Show simple item record

Metabolic flexibility of enigmatic SAR 324 revealed through metagenomics and metatranscriptomics

dc.contributor.authorSheik, Cody S.en_US
dc.contributor.authorJain, Suniten_US
dc.contributor.authorDick, Gregory J.en_US
dc.date.accessioned2014-01-08T20:34:51Z
dc.date.available2015-03-02T14:35:35Zen_US
dc.date.issued2014-01en_US
dc.identifier.citationSheik, Cody S.; Jain, Sunit; Dick, Gregory J. (2014). "Metabolic flexibility of enigmatic SAR 324 revealed through metagenomics and metatranscriptomics." Environmental Microbiology (1): 304-317.en_US
dc.identifier.issn1462-2912en_US
dc.identifier.issn1462-2920en_US
dc.identifier.urihttps://hdl.handle.net/2027.42/102166
dc.publisherWiley Periodicals, Inc.en_US
dc.titleMetabolic flexibility of enigmatic SAR 324 revealed through metagenomics and metatranscriptomicsen_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/2027.42/102166/1/emi12165.pdf
dc.description.bitstreamurlhttp://deepblue.lib.umich.edu/bitstream/2027.42/102166/2/emi12165-sup-0001-figure.pdf
dc.description.bitstreamurlhttp://deepblue.lib.umich.edu/bitstream/2027.42/102166/3/emi12165-sup-0002-table.pdf
dc.identifier.doi10.1111/1462-2920.12165en_US
dc.identifier.sourceEnvironmental Microbiologyen_US
dc.identifier.citedreferenceSayavedra‐Soto, L.A., Hamamura, N., Lui, C., 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.citedreferenceSorokin, D.Y. ( 2003 ) Oxidation of inorganic sulfur compounds by obligately organotrophic bacteria. Microbiology 72: 641 – 653.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.citedreferenceStamatakis, A., Hoover, P., and Rougemont, J. ( 2008 ) A rapid bootstrap algorithm for the RAxML web servers. Syst Biol 57: 758 – 771.en_US
dc.identifier.citedreferenceStockdreher, Y., Venceslau, S.S., Josten, M., Sahl, H., Pereira, I.A.C., and Dahl, C. ( 2012 ) Bacterium Allochromatium vinosum: evidence for sulfur transfer from DsrEFH to DsrC. PloS ONE.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.citedreferenceThauer, R.K., Jungerman, K., and Decker, K. ( 1977 ) Energy conservation in chemotrophic anaerobic bacteria. Bacteriol Rev 41: 100 – 180.en_US
dc.identifier.citedreferenceThorvaldsdóttir, H., Robinson, J., and Mesirov, J. ( 2013 ) Integrative Genomics Viewer (IGV): high‐performance genomics data visualization and exploration. Brief Bioinform 14: 178 – 192.en_US
dc.identifier.citedreferenceToner, B.M., Fakra, S.C., Manganini, S.J., Santelli, C.M., Marcus, M.A., Moffett, J.W., et al. ( 2009 ) Preservation of iron(II) by carbon‐rich matrices in a hydrothermal plume. Nat Geosci 2: 197 – 201.en_US
dc.identifier.citedreferenceVon Damm, 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.citedreferenceWalsh, D., Zaikova, E., Howes, C., Song, Y., Wright, J., Tringe, S., et al. ( 2009 ) Metagenome of a versatile chemolithoautotroph from expanding oceanic dead zones. Science 326: 578 – 582.en_US
dc.identifier.citedreferenceWelhan, J., and Lupton, J. ( 1987 ) Light hydrocarbon gases in Guaymas Basin hydrothermal fluids: thermogenic versus abiogenic origin. Am Assoc Petr Geol B 71: 215 – 223.en_US
dc.identifier.citedreferenceWinn, C.D., Karl, D.M., and Massoth, G.J. ( 1986 ) Microorganisms in deep‐sea hydrothermal plumes. Nature 320: 744 – 746.en_US
