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Volumn 6, Issue 3, 2003, Pages 295-301

Resolving functional diversity in relation to microbial community structure in soil: Exploiting genomics and stable isotope probing

Author keywords

[No Author keywords available]

Indexed keywords

DNA FRAGMENT; RNA; STABLE ISOTOPE; TOLUENE;

EID: 0038265142     PISSN: 13695274     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1369-5274(03)00066-3     Document Type: Review
Times cited : (116)

References (46)
  • 1
    • 0037335946 scopus 로고    scopus 로고
    • Community structure of ammonia-oxidizing bacteria within anoxic marine sediments
    • Freitag TE, Prosser JI: Community structure of ammonia-oxidizing bacteria within anoxic marine sediments. Appl Environ Microbiol 2003, 69:1359-1371. Natural microbial communities of ammonia-oxidising bacteria were characterised by analysis of 16S rRNA genes amplified using group-specific primers by PCR- and RT-PCR amplification of 16S rDNA and RNA, respectively. Phylogenetic analysis of sequences suggests dominance of Nitrosospira cluster-1-like organisms and of strains belonging to a novel cluster.
    • (2003) Appl Environ Microbiol , vol.69 , pp. 1359-1371
    • Freitag, T.E.1    Prosser, J.I.2
  • 2
    • 0031736834 scopus 로고    scopus 로고
    • Analysis of streptomycin biosynthetic gene clusters in streptomycetes isolated from soil
    • Egan S, Wiener P, Kallifidas D, Wellington EMH: Analysis of streptomycin biosynthetic gene clusters in streptomycetes isolated from soil. Appl Environ Microbiol 1998, 64:5061-5063.
    • (1998) Appl Environ Microbiol , vol.64 , pp. 5061-5063
    • Egan, S.1    Wiener, P.2    Kallifidas, D.3    Wellington, E.M.H.4
  • 4
    • 0038806464 scopus 로고    scopus 로고
    • Microbial ecology of soil biofilms: Substrate bioavailability, bioremediation and complexity
    • Burns RG, Stach JEM: Microbial ecology of soil biofilms: substrate bioavailability, bioremediation and complexity. Developments in Soil Science 2002, 28B:17-42.
    • (2002) Developments in Soil Science , vol.28 B , pp. 17-42
    • Burns, R.G.1    Stach, J.E.M.2
  • 5
    • 0342868796 scopus 로고    scopus 로고
    • Characterization of the dominant and rare members of a young Hawaiian soil bacterial community with small-subunit ribosomal DNA amplified from DNA fractionated on the basis of its guanine and cytosine composition
    • Nüsslein K, Tiedje JM: Characterization of the dominant and rare members of a young Hawaiian soil bacterial community with small-subunit ribosomal DNA amplified from DNA fractionated on the basis of its guanine and cytosine composition. Appl Environ Microbiol 1998, 64:1283-1289.
    • (1998) Appl Environ Microbiol , vol.64 , pp. 1283-1289
    • Nüsslein, K.1    Tiedje, J.M.2
  • 6
    • 0036795110 scopus 로고    scopus 로고
    • A molecular analysis of a bacterial chitinolytic community in an upland pasture
    • Metcalfe AC, Krsek M, Gooday GD, Prosser JI, Wellington EMH: A molecular analysis of a bacterial chitinolytic community in an upland pasture. Appl Environ Microbiol 2002, 68:5042-5050. Litter bags filled with chitin were used to enrich for chitinolytic bacterial community structure, which was studied using 16S rRNA genes and chitinase encoding genes. Sequence data revealed a major contribution of unexpected genera to the chitin degradation. Sludge application increased chitinolytic activity and concomitantly decreased diversity of chitinolytic communities.
    • (2002) Appl Environ Microbiol , vol.68 , pp. 5042-5050
    • Metcalfe, A.C.1    Krsek, M.2    Gooday, G.D.3    Prosser, J.I.4    Wellington, E.M.H.5
  • 8
    • 0028136885 scopus 로고
    • Bacterial gene transfer by natural genetic transformation in the environment
    • Lorenz MG, Wackernagel W: Bacterial gene transfer by natural genetic transformation in the environment. Microbiol Rev 1994, 58:563-602.
