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Volumn 9, Issue 4, 2014, Pages

Bioinformatic approaches reveal metagenomic characterization of soil microbial community

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BIODIVERSITY; BIOINFORMATICS; DESERT; FOREST; GRASSLAND; HIGH THROUGHPUT SEQUENCING; MANGROVE; METAGENOME; METAGENOMICS; MICROBIAL COMMUNITY; MICROBIOME; NONHUMAN; ORGANISMAL INTERACTION; PHYLOGENY; SOIL; SOIL MICROFLORA; BIOLOGY; ECOSYSTEM; METABOLOMICS; MICROBIOLOGY; PROCEDURES;

EID: 84898638322     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0093445     Document Type: Article
Times cited : (64)

References (53)
  • 1
    • 19144366982 scopus 로고    scopus 로고
    • The metagenomics of soil
    • DOI 10.1038/nrmicro1160
    • Daniel R (2005) The metagenomics of soi (Pubitemid 40716173)
    • (2005) Nature Reviews Microbiology , vol.3 , Issue.6 , pp. 470-478
    • Daniel, R.1
  • 4
    • 0036270789 scopus 로고    scopus 로고
    • Microbial diversity and function in soil: From genes to ecosystems
    • DOI 10.1016/S1369-5274(02)00324-7
    • Torsvik V, Øvreås L (2002) Microbial diversity and function in soil: from genes to ecosystems. Curr Opin Microbiol 5: 240-245. (Pubitemid 34614934)
    • (2002) Current Opinion in Microbiology , vol.5 , Issue.3 , pp. 240-245
    • Torsvik, V.1    Ovreas, L.2
  • 5
    • 0032863699 scopus 로고    scopus 로고
    • Construction of environmental DNA libraries in Escherichia coli and screening for the presence of genes conferring utilization of 4-hydroxybutyrate
    • Henne A, Daniel R, Schmitz RA, Gottschalk G (1999) Construction of environmental DNA libraries in Escherichia coli and screening for the presence of genes conferring utilization of 4-hydroxybutyrate. Appl Environ Microbiol 65: 3901-3907.
    • (1999) Appl Environ Microbiol , vol.65 , pp. 3901-3907
    • Henne, A.1    Daniel, R.2    Schmitz, R.A.3    Gottschalk, G.4
  • 7
    • 84859911168 scopus 로고    scopus 로고
    • Comparative metagenomic, phylogenetic and physiological analyses of soil microbial communities across nitrogen gradients
    • Fierer N, Lauber CL, Ramirez KS, Zaneveld J, Bradford MA, et al. (2012) Comparative metagenomic, phylogenetic and physiological analyses of soil microbial communities across nitrogen gradients. ISME J 6: 1007-1017.
    • (2012) ISME J , vol.6 , pp. 1007-1017
    • Fierer, N.1    Lauber, C.L.2    Ramirez, K.S.3    Zaneveld, J.4    Bradford, M.A.5
  • 8
    • 84855949949 scopus 로고    scopus 로고
    • Using network analysis to explore co-occurrence patterns in soil microbial communities
    • Barberán A, Bates ST, Casamayor EO, Fierer N (2012) Using network analysis to explore co-occurrence patterns in soil microbial communities. ISME J. 6: 343-351.
    • (2012) ISME J. , vol.6 , pp. 343-351
    • Barberán, A.1    Bates, S.T.2    Casamayor, E.O.3    Fierer, N.4
  • 9
    • 77952431173 scopus 로고    scopus 로고
    • Strategies for enhancing the effectiveness of metagenomic based enzyme discovery in lignocellulolytic microbial communities
    • De Angelis KM, Gladden JM, Allgaier M, Dhaeseleer P, Fortney JL, et al. (2010) Strategies for enhancing the effectiveness of metagenomic based enzyme discovery in lignocellulolytic microbial communities. Bioenerg Res 3: 146-158.
    • (2010) Bioenerg Res , vol.3 , pp. 146-158
    • De Angelis, K.M.1    Gladden, J.M.2    Allgaier, M.3    Dhaeseleer, P.4    Fortney, J.L.5
  • 10
    • 84865344067 scopus 로고    scopus 로고
    • Structure, fluctuation and magnitude of a natural grassland soil metagenome
    • Delmont TO, Prestat E, Keegan KP, Faubladier M, Robe P, et al. (2012) Structure, fluctuation and magnitude of a natural grassland soil metagenome. ISME J 6: 1677-1687.
