메뉴 건너뛰기




Volumn 407, Issue 12, 2009, Pages 3611-3619

DNA-based stable isotope probing: a link between community structure and function

Author keywords

16S rRNA genes; 13C; Bioremediation; DNA based stable isotope probing (SIP); Functional genes; Microbial diversity

Indexed keywords

16S RRNA GENES; 13C; ATTENTION TO DETAILS; COMMUNITY STRUCTURES; FUNCTIONAL GENES; LABELED SUBSTRATES; METAGENOME; MICROBIAL COMMUNITIES; MICROBIAL DIVERSITY; MICROBIAL ECOLOGIES; MOLECULAR TECHNIQUES; TAXONOMIC IDENTIFICATIONS;

EID: 65049087848     PISSN: 00489697     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.scitotenv.2008.05.012     Document Type: Article
Times cited : (70)

References (56)
  • 1
    • 0242573148 scopus 로고    scopus 로고
    • The isotope array, a new tool that employs substrate-mediated labeling of rRNA for determination of microbial community structure and function
    • Adamczyk J., Hesselsoe M., Iversen N., Horn M., Lehner A., Nielsen P.H., Schloter M., Roslev P., and Wagner M. The isotope array, a new tool that employs substrate-mediated labeling of rRNA for determination of microbial community structure and function. Appl Environ Microbiol 69 (2003) 6875-6887
    • (2003) Appl Environ Microbiol , vol.69 , pp. 6875-6887
    • Adamczyk, J.1    Hesselsoe, M.2    Iversen, N.3    Horn, M.4    Lehner, A.5    Nielsen, P.H.6    Schloter, M.7    Roslev, P.8    Wagner, M.9
  • 4
    • 34249684326 scopus 로고    scopus 로고
    • 15N achieved by disentangling the effects of genome G + C content and isotope enrichment on DNA density
    • 15N achieved by disentangling the effects of genome G + C content and isotope enrichment on DNA density. Appl Environ Microbiol 73 (2007) 3189-3195
    • (2007) Appl Environ Microbiol , vol.73 , pp. 3189-3195
    • Buckley, D.H.1    Huangyutitham, V.2    Hsu, S.F.3    Nelson, T.A.4
  • 8
    • 34547269835 scopus 로고    scopus 로고
    • The introduction of genetically modified microorganisms designed for rhizoremediation induces changes on native bacteria in the rhizosphere but not in the surrounding soil
    • de Cárcer D.A., Martín M., Mackova M., Macek T., Karlson U., and Rivilla R. The introduction of genetically modified microorganisms designed for rhizoremediation induces changes on native bacteria in the rhizosphere but not in the surrounding soil. ISME J 1 (2007) 215-223
    • (2007) ISME J , vol.1 , pp. 215-223
    • de Cárcer, D.A.1    Martín, M.2    Mackova, M.3    Macek, T.4    Karlson, U.5    Rivilla, R.6
  • 9
    • 24944587880 scopus 로고    scopus 로고
    • Two approaches to biological decontamination of groundwater and soil polluted by aromatics-characterization of microbial populations
    • Demnerová K., Mackova M., Spevákova V., Beranova K., Kochánková L., Lovecká P., Ryslavá E., and Macek T. Two approaches to biological decontamination of groundwater and soil polluted by aromatics-characterization of microbial populations. Int Microbiol 8 (2005) 205-211
    • (2005) Int Microbiol , vol.8 , pp. 205-211
    • Demnerová, K.1    Mackova, M.2    Spevákova, V.3    Beranova, K.4    Kochánková, L.5    Lovecká, P.6    Ryslavá, E.7    Macek, T.8
  • 10
    • 29144520930 scopus 로고    scopus 로고
