?Peter R. Girguis2003fGrowth and Methane Oxidation Rates of Anaerobic Methanotrophic Archaea in a Continuous-Flow Bioreactor 5472-5482&Applied and Environmental Microbiology699,~?&Werne, J. P. Baas, M. Damste, J. S. S.2002vMolecular isotopic tracing of carbon flow and trophic relationships in a methane-supported benthic microbial community 1694-1701Limnology and Oceanography476Nov://000179650200013ArticleISI:000179650200013~?%Tor, J. M. Amend, J. P. Lovley, D. R.2003]Metabolism of organic compounds in anaerobic, hydrothermal sulphate-reducing marine sediments583-591Environmental Microbiology57Jul://000183640700005ArticleISI:000183640700005~?"Teske, A. Dhillon, A. Sogin, M. L.2003qGenomic markers of ancient anaerobic microbial pathways: Sulfate reduction, methanogenesis, and methane oxidation186-191Biological Bulletin2042Apr://000182460500011ArticleISI:0001824605000113~?;Schouten, S. Wakeham, S. G. Hopmans, E. C. Damste, J. S. S.2003\Biogeochemical evidence that thermophilic archaea mediate the anaerobic oxidation of methane 1680-1686&Applied and Environmental Microbiology693Mar://000181435600046ArticleISI:000181435600046~? Schink, B.2002/Synergistic interactions in the microbial world257-261SAntonie Van Leeuwenhoek International Journal of General and Molecular Microbiology811-4://000178390200025ArticleISI:000178390200025*~? Weber, A. Jorgensen, B. B.2002fBacterial sulfate reduction in hydrothermal sediments of the Guaymas Basin, Gulf of California, Mexico827-8416Deep-Sea Research Part I-Oceanographic Research Papers495May://000175647600003ArticleISI:000175647600003T~? 7Sahm, K. MacGregor, B. J. Jorgensen, B. B. Stahl, D. A.1999Sulphate reduction and vertical distribution of sulphate-reducing bacteria quantified by rRNA slot-blot hybridization in a coastal marine sediment65-74Environmental Microbiology11Feb://000084961200010ArticleISI:000084961200010~? Boon, P. I. Lee, K.1997QMethane oxidation in sediments of a floodplain wetland in south-eastern Australia138-142Letters in Applied Microbiology252Aug://A1997XR12000015ArticleISI:A1997XR12000015d~? OOrphan, V. J. Ussler, W. Naehr, T. H. House, C. H. Hinrichs, K. U. Paull, C. K.2004Geological, geochemical, and microbiological heterogeneity of the seafloor around methane vents in the Eel River Basin, offshore California265-289Chemical Geology2053-4May 14://000221384300006ArticleISI:0002213843000065~?9Schrenk, M. O. Kelley, D. S. Delaney, J. R. Baross, J. A.2003`Incidence and diversity of microorganisms within the walls of an active deep-sea sulfide chimney 3580-3592&Applied and Environmental Microbiology696Jun://000187156200070ArticleISI:000187156200070M~?KHallam, S. J. Girguis, P. R. Preston, C. M. Richardson, P. M. DeLong, E. F.2003fIdentification of methyl coenzyme M reductase A (mcrA) genes associated with methane-oxidizing archaea 5483-5491&Applied and Environmental Microbiology699Sep://000185437000054ArticleISI:000185437000054?~?<Zhang, C. L. Pancost, R. D. Sassen, R. Qian, Y. Macko, S. A.2003Archaeal lipid biomarkers and isotopic evidence of anaerobic methane oxidation associated with gas hydrates in the Gulf of Mexico827-836Organic Geochemistry346://000183197400010ArticleISI:000183197400010<~?4Balk, M. Weijma, J. Friedrich, M. W. Stams, A. J. M.2003{Methanol utilization by a novel thermophilic homoacetogenic bacterium, Moorella mulderi sp nov., isolated from a bioreactor315-320Archives of Microbiology1795May://000183048100002ArticleISI:000183048100002"~?:Dhillon, A. Teske, A. Dillon, J. Stahl, D. A. Sogin, M. L.2003LMolecular characterization of sulfate-reducing bacteria in the Guaymas Basin 2765-2772&Applied and Environmental Microbiology695May://000182808300042ArticleISI:000182808300042p~?AChong, S. C. Liu, Y. T. Cummins, M. Valentine, D. L. Boone, D. R.2002lMethanogenium marinum sp nov., a H-2-using methanogen from Skan Bay, Alaska, and kinetics of H-2 utilization263-270SAntonie Van Leeuwenhoek International Journal of General and Molecular Microbiology811-4://000178390200026ArticleISI:000178390200026.~?Valentine, D. L.2002[Biogeochemistry and microbial ecology of methane oxidation in anoxic environments: a review271-282SAntonie Van Leeuwenhoek International Journal of General and Molecular Microbiology811-4://000178390200027ArticleISI:000178390200027~?Michaelis, W. Seifert, R. Nauhaus, K. Treude, T. Thiel, V. Blumenberg, M. Knittel, K. Gieseke, A. Peterknecht, K. Pape, T. Boetius, A. Amann, R. Jorgensen, B. B. Widdel, F. Peckmann, J. R. Pimenov, N. V. Gulin, M. B.2002IMicrobial reefs in the Black Sea fueled by anaerobic oxidation of methane 1013-1015Science2975583Aug 9://000177325400044ArticleISI:000177325400044\~?#Balk, M. Weijma, J. Stams, A. J. M.2002Thermotoga lettingae sp nov., a novel thermophilic, methanol-degrading bacterium isolated from a thermophilic anaerobic reactor 1361-1368AInternational Journal of Systematic and Evolutionary Microbiology52Jul://000176925200041Article Part 4ISI:000176925200041;~?