dc.identifier.citedreferenceWright, J., Konwar, K., and Hallam, S. ( 2012 ) Microbial ecology of expanding oxygen minimum zones. Nat Rev Microbiol 10: 381 – 475.en_US
dc.identifier.citedreferenceWright, T.D., Vergin, K.L., Boyd, P.W., and Giovannoni, S.J. ( 1997 ) A novel delta‐subdivision proteobacterial lineage from the lower ocean surface layer. Appl Environ Microb 63: 1441 – 1448.en_US
dc.identifier.citedreferenceZaikova, E., Walsh, D., Stilwell, C., Mohn, W., Tortell, P., and Hallam, S. ( 2010 ) Microbial community dynamics in a seasonally anoxic fjord: Saanich Inlet, British Columbia. Environ Microbiol 12: 172 – 191.en_US
dc.identifier.citedreferenceAnantharaman, K., Breier, J.A., Sheik, C.S., and Dick, G.J. ( 2013 ) Evidence for hydrogen oxidation and metabolic plasticity in widespread deep‐sea sulfur‐oxidizing bacteria. Proc Natl Acad Sci USA 110: 330 – 335.en_US
dc.identifier.citedreferenceArÍstegui, J., Gasol, J.M., Duarte, C.M., and Herndl, G.J. ( 2009 ) Microbial oceanography of the dark ocean's pelagic realm. Limnol Oceanogr 54: 1501 – 1529.en_US
dc.identifier.citedreferenceBadger, M.R., and Bek, E.J. ( 2008 ) Multiple Rubisco forms in proteobacteria: their functional significance in relation to CO2 acquisition by the CBB cycle. J Exp Bot 59: 1525 – 1541.en_US
dc.identifier.citedreferenceBaker, B.A., Lesniewski, R.A., and Dick, G.J. ( 2012 ) Genome‐enabled transcriptomics reveals archaeal populations that drive nitrification in a 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., and Dick, G.J. ( 2013 ) Community transcriptomic assembly reveals microbes that contribute to deep‐sea carbon and nitrogen cycling. ISME J 1–12. doi: 10.1038/ismej.2013.85en_US
dc.identifier.citedreferenceBrown, M.V., and Donachie, S.P. ( 2007 ) Evidence for tropical endemicity in the Deltaproteobacteria marine group B/SAR324 bacterioplankton clade. Aquat Microb Ecol 46: 107 – 115.en_US
dc.identifier.citedreferenceChevreux, B., Wetter, T., and Suhai, S. ( 1999 ) Genome sequence assembly using trace signals and additional sequence information. German Conference on Bioinformatics GCB'99 GCB. Comput Sci Biol Proc 45 – 56.en_US
dc.identifier.citedreferenceChistoserdova, L. ( 2011 ) Modularity of methylotrophy, revisited. Environ Microbiol 13: 2603 – 2622.en_US
dc.identifier.citedreferenceChistoserdova, L., Laukel, M., Portais, J., Vorholt, J.A., and Lindstrom, M.E. ( 2004 ) Multiple formate dehydrogenase enzymes in the facultative methylotrophy Methylobacterium extorquens AM1 are dispensable for growth on methanol. J Bacteriol 186: 22 – 28.en_US
dc.identifier.citedreferenceChitsaz, H., Yee‐Greenbaum, J.L., Tesler, G., Lombardo, M.J., Dupont, C.L., Badger, J.H., et al. ( 2011 ) Efficient de novo assembly of single‐cell bacterial genomes from short‐read data sets. Nat Biotechnol 29: 915 – 921.en_US
dc.identifier.citedreferenceColeman, N.V., Yau, S., WIlson, N.L., Nolan, L.M., Migocki, M.D., Ly, M., et al. ( 2011 ) Untangling the mulitple monooxygenases of Mycobacterium chubuense strain NBB4, a versatile hydrocarbon degrader. Environ Microbiol Rep 3: 297 – 307.en_US
