SEARCH

SEARCH BY CITATION

References

  • Amann RI , LudwigW & SchleiferKH (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev59: 143169.
  • Boetius A , RavenschlagK, SchubertCJet al. (2000) A marine microbial consortium apparently mediating anaerobic oxidation of methane. Nature407: 623626.
  • Brazelton WJ , SchrenkMO, KelleyDS & BarossJA (2006) Methane- and sulfur-metabolizing microbial communities dominate the Lost City hydrothermal field ecosystem. Appl Environ Microb72: 62576270.
  • Campbell BJ , EngelAS, PorterML & TakaiK (2006) The versatile epsilon-proteobacteria: key players in sulphidic habitats. Nat Rev Microbiol 4: 458468.
  • Chen Y , UsslerWIII, HaflidasonH, LeplandA, RiseL, HovlandM & HjelstuenBO (2010) Sources of methane inferred from pore-water δ13C of dissolved inorganic carbon in Pockmark G11, offshore Mid-Norway. Chem Geol275: 127138.
  • Christensen H , HansenM & SorensenJ (1999) Counting and size classification of active soil bacteria by fluorescence in situ hybridization with an rRNA oligonucleotide probe. Appl Environ Microb65: 17531761.
  • Daims HBA , AmannR, SchleiferKH & WagnerM (1999) The domain-specific probe EUB338 is insufficient for the detection of all Bacteria: development and evaluation of a more comprehensive probe set. Syst Appl Microbiol 22: 434444.
  • Edwards U , RogallT, BlockerH, EmdeM & BottgerEC (1989) Isolation and direct complete nucleotide determination of entire genes. Characterization of a gene coding for 16S ribosomal RNA. Nucleic Acids Res17: 78437853.
  • Einen J , ThorsethIH & OvreasL (2008) Enumeration of Archaea and Bacteria in seafloor basalt using real-time quantitative PCR and fluorescence microscopy. FEMS Microbiol Lett282: 182187.
  • Fang J , ShizukaA, KatoC & SchoutenS (2006) Microbial diversity of cold-seep sediments in Sagami Bay, Japan, as determined by 16S rRNA gene and lipid analyses. FEMS Microbiol Ecol57: 429441.
  • Glaubitz S , LabrenzM, JostG & JurgensK (2010) Diversity of active chemolithoautotrophic prokaryotes in the sulfidic zone of a Black Sea pelagic redoxcline as determined by rRNA-based stable isotope probing. FEMS Microbiol Ecol74: 3241.
  • Glöckner FO , AmannR, AlfreiderA, PernthalerJ, PsennerR, TrebesiusK & SchleiferKH (1996) An in situ hybridization protocol for detection and identification of planktonic bacteria. Syst Appl Microbiol19: 403406.
  • Harrison BK , ZhangH, BerelsonW & OrphanVJ (2009) Variations in archaeal and bacterial diversity associated with the sulfate-methane transition zone in continental margin sediments (Santa Barbara Basin, California). Appl Environ Microb75: 14871499.
  • Heijs SK , HaeseRR, van der WielenPW, ForneyLJ & van ElsasJD (2007) Use of 16S rRNA gene based clone libraries to assess microbial communities potentially involved in anaerobic methane oxidation in a Mediterranean cold seep. Microb Ecol53: 384398.
  • Hinrichs KU , HayesJM, SylvaSP, BrewerPG & DeLongEF (1999) Methane-consuming archaebacteria in marine sediments. Nature398: 802805.
  • Hjelstuen BO , HaflidasonH, SejrupHP & NygardA (2010) Sedimentary and structural control on pockmark development-evidence from the Nyegga pockmark field, NW European margin. Geo-Mar Lett30: 221230.
  • Hoehler TM , AlperinMJ, AlbertDB & MartensCS (1994) Field and laboratory studies of methane oxidation in an anoxic marine sediment – evidence for a methanogen-sulfate reducer consortium. Global Biogeochem Cy8: 451463.
  • Hovland M , SvensenH, ForsbergCF, JohansenH, FichlerC, FossaJH, JonssonR & RueslattenH (2005) Complex pockmarks with carbonate-ridges off mid-Norway: Products of sediment degassing. Mar Geol 218: 191206.
