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Novel hydrocarbon monooxygenase genes in the metatranscriptome of a natural deep‐sea hydrocarbon plume

dc.contributor.authorLi, Mengen_US
dc.contributor.authorJain, Suniten_US
dc.contributor.authorBaker, Brett J.en_US
dc.contributor.authorTaylor, Chrisen_US
dc.contributor.authorDick, Gregory J.en_US
dc.date.accessioned2014-01-08T20:35:09Z
dc.date.available2015-03-02T14:35:35Zen_US
dc.date.issued2014-01en_US
dc.identifier.citationLi, Meng; Jain, Sunit; Baker, Brett J.; Taylor, Chris; Dick, Gregory J. (2014). "Novel hydrocarbon monooxygenase genes in the metatranscriptome of a natural deep‐sea hydrocarbon plume." Environmental Microbiology (1): 60-71.en_US
dc.identifier.issn1462-2912en_US
dc.identifier.issn1462-2920en_US
dc.identifier.urihttps://hdl.handle.net/2027.42/102241
dc.publisherWiley Periodicals, Inc.en_US
dc.publisherAGUen_US
dc.titleNovel hydrocarbon monooxygenase genes in the metatranscriptome of a natural deep‐sea hydrocarbon plumeen_US
dc.typeArticleen_US
dc.rights.robotsIndexNoFollowen_US
dc.subject.hlbsecondlevelMicrobiology and Immunologyen_US
dc.subject.hlbtoplevelScienceen_US
dc.description.peerreviewedPeer Revieweden_US
dc.description.bitstreamurlhttp://deepblue.lib.umich.edu/bitstream/2027.42/102241/1/emi12182.pdf
dc.identifier.doi10.1111/1462-2920.12182en_US
dc.identifier.sourceEnvironmental Microbiologyen_US
dc.identifier.citedreferenceSievers, F., Wilm, A., Dineen, D., Gibson, T.J., Karplus, K., Li, W., et al. ( 2011 ) Fast, scalable generation of high‐quality protein multiple sequence alignments using Clustal Omega. Mol Syst Biol 7: 539.en_US
dc.identifier.citedreferenceSvenning, M.M., Hestnes, A.G., Wartiainen, I., Stein, L.Y., Klotz, M.G., Kalyuzhnaya, M.G., et al. ( 2011 ) Genome sequence of the Arctic methanotroph Methylobacter tundripaludum SV96. J Bacteriol 193: 6418 – 6419.en_US
dc.identifier.citedreferenceSwan, B.K., Martinez‐Garcia, M., Preston, C.M., Sczyrba, A., Woyke, T., Lamy, D., et al. ( 2011 ) Potential for chemolithoautotrophy among ubiquitous bacteria lineages in the dark ocean. Science 333: 1296 – 1300.en_US
dc.identifier.citedreferenceTavormina, P.L., Ussler, W., 3rd., and Orphan, V.J. ( 2008 ) Planktonic and sediment‐associated aerobic methanotrophs in two seep systems along the North American margin. Appl Environ Microbiol 74: 3985 – 39895.en_US
dc.identifier.citedreferenceTavormina, P.L., Ussler, W., 3rd., Joye, S.B., Harrison, B.K., and Orphan, V.J. ( 2010 ) Distributions of putative aerobic methanotrophs in diverse pelagic marine environments. ISME J 4: 700 – 710.en_US
dc.identifier.citedreferenceTavormina, P.L., Orphan, V.J., Kalyuzhnaya, M.G., Jetten, M.S.M., and Klotz, M.G. ( 2011 ) A novel family of functional operons encoding methane/ammonia monooxygenase‐related proteins in gammaproteobacterial methanotrophs. Environ Microbiol Rep 3: 91 – 100.en_US
dc.identifier.citedreferenceTavormina, P.L., Ussler, W., 3rd, Steele, J.A., Connon, S.A., Klotz, M.G., and Orphan, V.J. ( 2013 ) Abundance and distribution of diverse membrane‐bound monooxygenase (Cu‐MMO) genes within the Costa Rica oxygen minimum zone. Environ Microbiol Rep 3: 414 – 423. doi: 10.1111/1758‐2229.12025.en_US
dc.identifier.citedreferenceTeske, A., Hinrichs, K.U., Edgcomb, V., de Vera Gomez, A., Kysela, D., Sylva, S.P., et al. ( 2002 ) Microbial diversity of hydrothermal sediments in the Guaymas Basin: evidence for anaerobic methanotrophic communities. Appl Environ Microbiol 68: 1994 – 2007.en_US