    • Use of field-based stable isotope probing to identify adapted populations and track carbon flow through a phenol-degrading soil microbial community
    • DeRito C.M., Pumphrey G.M., and Madsen E.L. Use of field-based stable isotope probing to identify adapted populations and track carbon flow through a phenol-degrading soil microbial community. Appl Environ Microbiol 71 (2005) 7858-7865
    • (2005) Appl Environ Microbiol , vol.71 , pp. 7858-7865
    • DeRito, C.M.1    Pumphrey, G.M.2    Madsen, E.L.3
  • 11
    • 19144372182 scopus 로고    scopus 로고
    • Stable isotope probing - linking microbial identity to function
    • Dumont M.G., and Murrell J.C. Stable isotope probing - linking microbial identity to function. Nat Rev Microbiol 3 (2005) 499-504
    • (2005) Nat Rev Microbiol , vol.3 , pp. 499-504
    • Dumont, M.G.1    Murrell, J.C.2
  • 12
    • 33745134375 scopus 로고    scopus 로고
    • Identification of a complete methane monooxygenase operon from soil by combining stable isotope probing and metagenomic analysis
    • Dumont M.G., Radajewski S.M., Miguez C.B., McDonald I.R., and Murrell J.C. Identification of a complete methane monooxygenase operon from soil by combining stable isotope probing and metagenomic analysis. Environ Microbiol 8 (2006) 1240-1250
    • (2006) Environ Microbiol , vol.8 , pp. 1240-1250
    • Dumont, M.G.1    Radajewski, S.M.2    Miguez, C.B.3    McDonald, I.R.4    Murrell, J.C.5
  • 13
    • 33644841315 scopus 로고    scopus 로고
    • Changes in the community structure and activity of betaproteobacterial ammonia-oxidizing sediment bacteria along a freshwater-marine gradient
    • Freitag T.E., Chang L., and Prosser J.I. Changes in the community structure and activity of betaproteobacterial ammonia-oxidizing sediment bacteria along a freshwater-marine gradient. Environ Microbiol 8 (2006) 684-696
    • (2006) Environ Microbiol , vol.8 , pp. 684-696
    • Freitag, T.E.1    Chang, L.2    Prosser, J.I.3
  • 14
    • 31944434504 scopus 로고    scopus 로고
    • Stable-isotope probing of DNA: insights into the function of uncultivated microorganisms from isotopically labeled metagenomes
    • Friedrich M.W. Stable-isotope probing of DNA: insights into the function of uncultivated microorganisms from isotopically labeled metagenomes. Curr Opin Biotechnol 17 (2006) 59-66
    • (2006) Curr Opin Biotechnol , vol.17 , pp. 59-66
    • Friedrich, M.W.1
  • 15
    • 25144508465 scopus 로고    scopus 로고
    • 13C-carrier DNA shortens the incubation time needed to detect benzoate-utilizing denitrifying bacteria by stable-isotope probing
    • 13C-carrier DNA shortens the incubation time needed to detect benzoate-utilizing denitrifying bacteria by stable-isotope probing. Appl Environ Microbiol 71 (2005) 5192-5196
    • (2005) Appl Environ Microbiol , vol.71 , pp. 5192-5196
    • Gallagher, E.1    McGuinness, L.2    Phelps, C.3    Young, L.Y.4    Kerkhof, L.J.5
  • 16
    • 0030935768 scopus 로고    scopus 로고
    • Plant compounds that induce polychlorinated biphenyl biodegradation by Arthrobacter sp. strain B1B
    • Gilbert E.S., and Crowley D.E. Plant compounds that induce polychlorinated biphenyl biodegradation by Arthrobacter sp. strain B1B. Appl Environ Microbiol 63 (1997) 1933-1938