  • Hugler M , GartnerA & ImhoffJF (2010) Functional genes as markers for sulfur cycling and CO2 fixation in microbial communities of hydrothermal vents of the Logatchev field. FEMS Microbiol Ecol73: 526537.
  • Huson DH , AuchAF, QiJ & SchusterSC (2007) MEGAN analysis of metagenomic data. Genome Res17: 377386.
  • Inagaki F , TakaiK, KobayashiH, NealsonKH & HorikoshiK (2003) Sulfurimonas autotrophica gen. nov., sp. nov., a novel sulfur-oxidizing epsilon-proteobacterium isolated from hydrothermal sediments in the Mid-Okinawa Trough. Int J Syst Evol Micr53: 18011805.
  • Inagaki F , TakaiK, NealsonKH & HorikoshiK (2004) Sulfurovum lithotrophicum gen. nov., sp. nov., a novel sulfur-oxidizing chemolithoautotroph within the epsilon-Proteobacteria isolated from Okinawa Trough hydrothermal sediments. Int J Syst Evol Micr54: 14771482.
  • Inagaki F , NunouraT, NakagawaSet al. (2006) Biogeographical distribution and diversity of microbes in methane hydrate-bearing deep marine sediments on the Pacific Ocean Margin. P Natl Acad Sci USA103: 28152820.
  • Ivanov M , MazziniA, BlinovaV, KozlovaE, LabergJS, MatveevaT, TavianiM & KaskovN (2010) Seep mounds on the Southern Wiring Plateau (offshore Norway). Mar Petrol Geol27: 12351261.
  • Jagersma GC , MeulepasRJ, Heikamp-de JongI, GietelingJ, KlimiukA, SchoutenS, DamsteJS, LensPN & StamsAJ (2009) Microbial diversity and community structure of a highly active anaerobic methane-oxidizing sulfate-reducing enrichment. Environ Microbiol11: 32233232.
  • Knittel K & BoetiusA (2009) Anaerobic oxidation of methane: progress with an unknown process. Annu Rev Microbiol 63: 311334.
  • Knittel K , LösekannT, BoetiusA, KortR & AmannR (2005) Diversity and distribution of methanotrophic archaea at cold seeps. Appl Environ Microb71: 467479.
  • Könneke M , BernhardAE, de la TorreJR, WalkerCB, WaterburyJB & StahlDA (2005) Isolation of an autotrophic ammonia-oxidizing marine archaeon. Nature437: 543546.
  • Kvenvolden KA , GinsburgGD & SolovievVA (1993) Worldwide distribution of subaquatic gas hydrates. Geo-Mar Lett13: 3240.
  • Lane DJ (1991) 16S/23S rRNA sequencing. Nucleic Acid Techniques in Bacterial Systematics (StackebrandtE & GoodfellowM, eds), pp. 115175. Wiley, New York, NY.
  • Lane DJ , PaceB, OlsenGJ, StahlDA, SoginML & PaceNR (1985) Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses. P Natl Acad Sci USA82: 69556959.
  • Lanoil BD , SassenR, La DucMT, SweetST & NealsonKH (2001) Bacteria and Archaea physically associated with Gulf of Mexico gas hydrates. Appl Environ Microb67: 51435153.
  • Lanzen A , JorgensenSL, BengtssonMM, JonassenI, OverasL & UrichT (2011) Exploring the composition and diversity of microbial communities at the Jan Mayen hydrothermal vent field using RNA and DNA. FEMS Microbiol Ecol doi: DOI: 10.1111/j.1574-6941.2011.01138.x.
  • Leloup J , LoyA, KnabNJ, BorowskiC, WagnerM & JorgensenBB (2007) Diversity and abundance of sulfate-reducing microorganisms in the sulfate and methane zones of a marine sediment, Black Sea. Environ Microbiol9: 131142.
  • Liao L , XuXW, WangCS, ZhangDS & WuM (2009) Bacterial and archaeal communities in the surface sediment from the northern slope of the South China Sea. J Zhejiang Univ Sci B10: 890901.
  • Lloyd KG , LaphamL & TeskeA (2006) An anaerobic methane-oxidizing community of ANME-1b archaea in hypersaline Gulf of Mexico sediments. Appl Environ Microb72: 72187230.
  • Lloyd KG , AlbertDB, BiddleJF, ChantonJP, PizarroO & TeskeA (2010) Spatial structure and activity of sedimentary microbial communities underlying a Beggiatoa spp. mat in a Gulf of Mexico hydrocarbon seep. PLoS One5: e8738.
