메뉴 건너뛰기




Volumn 75, Issue 15, 2009, Pages 5111-5120

Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale

Author keywords

[No Author keywords available]

Indexed keywords

ACTINOBACTERIA; BACTERIAL COMMUNITY; BACTERIAL COMMUNITY COMPOSITION; BACTERIAL POPULATION; CONTINENTAL SCALE; PHYLOGENETIC DIVERSITY; PHYLOGENETIC STRUCTURES; PYROSEQUENCING; RELATIVE ABUNDANCE; SOIL BACTERIAL COMMUNITY; SOIL PH; SOUTH AMERICA; SPATIAL SCALE; TAXONOMIC RESOLUTION;

EID: 67651247607     PISSN: 00992240     EISSN: 10985336     Source Type: Journal    
DOI: 10.1128/AEM.00335-09     Document Type: Article
Times cited : (3197)

References (49)
  • 1
    • 53449086190 scopus 로고    scopus 로고
    • Tag-encoded pyrosequencing analysis of bacterial diversity in a single soil type as affected by management and land use
    • Acosta-Martínez, V., S. Dowd, Y. Sun, and V. Allen. 2008. Tag-encoded pyrosequencing analysis of bacterial diversity in a single soil type as affected by management and land use. Soil Biol. Biochem. 40:2762-2770.
    • (2008) Soil Biol. Biochem , vol.40 , pp. 2762-2770
    • Acosta-Martínez, V.1    Dowd, S.2    Sun, Y.3    Allen, V.4
  • 3
    • 0037628100 scopus 로고    scopus 로고
    • Comparison of soil fungal/bacterial ratios in a pH gradient using physiological and PLFA-based techniques
    • Bääth, E., and T. H. Anderson. 2003. Comparison of soil fungal/bacterial ratios in a pH gradient using physiological and PLFA-based techniques. Soil Biol. Biochem. 35:955-963.
    • (2003) Soil Biol. Biochem , vol.35 , pp. 955-963
    • Bääth, E.1    Anderson, T.H.2
  • 5
    • 0030860238 scopus 로고    scopus 로고
    • Molecular microbial diversity in soils from eastern Amazonia: Evidence for unusual microorganisms and microbial population shifts associated with deforestation
    • Borneman, J., and E. W. Triplett. 1997. Molecular microbial diversity in soils from eastern Amazonia: evidence for unusual microorganisms and microbial population shifts associated with deforestation. Appl. Environ. Microbiol. 63:2647-2653.
    • (1997) Appl. Environ. Microbiol , vol.63 , pp. 2647-2653
    • Borneman, J.1    Triplett, E.W.2
  • 7
    • 0034467820 scopus 로고    scopus 로고
    • Biogeography and degree of endemicity of fluorescent Pseudomonas strains in soil
    • Cho, J. C., and J. M. Tiedje. 2000. Biogeography and degree of endemicity of fluorescent Pseudomonas strains in soil. Appl. Environ. Microbiol. 66: 5448-5456.
    • (2000) Appl. Environ. Microbiol , vol.66 , pp. 5448-5456
    • Cho, J.C.1    Tiedje, J.M.2
  • 8
    • 0035816173 scopus 로고    scopus 로고
    • A further biodiversity index applicable to species lists: Variation in taxonomic distinctness
    • Clarke, K. R., and R. M. Warwick. 2001. A further biodiversity index applicable to species lists: variation in taxonomic distinctness. Mar. Ecol. Prog. Ser. 216:265-278.
    • (2001) Mar. Ecol. Prog. Ser , vol.216 , pp. 265-278
    • Clarke, K.R.1    Warwick, R.M.2
  • 12
    • 56849106496 scopus 로고    scopus 로고
    • The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing
    • Dethlefsen, L., S. Huse, M. L. Sogin, and D. A. Relman. 2008. The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing. PLoS Biol. 6:2383-2400.