dc.identifier.citedreferenceDeLong, E.F., Preston, C.M., Mincer, T., Rich, V., Hallam, S.J., Frigaard, N.‐U., et al. ( 2006 ) Community genomics among stratified microbial assemblages in the ocean's interior. Science 311: 496 – 503.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., Podell, S., Johnson, H.A., Rivera‐Espinoza, Y., Bernier‐Latmani, R., McCarthy, J.K., et al. ( 2008 ) Genomic insights into Mn(II) oxidation by the marine alphaproteobacterium Aurantimonas sp. strain SI85‐9A1. Appl Environ Microb 74: 2646 – 2658.en_US
dc.identifier.citedreferenceDick, G.J., Clement, B.G., Webb, S.M., Fodrie, F.J., Bargar, J.R., and Tebo, B.M. ( 2009a ) 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.citedreferenceDick, G.J., Andersson, A.F., Baker, B.J., Simmons, S.L., Thomas, B.C., Yelton, A.P., and Banfield, J.F. ( 2009b ) Community‐wide analysis of microbial genome sequence signatures. Genome Biol 10: R85.en_US
dc.identifier.citedreferenceDick, G.J., Anantharaman, K., Baker, B.J., Li, M., Reed, D.C., and Sheik, C.S. ( 2013 ) The microbiology of deep‐sea hydrothermal vent plumes: ecological and biogeographic linkages to seafloor and water column habitats. Front Ext Microbiol 4: 1 – 16.en_US
dc.identifier.citedreferenceEdgar, R.C. ( 2004 ) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32: 1792 – 1797.en_US
dc.identifier.citedreferenceFalkenby, L., Szymanska, M., Holkenbrink, C., Habicht, K., Andersen, J., Miller, M., and Frigaard, N.‐U. ( 2011 ) Quantitative proteomics of Chlorobaculum tepidum: insights into the sulfur metabolism of a phototrophic green sulfur bacterium. FEMS Microbiol Lett 323: 142 – 150.en_US
dc.identifier.citedreferenceFrias‐Lopez, J., Shi, Y., Tyson, G.W., Coleman, M.L., Schuster, S.C., Chisholm, S.W., and DeLong, E.F. ( 2008 ) Microbial community gene expression in ocean surface waters. Proc Natl Acad Sci USA 105: 3805 – 3810.en_US
dc.identifier.citedreferenceFuchsman, C.A., Kirkpatrick, J.B., Brazelton, W.J., Murray, J.W., and Staley, J.T. ( 2011 ) Metabolic strategies of free‐living and aggregate‐associated bacterial communities inferred from biologic and chemical profiles in the Black Sea suboxic zone. FEMS Microbiol Ecol 78: 586 – 603.en_US
dc.identifier.citedreferenceGerman, C., Bowen, A., Coleman, M., Honig, D., Huber, J., Jakuba, M., et al. ( 2010 ) Diverse styles of submarine venting on the ultraslow spreading Mid‐Cayman Rise. Proc Natl Acad Sci USA 107: 14020 – 14025.en_US
dc.identifier.citedreferenceGhiglione, J.‐F., Galand, P., Pommier, T., Pedrós‐Alió, C., Maas, E., Bakker, K., et al. ( 2012 ) Pole‐to‐pole biogeography of surface and deep marine bacterial communities. Proc Natl Acad Sci USA 109: 17633 – 17638.en_US
dc.identifier.citedreferenceGreene, E., Hubert, C., Nemati, M., Jenneman, G., and Voordouw, G. ( 2003 ) Nitrite reductase activity of sulphate‐reducing bacteria prevents their inhibition by nitrate‐reducing, sulphide‐oxidizing bacteria. Environ Microbiol 5: 607 – 617.en_US
dc.identifier.citedreferenceHensen, D., Sperling, D., Trüper, H.G., Brune, D.C., and Dahl, C. ( 2006 ) Thiosulphate oxidation in the phototrophic sulphur bacterium Allochromatium vinosum. Mol Microbiol 62: 794 – 810.en_US
dc.identifier.citedreferenceHolden, J., Breier, J., Rogers, K., Schulte, M., and Toner, B. ( 2012 ) Biogeochemical processes at hydrothermal vents: microbes and minerals, bioenergetics, and carbon fluxes. Oceanography 25: 196 – 208.en_US