  • Lösekann T , KnittelK, NadaligT, FuchsB, NiemannH, BoetiusA & AmannR (2007) Diversity and abundance of aerobic and anaerobic methane oxidizers at the Haakon Mosby Mud Volcano, Barents Sea. Appl Environ Microb73: 33483362.
  • Loy A , LehnerA, LeeN, AdamczykJ, MeierH, ErnstJ, SchleiferK-H & WagnerM (2002) Oligonucleotide microarray for 16S rRNA gene-based detection of all recognized lineages of sulfate-reducing prokaryotes in the environment. Appl Environ Microb68: 50645081.
  • Meulepas RJ , JagersmaCG, KhademAF, BuismanCJ, StamsAJ & LensPN (2009) Effect of environmental conditions on sulfate reduction with methane as electron donor by an Eckemforde Bay enrichment. Environ Sci Technol43: 65536559.
  • Michaelis W , SeifertR, NauhausKet al. (2002) Microbial reefs in the Black Sea fueled by anaerobic oxidation of methane. Science297: 10131015.
  • Morikawa K & YanagidaM (1981) Visualization of Individual DNA Molecules in Solution by Light Microscopy: DAPI Staining Method. J Biochem 89: 693696.
  • Muyzer G , de WaalEC & UitterlindenAG (1993) Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl Environ Microb59: 695700.
  • Muyzer G , TeskeA, WirsenCO & JannaschHW (1995) Phylogenetic relationships of Thiomicrospira species and their identification in deep-sea hydrothermal vent samples by denaturing gradient gel electrophoresis of 16S rDNA fragments. Arch Microbiol164: 165172.
  • Nauhaus K , BoetiusA, KrugerM & WiddelF (2002) In vitro demonstration of anaerobic oxidation of methane coupled to sulphate reduction in sediment from a marine gas hydrate area. Environ Microbiol4: 296305.
  • Niemann H , LösekannT, de BeerDet al. (2006) Novel microbial communities of the Haakon Mosby mud volcano and their role as a methane sink. Nature443: 854858.
  • Orcutt B & MeileC (2008) Constraints on mechanisms and rates of anaerobic oxidation of methane by microbial consortia: process-based modeling of ANME-2 archaea and sulfate reducing bacteria interactions. Biogeosciences 5: 15871599.
  • Orphan VJ , HinrichsKU, UsslerWIII, PaullCK, TaylorLT, SylvaSP, HayesJM & DelongEF (2001) Comparative analysis of methane-oxidizing archaea and sulfate-reducing bacteria in anoxic marine sediments. Appl Environ Microb67: 19221934.
  • Orphan VJ , HouseCH, HinrichsKU, McKeeganKD & DeLongEF (2002) Multiple archaeal groups mediate methane oxidation in anoxic cold seep sediments. P Natl Acad Sci USA99: 76637668.
  • Ovreas L , ForneyL, DaaeFL & TorsvikV (1997) Distribution of bacterioplankton in meromictic Lake Saelenvannet, as determined by denaturing gradient gel electrophoresis of PCR-amplified gene fragments coding for 16S rRNA. Appl Environ Microb63: 33673373.
  • Pachiadaki MG , LykousisV, StefanouEG & KormasKA (2010) Prokaryotic community structure and diversity in the sediments of an active submarine mud volcano (Kazan mud volcano, East Mediterranean Sea). FEMS Microbiol Ecol72: 429444.
  • Pernthaler A , DekasAE, BrownCT, GoffrediSK, EmbayeT & OrphanVJ (2008) Diverse syntrophic partnerships from deep-sea methane vents revealed by direct cell capture and metagenomics. P Natl Acad Sci USA105: 70527057.
  • Quince C , LanzenA, DavenportRJ & TurnbaughPJ (2011) Removing noise from pyrosequenced amplicons. BMC Bioinformatics12: 38.
  • Reeburgh WS (2007) Oceanic methane biogeochemistry. Chem Rev107: 486513.
  • Reiche S , HjelstuenBO & HaflidasonH (2011) High-resolution seismic stratigraphy, sedimentary processes and the origin of seabed cracks and pockmarks at Nyegga, mid-Norwegian margin. Mar Geol284: 2839.