    • (2008) PLoS Biol , vol.6 , pp. 2383-2400
    • Dethlefsen, L.1    Huse, S.2    Sogin, M.L.3    Relman, D.A.4
  • 13
    • 34247606048 scopus 로고    scopus 로고
    • Isolation and characterization of soil bacteria that define Teniglobus gen. nov., in the phylum Acidobacteria
    • Eichorst, S. A., J. A. Breznak, and T. M. Schmidt. 2007. Isolation and characterization of soil bacteria that define Teniglobus gen. nov., in the phylum Acidobacteria. Appl. Environ. Microbiol. 73:2708-2717.
    • (2007) Appl. Environ. Microbiol , vol.73 , pp. 2708-2717
    • Eichorst, S.A.1    Breznak, J.A.2    Schmidt, T.M.3
  • 15
    • 0026499429 scopus 로고
    • Conservation evaluation and phylogenetic diversity
    • Faith, D. P. 1992. Conservation evaluation and phylogenetic diversity. Biol. Conserv. 61:1-10.
    • (1992) Biol. Conserv , vol.61 , pp. 1-10
    • Faith, D.P.1
  • 16
    • 33947236971 scopus 로고    scopus 로고
    • Toward an ecological classification of soil bacteria
    • Fierer, N., M. A. Bradford, and R. B. Jackson. 2007. Toward an ecological classification of soil bacteria. Ecology 88:1354-1364.
    • (2007) Ecology , vol.88 , pp. 1354-1364
    • Fierer, N.1    Bradford, M.A.2    Jackson, R.B.3
  • 17
    • 56649124715 scopus 로고    scopus 로고
    • The influence of sex, handedness, and washing on the diversity of hand surface bacteria
    • Fierer, N., M. Hamady, C. L. Lauber, and R. Knight. 2008. The influence of sex, handedness, and washing on the diversity of hand surface bacteria. Proc. Natl. Acad. Sci. USA 105:17994-17999.
    • (2008) Proc. Natl. Acad. Sci. USA , vol.105 , pp. 17994-17999
    • Fierer, N.1    Hamady, M.2    Lauber, C.L.3    Knight, R.4
  • 18
    • 22144470189 scopus 로고    scopus 로고
    • Assessment of soil microbial community structure by use of taxon-specific quantitative PCR assays
    • Fierer, N., J. A. Jackson, R. Vilgalys, and R. B. Jackson. 2005. Assessment of soil microbial community structure by use of taxon-specific quantitative PCR assays. Appl. Environ. Microbiol. 71:4117-4120.
    • (2005) Appl. Environ. Microbiol , vol.71 , pp. 4117-4120
    • Fierer, N.1    Jackson, J.A.2    Vilgalys, R.3    Jackson, R.B.4
  • 19
    • 31444447130 scopus 로고    scopus 로고
    • The diversity and biogeography of soil bacterial communities
    • Fierer, N., and R. B. Jackson. 2006. The diversity and biogeography of soil bacterial communities. Proc. Natl. Acad. Sci. USA 103:626-631.
    • (2006) Proc. Natl. Acad. Sci. USA , vol.103 , pp. 626-631
    • Fierer, N.1    Jackson, R.B.2
  • 20
    • 51449115465 scopus 로고    scopus 로고
    • Fulthorpe, R. R., L. F. W. Roesch, A. Riva, and E. W. Triplett. 2008. Distantly sampled soils carry few species in common. ISME J. 2:901-910.
    • Fulthorpe, R. R., L. F. W. Roesch, A. Riva, and E. W. Triplett. 2008. Distantly sampled soils carry few species in common. ISME J. 2:901-910.
  • 21
    • 23944525404 scopus 로고    scopus 로고
    • Computational improvements reveal great bacterial diversity and high metal toxicity in soil
    • Gans, J., M. Wolinsky, and J. Dunbar. 2005. Computational improvements reveal great bacterial diversity and high metal toxicity in soil. Science 309: 1387-1390.
    • (2005) Science , vol.309 , pp. 1387-1390
    • Gans, J.1    Wolinsky, M.2    Dunbar, J.3
  • 22
    • 44449118067 scopus 로고    scopus 로고
    • Microbial biogeography: From taxonomy to traits
    • Green, J. L., B. J. M. Bohannan, and R. J. Whitaker. 2008. Microbial biogeography: from taxonomy to traits. Science 320:1039-1043.