    • (1994) Microbiol Rev , vol.58 , pp. 563-602
    • Lorenz, M.G.1    Wackernagel, W.2
  • 9
    • 0024334556 scopus 로고
    • Structural functional analysis of ribosomal subunits from vegetative Mycelium and spores of Streptomyces antibioticus
    • Quiros LM, Parra F, Hardisson C: Structural functional analysis of ribosomal subunits from vegetative Mycelium and spores of Streptomyces antibioticus. J Gen Microbiol 1989, 135:1661.
    • (1989) J Gen Microbiol , vol.135 , pp. 1661
    • Quiros, L.M.1    Parra, F.2    Hardisson, C.3
  • 10
    • 0030762263 scopus 로고    scopus 로고
    • Ribosome analysis reveals prominent activity of an uncultured member of the class Actinobacteria in grassland soils
    • Felske A, Rheims H, Wolterink A, Stackebrandt E, Akkermans AA: Ribosome analysis reveals prominent activity of an uncultured member of the class Actinobacteria in grassland soils. Microbiology 1997, 143:2983-2989.
    • (1997) Microbiology , vol.143 , pp. 2983-2989
    • Felske, A.1    Rheims, H.2    Wolterink, A.3    Stackebrandt, E.4    Akkermans, A.A.5
  • 11
    • 0027231336 scopus 로고
    • Quantitative relationship between naphthalene catabolic gene frequency and expression in predicting PAH degradation in soils at town gas manufacturing sites
    • Fleming JT, Sanseverino J, Sayler GS: Quantitative relationship between naphthalene catabolic gene frequency and expression in predicting PAH degradation in soils at town gas manufacturing sites. Environ Sci Technol 1993, 27:1068-1074.
    • (1993) Environ Sci Technol , vol.27 , pp. 1068-1074
    • Fleming, J.T.1    Sanseverino, J.2    Sayler, G.S.3
  • 12
    • 0027513639 scopus 로고
    • Effect of 2-hydroxybenzoate on the rate of naphthalene mineralization in soil
    • Ogunseitan OA, Olsen BH: Effect of 2-hydroxybenzoate on the rate of naphthalene mineralization in soil. Appl Microbiol Biotechnol 1993, 38:799-807.
    • (1993) Appl Microbiol Biotechnol , vol.38 , pp. 799-807
    • Ogunseitan, O.A.1    Olsen, B.H.2
  • 13
    • 0035476674 scopus 로고    scopus 로고
    • Gene expression monitoring in soils by mRNA analysis and gene lux fusions
    • Sayler GS, Fleming JT, Nivens DE: Gene expression monitoring in soils by mRNA analysis and gene lux fusions. Curr Opin Biotechnol 2001, 12:455-460.
    • (2001) Curr Opin Biotechnol , vol.12 , pp. 455-460
    • Sayler, G.S.1    Fleming, J.T.2    Nivens, D.E.3
  • 14
    • 0242668357 scopus 로고    scopus 로고
    • mRNA extraction and reverse transcription-PCR protocol for detection of nifH gene expression by Azotobacter vinelandii in soil
    • Burgmann H, Widmer F, Sigler WV, Zeyer J: mRNA extraction and reverse transcription-PCR protocol for detection of nifH gene expression by Azotobacter vinelandii in soil. Appl Environ Microbiol 2003, 69:1928-1935.
    • (2003) Appl Environ Microbiol , vol.69 , pp. 1928-1935
    • Burgmann, H.1    Widmer, F.2    Sigler, W.V.3    Zeyer, J.4
  • 15
    • 0002908439 scopus 로고    scopus 로고
    • Ecology of plasmid transfer and spread
    • Edited by Thomas CM. Amsterdam: Harwood Academic Publishers
    • van Elsas JD, Fry J, Hirsch P, Molin S: Ecology of plasmid transfer and spread. In The Horizontal Gene Pool. Edited by Thomas CM. Amsterdam: Harwood Academic Publishers; 2000:175-199.