-Nauhaus, K. Boetius, A. Kruger, M. Widdel, F.2002In vitro demonstration of anaerobic oxidation of methane coupled to sulphate reduction in sediment from a marine gas hydrate area296-305Environmental Microbiology45May://000175840900006ArticleISI:000175840900006x~?gTeske, A. Hinrichs, K. U. Edgcomb, V. Gomez, A. D. Kysela, D. Sylva, S. P. Sogin, M. L. Jannasch, H. W.2002uMicrobial diversity of hydrothermal sediments in the Guaymas Basin: Evidence for anaerobic methanotrophic communities 1994-2007&Applied and Environmental Microbiology684Apr://000174842200065ArticleISI:000174842200065~?5Weijma, J. Pol, L. W. H. Stams, A. J. M. Lettinga, G.2000hPerformance of a thermophilic sulfate and sulfite reducing high rate anaerobic reactor fed with methanol429-439Biodegradation116://000170725400013ArticleISI:0001707254000133~?;Valentine, D. L. Blanton, D. C. Reeburgh, W. S. Kastner, M.2001bWater column methane oxidation adjacent to an area of active hydrate dissociation, Eel River Basin 2633-2640Geochimica Et Cosmochimica Acta6516Aug://000170452300001ArticleISI:000170452300001h~?ancost, R. D. Bouloubassi, I. Aloisi, G. Hopmans, E. Werne, J. Pierre, C. Damste, J. S. S.2001TArchaeal and bacterial interactions during anaerobic methane oxidation at cold seeps U537-U5384Abstracts of Papers of the American Chemical Society221Apr 1://000168824703547Meeting Abstract Part 1ISI:000168824703547#~?HOrphan, V. J. House, C. H. Hinrichs, K. U. McKeegan, K. D. DeLong, E. F.2001YMethane-consuming archaea revealed by directly coupled isotopic and phylogenetic analysis484-487Science2935529Jul 20://000169966700045ArticleISI:000169966700045"~?.Pancost, R. D. Hopmans, E. C. Damste, J. S. S.2001^Archaeal lipids in Mediterranean cold seeps: Molecular proxies for anaerobic methane oxidation 1611-1627Geochimica Et Cosmochimica Acta6510May://000168762600007ArticleISI:000168762600007 ~?)Thomsen, T. R. Finster, K. Ramsing, N. B.2001[Biogeochemical and molecular signatures of anaerobic methane oxidation in a marine sediment 1646-1656&Applied and Environmental Microbiology674Apr://000167865500036ArticleISI:000167865500036q~?kOrphan, V. J. Hinrichs, K. U. Ussler, W. Paull, C. K. Taylor, L. T. Sylva, S. P. Hayes, J. M. Delong, E. F.2001jComparative analysis of methane-oxidizing archaea and sulfate-reducing bacteria in anoxic marine sediments 1922-1934&Applied and Environmental Microbiology674Apr://000167865500069ArticleISI:000167865500069~? /Valentine, D. L. Blanton, D. C. Reeburgh, W. S.2000@Hydrogen production by methanogens under low-hydrogen conditions415-421Archives of Microbiology1746Dec://000166252000006ArticleISI:000166252000006&~?!CHinrichs, K. U. Summons, R. E. Orphan, V. Sylva, S. P. Hayes, J. M.2000^Molecular and isotopic analysis of anaerobic methane-oxidizing communities in marine sediments 1685-1701Organic Geochemistry3112://000165957000031ArticleISI:000165957000031~?" Valentine, D. L. Reeburgh, W. S.2000/New perspectives on anaerobic methane oxidation477-484Environmental Microbiology25Oct://000165322900001ReviewISI:000165322900001S~?#Boetius, A. Ravenschlag, K. Schubert, C. J. Rickert, D. Widdel, F. Gieseke, A. Amann, R. Jorgensen, B. B. Witte, U. Pfannkuche, O.2000QA marine microbial consortium apparently mediating anaerobic oxidation of methane623-626Nature4076804Oct 5://000089772800045ArticleISI:000089772800045z~?$QPancost, R. D. Damste, J. S. S. de Lint, S. van der Maarel, Mjec Gottschal, J. C.2000Biomarker evidence for widespread anaerobic methane oxidation in Mediterranean sediments by a consortium of methanogenic archaea and bacteria 1126-1132&Applied and Environmental Microbiology663Mar://000085604800037ArticleISI:000085604800037+~?%5Weijma, J. Stams, A. J. M. Pol, L. W. H. Lettinga, G.2000`Thermophilic sulfate reduction and methanogenesis with methanol in a high rate anaerobic reactor354-363 Biotechnology and Bioengineering673Feb 5://000084740000012ArticleISI:000084740000012~?&EHinrichs, K. U. Hayes, J. M. Sylva, S. P. Brewer, P. G. DeLong, E. F.19994Methane-consuming archaebacteria in marine sediments802-805Nature3986730Apr 29://000080058100057ArticleISI:000080058100057i~?')Harmsen, H. J. M. Prieur, D. Jeanthon, C.1997Distribution of microorganisms in deep-sea hydrothermal vent chimneys investigated by whole-cell hybridization and enrichment culture of thermophilic subpopulations 2876-2883&Applied and Environmental Microbiology637Jul://A1997XJ18200057ArticleISI:A1997XJ18200057~?(Davidova, I. A. Stams, A. J. M.1996aSulfate reduction with methanol by a thermophilic consortium obtained from a methanogenic reactor297-302&Applied Microbiology and Biotechnology463Oct://A1996VQ22600015ArticleISI:A1996VQ22600015Z~?)[Ravot, G. Ollivier, B. Magot, M. Patel, B. K. C. Crolet, J. L. Fardeau, M. L. Garcia, J. L.1995fThiosulfate Reduction, an Important Physiological Feature Shared by Members of the Order Thermotogales 2053-2055&Applied and Environmental Microbiology615May://A1995QW18400067NoteISI:A1995QW18400067N~?*:Hoehler, T. M. Alperin, M. J. Albert, D. B. Martens, C. S.1994Field and Laboratory Studies of Methane Oxidation in an Anoxic Marine Sediment - Evidence for a Methanogen-Sulfate Reducer Consortium451-463Global Biogeochemical Cycles84Dec://A1994PU11800005ArticleISI:A1994PU11800005)~?+Jorgensen, B. B. Bak, F.1991wPathways and Microbiology of Thiosulfate Transformations and Sulfate Reduction in a Marine Sediment (Kattegat, Denmark)847-856&Applied and Environmental Microbiology573Mar://A1991FA76400037ArticleISI:A1991FA76400037~?, Grogan, D. W.1989gPhenotypic Characterization of the Archaebacterial Genus Sulfolobus - Comparison of 5 Wild-Type Strains 6710-6719Journal of Bacteriology17112Dec://A1989CB50400041ArticleISI:A1989CB50400041~?-'Iversen, N. Oremland, R. S. Klug, M. J.1987QBig Soda Lake (Nevada) .3. Pelagic Methanogenesis and Anaerobic Methane Oxidation804-814Limnology and Oceanography324Jul://A1987K372000003ArticleISI:A1987K372000003_~?.=Patel, R. N. Hou, C. T. Laskin, A. I. Felix, A. Derelanko, P.1980Microbial Oxidation of Gaseous Hydrocarbons - Production of Secondary Alcohols from Corresponding Normal-Alkanes by Methane-Utilizing Bacteria720-726&Applied and Environmental Microbiology394://A1980JR27900006ArticleISI:A1980JR27900006~?