    • (2008) Science , vol.320 , pp. 1039-1043
    • Green, J.L.1    Bohannan, B.J.M.2    Whitaker, R.J.3
  • 23
    • 40149103278 scopus 로고    scopus 로고
    • Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex
    • Hamady, M., J. J. Walker, J. K. Harris, N. J. Gold, and R. Knight. 2008. Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex. Nat. Methods 5:235-237.
    • (2008) Nat. Methods , vol.5 , pp. 235-237
    • Hamady, M.1    Walker, J.J.2    Harris, J.K.3    Gold, N.J.4    Knight, R.5
  • 24
    • 56649085249 scopus 로고    scopus 로고
    • Environmental and anthropogenic controls over bacterial communities in wetland soils
    • Hartman, W. H., C. J. Richardson, R. Vilgalys, and G. L. Bruland. 2008. Environmental and anthropogenic controls over bacterial communities in wetland soils. Proc. Natl. Acad. Sci. USA 105:17842-17847.
    • (2008) Proc. Natl. Acad. Sci. USA , vol.105 , pp. 17842-17847
    • Hartman, W.H.1    Richardson, C.J.2    Vilgalys, R.3    Bruland, G.L.4
  • 26
    • 57149093416 scopus 로고    scopus 로고
    • Huse, S. M., L. Dethlefsen, J. A. Huber, D. M. Welch, D. A. Relman, and M. L. Sogin. 2008. Exploring microbial diversity and taxonomy using SSU rRNA hypervariable tag sequencing. PLoS Genet. 4:e1000255.
    • Huse, S. M., L. Dethlefsen, J. A. Huber, D. M. Welch, D. A. Relman, and M. L. Sogin. 2008. Exploring microbial diversity and taxonomy using SSU rRNA hypervariable tag sequencing. PLoS Genet. 4:e1000255.
  • 27
    • 33644952722 scopus 로고    scopus 로고
    • Identifying the dominant soil bacterial taxa in libraries of 16S rRNA and 16S rRNA genes
    • Janssen, P. H. 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
  • 28
    • 63349105158 scopus 로고    scopus 로고
    • Jones, R. T., M. S. Robeson, C. L. Lauber, M. Hamady, R. Knight, and N. Fierer. 2009. A comprehensive survey of soil acidobacterial diversity using pyrosequencing and clone library analyses. ISME J. 4:442-453.
    • Jones, R. T., M. S. Robeson, C. L. Lauber, M. Hamady, R. Knight, and N. Fierer. 2009. A comprehensive survey of soil acidobacterial diversity using pyrosequencing and clone library analyses. ISME J. 4:442-453.
  • 29
    • 49249124904 scopus 로고    scopus 로고
    • The influence of soil properties on the structure of bacterial and fungal communities across land-use types
    • Lauber, C. L., M. S. Strickland, M. A. Bradford, and N. Fierer. 2008. The influence of soil properties on the structure of bacterial and fungal communities across land-use types. Soil Biol. Biochem. 40:2407-2415.
    • (2008) Soil Biol. Biochem , vol.40 , pp. 2407-2415
    • Lauber, C.L.1    Strickland, M.S.2    Bradford, M.A.3    Fierer, N.4
  • 30
    • 35549007148 scopus 로고    scopus 로고
    • Short pyrosequencing reads suffice for accurate microbial community analysis
    • Liu, Z. Z., C. Lozupone, M. Hamady, F. D. Bushman, and R. Knight. 2007. Short pyrosequencing reads suffice for accurate microbial community analysis. Nucleic Acids Res. 35:e120.
    • (2007) Nucleic Acids Res , vol.35
    • Liu, Z.Z.1    Lozupone, C.2    Hamady, M.3    Bushman, F.D.4    Knight, R.5
  • 32
    • 33748713890 scopus 로고    scopus 로고
    • UniFrac-an online tool for comparing microbial community diversity in a phylogenetic context
    • Lozupone, C., M. Hamady, and R. Knight. 2006. UniFrac-an online tool for comparing microbial community diversity in a phylogenetic context. BMC Bioinform. 7:731.