dc.identifier.citedreferenceHügler, M., and Sievert, S.M. ( 2011 ) Beyond the Calvin cycle: autotrophic carbon fixation in the ocean. Annu Rev Mar Sci 3: 261 – 289.en_US
dc.identifier.citedreferenceJannasch, H.W., and Mottl, M.J. ( 1985 ) Geomicrobiology of deep‐sea hydrothermal vents. Science 229: 717 – 725.en_US
dc.identifier.citedreferenceKarl, D.M., Wirsen, C.O., and Jannasch, H.W. ( 1980 ) Deep‐sea primary production at the Galapagos hydrothermal vents. Science 207: 1345 – 1347.en_US
dc.identifier.citedreferenceKarl, D.M., Knauer, G.A., Martin, J.H., and Ward, B.B. ( 1984 ) Bacterial chemolithotrophy in the ocean is associated with sinking particles. Nature 309: 54 – 56.en_US
dc.identifier.citedreferenceLang, S.Q., Butterfield, D.A., Schulte, M., Kelley, D.S., and Lilley, M.D. ( 2010 ) Elevated concentrations of formate, acetate and dissolved organic carbon found at the Lost City hydrothermal field. Geochim Cosmochim Acta 74: 941 – 952.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 lithotrophs. ISME J 6: 1 – 11.en_US
dc.identifier.citedreferenceLi, H., and Durbin, R. ( 2009 ) Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25: 1754 – 1760.en_US
dc.identifier.citedreferenceLi, H., and Durbin, R. ( 2010 ) Fast and accurate long‐read alignment with Burrows‐Wheeler transform. Bioinformatics 26: 589 – 595.en_US
dc.identifier.citedreferenceLi, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., et al. ( 2009 ) The Sequence Alignment/Map format and SAMtools. Bioinformatics 25: 2078 – 2079.en_US
dc.identifier.citedreferenceLi, M., Jain, S., Baker, B.J., Taylor, C., and Dick, G.J. ( 2013 ) Novel hydrocarbon monooxygenase genes in the metatranscriptome of a natural deep‐sea hydrocarbon plume. Environ Microbiol. doi: 10.1111/1462‐2920.12182.en_US
dc.identifier.citedreferenceLilley, M.D., de Angelis, M.A., and Gordon, L.I. ( 1982 ) CH 4, H 2, CO and N 2 O in submarine hydrothermal vent waters. Nature 300: 48 – 50.en_US
dc.identifier.citedreferenceLoy, A., Duller, S., Baranyi, C., Mussmann, M., Ott, J., Sharon, I., et al. ( 2009 ) Reverse dissimilatory sulfite reductase as phylogenetic marker for a subgroup of sulfur‐oxidizing prokaryotes. Environ Microbiol 11: 289 – 299.en_US
dc.identifier.citedreferenceLudwig, W., Strunk, O., Westram, R., Richter, L., Meier, H., and Yadhukumar, B.A. ( 2004 ) ARB: a software environment for sequence data. Nucleic Acids Res 32: 1363 – 1371.en_US
dc.identifier.citedreferenceMartens, C.S. ( 1990 ) Generation of short chain acid anions in hydrothermally altered sediments of the Guaymas Basin, Gulf of California. Appl Geochem 5: 71 – 76.en_US
dc.identifier.citedreferenceMartin, H.G., Ivanova, N., Kunin, V., Warnecke, F., Barry, K.W., McHardy, A.C., et al. ( 2006 ) Metagenomic analysis of two enhanced biological phosphorus removal (EBPR) sludge communities. Nat Biotechnol 24: 1263 – 1269.en_US
dc.identifier.citedreferenceMeyer, B., and Kuever, J. ( 2007 ) Phylogeny of the alpha and beta subunits of the dissimilatory adenosine‐5′‐phosphosulfate (APS) reductase from sulfate‐reducing prokaryotes–origin and evolution of the dissimilatory sulfate‐reduction pathway. Microbiology 153: 2026 – 2044.en_US
dc.identifier.citedreferenceMoran, M.A., Buchan, A., Gonzalez, J.M., Heidelberg, J.F., Whitman, W.B., Kiene, R.P., et al. ( 2004 ) Genome sequence of Silicibacter pomeroyi reveals adaptations to the marine environment. Nature 432: 910 – 913.en_US