/ Makula, R. A.19786Phospholipid Composition of Methane-Utilizing Bacteria771-777Journal of Bacteriology1343://A1978FC29900012ArticleISI:A1978FC29900012?0?Zbigniew Jan Mudryk Beata Podgorska Anetta Ameryk Jerzy Bolalek2000gThe occurrence and activity of sulphate-reducing bacteria in the bottom sediments of the Gulf of Gdansk105-117 Oceanologia421 23 FebruaryNiet online beschikbaar>~?1LMilkov, A. V. Vogt, P. R. Crane, K. Lein, A. Y. Sassen, R. Cherkashev, G. A.2004iGeological, geochemical, and microbial processes at the hydrate-bearing Hakon Mosby mud volcano: a review347-366Chemical Geology2053-4May 14://000221384300009ReviewISI:000221384300009|~?4LMuthumbi, W. Boon, N. Boterdaele, R. De Vreese, I. Top, E. M. Verstraete, W.2001Microbial sulfate reduction with acetate: process performance and composition of the bacterial communities in the reactor at different salinity levels787-793&Applied Microbiology and Biotechnology556Jun://000169585800020ArticleISI:000169585800020~?5Polprasert, C. Haas, C. N.1995AEffect of Sulfate on Anaerobic Processes Fed with Dual Substrates101-107Water Science and Technology319://A1995RT74400013ArticleISI:A1995RT74400013a~?6HOrphan, V. J. House, C. H. Hinrichs, K. U. McKeegan, K. D. DeLong, E. F.2002PMultiple archaeal groups mediate methane oxidation in anoxic cold seep sediments 7663-7668OProceedings of the National Academy of Sciences of the United States of America9911May 28://000175908600062ArticleISI:000175908600062/~?71Elvert, M. Suess, E. Greinert, J. Whiticar, M. J.2000yArchaea mediating anaerobic methane oxidation in deep-sea sediments at cold seeps of the eastern Aleutian subduction zone 1175-1187Organic Geochemistry3111://000165656900010ArticleISI:000165656900010-~?8HThiel, V. Peckmann, J. Richnow, H. H. Luth, U. Reitner, J. Michaelis, W.2001bMolecular signals for anaerobic methane oxidation in Black Sea seep carbonates and a microbial mat97-112Marine Chemistry732Feb://000166378900002ArticleISI:000166378900002*~?9BLanoil, B. D. Sassen, R. La Duc, M. T. Sweet, S. T. Nealson, K. H.2001KBacteria and Archaea physically associated with Gulf of Mexico gas hydrates 5143-5153&Applied and Environmental Microbiology6711Nov://000171914100027ArticleISI:000171914100027~?: Harder, J.1997gAnaerobic methane oxidation by bacteria employing C-14-methane uncontaminated with C-14-carbon monoxide13-23Marine Geology1371-2Feb://A1997WR72600003ArticleISI:A1997WR72600003u~?;'Kane, M. D. Poulsen, L. K. Stahl, D. A.1993Monitoring the Enrichment and Isolation of Sulfate-Reducing Bacteria by Using Oligonucleotide Hybridization Probes Designed from Environmentally Derived 16s Ribosomal-Rna Sequences682-686&Applied and Environmental Microbiology593Mar://A1993KQ12300005ArticleISI:A1993KQ12300005~?<;Beeder, J. Nilsen, R. K. Rosnes, J. T. Torsvik, T. Lien, T.1994CArchaeoglobus-Fulgidus Isolated from Hot North-Sea-Oil Field Waters 1227-1231&Applied and Environmental Microbiology604Apr://A1994ND82300025ArticleISI:A1994ND82300025~?= White, R. H.1988MStructural Diversity among Methanofurans from Different Methanogenic Bacteria 4594-4597Journal of Bacteriology17010Oct://A1988Q242300024ArticleISI:A1988Q242300024~?> Kelley, C.2003SMethane oxidation potential in the water column of two diverse coastal marine sites105-120Biogeochemistry651Aug://000185795900006ArticleISI:000185795900006~??/Islas-Lima, S. Thalasso, F. Gomez-Hernandez, J.2004?Evidence of anoxic methane oxidation coupled to denitrification13-16Water Research381Jan://000187881200002ArticleISI:000187881200002F~?@Grant, N. J. Whiticar, M. J.2002kStable carbon isotopic evidence for methane oxidation in plumes above Hydrate Ridge, Cascadia Oregon MarginGlobal Biogeochemical Cycles164Dec 10://000181103500001ArticleISI:000181103500001?AKotelnikova, S.2002@Microbial production and oxidation of methane in deep subsurface367-395Earth-Science Reviews583-4Oct://000178808300006ISI:000178808300006?C[Sassen, R. Roberts, H. H. Carney, R. Milkov, A. V. DeFreitas, D. A. Lanoil, B. Zhang, C. L.2004Free hydrocarbon gas, gas hydrate, and authigenic minerals in chemosynthetic communities of the northern Gulf of Mexico continental slope: relation to microbial processes195-217Chemical Geology2053-4May 14://000221384300002ISI:000221384300002,ӿ?DSBlumenberg, Martin Seifert, Richard Reitner, Joachim Pape, Thomas Michaelis, Walter2004JMembrane lipid patterns typify distinct anaerobic methanotrophic consortia 11111-11116PNAS10130 July 27, 2004The anaerobic oxidation of methane (AOM) is one of the major sinks of this substantial greenhouse gas in marine environments. Recent investigations have shown that diverse communities of anaerobic archaea and sulfate-reducing bacteria are involved in AOM. Most of the relevant archaea are assigned to two distinct phylogenetic clusters, ANME-1 and ANME-2. A suite of specific 13C-depleted lipids demonstrating the presence of consortia mediating AOM in fossil and recent environments has been established. Here we report on substantial differences in the lipid composition of microbial consortia sampled from distinct compartments of AOM-driven carbonate reefs growing in the northwestern Black Sea. Communities in which the dominant archaea are from the ANME-1 cluster yield internally cyclized tetraether lipids typical of thermophiles. Those in which ANME-2 archaea are dominant yield sn-2-hydroxyarchaeol accompanied by crocetane and crocetenes. The bacterial lipids from these communities are also distinct even though the sulfate-reducing bacteria all belong to the Desulfosarcina/Desulfococcus group. Nonisoprenoidal glycerol diethers are predominantly associated with ANME-1-dominated communities. Communities with ANME-2 yield mainly conventional, ester-linked diglycerides. ANME-1 archaea and associated sulfate-reducing bacteria seem to be enabled