platform-independent community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75: 7537-7541.
47. Schouten S, Middelburg JJ, Hopmans EC & Damste JSS (2010) Fossilization and degradation of intact polar lipids in deep subsurface sediments: a theoretical approach. Geochim Cosmochim Acta 74: 3806-3814.
48. 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.
49. Selesi D, Pattis I, Schmid M, Kandeler E & Hartmann A (2007) Quantification of bacterial RubisCO genes in soils by cbbL targeted real-time PCR. J Microbiol Methods 69: 497-503.
50. Smith DC, Spivack AJ, Fisk MR, Haveman SA, Staudigel H & ODP Leg 185 Shipboard Scientific Party (2000) Tracer-based estimates of drilling-induced microbial contamination of deep sea crust. Geomicrobiol J 17: 207-219.
51. Sørensen KB, Lauer A & Teske AP (2004) Archaeal phylotypes in a metal-rich and low-activity deep subsurface sediment of the Peru Basin, ODP Leg 201, Site 1231. Geobiology 2: 151-161.
52. Spang A, Hatzenpichler R, Brochier-Armanet C et al. (2010) Distinct gene set in two different lineages of ammonia oxidizing archaea supports the phylum Thaumarchaeota. Trends Microbiol 18: 331-340.
53. Takai K & Horikoshi K (1999) Genetic diversity of archaea in deep-sea hydrothermal vent environments. Genetics 152: 1285-1297.
54. Takai K & Horikoshi K (2000) Rapid detection and quantification of members of the archaeal community by quantitative PCR using fluorogenic probes. Appl Environ Microbiol 66: 5066-5072.
55. Takai K, Moser DP, Deflaun M, Onstott TC & Frederickson JK (2001) Archaeal diversity in waters from deep South African gold mines. Appl Environ Microbiol 67: 5750-5760.
56. Takai K, Oida H, Suzuki Y et al. (2004) Spatial distribution of marine Crenarchaeota Group I in the vicinity of deep-sea hydrothermal systems. Appl Environ Microbiol 70: 2404-2413.
57. Teske AP (2006) Microbial communities of deep marine subsurface sediments: molecular and cultivation surveys. Geomicrobiol J 23: 357-368.
58. Teske AP & Sørensen KB (2008) Uncultured archaea in deep marine subsurface sediments: have we caught them all? ISME J 2: 3-18.
59. Van Geldern R, Hayashi T, Böttcher ME, Mottl MJ, Barth JAC & Stadler S (2013) Stable isotope geochemistry of pore waters and marine sediments from the New Jersey shelf: methane formation and fluid origin. Geosphere 9: 96-112.
60. Vetriani C, Jannasch HM, MacGregor BJ, Stahl DA & Reysenbach AL (1999) Population structure and phylogenetic characterization of marine benthic archaea in deep-sea sediments. Appl Environ Microbiol 65: 4375-4384.
61. 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 Methods 55: 155-164.
62. Webster G, Parkes RJ, Fry JC & Weightman AJ (2004) Widespread occurrence of a novel division of bacteria identified by 16S rDNA gene sequences originally found in deep marine sediments. Appl Environ Microbiol 70: 5708-5713.
63. Webster G, Yarram L, Freese E, Köster J, Sass H, Parkes RJ & Weightman AJ (2007) Distribution of candidate division JS1 and other Bacteria in tidal sediments of the German Wadden Sea using targeted 16S rRNA gene PCR-DGGE. FEMS Microbiol Ecol 62: 78-89.
64. 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.
65. Webster G, Sass H, Cragg BA et al. (2011) Enrichment and cultivation of prokaryotes associated with the sulphate-methane transition zone of diffusion-controlled sediments of Aarhus Bay, Denmark, under heterotrophic conditions. FEMS Microbiol Ecol 77: 248-263.
66. Weinbauer MG, Beckmann C & Höfle MG (1998) Utility of green fluorescent nucleic acid dyes and aluminium oxide membrane filters for rapid epifluorescence enumeration of soil and sediment bacteria. Appl Environ Microbiol 64: 5000-5003.
67. Whitman WB, Coleman DC & Wiebe WJ (1998) Prokaryotes: the unseen majority. P Natl Acad Sci USA 95: 6578-6583.
68. Wilms R, Sass H, Köpke B, Cypionka H & Engelen B (2007) Methane and sulfate profiles within the subsurface of a tidal flat are reflected by the distribution of sulfate-reducing bacteria and methanogenic archaea. FEMS Microbiol Ecol 59: 611-621.