    • (2000) The Horizontal Gene Pool , pp. 175-199
    • Van Elsas, J.D.1    Fry, J.2    Hirsch, P.3    Molin, S.4
  • 16
    • 0032986790 scopus 로고    scopus 로고
    • Combination of fluorescent in situ hybridization and microautoradiography - A new tool for structure-function analyses in microbial ecology
    • Lee N, Nielsen PH, Andreasen KH, Juretschko S, Nielsen JL, Schleifer KH, Wagner M: Combination of fluorescent in situ hybridization and microautoradiography - a new tool for structure-function analyses in microbial ecology. Appl Environ Microbiol 1999, 65:1289-1297.
    • (1999) Appl Environ Microbiol , vol.65 , pp. 1289-1297
    • Lee, N.1    Nielsen, P.H.2    Andreasen, K.H.3    Juretschko, S.4    Nielsen, J.L.5    Schleifer, K.H.6    Wagner, M.7
  • 17
    • 0033775691 scopus 로고    scopus 로고
    • Use of combined microautoradiography and fluorescence in situ hybridization to determine carbon metabolism in mixed natural communities of uncultured bacteria from the genus Achromatium
    • Gray ND, Howarth R, Pickup RW, Jones JG, Head IM: Use of combined microautoradiography and fluorescence in situ hybridization to determine carbon metabolism in mixed natural communities of uncultured bacteria from the genus Achromatium. Appl Environ Microbiol 2000, 66:4518-4522.
    • (2000) Appl Environ Microbiol , vol.66 , pp. 4518-4522
    • Gray, N.D.1    Howarth, R.2    Pickup, R.W.3    Jones, J.G.4    Head, I.M.5
  • 18
    • 0037316061 scopus 로고    scopus 로고
    • Oligonucleotide microarray for the study of functional gene diversity in the nitrogen cycle in the environment
    • Taroncher-Oldenburg G, Griner EM, Francis CA, Ward BB: Oligonucleotide microarray for the study of functional gene diversity in the nitrogen cycle in the environment. Appl Environ Microbiol 2003, 69:1159-1171. This paper describes the development and optimisation of a DNA microarray method for the detection and quantification of functional genes in the environment and reports on their application to the study of the denitrification gene nirS.
    • (2003) Appl Environ Microbiol , vol.69 , pp. 1159-1171
    • Taroncher-Oldenburg, G.1    Griner, E.M.2    Francis, C.A.3    Ward, B.B.4
  • 19
    • 0028240270 scopus 로고
    • Molecular analysis of enrichment cultures of marine ammonia oxidisers
    • McCaig AE, Embley TM, Prosser JI: Molecular analysis of enrichment cultures of marine ammonia oxidisers. FEMS Microbiol Lett 1994, 120:363-368.
    • (1994) FEMS Microbiol Lett , vol.120 , pp. 363-368
    • McCaig, A.E.1    Embley, T.M.2    Prosser, J.I.3
  • 20
    • 0036135250 scopus 로고    scopus 로고
    • Grassland management regimens reduce small-scale heterogeneity and species diversity of β-proteobacterial ammonia oxidizer populations
    • Webster G, Embley TM, Prosser JI: Grassland management regimens reduce small-scale heterogeneity and species diversity of β-proteobacterial ammonia oxidizer populations. Appl Environ Microbiol 2002, 68:20-30.
    • (2002) Appl Environ Microbiol , vol.68 , pp. 20-30
    • Webster, G.1    Embley, T.M.2    Prosser, J.I.3
  • 21
    • 0037259086 scopus 로고    scopus 로고
    • Characterization of a nitrate-respiring bacterial community using the nitrate reductase gene (narG) as a functional marker
    • Gregory LG, Bond PL, Richardson DJ, Spiro S: Characterization of a nitrate-respiring bacterial community using the nitrate reductase gene (narG) as a functional marker. Microbiology 2003, 149:229-237.
    • (2003) Microbiology , vol.149 , pp. 229-237
    • Gregory, L.G.1    Bond, P.L.2    Richardson, D.J.3    Spiro, S.4
  • 22
    • 0034450921 scopus 로고    scopus 로고
    • Molecular detection of bacterial and streptomycete chitinases in the environment
    • Williamson N, Brian P, Wellington EMH: Molecular detection of bacterial and streptomycete chitinases in the environment. Antonie van Leeuwenhoek 2000, 78:315-321.
