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Volumn 69, Issue 3, 2007, Pages 523-528

Improved 16S rRNA-targeted probe set for analysis of sulfate-reducing bacteria by fluorescence in situ hybridization

Author keywords

16S rRNA targeted probes; Deltaproteobacteria; Fluorescence in situ hybridization; Sulfate reducing bacteria

Indexed keywords

RNA 16S;

EID: 34247592880     PISSN: 01677012     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.mimet.2007.02.009     Document Type: Article
Times cited : (94)

References (36)
  • 1
    • 0002890678 scopus 로고    scopus 로고
    • Nucleic acid probes and their application in environmental microbiology
    • Garrity G.M. (Ed), Springer, New York
    • Amann R., and Schleifer K.-H. Nucleic acid probes and their application in environmental microbiology. In: Garrity G.M. (Ed). Bergey's Manual of Systematic Bacteriology (2001), Springer, New York 67-82
    • (2001) Bergey's Manual of Systematic Bacteriology , pp. 67-82
    • Amann, R.1    Schleifer, K.-H.2
  • 2
    • 0025294528 scopus 로고
    • Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations
    • Amann R.I., Binder B.J., Olson R.J., Chisholm S.W., Devereux R., and Stahl D.A. Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations. Appl. Environ. Microbiol. 56 (1990) 1919-1925
    • (1990) Appl. Environ. Microbiol. , vol.56 , pp. 1919-1925
    • Amann, R.I.1    Binder, B.J.2    Olson, R.J.3    Chisholm, S.W.4    Devereux, R.5    Stahl, D.A.6
  • 3
    • 0029890507 scopus 로고    scopus 로고
    • In situ visualization of high genetic diversity in a natural microbial community
    • Amann R., Snaidr J., Wagner M., Ludwig W., and Schleifer K.H. In situ visualization of high genetic diversity in a natural microbial community. J. Bacteriol. 178 (1996) 3496-3500
    • (1996) J. Bacteriol. , vol.178 , pp. 3496-3500
    • Amann, R.1    Snaidr, J.2    Wagner, M.3    Ludwig, W.4    Schleifer, K.H.5
  • 4
    • 0035370087 scopus 로고    scopus 로고
    • The identification of microorganisms by fluorescence in situ hybridisation
    • Amann R., Fuchs B.M., and Behrens S. The identification of microorganisms by fluorescence in situ hybridisation. Curr. Opin. Biotechnol. 12 (2001) 231-236
    • (2001) Curr. Opin. Biotechnol. , vol.12 , pp. 231-236
    • Amann, R.1    Fuchs, B.M.2    Behrens, S.3
  • 5
    • 0036682224 scopus 로고    scopus 로고
    • PRIMROSE: a computer program for generating and estimating the phylogenetic range of 16S rRNA oligonucleotide probes and primers in conjunction with the RDP-II database
    • Ashelford K.E., Weightman A.J., and Fry J.C. PRIMROSE: a computer program for generating and estimating the phylogenetic range of 16S rRNA oligonucleotide probes and primers in conjunction with the RDP-II database. Nucleic Acids Res. 30 (2002) 3481-3489
    • (2002) Nucleic Acids Res. , vol.30 , pp. 3481-3489
    • Ashelford, K.E.1    Weightman, A.J.2    Fry, J.C.3
  • 6
    • 0344406194 scopus 로고    scopus 로고
    • In situ accessibility of small-subunit rRNA of members of the domains Bacteria, Archaea, and Eucarya to Cy3-labeled oligonucleotide probes
    • Behrens S., Ruhland C., Inacio J., Huber H., Fonseca A., Spencer-Martins I., Fuchs B.M., and Amann R. In situ accessibility of small-subunit rRNA of members of the domains Bacteria, Archaea, and Eucarya to Cy3-labeled oligonucleotide probes. Appl. Environ. Microbiol. 69 (2003) 1748-1758
    • (2003) Appl. Environ. Microbiol. , vol.69 , pp. 1748-1758
    • Behrens, S.1    Ruhland, C.2    Inacio, J.3    Huber, H.4    Fonseca, A.5    Spencer-Martins, I.6    Fuchs, B.M.7    Amann, R.8
  • 8
    • 0344172842 scopus 로고    scopus 로고