    • (2012) ISME J , vol.6 , pp. 1677-1687
    • Delmont, T.O.1    Prestat, E.2    Keegan, K.P.3    Faubladier, M.4    Robe, P.5
  • 11
    • 79953112264 scopus 로고    scopus 로고
    • Community transcriptomics reveals universal patterns of protein sequence conservation in natural microbial communities
    • Stewart FJ, Sharma AK, Bryant JA, Eppley JM, DeLong EF. (2011) Community transcriptomics reveals universal patterns of protein sequence conservation in natural microbial communities. Genome Biol 12: R26.
    • (2011) Genome Biol , vol.12
    • Stewart, F.J.1    Sharma, A.K.2    Bryant, J.A.3    Eppley, J.M.4    Delong, E.F.5
  • 12
    • 84871826193 scopus 로고    scopus 로고
    • Cross-biome metagenomic analyses of soil microbial communities and their functional attributes
    • Fierer N, Leff JW, Adams BJ, Nielsen UN, Bates ST, et al. (2012) Cross-biome metagenomic analyses of soil microbial communities and their functional attributes. Proc Natl Acad Sci U S A 109: 21390-21395.
    • (2012) Proc Natl Acad Sci U S A , vol.109 , pp. 21390-21395
    • Fierer, N.1    Leff, J.W.2    Adams, B.J.3    Nielsen, U.N.4    Bates, S.T.5
  • 13
    • 84855714036 scopus 로고    scopus 로고
    • Metagenomic analysis of the bioremediation of diesel-contaminated Canadian high arctic soils
    • Yergeau E, Sanschagrin S, Beaumier D, Greer CW (2012) Metagenomic analysis of the bioremediation of diesel-contaminated Canadian high arctic soils. PLoS One. 7: e30058.
    • (2012) PLoS One. , vol.7
    • Yergeau, E.1    Sanschagrin, S.2    Beaumier, D.3    Greer, C.W.4
  • 14
    • 84884127512 scopus 로고    scopus 로고
    • Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences
    • Langille MG, Zaneveld J, Caporaso JG, McDonald D, Knights D, et al. (2013) Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nat Biotechnol 31: 814-821.
    • (2013) Nat Biotechnol , vol.31 , pp. 814-821
    • Langille, M.G.1    Zaneveld, J.2    Caporaso, J.G.3    McDonald, D.4    Knights, D.5
  • 15
    • 53549118607 scopus 로고    scopus 로고
    • The metagenomics RAST server-a public resource for the automatic phylogenetic and functional analysis of metagenomes
    • Meyer F, Paarmann D, DSouza M, Olson R, Glass EM, et al. (2008) The metagenomics RAST server-a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics 9: 386.
    • (2008) BMC Bioinformatics , vol.9 , pp. 386
    • Meyer, F.1    Paarmann, D.2    Dsouza, M.3    Olson, R.4    Glass, E.M.5
  • 16
    • 84862024797 scopus 로고    scopus 로고
    • IMG/ M: The integrated metagenome data management and comparative analysis system
    • Markowitz VM, Chen IM, Chu K, Szeto E, Palaniappan K, et al. (2012) IMG/ M: the integrated metagenome data management and comparative analysis system. Nucleic Acids Res 40: D123-129.
    • (2012) Nucleic Acids Res , vol.40
    • Markowitz, V.M.1    Chen, I.M.2    Chu, K.3    Szeto, E.4    Palaniappan, K.5
  • 17
    • 78651266825 scopus 로고    scopus 로고
    • Community cyberinfrastructure for Advanced Microbial Ecology Research and Analysis: The CAMERA resource
    • Sun S, Chen J, Li W, Altintas I, Lin A, et al. (2011) Community cyberinfrastructure for Advanced Microbial Ecology Research and Analysis: the CAMERA resource. Nucleic Acids Res 39: D546-551.
    • (2011) Nucleic Acids Res , vol.39
    • Sun, S.1    Chen, J.2    Li, W.3    Altintas, I.4    Lin, A.5
  • 18
    • 80052606131 scopus 로고    scopus 로고
    • WebMGA: A customizable web server for fast metagenomic sequence analysis
    • Wu S, Zhu Z, Fu L, Niu B, Li W (2011) WebMGA: a customizable web server for fast metagenomic sequence analysis. BMC Genomics 12: 444.