    • (2006) BMC Bioinform , vol.7 , pp. 731
    • Lozupone, C.1    Hamady, M.2    Knight, R.3
  • 33
    • 29144464937 scopus 로고    scopus 로고
    • UniFrac: A new phylogenetic method for comparing microbial communities
    • Lozupone, C., and R. Knight. 2005. UniFrac: a new phylogenetic method for comparing microbial communities. Appl. Environ. Microbiol. 71:8228-8235.
    • (2005) Appl. Environ. Microbiol , vol.71 , pp. 8228-8235
    • Lozupone, C.1    Knight, R.2
  • 34
    • 34547433545 scopus 로고    scopus 로고
    • Global patterns in bacterial diversity
    • Lozupone, C. A., and R. Knight. 2007. Global patterns in bacterial diversity. Proc. Natl. Acad. Sci. USA 104:11436-11440.
    • (2007) Proc. Natl. Acad. Sci. USA , vol.104 , pp. 11436-11440
    • Lozupone, C.A.1    Knight, R.2
  • 35
    • 67651244836 scopus 로고    scopus 로고
    • Madigan, M. T., and J. M. Martinko. 2006. Brock biology of microorganisms, 11th ed. Pearson Benjamin Cummings, San Francisco, CA.
    • Madigan, M. T., and J. M. Martinko. 2006. Brock biology of microorganisms, 11th ed. Pearson Benjamin Cummings, San Francisco, CA.
  • 37
    • 0035487280 scopus 로고    scopus 로고
    • Numerical analysis of grassland bacterial community structure under different land management regimens by using 16S ribosomal DNA sequence data and denaturing gradient gel electrophoresis banding patterns
    • McCaig, A. E., L. A. Glover, and J. I. Prosser. 2001. Numerical analysis of grassland bacterial community structure under different land management regimens by using 16S ribosomal DNA sequence data and denaturing gradient gel electrophoresis banding patterns. Appl. Environ. Microbiol. 67: 4554-4559.
    • (2001) Appl. Environ. Microbiol , vol.67 , pp. 4554-4559
    • McCaig, A.E.1    Glover, L.A.2    Prosser, J.I.3
  • 38
    • 45749123195 scopus 로고    scopus 로고
    • Characterization of a bacterial community in an abandoned semiarid lead-zinc mine tailing site
    • Mendez, M. O., J. W. Neilson, and R. M. Maier. 2008. Characterization of a bacterial community in an abandoned semiarid lead-zinc mine tailing site. Appl. Environ. Microbiol. 74:3899-3907.
    • (2008) Appl. Environ. Microbiol , vol.74 , pp. 3899-3907
    • Mendez, M.O.1    Neilson, J.W.2    Maier, R.M.3
  • 39
    • 59649097910 scopus 로고    scopus 로고
    • Extensive phylogenetic analysis of a soil bacterial community illustrates extreme taxon evenness and the effects of amplicon length, degree of coverage, and DNA fractionation on classification and ecological parameters
    • Morales, S. E., T. F. Cosart, J. V. Johnson, and W. E. Holben. 2009. Extensive phylogenetic analysis of a soil bacterial community illustrates extreme taxon evenness and the effects of amplicon length, degree of coverage, and DNA fractionation on classification and ecological parameters. Appl. Environ. Microbiol. 75:668-675.
    • (2009) Appl. Environ. Microbiol , vol.75 , pp. 668-675
    • Morales, S.E.1    Cosart, T.F.2    Johnson, J.V.3    Holben, W.E.4
  • 40
    • 19344376606 scopus 로고    scopus 로고
    • Microbial macroecology: Highly structured prokaryotic soil assemblages in a tropical deciduous forest
    • Noguez, A. M., H. T. Arita, A. E. Escalante, L. J. Forney, F. Garcia-Oliva, and V. Souza. 2005. Microbial macroecology: highly structured prokaryotic soil assemblages in a tropical deciduous forest. Global Ecol. Biogeogr. 14: 241-248.