to use low concentrations of methane and to grow within a broad range of temperatures. Our results offer a tool for the study of recent and especially of fossil methane environments.5http://www.pnas.org/cgi/content/abstract/101/30/11111PNAS?E'Galchenko, V.F. Lein, A.Y. Ivanov, M.V.2004pRates of Microbial Production and Oxidation of Methane in the Bottom Sediments and Water Column of the Black Sea224-236 Microbiology732;http://content.kluweronline.com/article/488870/fulltext.pdf?FHDagurova, O.P. Namsaraev, B.B. Kozyreva, L.P. Zemskaya, T.I. Dulov, L.E.2004KBacterial Processes of the Methane Cycle in Bottom Sediments of Lake Baikal202-210 Microbiology732?G Burns, S. J.1998`Carbon isotopic evidence for coupled sulfate reduction methane oxidation in Amazon Fan sediments797-804Geochimica Et Cosmochimica Acta625Mar://000073250600005ISI:000073250600005ӿ?H2Vetriani, Costantino Tran, Hiep V. Kerkhof, Lee J.2003UFingerprinting Microbial Assemblages from the Oxic/Anoxic Chemocline of the Black Sea 6481-6488Appl. Environ. Microbiol.6911November 1, 2003Biomass samples from the Black Sea collected in 1988 were analyzed for SSU genes from Bacteria and Archaea after 10 years of storage at -80{degrees}C. Both clonal libraries and direct fingerprinting by terminal restriction fragment length polymorphism (T-RFLP) analyses were used to assess the microbial community. Uniform and discrete depth distributions of different SSU phylotypes were observed. However, most recombinant clones were not restricted to a specific depth in the water column, and many of the major T-RFLP peaks remain uncharacterized. Of the clones obtained, an {varepsilon}-Proteobacteria and a Pseudoalteromonas-like clone accounted for major peaks in the fingerprint, while deeply branching lineages of {alpha}- and {gamma}-Proteobacteria were associated with smaller peaks. Additionally, members were found among both the {delta}-Proteobacteria related to sulfate reducers and the Archaea related to phylotypes from the ANME groups that anaerobically oxidize methane.2http://aem.asm.org/cgi/content/abstract/69/11/6481Appl. Environ. Microbiol. ?IKruger, Martin Meyerdierks, Anke Glockner, Frank Oliver Amann, Rudolf Widdel, Friedrich Kube, Michael Reinhardt, Richard Kahnt, Jorg Bocher, Reinhard Thauer, Rudolf K Shima, Seigo2003QA conspicuous nickel protein in microbial mats that oxidize methane anaerobically878-881Nature426696810.1038/nature022072003/12/18/printuhttp://dx.doi.org/10.1038/nature02207 L3 - http://www.nature.com/nature/journal/v426/n6968/suppinfo/nature02207.htmlTY - JOUR 10.1038/nature02207 0028-0836?JZehnder, A. J. B. Brock, T. D.1979@Methane Formation and Methane Oxidation by Methanogenic Bacteria420-432Journal of Bacteriology1371://A1979GF08600057ISI:A1979GF08600057=?KGJorgensen, B. B. Bottcher, M. E. Luschen, H. Neretin, L. N. 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Detter, John C. Rokhsar, Daniel Richardson, Paul M. DeLong, Edward F.2004JReverse Methanogenesis: Testing the Hypothesis with Environmental Genomics 1457-1462Science3055689September 3, 2004Microbial methane consumption in anoxic sediments significantly impacts the global environment by reducing the flux of greenhouse gases from ocean to atmosphere. Despite its significance, the biological mechanisms controlling anaerobic methane oxidation are not well characterized. One current model suggests that relatives of methane-producing Archaea developed the capacity to reverse methanogenesis and thereby to consume methane to produce cellular carbon and energy. We report here a test of the "reverse-methanogenesis" hypothesis by genomic analyses of methane-oxidizing Archaea from deep-sea sediments. Our results show that nearly all genes typically associated with methane production are present in one specific group of archaeal methanotrophs. These genome-based observations support previous hypotheses and provide an informed foundation for metabolic modeling of anaerobic methane oxidation.<http://www.sciencemag.org/cgi/content/abstract/305/5689/1457Science߾?RStrous,Marc Jetten,Mike S.M.2004+Anaerobic oxidation of methane and ammonium99-117Annual Review of Microbiology581-http://arjournals.annualreviews.org/loi/microJournal ArticleAnnual Review of Microbiology4?SdSethunathan, N. Kumaraswamy, S. Rath, A. K. Ramakrishnan, B. Satpathy, S. N. Adhya, T. K. Rao, V. R.2000BMethane production, oxidation, and emission from Indian rice soils377-388"Nutrient Cycling in Agroecosystems581-3Nov://000166362400033ISI:000166362400033?T<Kumaraswamy, S. Rath, A. K. Ramakrishnan, B. Sethunathan, N.2000WWetland rice soils as sources and sinks of methane: a review and prospects for research449-461Biology and Fertility of Soils316Sep://000089292600001ISI:000089292600001?U Schouten, S.2001VEvidence for anaerobic methane oxidation by archaea in euxinic waters of the Black Sea 1277-1281Organic Geochemistry32K?V"van Breukelen, B. M. Griffioen, J.2004Biogeochemical processes at the fringe of a landfill leachate pollution plume: potential for dissolved organic carbon, Fe(II), Mn(II), NH4, and CH4 oxidation181-205 Journal of Contaminant Hydrology731-4Sep://000223882100008ISI:000223882100008?WKXin, J. Y. Cui, J. R. Niu, J. Z. Hua, S. F. Xia, C. G. Li, S. B. Zhu, L. M.2004>Production of methanol from methane by methanotrophic bacteria225-229"Biocatalysis and Biotransformation223May://000223975700010ISI:000223975700010&?X:Schreiber, M. E. Carey, G. R. Feinstein, D. T. Bahr, J. 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Woodside, J.2004wLife at cold seeps: a synthesis of biogeochemical and ecological data from Kazan mud volcano, eastern Mediterranean Sea367-390Chemical Geology2053-4May 14://000221384300010ISI:000221384300010?