dc.identifier.citedreferenceMoran, M.A., Satinsky, B., Gifford, S.M., Luo, H., Rivers, A., Chan, L.K., et al. ( 2013 ) Sizing up metatranscriptomics. ISME J 7: 237 – 243.en_US
dc.identifier.citedreferenceMussmann, M., Richter, M., Lombardot, T., Meyerdierks, A., Kuever, J., et al. ( 2005 ) Clustered genes related to sulfate respiration in uncultured prokaryotes support the theory of their concomitant horizontal transfer. J Bacteriol 187: 7126 – 7137.en_US
dc.identifier.citedreferenceOrcutt, B.N., Sylvan, J.B., Knab, N.J., and Edwards, K.J. ( 2011 ) Microbial ecology of the dark ocean above, at, and below the seafloor. Microbiol Mol Bio Rev 75: 361 – 422.en_US
dc.identifier.citedreferencePenn, K., Wu, D., Eisen, J., and Ward, N. ( 2006 ) Characterization of bacterial communities associated with deep‐sea corals on Gulf of Alaska seamounts. Appl Environ Microb 72: 1680 – 1683.en_US
dc.identifier.citedreferencePereira, I.A., Ramos, A.R., Grein, F., Marques, M.C., da Silva, S.M., and Venceslau, S.S. ( 2011 ) A comparative genomic analysis of energy metabolism in sulfate reducing bacteria and archaea. Front Microbiol 2: 69, 1 – 22.en_US
dc.identifier.citedreferencePham, V.D., Konstantinidis, K.T., Palden, T., and DeLong, E.F. ( 2008 ) Phylogenetic analyses of ribosomal DNA‐containing bacterioplankton genome fragments from a 4000 m vertical profile in the North Pacific Subtropical Gyre. Environ Microbiol 10: 2313 – 2330.en_US
dc.identifier.citedreferencePott, A.S., and Dahl, C. ( 1998 ) Sirohaem sulfite reductase and other proteins encoded by genes at the DSR locus of Chromatium vinosum are involved in the oxidation of intracellular sulfur. Microbiology 144: 1881 – 1894.en_US
dc.identifier.citedreferencePruesse, E., Quast, C., Knittel, K., Fuchs, B.M., Ludwig, W., Peplies, J., and Glockner, F.O. ( 2007 ) SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res 35: 7188 – 7196.en_US
dc.identifier.citedreferenceReinthaler, T., and Van, H. ( 2010 ) Major contribution of autotrophy to microbial carbon cycling in the deep North Atlantic's interior. Deep‐Sea Res PT II 57: 1572 – 1580.en_US
dc.identifier.citedreferenceRich, V.I., Pham, V.D., Eppley, J., Shi, Y., and DeLong, E.F. ( 2011 ) Time‐series analyses of Monterey Bay coastal microbial picoplankton using a ‘genome proxy’ microarray. Environ Microbiol 13: 116 – 134.en_US
dc.identifier.citedreferenceShi, Y., Tyson, G.W., and DeLong, E.F. ( 2009 ) Metatranscriptomics reveals unique microbial small RNAs in the ocean's water column. Nature 459: 266 – 269.en_US
dc.owningcollnameInterdisciplinary and Peer-Reviewed


Files in this item

Show simple item record

Remediation of Harmful Language

The University of Michigan Library aims to describe library materials in a way that respects the people and communities who create, use, and are represented in our collections. Report harmful or offensive language in catalog records, finding aids, or elsewhere in our collections anonymously through our metadata feedback form. More information at Remediation of Harmful Language.

Accessibility

If you are unable to use this file in its current format, please select the Contact Us link and we can modify it to make it more accessible to you.