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Volumn 15, Issue 1, 2014, Pages

Metagenomics reveals that detoxification systems are underrepresented in marine bacterial communities

Author keywords

Detoxification; Ecotoxicology; Global ocean sampling; Marine; Metagenomics; Oxidative stress; Toxic metals

Indexed keywords

BACTERIA (MICROORGANISMS);

EID: 84908068903     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-15-749     Document Type: Article
Times cited : (24)

References (50)
  • 1
    • 33747353951 scopus 로고    scopus 로고
    • Arsenic and selenium in microbial metabolism
    • 16704340
    • Stolz JF, Basu P, Santini JM, Oremland RS. Arsenic and selenium in microbial metabolism. Annu Rev Microbiol 2006, 60:107-130. 10.1146/annurev.micro.60.080805.142053, 16704340.
    • (2006) Annu Rev Microbiol , vol.60 , pp. 107-130
    • Stolz, J.F.1    Basu, P.2    Santini, J.M.3    Oremland, R.S.4
  • 2
    • 77954623707 scopus 로고    scopus 로고
    • Complications with remediation strategies involving the biodegradation and detoxification of recalcitrant contaminant aromatic hydrocarbons
    • 20542318
    • Frenzel M, Scarlett A, Rowland SJ, Galloway TS, Burton SK, Lappin-Scott HM, Booth AM. Complications with remediation strategies involving the biodegradation and detoxification of recalcitrant contaminant aromatic hydrocarbons. Sci Total Environ 2010, 408:4093-4101. 10.1016/j.scitotenv.2010.04.042, 20542318.
    • (2010) Sci Total Environ , vol.408 , pp. 4093-4101
    • Frenzel, M.1    Scarlett, A.2    Rowland, S.J.3    Galloway, T.S.4    Burton, S.K.5    Lappin-Scott, H.M.6    Booth, A.M.7
  • 3
    • 0028946084 scopus 로고
    • Phylogenetic identification and in situ detection of individual microbial cells without cultivation
    • 239358, 7535888
    • Amann RI, Ludwig W, Schleifer KH. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 1995, 59:143-169. 239358, 7535888.
    • (1995) Microbiol Rev , vol.59 , pp. 143-169
    • Amann, R.I.1    Ludwig, W.2    Schleifer, K.H.3
  • 4
    • 33947226782 scopus 로고    scopus 로고
    • Structural and functional diversity of the microbial kinome
    • 1821047, 17355172
    • Kannan N, Taylor SS, Zhai Y, Venter JC, Manning G. Structural and functional diversity of the microbial kinome. PLoS Biol 2007, 5:e17. 10.1371/journal.pbio.0050017, 1821047, 17355172.
    • (2007) PLoS Biol , vol.5 , pp. e17
    • Kannan, N.1    Taylor, S.S.2    Zhai, Y.3    Venter, J.C.4    Manning, G.5
  • 5
    • 58149505604 scopus 로고    scopus 로고
    • Discovering functional novelty in metagenomes: examples from light-mediated processes
    • 2612456, 18849420
    • Singh AH, Doerks T, Letunic I, Raes J, Bork P. Discovering functional novelty in metagenomes: examples from light-mediated processes. J Bacteriol 2009, 191:32-41. 10.1128/JB.01084-08, 2612456, 18849420.
    • (2009) J Bacteriol , vol.191 , pp. 32-41
    • Singh, A.H.1    Doerks, T.2    Letunic, I.3    Raes, J.4    Bork, P.5
  • 6
    • 84887212381 scopus 로고    scopus 로고
    • Biogeography of photosynthetic light-harvesting genes in marine phytoplankton
    • 2644788, 19240807
    • Bibby TS, Zhang Y, Chen M. Biogeography of photosynthetic light-harvesting genes in marine phytoplankton. PLoS ONE 2009, 4:e4601. 10.1371/journal.pone.0004601, 2644788, 19240807.
    • (2009) PLoS ONE , vol.4 , pp. e4601
    • Bibby, T.S.1    Zhang, Y.2    Chen, M.3
  • 7
    • 84875045322 scopus 로고    scopus 로고
    • Ecogenomic perspectives on domains of unknown function: correlation-based exploration of marine metagenomes
    • 3597751, 23516388
    • Buttigieg PL, Hankeln W, Kostadinov I, Kottmann R, Yilmaz P, Duhaime MB, Glöckner FO. Ecogenomic perspectives on domains of unknown function: correlation-based exploration of marine metagenomes. PLoS ONE 2013, 8:e50869. 10.1371/journal.pone.0050869, 3597751, 23516388.