^Hoffmeister, M. Martin, W.2003MInterspecific evolution: microbial symbiosis, endosymbiosis and gene transfer641-649Environmental Microbiology58Aug://000184266900002ISI:000184266900002?_Dzyuban, A. N.2002bIntensity of the microbiological processes of the methane cycle in different types of Baltic lakes98-104 Microbiology711Jan-Feb://000174112300013ISI:000174112300013?`)Larock, P. A. Hyun, J. H. Bennison, B. W.1994IBacterioplankton Growth and Production at the Louisiana Hydrocarbon Seeps104-109Geo-Marine Letters142-3Dec://A1994PZ71200006ISI:A1994PZ71200006 bӿ?bInagaki, Fumio Tsunogai, Urumu Suzuki, Masae Kosaka, Ayako Machiyama, Hideaki Takai, Ken Nunoura, Takuro Nealson, Kenneth H. Horikoshi, Koki2004Characterization of C1-Metabolizing Prokaryotic Communities in Methane Seep Habitats at the Kuroshima Knoll, Southern Ryukyu Arc, by Analyzing pmoA, mmoX, mxaF, mcrA, and 16S rRNA Genes 7445-7455Appl. Environ. Microbiol.7012December 1, 2004lSamples from three submerged sites (MC, a core obtained in the methane seep area; MR, a reference core obtained at a distance from the methane seep; and HC, a gas-bubbling carbonate sample) at the Kuroshima Knoll in the southern Ryuku arc were analyzed to gain insight into the organisms present and the processes involved in this oxic-anoxic methane seep environment. 16S rRNA gene analyses by quantitative real-time PCR and clone library sequencing revealed that the MC core sediments contained abundant archaea ([~]34% of the total prokaryotes), including both mesophilic methanogens related to the genus Methanolobus and ANME-2 members of the Methanosarcinales, as well as members of the {delta}-Proteobacteria, suggesting that both anaerobic methane oxidation and methanogenesis occurred at this site. In addition, several functional genes connected with methane metabolism were analyzed by quantitative competitive-PCR, including the genes encoding particulate methane monooxygenase (pmoA), soluble methane monooxygenase (mmoX), methanol dehydrogenese (mxaF), and methyl coenzyme M reductase (mcrA). In the MC core sediments, the most abundant gene was mcrA (2.5 x 106 copies/g [wet weight]), while the pmoA gene of the type I methanotrophs (5.9 x 106 copies/g [wet weight]) was most abundant at the surface of the MC core. These results indicate that there is a very complex environment in which methane production, anaerobic methane oxidation, and aerobic methane oxidation all occur in close proximity. The HC carbonate site was rich in {gamma}-Proteobacteria and had a high copy number of mxaF (7.1 x 106 copies/g [wet weight]) and a much lower copy number of the pmoA gene (3.2 x 102 copies/g [wet weight]). The mmoX gene was never detected. In contrast, the reference core contained familiar sequences of marine sedimentary archaeal and bacterial groups but not groups specific to C1 metabolism. Geochemical characterization of the amounts and isotopic composition of pore water methane and sulfate strongly supported the notion that in this zone both aerobic methane oxidation and anaerobic methane oxidation, as well as methanogenesis, occur.2http://aem.asm.org/cgi/content/abstract/70/12/7445Appl. Environ. Microbiol.L?c(Bidle, K. A. Kastner, M. Bartlett, D. H.1999A phylogenetic analysis of microbial communities associated with methane hydrate containing marine fluids and sediments in the Cascadia margin (ODP site 892B)101-108Fems Microbiology Letters1771Aug 1://000081777600015ISI:000081777600015ӿ?d7Glockner, Frank Oliver Fuchs, Bernhard M. Amann, Rudolf1999qBacterioplankton Compositions of Lakes and Oceans: a First Comparison Based on Fluorescence In Situ Hybridization 3721-3726Appl. Environ. Microbiol.658August 1, 19993Fluorescence in situ hybridization (FISH) with rRNA-targeted oligonucleotide probes was used to investigate the phylogenetic composition of bacterioplankton communities in several freshwater and marine samples. An average of about 50% of the cells were detected by probes for the domains Bacteria and Archaea, and of these, about half could be identified at the subdomain level with a set of group-specific probes. Beta subclass proteobacteria constituted a dominant fraction in freshwater systems, accounting for 16% (range, 3 to 32%) of the cells, although they were essentially absent in the marine samples examined. Members of the Cytophaga-Flavobacterium cluster were the most abundant group detected in the marine systems, accounting for 18% (range, 2 to 72%) of the 4',6-diamidino-2-phenylindole (DAPI) counts, and they were also important in freshwater systems (7%, range 0 to 18%). Furthermore, members of the alpha and gamma subclasses of Proteobacteria as well as members of the Planctomycetales were detected in both freshwater and marine water in abundances <7%.1http://aem.asm.org/cgi/content/abstract/65/8/3721Appl. Environ. Microbiol.