dc.identifier.citedreferenceTourna, M., Stieglmeier, M., Spang, A., Konneke, M., Schintlmeister, A., Urich, T., et al. ( 2011 ) Nitrososphaera viennensis, an ammonia oxidizing archaeon from soil. Proc Natl Acad Sci USA 108: 8420 – 8425.en_US
dc.identifier.citedreferenceValentine, D.L. ( 2010 ) Measure methane to quantify the oil spill. Nature 465: 421.en_US
dc.identifier.citedreferenceValentine, D.L. ( 2011 ) Emerging topics in marine methane biogeochemistry. Ann Rev Mar Sci 3: 147 – 171.en_US
dc.identifier.citedreferenceValentine, D.L., Kessler, J.D., Redmond, M.C., Mendes, S.D., Heintz, M.B., Farwell, C., et al. ( 2010 ) Propane respiration jump‐starts microbial response to a deep oil spill. Science 330: 208 – 211.en_US
dc.identifier.citedreferenceVondamm, K.L., Edmond, J.M., Measures, C.I., and Grant, B. ( 1985 ) Chemistry of submarine hydrothermal solutions at Guaymas Basin, Gulf of California. Geochim Cosmochim Acta 49: 2221 – 2237.en_US
dc.identifier.citedreferenceWard, N., Larsen, O., Sakwa, J., Bruseth, L., Khouri, H., Durkin, A.S., et al. ( 2004 ) Genomic insights into methanotrophy: the complete genome sequence of Methylococcus capsulatus (Bath). PLoS Biol 2: e303.en_US
dc.identifier.citedreferenceWasmund, K., Kurtboke, D.I., Burns, K.A., and Bourne, D.G. ( 2009 ) Microbial diversity in sediments associated with a shallow methane seep in the tropical Timor Sea of Australia reveals a novel aerobic methanotroph diversity. FEMS Microbiol Ecol 68: 142 – 151.en_US
dc.identifier.citedreferenceWelhan, J.A., and Lupton, J.E. ( 1987 ) Light hydrocarbon gases in Guaymas Basin hydrothermal fluids: thermogenic versus abiogenic orign. Am Assoc Pet Geol Bull 71: 215 – 223.en_US
dc.identifier.citedreferenceYan, T., Ye, Q., Zhou, J., and Zhang, C.L. ( 2006 ) Diversity of functional genes for methanotrophs in sediments associated with gas hydrates and hydrocarbon seeps in the Gulf of Mexico. FEMS Microbiol Ecol 57: 251 – 259.en_US
dc.identifier.citedreferenceZbinden, M., Shillito, B., Le Bris, N., De Villardi de Montlaur, C., Roussel, E., Guyot, F., et al. ( 2008 ) New insights on the metabolic diversity among the epibiotic microbial community of the hydrothermal shrimp Rimicaris exoculata. J Expe Mar Biol Ecol 359: 131 – 140.en_US
dc.identifier.citedreferenceZerbino, D.R., and Birney, E. ( 2008 ) Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18: 821 – 829.en_US
dc.identifier.citedreferenceAbascal, F., Zardoya, R., and Posada, D. ( 2005 ) ProtTest: selection of best‐fit models of protein evolution. Bioinformatics 21: 2104 – 2105.en_US
dc.identifier.citedreferenceArp, D.J., Chain, P.S.G., and Klotz, M.G. ( 2007 ) The impact of genome analyses on our understanding of ammonia‐oxidizing bacteria. Annu Rev Microbiol 61: 503 – 528.en_US
dc.identifier.citedreferenceBaani, M., and Liesack, W. ( 2008 ) Two isozymes of particulate methane monooxygenase with different methane oxidation kinetics are found in Methylocystis sp. strain SC2. Proc Natl Acad Sci USA 105: 10203 – 10208.en_US
dc.identifier.citedreferenceBaelum, J., Borglin, S., Chakraborty, R., Fortney, J.L., Lamendella, R., Mason, O.U., et al. ( 2012 ) Deep‐sea bacteria enriched by oil and dispersant from the Deepwater Horizon spill. Environ Microbiol 14: 2405 – 2416.en_US