  • Roesch LF , FulthorpeRR, RivaAet al. (2007) Pyrosequencing enumerates and contrasts soil microbial diversity. ISME J1: 283290.
  • Ronimus RS , ReysenbachA, MusgraveDR & MorganHW (1997) The phylogenetic position of the Thermococcus isolate AN1 based on 16S rRNA gene sequence analysis: a proposal that AN1 represents a new species, Thermococcus zilligii sp. nov. Arch Microbiol 168: 245248.
  • Sassen R , RobertsHH, AharonP, LarkinJ, ChinnEW & CarneyR (1993) Chemosynthetic bacterial mats at cold hydrocarbon seeps, Gulf of Mexico continental-slope. Org Geochem20: 7789.
  • Schreiber L , HollerT, KnittelK, MeyerdierksA & AmannR (2010) Identification of the dominant sulfate-reducing bacterial partner of anaerobic methanotrophs of the ANME-2 clade. Environ Microbiol12: 23272340.
  • Steinsbu BO , ThorsethIH, NakagawaS, InagakiF, LeverMA, EngelenB, OvreasL & PedersenRB (2010) Archaeoglobus sulfaticallidus sp. nov., a novel thermophilic and facultatively lithoautotrophic sulfate-reducer isolated from black rust exposed to hot ridge flank crustal fluids. Int J Syst Evol Micr1: 12.
  • Stoecker K , DorningerC, DaimsH & WagnerM (2010) Double labeling of oligonucleotide probes for fluorescence in situ hybridization (DOPE-FISH) improves signal intensity and increases rRNA accessibility. Appl Environ Microb76: 922926.
  • Takai K , SuzukiM, NakagawaS, MiyazakiM, SuzukiY, InagakiF & HorikoshiK (2006) Sulfurimonas paralvinellae sp. nov., a novel mesophilic, hydrogen- and sulfur-oxidizing chemolithoautotroph within the Epsilonproteobacteria isolated from a deep-sea hydrothermal vent polychaete nest, reclassification of Thiomicrospira denitrificans as Sulfurimonas denitrificans comb. nov. and emended description of the genus Sulfurimonas. Int J Syst Evol Micr56: 17251733.
  • Treude T , KrugerM, BoetiusA & JorgensenBB (2005) Environmental control on anaerobic oxidation of methane in the gassy sediments of Eckernforde Bay (German Baltic). Limnol Oceanogr50: 17711786.
  • Treude T , OrphanV, KnittelK, GiesekeA, HouseCH & BoetiusA (2007) Consumption of methane and CO2 by methanotrophic microbial mats from gas seeps of the anoxic Black Sea. Appl Environ Microb73: 22712283.
  • Treusch AH , LeiningerS, KletzinA, SchusterSC, KlenkHP & SchleperC (2005) Novel genes for nitrite reductase and Amo-related proteins indicate a role of uncultivated mesophilic crenarchaeota in nitrogen cycling. Environ Microbiol7: 19851995.
  • Walker CB , de la TorreJR, KlotzMGet al. (2010) Nitrosopumilus maritimus genome reveals unique mechanisms for nitrification and autotrophy in globally distributed marine crenarchaea. P Natl Acad Sci USA107: 88188823.
  • Webster G , ParkesRJ, CraggBA, NewberryCJ, WeightmanAJ & FryJC (2006) Prokaryotic community composition and biogeochemical processes in deep subseafloor sediments from the Peru Margin. FEMS Microbiol Ecol58: 6585.
  • Webster G , YarramL, FreeseE, KosterJ, SassH, ParkesRJ & WeightmanAJ (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 Ecol62: 7889.
  • Wegener G , ShovitriM, KnittelK, NiemannH, HovlandM & BoetiusA (2008) Biogeochemical processes and microbial diversity of the Gullfaks and Tommeliten methane seeps (Northern North Sea). Biogeosciences5: 11271144.
  • Whelan JA , RussellNB & WhelanMA (2003) A method for the absolute quantification of cDNA using real-time PCR. J Immunol Methods278: 261269.
  • Zipper H , ButaC, LammleK, BrunnerH, BernhagenJ & VitzthumF (2003) Mechanisms underlying the impact of humic acids on DNA quantification by SYBR Green I and consequences for the analysis of soils and aquatic sediments. Nucleic Acids Res31: e39.