+ۿ?e3Snaidr, J Amann, R Huber, I Ludwig, W Schleifer, KH1997PPhylogenetic analysis and in situ identification of bacteria in activated sludge 2884-2896Appl. Environ. Microbiol.637 July 1, 19971http://aem.asm.org/cgi/content/abstract/63/7/2884Appl. Environ. Microbiol.?fKelly, D. P. Murrell, J. C.1999,Microbial metabolism of methanesulfonic acid341-348Archives of Microbiology1726Dec://000083877800001ISI:0000838778000011?g1Ishii, K. Mussmann, M. MacGregor, B. J. Amann, R.2004zAn improved fluorescence in situ hybridization protocol for the identification of bacteria and archaea in marine sediments203-212Fems Microbiology Ecology503Nov 22://000225366900008ISI:000225366900008 Tӿ?hHKnittel, Katrin Losekann, Tina Boetius, Antje Kort, Renate Amann, Rudolf2005BDiversity and Distribution of Methanotrophic Archaea at Cold Seeps467-479Appl. Environ. Microbiol.711January 1, 2005 In this study we investigated by using 16S rRNA-based methods the distribution and biomass of archaea in samples from (i) sediments above outcropping methane hydrate at Hydrate Ridge (Cascadia margin off Oregon) and (ii) massive microbial mats enclosing carbonate reefs (Crimea area, Black Sea). The archaeal diversity was low in both locations; there were only four (Hydrate Ridge) and five (Black Sea) different phylogenetic clusters of sequences, most of which belonged to the methanotrophic archaea (ANME). ANME group 2 (ANME-2) sequences were the most abundant and diverse sequences at Hydrate Ridge, whereas ANME-1 sequences dominated the Black Sea mats. Other seep-specific sequences belonged to the newly defined group ANME-3 (related to Methanococcoides spp.) and to the Crenarchaeota of marine benthic group B. Quantitative analysis of the samples by fluorescence in situ hybridization (FISH) showed that ANME-1 and ANME-2 co-occurred at the cold seep sites investigated. At Hydrate Ridge the surface sediments were dominated by aggregates consisting of ANME-2 and members of the Desulfosarcina-Desulfococcus branch (DSS) (ANME-2/DSS aggregates), which accounted for >90% of the total cell biomass. The numbers of ANME-1 cells increased strongly with depth; these cells accounted 1% of all single cells at the surface and more than 30% of all single cells (5% of the total cells) in 7- to 10-cm sediment horizons that were directly above layers of gas hydrate. In the Black Sea microbial mats ANME-1 accounted for about 50% of all cells. ANME-2/DSS aggregates occurred in microenvironments within the mat but accounted for only 1% of the total cells. FISH probes for the ANME-2a and ANME-2c subclusters were designed based on a comparative 16S rRNA analysis. In Hydrate Ridge sediments ANME-2a/DSS and ANME-2c/DSS aggregates differed significantly in morphology and abundance. The relative abundance values for these subgroups were remarkably different at Beggiatoa sites (80% ANME-2a, 20% ANME-2c) and Calyptogena sites (20% ANME-2a, 80% ANME-2c), indicating that there was preferential selection of the groups in the two habitats. These variations in the distribution, diversity, and morphology of methanotrophic consortia are discussed with respect to the presence of microbial ecotypes, niche formation, and biogeography.0http://aem.asm.org/cgi/content/abstract/71/1/467Appl. Environ. Microbiol.F?iKMoran, James J. House, Christopher H. Freeman, Katherine H. Ferry, James G.2004QTrace methane oxidation studied in several Euryarchaeota under diverse conditions Archaea 11online?jAloisi, Giovanni Bouloubassi, Ioanna Heijs, Sander K. Pancost, Richard D. Pierre, Catherine Sinninghe Damste, Jaap S. Gottschal, Jan C. Forney, Larry J. Rouchy, Jean-Marie2002PCH4-consuming microorganisms and the formation of carbonate crusts at cold seeps195-203#Earth and Planetary Science Letters2031 2002/10/15_http://www.sciencedirect.com/science/article/B6V61-46TBBMG-4/2/6e002101c9cacaa000d03024b76e5821 TY - JOURd?kZKnittel, K. Boetius, A. Lemke, A. Eilers, H. Lochte, K. Pfannkuche, O. Linke, P. Amann, R.2003Activity, distribution, and diversity of sulfate reducers and other bacteria in sediments above gas hydrate (Cascadia margin, Oregon)269-294Geomicrobiology Journal204Jul-Aug://000184575800002ISI:000184575800002?lIversen, N. Blackburn, T. H.1981>Seasonal Rates of Methane Oxidation in Anoxic Marine-Sediments 1295-1300&Applied and Environmental Microbiology416://A1981LS99600002ISI:A1981LS996000021?nKallmeyer, J. Boetius, A.2004Effects of temperature and pressure on sulfate reduction and anaerobic oxidation of methane in hydrothermal sediments of Guaymas Basin 1231-1233&Applied and Environmental Microbiology702Feb://000188854900075ISI:000188854900075ۿ?p DeLong, EF1992&Archaea in Coastal Marine Environments 5685-5689PNAS8912 June 15, 19923http://www.pnas.org/cgi/content/abstract/89/12/5685PNASd׽?q4Chistoserdova, Ludmila Vorholt, Julia Lidstrom, Mary2005MA genomic view of methane oxidation by aerobic bacteria and anaerobic archaea208Genome Biology62dRecent sequencing of the genome and proteomic analysis of a model aerobic methanotrophic bacterium, Methylococcus capsulatus (Bath) has revealed a highly versatile metabolic potential. In parallel, environmental genomics has provided glimpses into anaerobic methane oxidation by certain archaea, further supporting the hypothesis of reverse methanogenesis.%http://genomebiology.com/2005/6/2/208 1465-6906Genome Biology?r(Arvidson, R. S. Morse, J. W. Joye, S. B.2004WThe sulfur biogeochemistry of chemosynthetic cold seep communities, Gulf of Mexico, USA97-119Marine Chemistry873-4Jul://000221581300003ISI:000221581300003 Iӿ?sWCasamayor, Emilio O. Schafer, Hendrik Baneras, Lluis Pedros-Alio, Carlos Muyzer, Gerard2000Identification of and Spatio-Temporal Differences between Microbial Assemblages from Two Neighboring Sulfurous Lakes: Comparison by Microscopy and Denaturing Gradient Gel Electrophoresis499-508Appl. Environ. Microbiol.662February 1, 2000 The microbial assemblages of Lake Ciso and Lake Vilar (Banyoles, northeast Spain) were analyzed in space and time by microscopy and by performing PCR-denaturing gradient gel electrophoresis (DGGE) and sequence analysis of 16S rRNA gene fragments. Samples obtained from different water depths and at two different times of the year (in the winter during holomixis and in the early spring during a phytoplankton bloom) were analyzed. Although the lakes have the same climatic conditions and the same water source, the limnological