dc.identifier.citedreferenceBaker, B.J., Lesniewski, R.A., and Dick, G.J. ( 2012 ) Genome‐enabled transcriptomics reveals archaeal populations that drive nitrification in deep‐sea hydrothermal plume. ISME J 6: 2269 – 2279.en_US
dc.identifier.citedreferenceBaker, B.J., Sheik, C.S., Taylor, C.A., Jain, S., Bhasi, A., Cavalcoli, J.D., et al. ( 2013 ) Community transcriptomic assembly reveals microbes that contribute to deep‐sea carbon and nitrogen cycling. ISME J. doi: 10.1038/ismej.2013.85. (in press).en_US
dc.identifier.citedreferenceBalasubramanian, R., Smith, S.M., Rawat, S., Yatsunyk, L.A., Stemmler, T.L., and Rosenzweig, A.C. ( 2010 ) Oxidation of methane by a biological dicopper centre. Nature 465: 115 – 119.en_US
dc.identifier.citedreferenceBeaulieu, S.E. ( 2010 ) InterRidge global database of active submarine hydrothermal vent fields: prepared for InterRidge, Version 2.0. World Wide Web electronic publication [WWW document]. URL http://www.interridge.org/IRvents.en_US
dc.identifier.citedreferencevan Beilen, J.B., and Funhoff, E.G. ( 2007 ) Alkane hydroxylases involved in microbial alkane degradation. Appl Microbiol Biotechnol 74: 13 – 21.en_US
dc.identifier.citedreferencevan Beilen, J.B., Li, Z., Duetz, W.A., Smits, T.H.M., and Witholt, B. ( 2003 ) Diversity of alkane hydroxylase systems in the environment. Oil Gas Sci Technol 58: 427 – 440.en_US
dc.identifier.citedreferenceBerger, S.A., Krompaß, D., and Stamatakis, A. ( 2011 ) Performance, accuracy and web‐server for evolutionary placement of short sequence reads under maximum‐likelihood. Syst Biol 60: 291 – 302.en_US
dc.identifier.citedreferenceBerube, P.M., and Stahl, D.A. ( 2012 ) The divergent AmoC3 subunit of ammonia monooxygenase functions as part of a stress response system in Nitrosomonas europaea. J Bacteriol 194: 3448 – 3456.en_US
dc.identifier.citedreferenceBiddle, J.F., Cardman, Z., Mendlovitz, H., Albert, D.B., Lloyd, K.G., Boetius, A., et al. ( 2011 ) Anaerobic oxidation of methane at different temperature regimes in Guaymas Basin hydrothermal sediments. ISME J 5: 1 – 14.en_US
dc.identifier.citedreferenceBoden, R., Cunliffe, M., Scanlan, J., Moussard, H., Kits, K.D., Klotz, M.G., et al. ( 2011 ) Complete genome sequence of the aerobic marine methanotroph Methylomonas methanica MC09. J Bacteriol 193: 7001 – 7002.en_US
dc.identifier.citedreferenceCampbell, K.A. ( 2006 ) Hydrocarbon seep and hydrothermal vent paleoenvironments and paleontology: past developments and future research directions. Palaeogeogr Palaeoclimatol Palaeoecol 232: 362 – 407.en_US
dc.identifier.citedreferenceCapella‐Gutierrez, S., Silla‐Martinez, J.M., and Gabaldon, T. ( 2009 ) TrimAl: a tool for automated alignment trimming in large‐scale phylogenetic analyses. Bioinformatics 25: 1972 – 1973.en_US
dc.identifier.citedreferenceChen, Y., Crombie, A., Rahman, M.T., Dedysh, S.N., Liesack, W., Stott, M.B., et al. ( 2010 ) Complete genome sequence of the aerobic facultative methanotroph Methylocella silvestris BL2. J Bacteriol 192: 3840 – 3841.en_US
dc.identifier.citedreferenceChevreux, B., Pfisterer, T., Drescher, B., Driesel, A.J., Muller, W.E.G., Wetter, T., et al. ( 2004 ) Using the miraEST assembler for reliable and automated mRNA transcript assembly and SNP detection in sequenced ESTs. Genome Res 14: 1147 – 1159.en_US
dc.identifier.citedreferenceChistoserdova, L. ( 2011 ) Modularity of methylotrophy, revisited. Environ Microbiol 13: 2603 – 2622.en_US