    • The domain-specific probe EUB338 is insufficient for the detection of all bacteria: development and evaluation of a more comprehensive probe set
    • Daims H., Brühl A., Amann R., Schleifer K.-H., and Wagner M. The domain-specific probe EUB338 is insufficient for the detection of all bacteria: development and evaluation of a more comprehensive probe set. Syst. Appl. Microbiol. 22 (1999) 434-444
    • (1999) Syst. Appl. Microbiol. , vol.22 , pp. 434-444
    • Daims, H.1    Brühl, A.2    Amann, R.3    Schleifer, K.-H.4    Wagner, M.5
  • 9
    • 13444308853 scopus 로고    scopus 로고
    • Fluorescence in situ hybridization for the detection of prokaryotes
    • BIOS Scientific Publishers, Abingdon, UK
    • Daims H., Stoecker K., and Wagner M. Fluorescence in situ hybridization for the detection of prokaryotes. Advanced Methods in Molecular Microbial Ecology (2005), BIOS Scientific Publishers, Abingdon, UK 213-239
    • (2005) Advanced Methods in Molecular Microbial Ecology , pp. 213-239
    • Daims, H.1    Stoecker, K.2    Wagner, M.3
  • 10
    • 33644868597 scopus 로고    scopus 로고
    • daime, a novel image analysis program for microbial ecology and biofilm research
    • Daims H., Lücker S., and Wagner M. daime, a novel image analysis program for microbial ecology and biofilm research. Environ. Microbiol. 8 (2006) 200-213
    • (2006) Environ. Microbiol. , vol.8 , pp. 200-213
    • Daims, H.1    Lücker, S.2    Wagner, M.3
  • 12
    • 0033855457 scopus 로고    scopus 로고
    • Unlabeled helper oligonucleotides increase the in situ accessibility to 16S rRNA of fluorescently labeled oligonucleotide probes
    • Fuchs B.M., Glockner F.O., Wulf J., and Amann R. Unlabeled helper oligonucleotides increase the in situ accessibility to 16S rRNA of fluorescently labeled oligonucleotide probes. Appl. Environ. Microbiol. 66 (2000) 3603-3607
    • (2000) Appl. Environ. Microbiol. , vol.66 , pp. 3603-3607
    • Fuchs, B.M.1    Glockner, F.O.2    Wulf, J.3    Amann, R.4
  • 13
    • 0021781839 scopus 로고
    • Sulphate-reducing bacteria and anaerobic corrosion
    • Hamilton W.A. Sulphate-reducing bacteria and anaerobic corrosion. Annu. Rev. Microbiol. 39 (1985) 195-217
    • (1985) Annu. Rev. Microbiol. , vol.39 , pp. 195-217
    • Hamilton, W.A.1
  • 14
    • 0019999242 scopus 로고
    • Mineralization of organic matter in the sea-bed-the role of sulphate reduction
    • Jørgensen B.B. Mineralization of organic matter in the sea-bed-the role of sulphate reduction. Nature 296 (1982) 643-645
    • (1982) Nature , vol.296 , pp. 643-645
    • Jørgensen, B.B.1
  • 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 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
  • 17
    • 33846033212 scopus 로고    scopus 로고
    • Diversity and abundance of sulfate-reducing microorganisms in the sulfate and methane zones of a marine sediment, Black Sea
    • Leloup J., Loy A., Knab N.J., Borowski C., Wagner M., and Jørgensen B.B. Diversity and abundance of sulfate-reducing microorganisms in the sulfate and methane zones of a marine sediment, Black Sea. Environ. Microbiol. 9 (2007) 131-142
    • (2007) Environ. Microbiol. , vol.9 , pp. 131-142
    • Leloup, J.1    Loy, A.2    Knab, N.J.3    Borowski, C.4    Wagner, M.5    Jørgensen, B.B.6
  • 18
    • 0033952908 scopus 로고    scopus 로고
    • Bacteremia caused by a strain of Desulfovibrio related to the provisionally named Desulfovibrio fairfieldensis
    • Loubinoux J., Mory F., Pereira I.A., and Le Faou A.E. Bacteremia caused by a strain of Desulfovibrio related to the provisionally named Desulfovibrio fairfieldensis. J. Clin. Microbiol. 38 (2000) 931-934
    • (2000) J. Clin. Microbiol. , vol.38 , pp. 931-934
    • Loubinoux, J.1    Mory, F.2    Pereira, I.A.3    Le Faou, A.E.4
  • 19