    • (2011) BMC Genomics , vol.12 , pp. 444
    • Wu, S.1    Zhu, Z.2    Fu, L.3    Niu, B.4    Li, W.5
  • 19
    • 84865741828 scopus 로고    scopus 로고
    • The Human Microbiome Project: A community resource for the healthy human microbiome
    • Gevers D, Knight R, Petrosino JF, Huang K, McGuire AL, et al. (2012) The Human Microbiome Project: a community resource for the healthy human microbiome. PLoS Biol 10: e1001377.
    • (2012) PLoS Biol , vol.10
    • Gevers, D.1    Knight, R.2    Petrosino, J.F.3    Huang, K.4    McGuire, A.L.5
  • 24
    • 84864440400 scopus 로고    scopus 로고
    • Metagenomic microbial community profiling using unique clade-specific marker genes
    • Segata N, Waldron L, Ballarini A, Narasimhan V, Jousson O, et al. (2012) Metagenomic microbial community profiling using unique clade-specific marker genes. Nat Methods 9: 811-814.
    • (2012) Nat Methods , vol.9 , pp. 811-814
    • Segata, N.1    Waldron, L.2    Ballarini, A.3    Narasimhan, V.4    Jousson, O.5
  • 26
    • 0000286531 scopus 로고
    • An ordination of the upland forest communities of southern Wisconsin
    • Bray JR, Curtis JT (1957) An ordination of the upland forest communities of southern Wisconsin. Ecol Monographs, 27: 325-349.
    • (1957) Ecol Monographs , vol.27 , pp. 325-349
    • Bray, J.R.1    Curtis, J.T.2
  • 28
    • 84863304598 scopus 로고    scopus 로고
    • R Foundation for Statistical Computing, Vienna, Austria
    • R Development Core Team (2007) R: A language and environment for statistical computing [http://www.R-project.org].R Foundation for Statistical Computing, Vienna, Austria.
    • (2007) R: A Language and Environment for Statistical Computing
  • 29
    • 84864037467 scopus 로고    scopus 로고
    • Metabolic reconstruction for metagenomic data and its application to the human microbiome
    • Abubucker S, Segata N, Goll J, Schubert AM, Izard J, et al. (2012) Metabolic reconstruction for metagenomic data and its application to the human microbiome. PLoS Comput Biol 8: e1002358.
    • (2012) PLoS Comput Biol , vol.8
    • Abubucker, S.1    Segata, N.2    Goll, J.3    Schubert, A.M.4    Izard, J.5
  • 30
    • 75549090213 scopus 로고    scopus 로고
    • KEGG for representation and analysis of molecular networks involving diseases and drugs
    • Kanehisa M, Goto S, Furumichi M, Tanabe M, Hirakawa M. (2010) KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Res 38: D355-360.
    • (2010) Nucleic Acids Res , vol.38
    • Kanehisa, M.1    Goto, S.2    Furumichi, M.3    Tanabe, M.4    Hirakawa, M.5
  • 31
    • 77957244650 scopus 로고    scopus 로고
    • Search and clustering orders of magnitude faster than BLAST
    • Edgar RC (2010) Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26: 2460-2461.
    • (2010) Bioinformatics , vol.26 , pp. 2460-2461
    • Edgar, R.C.1
  • 32
    • 70049085269 scopus 로고    scopus 로고
    • A parsimony approach to biological pathway reconstruction/inference for genomes and metagenomes
    • Ye Y, Doak TG (2009) A parsimony approach to biological pathway reconstruction/inference for genomes and metagenomes. PLoS Comput Biol 5: e1000465.
    • (2009) PLoS Comput Biol , vol.5
    • Ye, Y.1    Doak, T.G.2
  • 33
    • 77955801615 scopus 로고    scopus 로고
    • Galaxy: A comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences
    • Goecks J, Nekrutenko A, Taylor J, Galaxy Team (2010) Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol 11: R86.
    • (2010) Genome Biol , vol.11
    • Goecks, J.1    Nekrutenko, A.2    Taylor, J.3
  • 34
    • 0031321241 scopus 로고    scopus 로고
    • The Simes method for multiple hypothesis testing with positively dependent test statistics
    • Sarkar SK, Chang CK (1997) The Simes method for multiple hypothesis testing with positively dependent test statistics. J Am Stat Assoc 92: 1601-1608.
    • (1997) J Am Stat Assoc , vol.92 , pp. 1601-1608
    • Sarkar, S.K.1    Chang, C.K.2
  • 35
    • 0001677717 scopus 로고
    • Controlling the false discovery rate: A practical and powerful approach to multiple testing
    • Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J Royal Statis Soc B 57: 289-300.