    • (1997) Appl Environ Microbiol , vol.63 , pp. 1933-1938
    • Gilbert, E.S.1    Crowley, D.E.2
  • 17
    • 29144450332 scopus 로고    scopus 로고
    • Investigation of an acetate-fed denitrifying microbial community by stable isotope probing, full-cycle rRNA analysis, and fluorescent in situ hybridization-microautoradiography
    • Ginige M.P., Keller J., and Blackall L.L. Investigation of an acetate-fed denitrifying microbial community by stable isotope probing, full-cycle rRNA analysis, and fluorescent in situ hybridization-microautoradiography. Appl Environ Microbiol 71 (2005) 8683-8691
    • (2005) Appl Environ Microbiol , vol.71 , pp. 8683-8691
    • Ginige, M.P.1    Keller, J.2    Blackall, L.L.3
  • 20
    • 0345686678 scopus 로고    scopus 로고
    • Discovery of a bacterium, with distinctive dioxygenase, that is responsible for in situ biodegradation in contaminated sediment
    • Jeon C.O., Park W., Padmanabhan P., DeRito C., Snape J.R., and Madsen E.L. Discovery of a bacterium, with distinctive dioxygenase, that is responsible for in situ biodegradation in contaminated sediment. Proc Natl Acad Sci U S A 100 (2003) 13591-13596
    • (2003) Proc Natl Acad Sci U S A , vol.100 , pp. 13591-13596
    • Jeon, C.O.1    Park, W.2    Padmanabhan, P.3    DeRito, C.4    Snape, J.R.5    Madsen, E.L.6
  • 21
    • 0842345383 scopus 로고    scopus 로고
    • Polaromonas naphthalenivorans sp. nov., a naphthalene-degrading bacterium from naphthalene-contaminated sediment
    • Jeon C.O., Park W., Ghiorse W.C., and Madsen E.L. Polaromonas naphthalenivorans sp. nov., a naphthalene-degrading bacterium from naphthalene-contaminated sediment. Int J Syst Evol Microbiol 54 (2004) 93-97
    • (2004) Int J Syst Evol Microbiol , vol.54 , pp. 93-97
    • Jeon, C.O.1    Park, W.2    Ghiorse, W.C.3    Madsen, E.L.4
  • 22
    • 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 P.H., Andreasen K.H., Juretschko S., Nielsen J.L., Schleifer K.H., and Wagner M. Combination of fluorescent in situ hybridization and microautoradiography - a new tool for structure-function analyses in microbial ecology. Appl Environ Microbiol 65 (1999) 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
  • 23
    • 43049117987 scopus 로고    scopus 로고
    • Methods for rhizoremediation research. Approaches to experimental design and microbial analysis
    • Phytoremediation and rhizoremediation. Theoretical background. Mackova M., Dowling D., and Macek T. (Eds), Springer, Dordrecht
    • Leigh M.B. Methods for rhizoremediation research. Approaches to experimental design and microbial analysis. In: Mackova M., Dowling D., and Macek T. (Eds). Phytoremediation and rhizoremediation. Theoretical background. Focus on biotechnology vol. 9A (2006), Springer, Dordrecht 33-55
    • (2006) Focus on biotechnology , vol.9 A , pp. 33-55
    • Leigh, M.B.1
  • 24
    • 33646086019 scopus 로고    scopus 로고
    • Polychlorinated biphenyl (PCB)-degrading bacteria associated with trees in a PCB-contaminated site
    • Leigh M.B., Prouzová P., Macková M., Macek T., Nagle D.P., and Fletcher J.S. Polychlorinated biphenyl (PCB)-degrading bacteria associated with trees in a PCB-contaminated site. Appl Environ Microbiol 72 (2006) 2331-2342