    • 0036795787 scopus 로고    scopus 로고
    • Oligonucleotide microarray for 16S rRNA gene-based detection of all recognized lineages of sulfate-reducing prokaryotes in the environment
    • Loy A., Lehner A., Lee N., Adamczyk J., Meier H., Ernst J., Schleifer K.-H., and Wagner M. Oligonucleotide microarray for 16S rRNA gene-based detection of all recognized lineages of sulfate-reducing prokaryotes in the environment. Appl. Environ. Microbiol. 68 (2002) 5064-5081
    • (2002) Appl. Environ. Microbiol. , vol.68 , pp. 5064-5081
    • Loy, A.1    Lehner, A.2    Lee, N.3    Adamczyk, J.4    Meier, H.5    Ernst, J.6    Schleifer, K.-H.7    Wagner, M.8
  • 20
    • 10444242668 scopus 로고    scopus 로고
    • Microarray and functional gene analyses of sulfate-reducing prokaryotes in low sulfate, acidic fens reveal co-occurrence of recognized genera and novel lineages
    • Loy A., Küsel K., Lehner A., Drake H.L., and Wagner M. Microarray and functional gene analyses of sulfate-reducing prokaryotes in low sulfate, acidic fens reveal co-occurrence of recognized genera and novel lineages. Appl. Environ. Microbiol. 70 (2004) 6998-7009
    • (2004) Appl. Environ. Microbiol. , vol.70 , pp. 6998-7009
    • Loy, A.1    Küsel, K.2    Lehner, A.3    Drake, H.L.4    Wagner, M.5
  • 21
    • 33846102841 scopus 로고    scopus 로고
    • probeBase-an online resource for rRNA-targeted oligonucleotide probes: New features 2007
    • Loy A., Maixner F., Wagner M., and Horn M. probeBase-an online resource for rRNA-targeted oligonucleotide probes: New features 2007. Nucleic Acids Res. 35 (2007) D800-D804
    • (2007) Nucleic Acids Res. , vol.35
    • Loy, A.1    Maixner, F.2    Wagner, M.3    Horn, M.4
  • 24
    • 0027068041 scopus 로고
    • Phylogenetic oligodeoxynucleotide probes for the major subclasses of Proteobacteria: problems and solutions
    • Manz W., Amann R., Ludwig W., Wagner M., and Schleifer K.-H. Phylogenetic oligodeoxynucleotide probes for the major subclasses of Proteobacteria: problems and solutions. Syst. Appl. Microbiol. 15 (1992) 593-600
    • (1992) Syst. Appl. Microbiol. , vol.15 , pp. 593-600
    • Manz, W.1    Amann, R.2    Ludwig, W.3    Wagner, M.4    Schleifer, K.-H.5
  • 25
    • 0035919654 scopus 로고    scopus 로고
    • Methane-consuming archaea revealed by directly coupled isotopic and phylogenetic analysis
    • Orphan V.J., House C.H., Hinrichs K.U., McKeegan K.D., and DeLong E.F. Methane-consuming archaea revealed by directly coupled isotopic and phylogenetic analysis. Science 293 (2001) 484-487
    • (2001) Science , vol.293 , pp. 484-487
    • Orphan, V.J.1    House, C.H.2    Hinrichs, K.U.3    McKeegan, K.D.4    DeLong, E.F.5
  • 26
    • 0038221073 scopus 로고    scopus 로고
    • Automated enumeration of groups of marine picoplankton after fluorescence in situ hybridization
    • Pernthaler J., Pernthaler A., and Amann R. Automated enumeration of groups of marine picoplankton after fluorescence in situ hybridization. Appl. Environ. Microbiol. 69 (2003) 2631-2637
    • (2003) Appl. Environ. Microbiol. , vol.69 , pp. 2631-2637
    • Pernthaler, J.1    Pernthaler, A.2    Amann, R.3
  • 27
    • 0029739071 scopus 로고    scopus 로고
    • Degradative capacities and 16S rRNA-targeted whole-cell hybridization of sulfate-reducing bacteria in an anaerobic enrichment culture utilizing alkylbenzenes from crude oil
    • Rabus R., Fukui M., Wilkes H., and Widdle F. Degradative capacities and 16S rRNA-targeted whole-cell hybridization of sulfate-reducing bacteria in an anaerobic enrichment culture utilizing alkylbenzenes from crude oil. Appl. Environ. Microbiol. 62 (1996) 3605-3613
    • (1996) Appl. Environ. Microbiol. , vol.62 , pp. 3605-3613
    • Rabus, R.1    Fukui, M.2    Wilkes, H.3    Widdle, F.4