dc.identifier.citedreferenceColeman, N.V., Yau, S., Wilson, N.L., Nolan, L.M., Migocki, M.D., Ly, M.A., et al. ( 2011 ) Untangling the multiple monooxygenases of Mycobacterium chubuense strain NBB4, a versatile hydrocarbon degrader. Environ Microbiol 3: 297 – 307.en_US
dc.identifier.citedreferenceColeman, N.V., Le, N.B., Ly, M.A., Ogawa, H.E., McCarl, V., Wilson, N.L., et al. ( 2012 ) Hydrocarbon monooxygenase in Mycobacterium: recombinant expression of a member of the ammonia monooxygenase superfamily. ISME J 6: 171 – 182.en_US
dc.identifier.citedreferenceCostello, A.M., and Lidstrom, M.E. ( 1999 ) Molecular characterization of functional and phylogenetic genes from natural populations of methanotrophs in lake sediments. Appl Environ Microbiol 65: 5066 – 5074.en_US
dc.identifier.citedreferenceCrépeau, V., Cambon Bonavita, M.A., Lesongeur, F., Randrianalivelo, H., Sarradin, P.M., Sarrazin, J., et al. ( 2011 ) Diversity and function in microbial mats from the Lucky Strike hydrothermal vent field. FEMS Microbiol Ecol 76: 524 – 540.en_US
dc.identifier.citedreferenceDeSantis, T.Z., Hugenholtz, P., Jr, Keller, K., Brodie, E.L., Larsen, N., Piceno, Y.M., et al. ( 2006 ) NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes. Nucleic Acids Res 34: W394 – W399.en_US
dc.identifier.citedreferenceDick, G.J., and Tebo, B.M. ( 2010 ) Microbial diversity and biogeochemistry of the Guaymas Basin deep‐sea hydrothermal plume. Environ Microbiol 12: 1334 – 1347.en_US
dc.identifier.citedreferenceDick, G.J., Clement, B.G., Webb, S.M., Fodrie, F.J., Bargar, J.R., and Tebo, B.M. ( 2009 ) Enzymatic microbial Mn(II) oxidation and Mn biooxide production in the Guaymas Basin deep‐sea hydrothermal plume. Geochim Cosmochim Acta 73: 6517 – 6530.en_US
dc.identifier.citedreferenceDunfield, P.F., Yimga, M.T., Dedysh, S.N., Berger, U., Liesack, W., and Heyer, J. ( 2002 ) Isolation of a Methylocystis strain containing a novel pmoA ‐like gene. FEMS Microbiol Ecol 41: 17 – 26.en_US
dc.identifier.citedreferenceDunfield, P.F., Yuryev, A., Senin, P., Smirnova, A.V., Stott, M.B., Hou, S., et al. ( 2007 ) Methane oxidation by an extremely acidophilic bacterium of the phylum Verrucomicrobia. Nature 450: 879 – 882.en_US
dc.identifier.citedreferenceDuperron, S., Sibuet, M., MacGregor, B.J., Kuypers, M.M., Fisher, C.R., and Dubilier, N. ( 2007 ) Diversity, relative abundance and metabolic potential of bacterial endosymbionts in three Bathymodiolus mussel species from cold seeps in the Gulf of Mexico. Environ Microbiol 9: 1423 – 1438.en_US
dc.identifier.citedreferenceElsaied, H.E., Hayashi, T., and Naganuma, T. ( 2004 ) Molecular analysis of deep‐sea hydrothermal vent aerobic methanotrophs by targeting genes of 16S rRNA and particulate methane monooxygenase. Mar Biotechnol 6: 503 – 509.en_US
dc.identifier.citedreferenceErikstad, H.A., Jensen, S., Keen, T.J., and Birkeland, N.K. ( 2012 ) Differential expression of particulate methane monooxygenase genes in the verrucomicrobial methanotroph ‘Methylacidiphilum kamchatkense’ Kam1. Extremophiles 16: 405 – 409.en_US
dc.identifier.citedreferenceEttwig, K.F., Butler, M.K., Le Paslier, D., Pelletier, E., Mangenot, S., Kuypers, M.M., et al. ( 2010 ) Nitrite‐driven anaerobic methane oxidation by oxygenic bacteria. Nature 464: 543 – 548.en_US
dc.identifier.citedreferenceFrancis, C.A., Roberts, K.J., Beman, J.M., Santoro, A.E., and Oakley, B.B. ( 2005 ) Ubiquity and diversity of ammonia‐oxidizing archaea in water columns and sediments of the ocean. Proc Natl Acad Sci USA 102: 14683 – 14688.en_US