    • (2005) Global Ecol. Biogeogr , vol.14 , pp. 241-248
    • Noguez, A.M.1    Arita, H.T.2    Escalante, A.E.3    Forney, L.J.4    Garcia-Oliva, F.5    Souza, V.6
  • 41
    • 33847327474 scopus 로고    scopus 로고
    • Biogeography: An emerging cornerstone for understanding prokaryotic diversity, ecology, and evolution
    • Ramette, A., and J. M. Tiedje. 2007. Biogeography: an emerging cornerstone for understanding prokaryotic diversity, ecology, and evolution. Microb. Ecol. 53:197-207.
    • (2007) Microb. Ecol , vol.53 , pp. 197-207
    • Ramette, A.1    Tiedje, J.M.2
  • 42
    • 34547800097 scopus 로고    scopus 로고
    • Roesch, L. F. W., R. R. Fulthorpe, A. Riva, G. Casella, A. K. M. Hadwin, A. D. Kent, S. H. Daroub, F. A. O. Camargo, W. G. Farmerie, and E. W. Triplett. 2007. Pyrosequencing enumerates and contrasts soil microbial diversity. ISME J. 1:283-290.
    • Roesch, L. F. W., R. R. Fulthorpe, A. Riva, G. Casella, A. K. M. Hadwin, A. D. Kent, S. H. Daroub, F. A. O. Camargo, W. G. Farmerie, and E. W. Triplett. 2007. Pyrosequencing enumerates and contrasts soil microbial diversity. ISME J. 1:283-290.
  • 43
    • 33644962444 scopus 로고    scopus 로고
    • Effect of pH on isolation and distribution of members of subdivision 1 of the phylum Acidobacteria occurring in soil
    • Sait, M., K. E. R. Davis, and P. H. Janssen. 2006. Effect of pH on isolation and distribution of members of subdivision 1 of the phylum Acidobacteria occurring in soil. Appl. Environ. Microbiol. 72:1852-1857.
    • (2006) Appl. Environ. Microbiol , vol.72 , pp. 1852-1857
    • Sait, M.1    Davis, K.E.R.2    Janssen, P.H.3
  • 44
    • 40249113895 scopus 로고    scopus 로고
    • Schloss, P. D. 2008. Evaluating different approaches that test whether microbial communities have the same structure. ISME J. 2:265-275.
    • Schloss, P. D. 2008. Evaluating different approaches that test whether microbial communities have the same structure. ISME J. 2:265-275.
  • 46
    • 33750983947 scopus 로고    scopus 로고
    • Clearcut: A fast implementation of relaxed neighbor joining
    • Sheneman, L., J. Evans, and J. A. Foster. 2006. Clearcut: a fast implementation of relaxed neighbor joining. Bioinformatics 22:2823-2824.
    • (2006) Bioinformatics , vol.22 , pp. 2823-2824
    • Sheneman, L.1    Evans, J.2    Foster, J.A.3
  • 47
    • 33645054591 scopus 로고    scopus 로고
    • Investigating microbial community structure in soils by physiological, biochemical and molecular fingerprinting methods
    • Singh, B. K., S. Munro, E. Reid, B. Ord, J. M. Potts, E. Paterson, and P. Millard. 2006. Investigating microbial community structure in soils by physiological, biochemical and molecular fingerprinting methods. Eur. J. Soil Sci. 57:72-82.
    • (2006) Eur. J. Soil Sci , vol.57 , pp. 72-82
    • Singh, B.K.1    Munro, S.2    Reid, E.3    Ord, B.4    Potts, J.M.5    Paterson, E.6    Millard, P.7
  • 49
    • 43649086777 scopus 로고    scopus 로고
    • Differences in the composition and diversity of bacterial communities from agricultural and forest soils
    • Upchurch, R., C. Y. Chi, K. Everett, G. Dyszynski, D. C. Coleman, and W. B. Whitman. 2008. Differences in the composition and diversity of bacterial communities from agricultural and forest soils. Soil Biol. Biochem. 40:1294-1305.
    • (2008) Soil Biol. Biochem , vol.40 , pp. 1294-1305
    • Upchurch, R.1    Chi, C.Y.2    Everett, K.3    Dyszynski, G.4    Coleman, D.C.5    Whitman, W.B.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.