parameters were different, as were most of the morphologically distinguishable photosynthetic bacteria enumerated by microscopy. The phylogenetic affiliations of the predominant DGGE bands were inferred by performing a comparative 16S rRNA sequence analysis. Sequences obtained from Lake Ciso samples were related to gram-positive bacteria and to members of the division Proteobacteria. Sequences obtained from Lake Vilar samples were related to members of the Cytophaga-Flavobacterium-Bacteroides phylum and to cyanobacteria. Thus, we found that like the previously reported differences between morphologically distinct inhabitants of the two lakes, there were also differences among the community members whose morphologies did not differ conspicuously. The changes in the species composition from winter to spring were also marked. The two lakes both contained sequences belonging to phototrophic green sulfur bacteria, which is consistent with microscopic observations, but these sequences were different from the sequences of cultured strains previously isolated from the lakes. Euryarchaeal sequences (i.e., methanogen- and thermoplasma-related sequences) also were present in both lakes. These euryarchaeal group sequences dominated the archaeal sequences in Lake Ciso but not in Lake Vilar. In Lake Vilar, a new planktonic population related to the crenarchaeota produced the dominant archaeal band. The phylogenetic analysis indicated that new bacterial and archaeal lineages were present and that the microbial diversity of these assemblages was greater than previously known. We evaluated the correspondence between the abundances of several morphotypes and DGGE bands by comparing microscopy and sequencing results. Our data provide evidence that the sequences obtained from the DGGE fingerprints correspond to the microorganisms that are actually present at higher concentrations in the natural system.0http://aem.asm.org/cgi/content/abstract/66/2/499Appl. Environ. Microbiol.s?t2Watanabe, Kazuya Kodama, Yumiko Harayama, Shigeaki2001wDesign and evaluation of PCR primers to amplify bacterial 16S ribosomal DNA fragments used for community fingerprinting253-262"Journal of Microbiological Methods4432001/4/2_http://www.sciencedirect.com/science/article/B6T30-42G0M1Y-8/2/577eab17de3b1b3eccfade31668f1f4a TY - JOUR^?uFMarchesi, J. R. Weightman, A. J. Cragg, B. A. Parkes, R. J. Fry, J. C.2001Methanogen and bacterial diversity and distribution in deep gas hydrate sediments from the Cascadia Margin as revealed by 16S rRNA molecular analysis221-228Fems Microbiology Ecology343Jan://000166468400006ISI:000166468400006E?vYu, Z. T. Morrison, M.2004Comparisons of different hypervariable regions of rrs genes for use in fingerprinting of microbial communities by PCR-denaturing gradient gel electrophoresis 4800-4806&Applied and Environmental Microbiology708Aug://000223290100051ISI:000223290100051c?w Reeburgh, W S1982&Dynamic Environment of the Ocean Floor1982/// TY - GEN?xMartens, C S Berner, R A1977PInterstitial water chemistry of Long Island Sound sediments. I, Dissolved gases.10-25Limnol. Oceanogr.221977/// TY - JOUR?z)Alperin, M J Reeburgh, W S Whiticar, M J1988UCarbon and hydrogen isotope fractionation resulting from anaerobic methane oxidation.279-288Glob. Biochem. Cycles21988/// TY - JOUR?|,Hansen, L B Finster, K Fossing, H Iversen, N1998fAnaerobic methane oxidation in sulfate depleted sediments: effects of sulfate and molybdate additions.195-204Aquat. Microb. Ecol.141998/// TY - JOUR?~Suess, E1999Gas hydrate destabilization: enhanced dewatering, benthic material turnover and large methane plumes at the Cascadia convergent margin.1-5Earth Planet. Sci. Lett.1701999/// TY - JOUR?Linke, P1994PIn situ measurement of fluid flow from cold seeps at active continental margins.721-739 Deep Sea Res.411994/// TY - JOURF?+Bohrmann, G Linke, P Suess, P Pfannkuche, O2000-RV SONNE Cruise Report SO143: TECFLUX-I-1999. GEOMAR Rep.932000/// TY - JOUR?Aharon, P Fu, B2000Microbial sulfate reduction rates and sulfur and oxygen isotope fractionations at oil and gas seeps in deepwater Gulf of Mexico.233-246Geochim. Cosmochim. 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Treude, T. Boetius, A. Kruger, M.2005nEnvironmental regulation of the anaerobic oxidation of methane: a comparison of ANME-I and ANME-II communities98-106Environmental Microbiology71Jan://000225955800011ISI:000225955800011?WSchmidt, M. Hensen, C. Morz, T. Muller, C. Grevemeyer, I. Wallmann, K. Mau, S. Kaul, N.2005JMethane hydrate accumulation in "Mound 11" mud volcano, Costa Rica forearc83-100Marine Geology2161-2Mar 30://000228138900007ISI:000228138900007+?!Tsunogai, U. Yoshida, N. Gamo, T.2002Carbon isotopic evidence of methane oxidation through sulfate reduction in sediment beneath cold seep vents on the seafloor at Nankai Trough145-160Marine Geology1871-2Jul 20://000178093200008ISI:000178093200008?