dc.identifier.citedreferenceFrias‐Lopez, J., Shi, Y., Tyson, G.W., Coleman, M.L., Schuster, S.C., Chisholm, S.W., et al. ( 2008 ) Microbial community gene expression in ocean surface waters. Proc Natl Acad Sci USA 105: 3805 – 3810.en_US
dc.identifier.citedreferenceGilbert, J.A., and Dupont, C.L. ( 2011 ) Microbial metagenomics: beyond the genome. Ann Rev Mar Sci 3: 347 – 371.en_US
dc.identifier.citedreferenceGilbert, J.A., Field, D., Huang, Y., Edwards, R., Li, W.Z., Gilna, P., et al. ( 2008 ) Detection of large numbers of novel sequences in the metatranscriptomes of complex marine microbial communities. PLoS One 3: e3042.en_US
dc.identifier.citedreferenceHamamura, N., and Arp, D.J. ( 2000 ) Isolation and characterization of alkane‐utilizing Nocardioides sp. strain CF8. FEMS Microbiol Lett 186: 21 – 26.en_US
dc.identifier.citedreferenceHamamura, N., Storfa, R.T., Semprini, L., and Arp, D.J. ( 1999 ) Diversity in butane monooxygenases among butane‐grown bacteria. Appl Environ Microbiol 65: 4586 – 4593.en_US
dc.identifier.citedreferenceHamamura, N., Yeager, C.M., and Arp, D.J. ( 2001 ) Two distinct monooxygenases for alkane oxidation in Nocardioides sp. strain CF8. Appl Environ Microbiol 67: 4992 – 4998.en_US
dc.identifier.citedreferenceHanson, R.S., and Hanson, T.E. ( 1996 ) Methanotrophic bacteria. Microbiol Rev 60: 439 – 471.en_US
dc.identifier.citedreferenceHavelsrud, O.E., Haverkamp, T.H., Kristensen, T., Jakobsen, K.S., and Rike, A.G. ( 2011 ) A metagenomic study of methanotrophic microorganisms in Coal Oil Point seep sediments. BMC Microbiol 11: 221.en_US
dc.identifier.citedreferenceHayashi, T., Obata, H., Gamo, T., Sano, Y., and Naganuma, T. ( 2007 ) Distribution and phylogenetic characteristics of the genes encoding enzymes relevant to methane oxidation in oxygen minimum zones of the eastern Pacific Ocean. J Environ Sci 1: 275 – 284.en_US
dc.identifier.citedreferenceHou, S., Makarova, K.S., Saw, J.H., Senin, P., Ly, B.V., Zhou, Z., et al. ( 2008 ) Complete genome sequence of the extremely acidophilic methanotroph isolate V4, Methylacidiphilum infernorum, a representative of the bacterial phylum Verrucomicrobia. Biol Direct 3: 26.en_US
dc.identifier.citedreferenceHuang, X.Q., and Miller, W. ( 1991 ) A time‐efficient, linear‐space local similarity algorithm. Adv Appl Math 12: 337 – 357.en_US
dc.identifier.citedreferenceInagaki, F., Tsunogai, U., Suzuki, M., Kosaka, A., Machiyama, H., Takai, K., et al. ( 2004 ) Characterization 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. Appl Environ Microbiol 70: 7445 – 7455.en_US
dc.identifier.citedreferenceKessler, J.D., Valentine, D.L., Redmond, M.C., Du, M., Chan, E.W., Mendes, S.D., et al. ( 2011 ) A persistent oxygen anomaly reveals the fate of spilled methane in the deep Gulf of Mexico. Science 331: 312 – 315.en_US
dc.identifier.citedreferenceKönneke, M., Bernhard, A.E., Torre, J.R., Walker, C.B., Waterbury, J.B., and Stahl, D.A. ( 2005 ) Isolation of an autotrophic ammonia‐oxidizing marine archaeon. Nature 437: 543 – 546.en_US
dc.identifier.citedreferenceLam, P. ( 2004 ) Microbial ammonia oxidation in deep‐sea hydrothermal plumes. PhD Thesis. Hawaii, USA: University of Hawaii.en_US
dc.identifier.citedreferenceLangmead, B., Trapnell, C., Pop, M., and Salzberg, S.L. ( 2009 ) Ultrafast and memory‐efficient alignment of short DNA sequences to the human genome. Genome Biol 10: R25.en_US