    • (2006) Appl Environ Microbiol , vol.72 , pp. 2331-2342
    • Leigh, M.B.1    Prouzová, P.2    Macková, M.3    Macek, T.4    Nagle, D.P.5    Fletcher, J.S.6
  • 25
    • 34249939326 scopus 로고    scopus 로고
    • Biphenyl-utilizing bacteria and their functional genes in a pine root zone contaminated with polychlorinated biphenyls (PCBs)
    • Leigh M.B., Pellizari V.H., Uhlík O., Sutka R., Rodrigues J., Ostrom N.E., Zhou J., and Tiedje J.M. Biphenyl-utilizing bacteria and their functional genes in a pine root zone contaminated with polychlorinated biphenyls (PCBs). ISME J 1 (2007) 134-148
    • (2007) ISME J , vol.1 , pp. 134-148
    • Leigh, M.B.1    Pellizari, V.H.2    Uhlík, O.3    Sutka, R.4    Rodrigues, J.5    Ostrom, N.E.6    Zhou, J.7    Tiedje, J.M.8
  • 26
    • 4644335844 scopus 로고    scopus 로고
    • Molecular diversity of methanotrophs in Transbaikal soda lake sediments and identification of potentially active populations by stable isotope probing
    • Lin J.L., Radajewski S., Eshinimaev B.T., Trotsenko Y.A., McDonald I.R., and Murrell J.C. Molecular diversity of methanotrophs in Transbaikal soda lake sediments and identification of potentially active populations by stable isotope probing. Environ Microbiol 6 (2004) 1049-1060
    • (2004) Environ Microbiol , vol.6 , pp. 1049-1060
    • Lin, J.L.1    Radajewski, S.2    Eshinimaev, B.T.3    Trotsenko, Y.A.4    McDonald, I.R.5    Murrell, J.C.6
  • 27
    • 0027998116 scopus 로고
    • Bacterial phylogeny based on 16S and 23S rRNA sequence analysis
    • Ludwig W., and Schleifer K.H. Bacterial phylogeny based on 16S and 23S rRNA sequence analysis. FEMS Microbiol Rev 15 (1994) 155-173
    • (1994) FEMS Microbiol Rev , vol.15 , pp. 155-173
    • Ludwig, W.1    Schleifer, K.H.2
  • 28
    • 0842266321 scopus 로고    scopus 로고
    • Stable isotope probing of rRNA and DNA reveals a dynamic methylotroph community and trophic interactions with fungi and protozoa in oxic rice field soil
    • Lueders T., Wagner B., Claus P., and Friedrich M.W. Stable isotope probing of rRNA and DNA reveals a dynamic methylotroph community and trophic interactions with fungi and protozoa in oxic rice field soil. Environ Microbiol 6 (2004) 60-72
    • (2004) Environ Microbiol , vol.6 , pp. 60-72
    • Lueders, T.1    Wagner, B.2    Claus, P.3    Friedrich, M.W.4
  • 29
    • 0842266326 scopus 로고    scopus 로고
    • Enhanced sensitivity of DNA- and rRNA-based stable isotope probing by fractionation and quantitative analysis of isopycnic centrifugation gradients
    • Lueders T., Manefield M., and Friedrich M.W. Enhanced sensitivity of DNA- and rRNA-based stable isotope probing by fractionation and quantitative analysis of isopycnic centrifugation gradients. Environ Microbiol 6 (2004) 73-78
    • (2004) Environ Microbiol , vol.6 , pp. 73-78
    • Lueders, T.1    Manefield, M.2    Friedrich, M.W.3
  • 32
    • 39149087111 scopus 로고    scopus 로고
    • Phytoremediation and rhizoremediation
    • Theoretical background, Springer, Dordrecht 300 pp.
    • Mackova M., Dowling D., and Macek T. Phytoremediation and rhizoremediation. Theoretical background. Focus on biotechnology vol. 9A (2006), Springer, Dordrecht 300 pp.
