SEARCH

SEARCH BY CITATION

References

  • Altschul SF, Madden TL, Schaffer AA, Zhang JH, Zhang Z, Miller W & Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 33893402.
  • Baldwin BR, Nakatsu CH & Nies L (2003) Detection and enumeration of aromatic oxygenase genes by multiplex and real-time PCR. Appl Environ Microb 69: 33503358.
  • Biddle JF, Lipp JS, Lever MA et al. (2006) Heterotrophic Archaea dominate sedimentary subsurface ecosystems off Peru. P Natl Acad Sci USA 103: 38463851.
  • Böning P, Brumsack H-J, Böttcher ME, Schnetger B, Kriete C, Kallmeyer J & Borchers SL (2004) Geochemistry of Peruvian near-surface sediments. Geochim Cosmochim Ac 68: 44294451.
  • Coolen MJL, Cypionka H, Sass AM, Sass H & Overmann J (2002) Ongoing modification of mediterranean pleistocene sapropels mediated by prokaryotes. Science 296: 24072410.
  • D'Hondt SL, Jørgensen BB, Miller DJ and Shipboard Scientific Party (2003) Leg 201 Initial Report – controls on microbial communities in deeply buried sediments, Eastern Equatorial Pacific and Peru Margin. Proceedings of the Ocean Drilling Program Initial Reports, 201 College Station, TX. DOI: DOI: 10.2973/odp.proc.ir.201.2003.
  • D'Hondt SL, Jørgensen BB, Miller DJ et al. (2004) Distributions of microbial activities in deep subseafloor sediments. Science 306: 22162221.
  • Fry JC, Parkes JR, Cragg BA, Weightman AJ & Webster G (2008) Prokaryotic biodiversity and activity in the deep subseafloor biosphere. FEMS Microbiol Ecol 66: 181196.
  • Hamburg University (2007) Investigations of Microbiological, Biogeochemical and Paleo-Climatological Processes in the Stratified Water Column and in the Sediments from the Black Sea R/V Meteor M72-5 Cruise Report. University of Hamburg, Hamburg, Germany.
  • Hugenholtz P & Stackebrandt E (2004) Reclassification of Sphaerobacter thermophilus from the subclass Sphaerobacteridae in the phylum Actinobacteria to the class Thermomicrobia (emended description) in the phylum Chloroflexi (emended description). Int J Syst Evol Micr 54: 20492051.
  • Hugenholtz P, Goebel BM & Pace NR (1998) Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. J Bacteriol 180: 47654774.
  • Inagaki F, Suzuki M, Takai K et al. (2003) Microbial communities associated with geological horizons in coastal subseafloor sediments from the Sea of Okhotsk. Appl Environ Microb 69: 72247235.
  • 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: 28152820.
  • Jørgensen BB & Boetius A (2007) Feast and famine – microbial life in the deep-sea bed. Nat Rev Microbiol 5: 770781.
  • JørgensenBB, D'HondtS & MillerDJ, eds (2005) Proceedings of the Ocean Drilling Program, Sci Results, Vol. 201 College Station, TX. DOI: DOI: 10.2973/odp.proc.sr.201.2006.
  • Kolb S, Knief C, Stubner S & Conrad R (2003) Quantitative detection of methanotrophs in soil by novel pmoA-targeted real-time PCR assays. Appl Environ Microb 69: 24232429.
  • Kormas KA, 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: 115125.
  • KudrassHK, ed (2000) Cruise Report SO147 Peru Upwelling:Valparaiso-Callao, 29.05.-03.07.2000. BGR Hannover, Hannover, Germany.
  • Labrenz M, Brettar I, Christen R, Flavier S, Bötel J & Höfle MG (2004) Development and application of a real-time PCR approach for quantification of uncultured bacteria in the Central Baltic Sea. Appl Environ Microb 70: 49714979.
  • Lipp JS, Morono Y, Inagaki F & Hinrichs K-U (2008) Significant contribution of Archaea to extant biomass in marine subsurface sediments. Nature 454: 991994.