dc.identifier.citedreferenceLesniewski, R.A., Jain, S., Anantharaman, K., Schloss, P.D., and Dick, G.J. ( 2012 ) The metatranscriptome of a deep‐sea hydrothermal plume is dominated by water column methanotrophs and chemolithotrophs. ISME J 6: 2257 – 2268.en_US
dc.identifier.citedreferenceLieberman, R.L., and Rosenzweig, A.C. ( 2005 ) Crystal structure of a membrane‐bound metalloenzyme that catalyses the biological oxidation of methane. Nature 434: 177 – 182.en_US
dc.identifier.citedreferenceLudwig, W., Strunk, O., Westram, R., Richter, L., Meier, H., Yadhukumar, et al. ( 2004 ) ARB: a software environment for sequence data. Nucleic Acids Res 32: 1363 – 1371.en_US
dc.identifier.citedreferenceLüke, C., and Frenzel, P. ( 2011 ) Potential of pmoA amplicon pyrosequencing for methanotroph diversity studies. Appl Environ Microbiol 77: 6305 – 6309.en_US
dc.identifier.citedreferenceMcCollom, T. ( 2008 ) Observational, experimental, and theoretical constraints on carbon cycling in mid‐ocean ridge hydrothermal systems. In Geophysical Monograph Series. Vol. 178. Lowell, R.P., Seewald, J.S., Metaxas, A., and Perfit, M. (eds). Washington, DC, USA: AGU, pp. 193 – 213.en_US
dc.identifier.citedreferenceMcDonald, I.R., Bodrossy, L., Chen, Y., and Murrell, J.C. ( 2008 ) Molecular ecology techniques for the study of aerobic methanotrophs. Appl Environ Microbiol 74: 1305 – 1315.en_US
dc.identifier.citedreferenceMason, O.U., Hazen, T.C., Borglin, S., Chain, P., Dubinsky, E.A., Fortney, J.L., et al. ( 2012 ) Metagenome, metatranscriptome and single‐cell sequencing reveal microbial response to Deepwater Horizon oil spill. ISME J 6: 1715 – 1727.en_US
dc.identifier.citedreferenceMilkov, A.V., Sassen, R., Apanasovich, T.V., and Dadashev, F.G. ( 2003 ) Global gas flux from mud volcanoes: a significant source of fossil methane in the atmosphere and the ocean. Geophys Res Lett 30: 1037. doi: 10.1029/2002GL016358.en_US
dc.identifier.citedreferenceMuyzer, G., and van der Kraan, G.M. ( 2008 ) Bacteria from hydrocarbon seep areas growing on short‐chain alkanes. Trends Microbiol 16: 138 – 141.en_US
dc.identifier.citedreferenceNercessian, O., Fouquet, Y., Pierre, C., Prieur, D., and Jeanthon, C. ( 2005 ) Diversity of Bacteria and Archaea associated with a carbonate‐rich metalliferous sediment sample from the Rainbow vent field on the Mid‐Atlantic Ridge. Environ Microbiol 7: 698 – 714.en_US
dc.identifier.citedreferenceNorton, J.M., Alzerreca, J.J., Suwa, Y., and Klotz, M.G. ( 2002 ) Diversity of ammonia monooxygenase operon in autotrophic ammonia‐oxidizing bacteria. Arch Microbiol 177: 139 – 149.en_US
dc.identifier.citedreferencePol, A., Heijmans, K., Harhangi, H.R., Tedesco, D., Jetten, M.S., and Op den Camp, H.J. ( 2007 ) Methanotrophy below pH 1 by a new Verrucomicrobia species. Nature 450: 874 – 878.en_US
dc.identifier.citedreferenceRaggi, L., Schubtz, F., Hinrichs, K.U., Dubilier, N., and Petersen, J.M. ( 2012 ) Bacterial symbionts of Bathymodiolus mussels and Escarpia tubeworms from Chapopote, an asphalt seep in the southern Gulf of Mexico. Environ Microbiol. doi: 10.1111/1462‐2920.12051 (in press).en_US
dc.identifier.citedreferenceRedmond, M.C., Valentine, D.L., and Sessions, A.L. ( 2010 ) Identification of novel methane‐, ethane‐, and propane‐oxidizing bacteria at marine hydrocarbon seeps by stable isotope probing. Appl Environ Microbiol 76: 6412 – 6422.en_US