    • (2006) Focus on biotechnology , vol.9 A
    • Mackova, M.1    Dowling, D.2    Macek, T.3
  • 34
    • 0036840287 scopus 로고    scopus 로고
    • RNA stable isotope probing, a novel means of linking microbial community function to phylogeny
    • Manefield M., Whiteley A.S., Griffiths R.I., and Bailey M.J. RNA stable isotope probing, a novel means of linking microbial community function to phylogeny. Appl Environ Microbiol 68 (2002) 5367-5373
    • (2002) Appl Environ Microbiol , vol.68 , pp. 5367-5373
    • Manefield, M.1    Whiteley, A.S.2    Griffiths, R.I.3    Bailey, M.J.4
  • 36
    • 17544368805 scopus 로고    scopus 로고
    • Degradation of methyl bromide and methyl chloride in soil microcosms: use of stable C isotope fractionation and stable isotope probing to identify reactions and the responsible microorganisms
    • Miller L.G., Warner K.L., Baesman S.M., Oremland R.S., McDonald I.R., Radajewski S., and Murrell J.C. Degradation of methyl bromide and methyl chloride in soil microcosms: use of stable C isotope fractionation and stable isotope probing to identify reactions and the responsible microorganisms. Geochim Cosmochim Acta 68 (2004) 3271-3283
    • (2004) Geochim Cosmochim Acta , vol.68 , pp. 3271-3283
    • Miller, L.G.1    Warner, K.L.2    Baesman, S.M.3    Oremland, R.S.4    McDonald, I.R.5    Radajewski, S.6    Murrell, J.C.7
  • 37
    • 0036200066 scopus 로고    scopus 로고
    • Identification of the functionally active methanotroph population in a peat soil microcosm by stable-isotope probing
    • Morris S.A., Radajewski S., Willison T.W., and Murrell J.C. Identification of the functionally active methanotroph population in a peat soil microcosm by stable-isotope probing. Appl Environ Microbiol 68 (2002) 1446-1453
    • (2002) Appl Environ Microbiol , vol.68 , pp. 1446-1453
    • Morris, S.A.1    Radajewski, S.2    Willison, T.W.3    Murrell, J.C.4
  • 39
    • 34248137874 scopus 로고    scopus 로고
    • Methodological considerations for the use of stable isotope probing in microbial ecology
    • Neufeld J.D., Dumont M.G., Vohra J., and Murrell J.C. Methodological considerations for the use of stable isotope probing in microbial ecology. Microb Ecol 53 (2007) 435-442
    • (2007) Microb Ecol , vol.53 , pp. 435-442
    • Neufeld, J.D.1    Dumont, M.G.2    Vohra, J.3    Murrell, J.C.4
  • 40
    • 34848869322 scopus 로고    scopus 로고
    • Microbial degradation of the biocide polyhexamethylene biguanide: isolation and characterization of enrichment consortia and determination of degradation by measurement of stable isotope incorporation into DNA
    • O'Malley L.P., Shaw C.H., and Collins A.N. Microbial degradation of the biocide polyhexamethylene biguanide: isolation and characterization of enrichment consortia and determination of degradation by measurement of stable isotope incorporation into DNA. J Appl Microbiol 103 (2007) 1158-1169
    • (2007) J Appl Microbiol , vol.103 , pp. 1158-1169
    • O'Malley, L.P.1    Shaw, C.H.2    Collins, A.N.3
  • 42
    • 0034628432 scopus 로고    scopus 로고
    • Stable-isotope probing as a tool in microbial ecology
    • Radajewski S., Ineson P., Parekh N.R., and Murrell J.C. Stable-isotope probing as a tool in microbial ecology. Nature 403 (2000) 646-649
    • (2000) Nature , vol.403 , pp. 646-649
    • Radajewski, S.1    Ineson, P.2    Parekh, N.R.3    Murrell, J.C.4
  • 44
    • 0038482074 scopus 로고    scopus 로고
    • Stable-isotope probing of nucleic acids: a window to the function of uncultured microorganisms
    • Radajewski S., McDonald I.R., and Murrell J.C. Stable-isotope probing of nucleic acids: a window to the function of uncultured microorganisms. Curr Opin Biotechnol 14 (2003) 296-302
    • (2003) Curr Opin Biotechnol , vol.14 , pp. 296-302
    • Radajewski, S.1    McDonald, I.R.2    Murrell, J.C.3
  • 45
    • 38349114175 scopus 로고    scopus 로고