    • (2013) PLoS ONE , vol.8 , pp. e50869
    • Buttigieg, P.L.1    Hankeln, W.2    Kostadinov, I.3    Kottmann, R.4    Yilmaz, P.5    Duhaime, M.B.6    Glöckner, F.O.7
  • 9
    • 79951882096 scopus 로고    scopus 로고
    • Pyrosequencing of antibiotic-contaminated river sediments reveals high levels of resistance and gene transfer elements
    • 3040208, 21359229
    • Kristiansson E, Fick J, Janzon A, Grabic R, Rutgersson C, Weijdegård B, Söderström H, Larsson DGJ. Pyrosequencing of antibiotic-contaminated river sediments reveals high levels of resistance and gene transfer elements. PLoS ONE 2011, 6:e17038. 10.1371/journal.pone.0017038, 3040208, 21359229.
    • (2011) PLoS ONE , vol.6 , pp. e17038
    • Kristiansson, E.1    Fick, J.2    Janzon, A.3    Grabic, R.4    Rutgersson, C.5    Weijdegård, B.6    Söderström, H.7    Larsson, D.G.J.8
  • 15
    • 84949130073 scopus 로고    scopus 로고
    • HMMER
    • Eddy S. HMMER. [http://hmmer.janelia.org/].
    • Eddy, S.1
  • 17
    • 33845986334 scopus 로고    scopus 로고
    • Exploring genomic dark matter: a critical assessment of the performance of homology search methods on noncoding RNA
    • 1716261, 17151342
    • Freyhult EK, Bollback JP, Gardner PP. Exploring genomic dark matter: a critical assessment of the performance of homology search methods on noncoding RNA. Genome Res 2007, 17:117-125. 1716261, 17151342.
    • (2007) Genome Res , vol.17 , pp. 117-125
    • Freyhult, E.K.1    Bollback, J.P.2    Gardner, P.P.3
  • 20
    • 72749084211 scopus 로고    scopus 로고
    • An atlas of the thioredoxin fold class reveals the complexity of function-enabling adaptations
    • 2757866, 19851441
    • Atkinson HJ, Babbitt PC. An atlas of the thioredoxin fold class reveals the complexity of function-enabling adaptations. PLoS Comput Biol 2009, 5:e1000541. 10.1371/journal.pcbi.1000541, 2757866, 19851441.
    • (2009) PLoS Comput Biol , vol.5 , pp. e1000541
    • Atkinson, H.J.1    Babbitt, P.C.2
  • 21
    • 33744784298 scopus 로고    scopus 로고
    • An application of statistics to comparative metagenomics
    • 1473205, 16549025
    • Rodriguez-Brito B, Rohwer F, Edwards RA. An application of statistics to comparative metagenomics. BMC Bioinformatics 2006, 7:162. 10.1186/1471-2105-7-162, 1473205, 16549025.
    • (2006) BMC Bioinformatics , vol.7 , pp. 162
    • Rodriguez-Brito, B.1    Rohwer, F.2    Edwards, R.A.3
  • 22
    • 70349993601 scopus 로고    scopus 로고
    • ShotgunFunctionalizeR: an R-package for functional comparison of metagenomes
    • 19696045
    • Kristiansson E, Hugenholtz P, Dalevi D. ShotgunFunctionalizeR: an R-package for functional comparison of metagenomes. Bioinformatics 2009, 25:2737-2738. 10.1093/bioinformatics/btp508, 19696045.
    • (2009) Bioinformatics , vol.25 , pp. 2737-2738
    • Kristiansson, E.1    Hugenholtz, P.2    Dalevi, D.3
  • 23
    • 71749111168 scopus 로고    scopus 로고
    • Analysis and comparison of very large metagenomes with fast clustering and functional annotation
    • 2774329, 19863816
    • Li W. Analysis and comparison of very large metagenomes with fast clustering and functional annotation. BMC Bioinformatics 2009, 10:359. 10.1186/1471-2105-10-359, 2774329, 19863816.
    • (2009) BMC Bioinformatics , vol.10 , pp. 359
    • Li, W.1
  • 26
    • 57349122987 scopus 로고    scopus 로고
    • Comparative genomics of two ecotypes of the marine planktonic copiotroph Alteromonas macleodii suggests alternative lifestyles associated with different kinds of particulate organic matter
    • 18670397