    • (2000) Antonie van Leeuwenhoek , vol.78 , pp. 315-321
    • Williamson, N.1    Brian, P.2    Wellington, E.M.H.3
  • 23
    • 0242668357 scopus 로고    scopus 로고
    • mRNA extraction and reverse transcription- PCR protocol for detection of nifH gene expression by Azotobacter vinelandii in soil
    • Burgmann H, Widmer F, Sigler WV, Zeyer J: mRNA extraction and reverse transcription- PCR protocol for detection of nifH gene expression by Azotobacter vinelandii in soil. Appl Environ Microbiol 2003, 69:1928-1935.
    • (2003) Appl Environ Microbiol , vol.69 , pp. 1928-1935
    • Burgmann, H.1    Widmer, F.2    Sigler, W.V.3    Zeyer, J.4
  • 24
    • 0036793715 scopus 로고    scopus 로고
    • Detection and diversity of expressed denitrification genes in estuarine sediments after reverse transcription-PCR amplification from mRNA
    • Nogales B, Timmis KN, Nedwell DB, Osborn AM: Detection and diversity of expressed denitrification genes in estuarine sediments after reverse transcription-PCR amplification from mRNA. Appl Environ Microbiol 2002, 68:5017-5025. Five denitrification genes were analysed by RT-PCR of mRNA from river sediments. Active expression of nirS and nosZ was confirmed. High diversity of nirS was observed and distribution of sequence variants was specific to sampling sites.
    • (2002) Appl Environ Microbiol , vol.68 , pp. 5017-5025
    • Nogales, B.1    Timmis, K.N.2    Nedwell, D.B.3    Osborn, A.M.4
  • 25
    • 0034628432 scopus 로고    scopus 로고
    • Stable-isotope probing as a tool in microbial ecology
    • Radajewski S, Ineson P, Parekh NR, Murrell JC: Stable-isotope probing as a tool in microbial ecology. Nature 2000, 403:646-649.
    • (2000) Nature , vol.403 , pp. 646-649
    • Radajewski, S.1    Ineson, P.2    Parekh, N.R.3    Murrell, J.C.4
  • 27
    • 0034995535 scopus 로고    scopus 로고
    • C-13 incorporation into DNA as a means of identifying the active components of ammonia-oxidizer populations
    • Whitby CB, Hall G, Pickup R, Saunders JR, Ineson P, Parekh NR, McCarthy A: C-13 incorporation into DNA as a means of identifying the active components of ammonia-oxidizer populations. Lett Appl Microbiol 2001, 32:398-401. Using group-specific 16S rRNA primers, this paper shows the identification of different active autotrophic ammonia-oxidising bacteria in freshwater enrichment cultures.
    • (2001) Lett Appl Microbiol , vol.32 , pp. 398-401
    • Whitby, C.B.1    Hall, G.2    Pickup, R.3    Saunders, J.R.4    Ineson, P.5    Parekh, N.R.6    McCarthy, A.7
  • 28
    • 0036840287 scopus 로고    scopus 로고
    • RNA stable isotope probing, a novel means of linking microbial community function to phylogeny
    • Manefield M, Whiteley AS, Griffiths RI, Bailey MJ: RNA stable isotope probing, a novel means of linking microbial community function to phylogeny. Appl Environ Microbiol 2002, 68:5367-5373. This paper deals with the RNA-SIP approach combined with profiling techniques of RT-PCR products recovered from the density gradient centrifugation fractions and shows how active phenol-degrading bacteria can be identified in an industrial bioreactor.
    • (2002) Appl Environ Microbiol , vol.68 , pp. 5367-5373
    • Manefield, M.1    Whiteley, A.S.2    Griffiths, R.I.3    Bailey, M.J.4
  • 29
    • 0035035778 scopus 로고    scopus 로고
    • Use of isotopic and molecular techniques to link toluene degradation in denitrifying aquifer microcosms to specific microbial populations
    • Pelz O, Chatzinotas A, Andersen N, Bernasconi SM, Hesse C, Abraham WR, Zeyer J: Use of isotopic and molecular techniques to link toluene degradation in denitrifying aquifer microcosms to specific microbial populations. Arch Microbiol 2001, 175:270-281.