  • 28
    • 0027375701 scopus 로고
    • 2S in photosynthetic biofilms determined by oligonucleotide probes and microelectrodes
    • 2S in photosynthetic biofilms determined by oligonucleotide probes and microelectrodes. Appl. Environ. Microbiol. 59 (1993) 3840-3849
    • (1993) Appl. Environ. Microbiol. , vol.59 , pp. 3840-3849
    • Ramsing, N.B.1    Kühl, M.2    Jørgensen, B.B.3
  • 30
    • 0034940124 scopus 로고    scopus 로고
    • Structure and diversity of Gram-negative sulfate-reducing bacteria on rice roots
    • Scheid D., and Stubner S. Structure and diversity of Gram-negative sulfate-reducing bacteria on rice roots. FEMS Microbiol. Ecol. 36 (2001) 175-183
    • (2001) FEMS Microbiol. Ecol. , vol.36 , pp. 175-183
    • Scheid, D.1    Stubner, S.2
  • 31
    • 0002007445 scopus 로고    scopus 로고
    • Nucleic acid based techniques for analyzing the diversity, structure, and dynamics of microbial communities in wastewater treatment
    • Rehm H.-J., Reed G., Pühler A., and Stadler P. (Eds), Wiley-VCH, Weinheim
    • Schramm A., and Amann R. Nucleic acid based techniques for analyzing the diversity, structure, and dynamics of microbial communities in wastewater treatment. In: Rehm H.-J., Reed G., Pühler A., and Stadler P. (Eds). Environmental Processes-Wastewater and Waste Treatment (1999), Wiley-VCH, Weinheim 85-108
    • (1999) Environmental Processes-Wastewater and Waste Treatment , pp. 85-108
    • Schramm, A.1    Amann, R.2
  • 32
    • 18744372991 scopus 로고    scopus 로고
    • Fluorescence in situ hybridization of 16S rRNA gene clones (Clone-FISH) for probe validation and screening of clone libraries
    • Schramm A., Fuchs B.M., Nielsen J.L., Tonolla M., and Stahl D.A. Fluorescence in situ hybridization of 16S rRNA gene clones (Clone-FISH) for probe validation and screening of clone libraries. Environ. Microbiol. 4 (2002) 713-720
    • (2002) Environ. Microbiol. , vol.4 , pp. 713-720
    • Schramm, A.1    Fuchs, B.M.2    Nielsen, J.L.3    Tonolla, M.4    Stahl, D.A.5
  • 33
    • 34247619100 scopus 로고    scopus 로고
    • Stahl, D.A., Loy, A., Wagner, M., in press. Molecular strategies for studies of natural populations of sulphate-reducing microorganisms. In: Barton, L.L., Hamilton, W.A. (Eds.), Sulfate-Reducing Bacteria: Environmental and Engineered Systems. Cambridge University Press.
  • 34
    • 0029943094 scopus 로고    scopus 로고
    • Probable new species of Desulfovibrio isolated from a pyogenic liver abscess
    • Tee W., Dyall-Smith M., Woods W., and Eisen D. Probable new species of Desulfovibrio isolated from a pyogenic liver abscess. J. Clin. Microbiol. 34 (1996) 1760-1764
    • (1996) J. Clin. Microbiol. , vol.34 , pp. 1760-1764
    • Tee, W.1    Dyall-Smith, M.2    Woods, W.3    Eisen, D.4
  • 35
    • 0038265129 scopus 로고    scopus 로고
    • Fluorescence in situ hybridisation for the identification and characterisation of prokaryotes
    • Wagner M., Horn M., and Daims H. Fluorescence in situ hybridisation for the identification and characterisation of prokaryotes. Curr. Opin. Microbiol. 6 (2003) 302-309
    • (2003) Curr. Opin. Microbiol. , vol.6 , pp. 302-309
    • Wagner, M.1    Horn, M.2    Daims, H.3
  • 36
    • 33644856670 scopus 로고    scopus 로고
    • Making all parts of the 16S rRNA of Escherichia coli accessible in situ to single DNA oligonucleotides
    • Yilmaz L.S., Okten H.E., and Noguera D.R. Making all parts of the 16S rRNA of Escherichia coli accessible in situ to single DNA oligonucleotides. Appl. Environ. Microbiol. 72 (2006) 733-744
    • (2006) Appl. Environ. Microbiol. , vol.72 , pp. 733-744
    • Yilmaz, L.S.1    Okten, H.E.2    Noguera, D.R.3


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