/Tsunogai, U. Yoshida, N. Ishibashi, J. Gamo, T.2000Carbon isotopic distribution of methane in deep-sea hydrothermal plume, Myojin Knoll Caldera, Izu-Bonin arc: Implications for microbial methane oxidation in the oceans and applications to heat flux estimation 2439-2452Geochimica Et Cosmochimica Acta6414Jul://000088021000007ISI:000088021000007??Madsen, Eugene L.2005\IDENTIFYING MICROORGANISMS RESPONSIBLE FOR ECOLOGICALLY SIGNIFICANT BIOGEOCHEMICAL PROCESSES439-446)Nature Reviews Microbiology Nat Rev Micro3510.1038/nrmicro11512005/05//print%http://dx.doi.org/10.1038/nrmicro1151TY - JOUR 10.1038/nrmicro1151 1740-1526?ELie, T. J. Pitta, T. Leadbetter, E. R. Godchaux, W. Leadbetter, J. R.1996=Sulfonates: Novel electron acceptors in anaerobic respiration204-210Archives of Microbiology1663Sep://A1996VH79400008ISI:A1996VH79400008?Cook, A. M. Denger, K.2002#Dissimilation of the C-2 sulfonates1-6Archives of Microbiology1791Dec://000180587500001ISI:000180587500001@?Mogensen, A. S. Ahring, B. K.2002Formation of metabolites during biodegradation of linear alkylbenzene sulfonate in an upflow anaerobic sludge bed reactor under thermophilic conditions483-488 Biotechnology and Bioengineering775Mar 5://000173839300001ISI:000173839300001 ?DeLong, Edward F.2005)MICROBIAL COMMUNITY GENOMICS IN THE OCEAN459-469)Nature Reviews Microbiology Nat Rev Micro3610.1038/nrmicro11582005/06//print%http://dx.doi.org/10.1038/nrmicro1158TY - JOUR 10.1038/nrmicro1158 1740-1526.?5Schleper, Christa Jurgens, German Jonuscheit, Melanie2005'GENOMIC STUDIES OF UNCULTIVATED ARCHAEA479-488)Nature Reviews Microbiology Nat Rev Micro3610.1038/nrmicro11592005/06//print%http://dx.doi.org/10.1038/nrmicro1159TY - JOUR 10.1038/nrmicro1159 1740-1526)?+Martens, C. S. Albert, D. B. Alperin, M. J.1999rStable isotope tracing of anaerobic methane oxidation in the gassy sediments of Eckernforde Bay, German Baltic Sea589-610American Journal of Science2997-9Sep-Nov://000084139100005ISI:000084139100005V?+Martens, C. S. Albert, D. B. Alperin, M. J.1998Biogeochemical processes controlling methane in gassy coastal sediments - Part 1. A model coupling organic matter flux to gas production, oxidation and transport 1741-1770Continental Shelf Research1814-15Dec://000077953300005ISI:000077953300005 ?Whiticar, M. J.2002Diagenetic relationships of methanogenesis, nutrients, acoustic turbidity, pockmarks and freshwater seepages in Eckernforde Bay29-53Marine Geology1821-2Apr 10://000175747000003ISI:000175747000003?@Treude, T. Boetius, A. Knittel, K. Wallmann, K. Jorgensen, B. B.2003TAnaerobic oxidation of methane above gas hydrates at Hydrate Ridge, NE Pacific Ocean1-14Marine Ecology-Progress Series264://000188586200001ISI:000188586200001*?2Treude, T. Kruger, M. Boetius, A. Jorgensen, B. B.2005qEnvironmental control on anaerobic oxidation of methane in the gassy sediments of Eckernforde Bay (German Baltic) 1771-1786Limnology And Oceanography506Nov://000233370600007 ISI:000233370600007<?dMeyerdierks, A. Kube, M. Lombardot, T. Knittel, K. Bauer, M. Glockner, F. O. Reinhardt, R. Amann, R.2005QInsights into the genomes of archaea mediating the anaerobic oxidation of methane 1937-1951Environmental Microbiology712Dec://000233313400009 ISI:000233313400009 ?9Kruger, M. Treude, T. Wolters, H. Nauhaus, K. Boetius, A.20057Microbial methane turnover in different marine habitats6-17/Palaeogeography Palaeoclimatology Palaeoecology2271-3Oct 28://000233028600002 ISI:000233028600002y?Savvichev, A. S. Rusanov,, II Rogozin, D. Y. Zakharova, E. E. Lunina, O. N. Bryantseva, I. A. Yusupov, S. K. Pimenov, N. V. Degermendzhi, A. G. Ivanov, M. V.2005aMicrobiological and isotopic-geochemical investigations of meromictic lakes in Khakasia in winter477-485 Microbiology744Jul-Aug://000232561700016 ISI:000232561700016??NLanoil, B. D. La Duc, M. T. Wright, M. Kastner, M. Nealson, K. H. Bartlett, D.2005kArchaeal diversity in ODP legacy borehole 892b and associated seawater and sediments of the Cascadia Margin167-177Fems Microbiology Ecology542Oct 1://000232428100001 ISI:000232428100001_??Scholten, J. C. M. Joye, S. B. Hollibaugh, J. T. Murrell, J. C.2005Molecular analysis of the sulfate reducing and archaeal community in a meromictic soda lake (Mono Lake, California) by targeting 16S rRNA, mcrA, apsA, and dsrAB genes29-39Microbial Ecology501Jul://000232267300004 ISI:000232267300004D?<Huguen, C. Mascle, J. Woodside, J. Zitter, T. Foucher, J. P.2005dMud volcanoes and mud domes of the Central Mediterranean Ridge: Near-bottom and in situ observations 1911-19316Deep-Sea Research Part I-Oceanographic Research Papers5210Oct://000232212200008 ISI:000232212200008/?+Heijs, S. K. Damste, J. S. S. Forney, L. 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Kaul, N.2005JMethane hydrate accumulation in "Mound 11" mud volcano, Costa Rica forearc83-100Marine Geology2161-2Mar 30://000228138900007 ISI:000228138900007F~?0Chistoserdova, L. Vorholt, J. A. Lidstrom, M. E.2005MA genomic view of methane oxidation by aerobic bacteria and anaerobic archaeaGenome Biology62://000227026500005 208ISI:000227026500005R?#Buhring, S. I. Elvert, M. Witte, U.2005The microbial community structure of different permeable sandy sediments characterized by the investigation of bacterial fatty acids and fluorescence in situ hybridization281-293Environmental Microbiology72Feb://000226376800014 ISI:000226376800014 ?7Knittel, K. Losekann, T. Boetius, A. Kort, R. 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Both the stable carbon isotopic composition of dissolved methane and the microbial community structure analyzed by fluorescent in situ hybridization provide strong evidence that microbially mediated methane oxidation occurs. At the shelf, strong isotope fractionation was observed above high-intensity seeps. This effect was attributed to bacterial type I and II methanotrophs, which on average accounted for 2.5% of the DAPI (4',6'-diamidino-2-phenylindole)-stained cells in the whole oxic water column. At deep sites, in the oxic-anoxic transition zone, strong isotopic fractionation of methane overlapped with an increased abundance of Archaea and Bacteria, indicating that these organisms are involved in the oxidation of methane. In underlying anoxic water, we successfully identified the archaeal methanotrophs ANME-1 and ANME-2, eachof which accounted for 3 to 4% of the total cell counts. 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