  • Morris RM, Rappe MS, Urbach E, Connon SA & Giovannoni SJ (2004) Prevalence of the Chloroflexi-related SAR202 bacterioplankton cluster throughout the mesopelagic zone and deep ocean. Appl Environ Microb 70: 28362842.
  • Nadkarni MA, Martin FE, Jacques NA & Hunter N (2002) Determination of bacterial load by real-time PCR using a broad-range (universal) probe and primers set. Microbiology 148: 257266.
  • Parkes RJ, Cragg BA & Wellsbury P (2000) Recent studies on bacterial populations and processes in subseafloor sediments: a review. Hydrogeol J 8: 1128.
  • Parkes RJ, Webster G, Cragg BA et al. (2005) Deep sub-seafloor prokaryotes stimulated at interfaces over geological time. Nature 436: 390394.
  • Rappe MS & Giovannoni SJ (2003) The uncultured microbial majority. Annu Rev Microbiol 57: 369394.
  • 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 Microb 68: 37593770.
  • Rochelle PA, Cragg BA, Fry JC, Parkes RJ & Weightman AJ (1994) Effect of sample handling on estimation of bacterial diversity in marine sediments by 16S rRNA gene sequence analysis. FEMS Microbiol Ecol 15: 215225.
  • Roussel EG, Bonavita M-AC, Querellou J, Cragg BA, Webster G, Prieur D & Parkes RJ (2008) Extending the sub-sea-floor biosphere. Science 320: 1046.
  • 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: 12511260.
  • 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: 861864.
  • 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 Micr 53: 18431851.
  • Tatusova TA & Madden TL (1999) BLAST 2 sequences, a new tool for comparing protein and nucleotide sequences. FEMS Microbiol Lett 174: 247250.
  • Teske AP (2006) Microbial community composition in deep marine subsurface sediments of ODP Leg 201: sequencing surveys and cultivations. Proceedings of the Ocean Drilling Program, Sci. Results, 201 (JørgensenBB, D'HondtSL & MillerDJ, eds), pp. 1–19. College Station, TX (Ocean Drilling Program). DOI: DOI: 10.2973/odp.proc.sr.201.120.2006.
  • 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: 155164.
  • Webster G, Parkes RJ, Fry JC & Weightman AJ (2004) Widespread occurrence of a novel division of bacteria identified by 16S rRNA gene sequences originally found in deep marine sediments. Appl Environ Microb 70: 57085713.
  • Webster G, Watt LC, Rinna J, Fry JC, Evershed RP, Parkes J & Weightman AJ (2006) A comparison of stable-isotope probing of DNA and phospholipid fatty acids to study prokaryotic functional diversity in sulfate-reducing marine sediment enrichment slurries. Environ Microbiol 8: 15751589.
  • 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: 7889.
  • Whitman WB, Coleman DC & Wiebe WJ (1998) Prokaryotes: the unseen majority. P Natl Acad Sci USA 95: 65786583.
  • Wiedicke-Hombach M (2006) Sumatra–The Hydrocarbon System of the Sumatra Forearc-SO189-2 Cruise Report. Archive Number 0126492. Federal Institute for Geosciences and Natural Resources (BGR), Hannover, Germany.
  • Yamada T, Sekiguchi Y, Hanada S, Imachi H, Ohashi A, Harada H & Kamagata Y (2006) Anaerolinea thermolimosa sp. nov., Levilinea saccharolytica gen. nov., sp. nov. and Leptolinea tardivitalis gen. nov., sp. nov., novel filamentous anaerobes, and description of the new classes Anaerolineae classis nov. and Caldilineae classis nov. in the bacterial phylum Chloroflexi. Int J Syst Evol Micr 56: 13311340.
  • Yamada T, Imachi H, Ohashi A, Harada H, Hanada S, Kamagata Y & Sekiguchi Y (2007) 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. Int J Syst Evol Micr 57: 22992306.