    • Ivars-Martinez E, Martín-Cuadrado A-B, D'Auria G, Mira A, Ferriera S, Johnson J, Friedman R, Rodríguez-Valera F. Comparative genomics of two ecotypes of the marine planktonic copiotroph Alteromonas macleodii suggests alternative lifestyles associated with different kinds of particulate organic matter. ISME J 2008, 2:1194-1212. 10.1038/ismej.2008.74, 18670397.
    • (2008) ISME J , vol.2 , pp. 1194-1212
    • Ivars-Martinez, E.1    Martín-Cuadrado, A.-B.2    D'Auria, G.3    Mira, A.4    Ferriera, S.5    Johnson, J.6    Friedman, R.7    Rodríguez-Valera, F.8
  • 27
    • 79251649939 scopus 로고    scopus 로고
    • Characterization of cyanate metabolism in marine Synechococcus and Prochlorococcus spp
    • 3019706, 21057026
    • Kamennaya NA, Post AF. Characterization of cyanate metabolism in marine Synechococcus and Prochlorococcus spp. Appl Environ Microbiol 2011, 77:291-301. 10.1128/AEM.01272-10, 3019706, 21057026.
    • (2011) Appl Environ Microbiol , vol.77 , pp. 291-301
    • Kamennaya, N.A.1    Post, A.F.2
  • 31
    • 33947215475 scopus 로고    scopus 로고
    • CAMERA: a community resource for metagenomics
    • 1821059, 17355175
    • Seshadri R, Kravitz SA, Smarr L, Gilna P, Frazier M. CAMERA: a community resource for metagenomics. PLoS Biol 2007, 5:e75. 10.1371/journal.pbio.0050075, 1821059, 17355175.
    • (2007) PLoS Biol , vol.5 , pp. e75
    • Seshadri, R.1    Kravitz, S.A.2    Smarr, L.3    Gilna, P.4    Frazier, M.5
  • 32
    • 19144362371 scopus 로고    scopus 로고
    • Microbial community genomics in the ocean
    • 15886695
    • Delong EF. Microbial community genomics in the ocean. Nat Rev Microbiol 2005, 3:459-469. 10.1038/nrmicro1158, 15886695.
    • (2005) Nat Rev Microbiol , vol.3 , pp. 459-469
    • Delong, E.F.1
  • 33
    • 77954227260 scopus 로고    scopus 로고
    • Analysis of membrane proteins in metagenomics: networks of correlated environmental features and protein families
    • 2892097, 20430783
    • Patel PV, Gianoulis TA, Bjornson RD, Yip KY, Engelman DM, Gerstein MB. Analysis of membrane proteins in metagenomics: networks of correlated environmental features and protein families. Genome Res 2010, 20:960-971. 10.1101/gr.102814.109, 2892097, 20430783.
    • (2010) Genome Res , vol.20 , pp. 960-971
    • Patel, P.V.1    Gianoulis, T.A.2    Bjornson, R.D.3    Yip, K.Y.4    Engelman, D.M.5    Gerstein, M.B.6
  • 35
    • 0026773382 scopus 로고
    • Amplification and rearrangement of a prokaryotic metallothionein locus smt in Synechococcus PCC 6301 selected for tolerance to cadmium
    • 1354365
    • Gupta A, Whitton BA, Morby AP, Huckle JW, Robinson NJ. Amplification and rearrangement of a prokaryotic metallothionein locus smt in Synechococcus PCC 6301 selected for tolerance to cadmium. Proc Biol Sci 1992, 248:273-281. 10.1098/rspb.1992.0072, 1354365.
    • (1992) Proc Biol Sci , vol.248 , pp. 273-281
    • Gupta, A.1    Whitton, B.A.2    Morby, A.P.3    Huckle, J.W.4    Robinson, N.J.5
  • 38
    • 79958071293 scopus 로고    scopus 로고
    • Metagenomics and the protein universe
    • 3118404, 21497084
    • Godzik A. Metagenomics and the protein universe. Curr Opin Struct Biol 2011, 21:398-403. 10.1016/j.sbi.2011.03.010, 3118404, 21497084.
    • (2011) Curr Opin Struct Biol , vol.21 , pp. 398-403
    • Godzik, A.1
  • 39
    • 33645220455 scopus 로고    scopus 로고
    • Oxidative stress in marine environments: biochemistry and physiological ecology
    • 16460273
    • Lesser MP. Oxidative stress in marine environments: biochemistry and physiological ecology. Annu Rev Physiol 2006, 68:253-278. 10.1146/annurev.physiol.68.040104.110001, 16460273.
    • (2006) Annu Rev Physiol , vol.68 , pp. 253-278
    • Lesser, M.P.1
  • 40
    • 67650859628 scopus 로고    scopus 로고
    • Occurrence, phylogeny, structure, and function of catalases and peroxidases in cyanobacteria
    • 19129167