    • (1995) J Royal Statis Soc B , vol.57 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 36
    • 79551587720 scopus 로고    scopus 로고
    • Cytoscape 2.8: New features for data integration and network visualization
    • Smoot ME, Ono K, Ruscheinski J, Wang PL, Ideker T. (2011) Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics 27: 431-432.
    • (2011) Bioinformatics , vol.27 , pp. 431-432
    • Smoot, M.E.1    Ono, K.2    Ruscheinski, J.3    Wang, P.L.4    Ideker, T.5
  • 37
    • 77950251400 scopus 로고    scopus 로고
    • A human gut microbial gene catalogue established by metagenomic sequencing
    • Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, et al. (2010) A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464: 59-65.
    • (2010) Nature , vol.464 , pp. 59-65
    • Qin, J.1    Li, R.2    Raes, J.3    Arumugam, M.4    Burgdorf, K.S.5
  • 38
    • 84862162269 scopus 로고    scopus 로고
    • Composition of the adult digestive tract bacterial microbiome based on seven mouth surfaces, tonsils, throat and stool samples
    • Segata N, Haake SK, Mannon P, Lemon KP, Waldron L, et al. (2012) Composition of the adult digestive tract bacterial microbiome based on seven mouth surfaces, tonsils, throat and stool samples. Genome Biol 13: R42.
    • (2012) Genome Biol , vol.13
    • Segata, N.1    Haake, S.K.2    Mannon, P.3    Lemon, K.P.4    Waldron, L.5
  • 39
    • 33644952722 scopus 로고    scopus 로고
    • Identifying the dominant soil bacterial taxa in libraries of 16S rRNA and 16S rRNA genes
    • Janssen PH (2006) Identifying the dominant soil bacterial taxa in libraries of 16S rRNA and 16S rRNA genes. Appl Environ Microbiol 72: 1719-1728.
    • (2006) Appl Environ Microbiol , vol.72 , pp. 1719-1728
    • Janssen, P.H.1
  • 40
    • 71549170264 scopus 로고    scopus 로고
    • Exploring methanotrophs diversity in acidic northern wetlands: Molecular and cultivation-based studies
    • Dedysh SN (2009) Exploring methanotrophs diversity in acidic northern wetlands: molecular and cultivation-based studies. Microbiology 78: 655-669.
    • (2009) Microbiology , vol.78 , pp. 655-669
    • Dedysh, S.N.1
  • 41
    • 84865186665 scopus 로고    scopus 로고
    • Cultivating uncultured bacteria from northern wetlands: Knowledge gained and remaining gaps
    • Dedysh SN (2011) Cultivating uncultured bacteria from northern wetlands: knowledge gained and remaining gaps. Front Microbiol 2: 184.
    • (2011) Front Microbiol , vol.2 , pp. 184
    • Dedysh, S.N.1
  • 42
    • 0027403792 scopus 로고
    • Effect of land use change on methane oxidation in temperate forest and grassland soils
    • Ojima DS, Valentine DW, Mosier AR, Parton WJ, Schimel (1993) Effect of land use change on methane oxidation in temperate forest and grassland soils. Chemosphere 26: 675-685. (Pubitemid 23087876)
    • (1993) Chemosphere , vol.26 , Issue.1-4 , pp. 675-685
    • Ojima, D.S.1    Valentine, D.W.2    Mosier, A.R.3    Parton, W.J.4    Schimel, D.S.5
  • 43
    • 33751070097 scopus 로고    scopus 로고
    • Methane oxidation rates in forest soils and their controlling variables: A review and a case study in Korea
    • DOI 10.1007/s11284-006-0041-9, Special Issue on Global Changes in Terrestrial Ecosystems
    • Jang I, Lee S, Hong JH, Kang H (2006) Methane oxidation rates in forest soils and their controlling variables, a review and a case study in Korea. Ecol Res 21: 849-854. (Pubitemid 44760456)
    • (2006) Ecological Research , vol.21 , Issue.6 , pp. 849-854
    • Jang, I.1    Lee, S.2    Hong, J.-H.3    Kang, H.4
  • 44
    • 33747884210 scopus 로고    scopus 로고
    • Family II. Ectothiorhodospiraceae
    • Brenner DJ, Krieg NR, Staley JT, Garrity GM, editors 2nd. Springer, New York, NY.