    • (2001) Arch Microbiol , vol.175 , pp. 270-281
    • Pelz, O.1    Chatzinotas, A.2    Andersen, N.3    Bernasconi, S.M.4    Hesse, C.5    Abraham, W.R.6    Zeyer, J.7
  • 30
    • 0036790017 scopus 로고    scopus 로고
    • Microbial population genomics and ecology
    • DeLong E: Microbial population genomics and ecology. Curr Opin Microbiol 2002, 5:520-524.
    • (2002) Curr Opin Microbiol , vol.5 , pp. 520-524
    • DeLong, E.1
  • 32
    • 0036270789 scopus 로고    scopus 로고
    • Microbial diversity and function in soil: From genes to ecosystems
    • Torsvik V, Ovreas L: Microbial diversity and function in soil: from genes to ecosystems. Curr Opin Microbiol 2002, 5:240-245.
    • (2002) Curr Opin Microbiol , vol.5 , pp. 240-245
    • Torsvik, V.1    Ovreas, L.2
  • 35
    • 0037772204 scopus 로고    scopus 로고
    • Microarrays for bacterial detection and microbial community analysis
    • in press
    • Zhou J: Microarrays for bacterial detection and microbial community analysis. Curr Opin Microbiol 2003, in press.
    • (2003) Curr Opin Microbiol
    • Zhou, J.1
  • 38
    • 85031152579 scopus 로고    scopus 로고
    • Stable isotope probing of nucleic acids: A window to the function of uncultured organisms
    • in press
    • Radajewski S, McDonald IR, Murrell JC: Stable isotope probing of nucleic acids: a window to the function of uncultured organisms. Curr Opin Biotechnol, in press.
    • Curr Opin Biotechnol
    • Radajewski, S.1    McDonald, I.R.2    Murrell, J.C.3
  • 40
    • 0036727242 scopus 로고    scopus 로고
    • Isolation of antibiotics turbomycin A and B from a metagenomic library of soil microbial DNA
    • Gillespie DE, Brady SF, Bettermann AD, Cianciotto NP, Liles MR, Rondon MR, Clardy J, Goodman RM, Handelsman J: Isolation of antibiotics turbomycin A and B from a metagenomic library of soil microbial DNA. Appl Environ Microbiol 2002, 68:4301-4306. A description of the screening of a large BAC library that led to the discovery of two closely related triaryl cation antibiotics with a broad spectrum of activity. The capacity of the host, E. coli, to produce these antibiotics was stimulated by the cloning of a single operon. The interaction of the gene product with the tyrosine degradation pathway of the host results in its production.
    • (2002) Appl Environ Microbiol , vol.68 , pp. 4301-4306
    • Gillespie, D.E.1    Brady, S.F.2    Bettermann, A.D.3    Cianciotto, N.P.4    Liles, M.R.5    Rondon, M.R.6    Clardy, J.7    Goodman, R.M.8    Handelsman, J.9
  • 41
    • 0035963668 scopus 로고    scopus 로고
    • Cloning and heterologous expression of a natural product biosynthetic gene cluster from eDNA
    • Brady SF, Choa CJ, Handelsman J, Clardy J: Cloning and heterologous expression of a natural product biosynthetic gene cluster from eDNA. Org Lett 2001, 13:1981-1984.
    • (2001) Org Lett , vol.13 , pp. 1981-1984
    • Brady, S.F.1    Choa, C.J.2    Handelsman, J.3    Clardy, J.4
  • 44
    • 0346035740 scopus 로고    scopus 로고
    • Recombinant environmental libraries provide access to microbial diversity for drug discovery from natural products
    • Courtois S, Cappellano CM, Ball M, Francou FX, Normand P, Helynck G, Martinez A, Kolvek SJ, Hopke J, Osburne MS et al.: Recombinant environmental libraries provide access to microbial diversity for drug discovery from natural products. Appl Environ Microbiol 2003, 69:49-55. Total community DNA from soil was cloned into a cosmid vector designed so that it could be transformed into S. Iividans. PCR screening revealed eight novel PKS I genes.
    • (2003) Appl Environ Microbiol , vol.69 , pp. 49-55
    • Courtois, S.1    Cappellano, C.M.2    Ball, M.3    Francou, F.X.4    Normand, P.5    Helynck, G.6    Martinez, A.7    Kolvek, S.J.8    Hopke, J.9    Osburne, M.S.10


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