    • The effect of ryegrass (Lolium perenne) on decrease of PAH content in long term contaminated soil
    • Rezek J., in der Wiesche C., Mackova M., Zadrazil F., and Macek T. The effect of ryegrass (Lolium perenne) on decrease of PAH content in long term contaminated soil. Chemosphere 70 (2008) 1603-1608
    • (2008) Chemosphere , vol.70 , pp. 1603-1608
    • Rezek, J.1    in der Wiesche, C.2    Mackova, M.3    Zadrazil, F.4    Macek, T.5
  • 48
  • 49
    • 38349181832 scopus 로고    scopus 로고
    • The chemical ecology of pollutant biodegradation. Bioremediation and phytoremediation from mechanistic and ecological perspectives
    • Phytoremediation and rhizoremediation. Theoretical background. Mackova M., Dowling D., and Macek T. (Eds), Springer, Dordrecht
    • Singer A.C. The chemical ecology of pollutant biodegradation. Bioremediation and phytoremediation from mechanistic and ecological perspectives. In: Mackova M., Dowling D., and Macek T. (Eds). Phytoremediation and rhizoremediation. Theoretical background. Focus on Biotechnology vol. 9A (2006), Springer, Dordrecht 5-21
    • (2006) Focus on Biotechnology , vol.9 A , pp. 5-21
    • Singer, A.C.1
  • 50
    • 2942596158 scopus 로고    scopus 로고
    • The tritrophic trinity: a source of pollutant-degrading enzymes and its implications for phytoremediation
    • Singer A.C., Thompson I.P., and Bailey M.J. The tritrophic trinity: a source of pollutant-degrading enzymes and its implications for phytoremediation. Curr Opin Microbiol 7 (2004) 239-244
    • (2004) Curr Opin Microbiol , vol.7 , pp. 239-244
    • Singer, A.C.1    Thompson, I.P.2    Bailey, M.J.3
  • 51
    • 15444374754 scopus 로고    scopus 로고
    • Stable-isotope probing of bacteria capable of degrading salicylate, naphthalene, or phenanthrene in a bioreactor treating contaminated soil
    • Singleton D.R., Powell S.N., Sangaiah R., Gold A., Ball L.M., and Aitken M.D. Stable-isotope probing of bacteria capable of degrading salicylate, naphthalene, or phenanthrene in a bioreactor treating contaminated soil. Appl Environ Microbiol 71 (2005) 1202-1209
    • (2005) Appl Environ Microbiol , vol.71 , pp. 1202-1209
    • Singleton, D.R.1    Powell, S.N.2    Sangaiah, R.3    Gold, A.4    Ball, L.M.5    Aitken, M.D.6
  • 52
    • 0036270789 scopus 로고    scopus 로고
    • Microbial diversity and function in soil: from genes to ecosystems
    • Torsvik V., and Øvreås L. Microbial diversity and function in soil: from genes to ecosystems. Curr Opin Microbiol 3 (2002) 240-245
    • (2002) Curr Opin Microbiol , vol.3 , pp. 240-245
    • Torsvik, V.1    Øvreås, L.2
  • 54
    • 33746778517 scopus 로고    scopus 로고
    • A comparison of stable-isotope probing of DNA and phospholipid fatty acids to study prokaryotic functional diversity in sulfate-reducing marine sediment enrichment slurries
    • Webster G., Watt L.C., Rinna J., Fry J.C., Evershed R.P., Parkes R.J., and Weightman A.J. A comparison of stable-isotope probing of DNA and phospholipid fatty acids to study prokaryotic functional diversity in sulfate-reducing marine sediment enrichment slurries. Environ Microbiol 8 (2006) 1575-1589
    • (2006) Environ Microbiol , vol.8 , pp. 1575-1589
    • Webster, G.1    Watt, L.C.2    Rinna, J.3    Fry, J.C.4    Evershed, R.P.5    Parkes, R.J.6    Weightman, A.J.7
  • 55
    • 0038265142 scopus 로고    scopus 로고
    • Resolving functional diversity in relation to microbial community structure in soil: exploiting genomics and stable isotope probing
    • Wellington E.M., Berry A., and Krsek M. Resolving functional diversity in relation to microbial community structure in soil: exploiting genomics and stable isotope probing. Curr Opin Microbiol 6 (2003) 295-301
    • (2003) Curr Opin Microbiol , vol.6 , pp. 295-301
    • Wellington, E.M.1    Berry, A.2    Krsek, M.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.