dc.identifier.citedreferenceReed, A.J., Dorn, R., van Dover, C.L., Lutz, R.A., and Vetriani, C. ( 2009 ) Phylogenetic diversity of methanogenic, sulfate‐reducing and methanotrophic prokaryotes from deep‐sea hydrothermal vents and cold seeps. Deep‐Sea Res Part II 56: 1665 – 1674.en_US
dc.identifier.citedreferenceRobinson, J.T., Thorvaldsdottir, H., Winckler, W., Guttman, M., Lander, E.S., Getz, G., et al. ( 2011 ) Integrative genomics viewer. Nat Biotechnol 29: 24 – 26.en_US
dc.identifier.citedreferenceSayavedra‐Soto, L.A., Hamamura, N., Liu, C.W., Kimbrel, J.A., Chang, J.H., and Arp, D.J. ( 2011 ) The membrane‐associated monooxygenase in the butane‐oxidizing Gram‐positive bacterium Nocardioides sp. strain CF8 is a novel member of the AMO/PMO family. Environ Microbiol Rep 3: 390 – 396.en_US
dc.identifier.citedreferenceSchloss, P.D., Westcott, S.L., Ryabin, T., Hall, J.R., Hartmann, M., Hollister, E.B., et al. ( 2009 ) Introducing mothur: open‐source, platform‐independent, community‐supported software for describing and comparing microbial communities. Appl Environ Microbiol 75: 7537 – 7541.en_US
dc.identifier.citedreferenceSchulz, M.H., Zerbino, D.R., Vingron, M., and Birney, E. ( 2012 ) Oases: robust de novo RNA‐seq assembly across the dynamic range of expression levels. Bioinformatics 28: 1086 – 1092.en_US
dc.identifier.citedreferenceSheik, C.S., Jain, S., and Dick, G.J. ( 2013 ) Metabolic flexibility of enigmatic SAR324 revealed through metagenomics and metatranscriptomics. Environ Microbiol. doi: 10.1111/1462‐2920.12165. (in press).en_US
dc.identifier.citedreferenceShi, Y., Tyson, G.W., Eppley, J.M., and DeLong, E.F. ( 2011 ) Integrated metatranscriptomic and metagenomic analyses of stratified microbial assemblages in the open ocean. ISME J 5: 999 – 1013.en_US
dc.identifier.citedreferenceSpiridonova, E.M., Kuznetsov, B.B., Pimenov, N.V., and Tourova, T.P. ( 2006 ) Phylogenetic characterization of endosymbionts of the hydrothermal vent mussel Bathymodiolus azoricus by analysis of the 16S rRNA, cbbL, and pmoA genes. Microbiology 75: 694 – 701.en_US
dc.identifier.citedreferenceStamatakis, A. ( 2006 ) RAxML‐VI‐HPC: maximum likelihood‐based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22: 2688 – 2690.en_US
dc.identifier.citedreferenceStein, L.Y., Bringel, F., DiSpirito, A.A., Han, S., Jetten, M.S., Kalyuzhnaya, M.G., et al. ( 2011 ) Genome sequence of the methanotrophic alphaproteobacterium Methylocystis sp. strain Rockwell (ATCC 49242). J Bacteriol 193: 2668 – 2669.en_US
dc.identifier.citedreferenceStoecker, K., Bendinger, B., Schoning, B., Nielsen, P.H., Nielsen, J.L., Baranyi, C., et al. ( 2006 ) Cohn's Crenothrix is a filamentous methane oxidizer with an unusual methane monooxygenase. Proc Natl Acad Sci USA 103: 2363 – 2367.en_US
dc.identifier.citedreferenceStolyar, S., Costello, A.M., Peeples, T.L., and Lidstrom, M.E. ( 1999 ) Role of multiple gene copies in particulate methane monooxygenase activity in the methane‐oxidizing bacterium Methylococcus capsulatus Bath. Microbiology 145: 1235 – 1244.en_US
dc.identifier.citedreferenceSuzuki, T., Nakamura, T., and Fuse, H. ( 2012 ) Isolation of two novel marine ethylene‐assimilating bacteria, Haliea Species ETY‐M and ETY‐NAG, containing particulate methane monooxygenase‐like genes. Microbes Environ 27: 54 – 60.en_US
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