    • Imhoff JF (2005) Family II. Ectothiorhodospiraceae. In: Brenner DJ, Krieg NR, Staley JT, Garrity GM, editors. Bergey's manual of systematic bacteriology, 2nd. Springer, New York, NY. pp. 41-52.
    • (2005) Bergey's Manual of Systematic Bacteriology , pp. 41-52
    • Imhoff, J.F.1
  • 45
    • 19544364328 scopus 로고    scopus 로고
    • Family II. Desulfobulbaceae fam
    • Brenner DJ, Krieg NR, Staley JT, Garrity GM, editors 2nd. New York: Springer
    • Kuever J, Rainey FA, Widdel F (2005) Family II. Desulfobulbaceae fam. nov. In: Brenner DJ, Krieg NR, Staley JT, Garrity GM, editors. p.Bergey's manual of systematic bacteriology, 2nd. New York: Springer, p.988.
    • (2005) Bergey's Manual of Systematic Bacteriology , pp. 988
    • Kuever, J.1    Rainey, F.A.2    Widdel, F.3
  • 46
    • 84874336197 scopus 로고    scopus 로고
    • The methanol dehydrogenase gene, mxaF, as a functional and phylogenetic marker for proteobacterial methanotrophs in natural environments
    • Lau E, Fisher MC, Steudler PA, Cavanaugh CM (2013) The methanol dehydrogenase gene, mxaF, as a functional and phylogenetic marker for proteobacterial methanotrophs in natural environments. PLoS One 8: e56993.
    • (2013) PLoS One , vol.8
    • Lau, E.1    Fisher, M.C.2    Steudler, P.A.3    Cavanaugh, C.M.4
  • 48
    • 80051940088 scopus 로고    scopus 로고
    • Diversity, biological roles and biosynthetic pathways for sugar-glycerate containing compatible solutes in bacteria and archaea
    • Empadinhas N, da Costa MS (2011) Diversity, biological roles and biosynthetic pathways for sugar-glycerate containing compatible solutes in bacteria and archaea. Environ Microbiol 13: 2056-2077.
    • (2011) Environ Microbiol , vol.13 , pp. 2056-2077
    • Empadinhas, N.1    Da Costa, M.S.2
  • 50
    • 34250634316 scopus 로고    scopus 로고
    • 2+ (Znu) transporters in Treponema pallidum: Analysis of metal specificities and expression profiles
    • DOI 10.1111/j.1365-2958.2007.05771.x
    • Desrosiers DC, Sun YC, Zaidi AA, Eggers CH, Cox DL, et al. (2007) The general transition metal (Tro) and Zn2+ (Znu) transporters in Treponema pallidum: analysis of metal specificities and expression profiles. Mol Microbiol 65: 137-152. (Pubitemid 46934485)
    • (2007) Molecular Microbiology , vol.65 , Issue.1 , pp. 137-152
    • Desrosiers, D.C.1    Sun, Y.C.2    Zaidi, A.A.3    Eggers, C.H.4    Cox, D.L.5    Radolf, J.D.6
  • 51
    • 0027252509 scopus 로고
    • 2 assimilation: Enzyme modulation
    • Wolosiuk RA, Ballicora MA, Hagelin K (1993) The reductive pentose phosphate cycle for photosynthetic CO2 assimilation: enzyme modulation. FASEB J 7: 622-637. (Pubitemid 23163597)
    • (1993) FASEB Journal , vol.7 , Issue.8 , pp. 622-637
    • Wolosiuk, R.A.1    Ballicora, M.A.2    Hagelin, K.3
  • 52
    • 77954266751 scopus 로고    scopus 로고
    • Characterization of the branched-chain amino acid aminotransferase enzyme family in tomato
    • Maloney GS, Kochevenko A, Tieman DM, Tohge T, Krieger U, et al. (2010) Characterization of the branched-chain amino acid aminotransferase enzyme family in tomato. Plant Physiol 153: 925-936.
    • (2010) Plant Physiol , vol.153 , pp. 925-936
    • Maloney, G.S.1    Kochevenko, A.2    Tieman, D.M.3    Tohge, T.4    Krieger, U.5
  • 53
    • 84869808716 scopus 로고    scopus 로고
    • The Shikimate pathway and aromatic amino acid biosynthesis in plants
    • Maeda H, Dudareva N (2012) The Shikimate pathway and aromatic amino acid biosynthesis in plants. Annu Rev Plant Biol 63: 73-105.
    • (2012) Annu Rev Plant Biol , vol.63 , pp. 73-105
    • Maeda, H.1    Dudareva, N.2


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