    • Bernroitner M, Zamocky M, Furtmüller PG, Peschek GA, Obinger C. Occurrence, phylogeny, structure, and function of catalases and peroxidases in cyanobacteria. J Exp Bot 2009, 60:423-440. 10.1093/jxb/ern309, 19129167.
    • (2009) J Exp Bot , vol.60 , pp. 423-440
    • Bernroitner, M.1    Zamocky, M.2    Furtmüller, P.G.3    Peschek, G.A.4    Obinger, C.5
  • 41
    • 84864611407 scopus 로고    scopus 로고
    • Molecular evolution of hydrogen peroxide degrading enzymes
    • 3523812, 22330759
    • Zamocky M, Gasselhuber B, Furtmüller PG, Obinger C. Molecular evolution of hydrogen peroxide degrading enzymes. Arch Biochem Biophys 2012, 525:131-144. 10.1016/j.abb.2012.01.017, 3523812, 22330759.
    • (2012) Arch Biochem Biophys , vol.525 , pp. 131-144
    • Zamocky, M.1    Gasselhuber, B.2    Furtmüller, P.G.3    Obinger, C.4
  • 43
    • 84870854383 scopus 로고    scopus 로고
    • Cyanobacterial toxins: biosynthetic routes and evolutionary roots
    • 23051004
    • Dittmann E, Fewer DP, Neilan BA. Cyanobacterial toxins: biosynthetic routes and evolutionary roots. FEMS Microbiol Rev 2013, 37:23-43. 10.1111/j.1574-6976.2012.12000.x, 23051004.
    • (2013) FEMS Microbiol Rev , vol.37 , pp. 23-43
    • Dittmann, E.1    Fewer, D.P.2    Neilan, B.A.3
  • 44
    • 77955299705 scopus 로고    scopus 로고
    • Neurotoxic alkaloids: saxitoxin and its analogs
    • 2920551, 20714432
    • Wiese M, D'Agostino PM, Mihali TK, Moffitt MC, Neilan BA. Neurotoxic alkaloids: saxitoxin and its analogs. Mar Drugs 2010, 8:2185-2211. 10.3390/md8072185, 2920551, 20714432.
    • (2010) Mar Drugs , vol.8 , pp. 2185-2211
    • Wiese, M.1    D'Agostino, P.M.2    Mihali, T.K.3    Moffitt, M.C.4    Neilan, B.A.5
  • 45
    • 0033968660 scopus 로고    scopus 로고
    • Cyanobacterial cell walls: news from an unusual prokaryotic envelope
    • 94402, 10671437
    • Hoiczyk E, Hansel A. Cyanobacterial cell walls: news from an unusual prokaryotic envelope. J Bacteriol 2000, 182:1191-1199. 10.1128/JB.182.5.1191-1199.2000, 94402, 10671437.
    • (2000) J Bacteriol , vol.182 , pp. 1191-1199
    • Hoiczyk, E.1    Hansel, A.2
  • 46
    • 57749084589 scopus 로고    scopus 로고
    • A new family of cyanobacterial penicillin-binding proteins. A missing link in the evolution of class A beta-lactamases
    • 18801739
    • Urbach C, Fastrez J, Soumillion P. A new family of cyanobacterial penicillin-binding proteins. A missing link in the evolution of class A beta-lactamases. J Biol Chem 2008, 283:32516-32526. 10.1074/jbc.M805375200, 18801739.
    • (2008) J Biol Chem , vol.283 , pp. 32516-32526
    • Urbach, C.1    Fastrez, J.2    Soumillion, P.3
  • 47
    • 79961135005 scopus 로고    scopus 로고
    • Vienna, Austria: R Foundation for Statistical Computing
    • R Development Core Team R: a Language and Environment for Statistical Computing 2011, Vienna, Austria: R Foundation for Statistical Computing, R Development Core Team.
    • (2011) R: a Language and Environment for Statistical Computing
  • 48
    • 0242281980 scopus 로고    scopus 로고
    • Bioconductor R packages for exploratory analysis and normalization of cDNA microarray data
    • New York: Springer, Parmingiani G, Garrett ES, Irizarry RA, Zeger SL
    • Dudoit S, Yang YH. Bioconductor R packages for exploratory analysis and normalization of cDNA microarray data. The Analysis of Gene Expression Data: Methods and Software 2002, New York: Springer, Parmingiani G, Garrett ES, Irizarry RA, Zeger SL.
    • (2002) The Analysis of Gene Expression Data: Methods and Software
    • Dudoit, S.1    Yang, Y.H.2
  • 49
    • 84855739893 scopus 로고    scopus 로고
    • Another Multidimensional Analysis Package
    • Lucas A. Another Multidimensional Analysis Package. [http://CRAN.R-project.org/package=amap].
    • Lucas, A.1


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