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Volumn 9, Issue 4, 2016, Pages 519-524

Underestimation of ammonia-oxidizing bacteria abundance by amplification bias in amoA-targeted qPCR

Author keywords

[No Author keywords available]

Indexed keywords

AMMONIA OXIDIZING BACTERIUM; AMOA GENE; AMPLICON; ARTICLE; BACTERIAL GENE; BACTERIUM IDENTIFICATION; COMPUTER MODEL; GENE AMPLIFICATION; GENE CLUSTER; GENE TARGETING; GENETIC ANALYSIS; MICROBIAL COMMUNITY; MICROBIAL DIVERSITY; MOLECULAR CLONING; NITROSOMONAS; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; POLYMERASE CHAIN REACTION; POPULATION ABUNDANCE; QUANTITATIVE ANALYSIS; SEQUENCE ANALYSIS;

EID: 84976536097     PISSN: 17517907     EISSN: 17517915     Source Type: Journal    
DOI: 10.1111/1751-7915.12366     Document Type: Article
Times cited : (26)

References (17)
  • 1
    • 84907020140 scopus 로고    scopus 로고
    • Agreement between amoA gene-specific quantitative PCR and fluorescence in situ hybridization in the measurement of ammonia-oxidizing bacteria in activated sludge
    • Baptista, J.D.C., Lunn, M., Davenport, R.J., Swan, D.L., Read, L.F., Brown, M.R., et al. (2014) Agreement between amoA gene-specific quantitative PCR and fluorescence in situ hybridization in the measurement of ammonia-oxidizing bacteria in activated sludge. Appl Environ Microbiol 80: 5901–5910.
    • (2014) Appl Environ Microbiol , vol.80 , pp. 5901-5910
    • Baptista, J.D.C.1    Lunn, M.2    Davenport, R.J.3    Swan, D.L.4    Read, L.F.5    Brown, M.R.6
  • 2
    • 40549109538 scopus 로고    scopus 로고
    • Quantification of the detrimental effect of a single primer-template mismatch by real-time PCR using the 16S rRNA gene as an example
    • Bru, D., Martin-Laurent, F., and Philippot, L. (2008) Quantification of the detrimental effect of a single primer-template mismatch by real-time PCR using the 16S rRNA gene as an example. Appl Environ Microbiol 74: 1660–1663.
    • (2008) Appl Environ Microbiol , vol.74 , pp. 1660-1663
    • Bru, D.1    Martin-Laurent, F.2    Philippot, L.3
  • 3
    • 84891787231 scopus 로고    scopus 로고
    • Ribosomal Database Project: data and tools for high throughput rRNA analysis
    • Cole, J.R., Wang, Q., Fish, J.A., Chai, B., McGarrell, D.M., Sun, Y., et al. (2014) Ribosomal Database Project: data and tools for high throughput rRNA analysis. Nucleic Acids Res 42: D633–D642.
    • (2014) Nucleic Acids Res , vol.42 , pp. D633-D642
    • Cole, J.R.1    Wang, Q.2    Fish, J.A.3    Chai, B.4    McGarrell, D.M.5    Sun, Y.6
  • 5
    • 0035144174 scopus 로고    scopus 로고
    • Quantification of ammonia-oxidizing bacteria in arable soil by real-time PCR
    • Hermansson, A., and Lindgren, P.E. (2001) Quantification of ammonia-oxidizing bacteria in arable soil by real-time PCR. Appl Environ Microbiol 67: 972–976.
    • (2001) Appl Environ Microbiol , vol.67 , pp. 972-976
    • Hermansson, A.1    Lindgren, P.E.2
  • 6
    • 74149086631 scopus 로고    scopus 로고
    • Phylogenetic and functional marker genes to study ammonia-oxidizing microorganisms (AOM) in the environment
    • Junier, P., Molina, V., Dorador, C., Hadas, O., Kim, O.-S., Junier, T., et al. (2010) Phylogenetic and functional marker genes to study ammonia-oxidizing microorganisms (AOM) in the environment. Appl Microbiol Biotechnol 85: 425–440.
    • (2010) Appl Microbiol Biotechnol , vol.85 , pp. 425-440
    • Junier, P.1    Molina, V.2    Dorador, C.3    Hadas, O.4    Kim, O.-S.5    Junier, T.6
  • 7
    • 0030901922 scopus 로고    scopus 로고
    • Analysis of ammonia-oxidizing bacteria of the beta subdivision of the class Proteobacteria in coastal sand dunes by denaturing gradient gel electrophoresis and sequencing of PCR-amplified 16S ribosomal DNA fragments
    • Kowalchuk, G.A., Stephen, J.R., De Boer, W., Prosser, J.I., Embley, T.M., and Woldendorp, J.W. (1997) Analysis of ammonia-oxidizing bacteria of the beta subdivision of the class Proteobacteria in coastal sand dunes by denaturing gradient gel electrophoresis and sequencing of PCR-amplified 16S ribosomal DNA fragments. Appl Environ Microbiol 63: 1489–1497.
    • (1997) Appl Environ Microbiol , vol.63 , pp. 1489-1497
    • Kowalchuk, G.A.1    Stephen, J.R.2    De Boer, W.3    Prosser, J.I.4    Embley, T.M.5    Woldendorp, J.W.6
  • 8
    • 85022158148 scopus 로고    scopus 로고
    • MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets
    • In press
    • Kumar, S., Stecher, G., and Tamura, K. (2016) MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets. Mol Biol Evol In press.
    • (2016) Mol Biol Evol
    • Kumar, S.1    Stecher, G.2    Tamura, K.3
  • 9
    • 33646565655 scopus 로고    scopus 로고
    • Comparison of PCR primer-based strategies for characterization of ammonia oxidizer communities in environmental samples
    • Mahmood, S., Freitag, T.E., and Prosser, J.I. (2006) Comparison of PCR primer-based strategies for characterization of ammonia oxidizer communities in environmental samples. FEMS Microbiol Ecol 56: 482–493.
    • (2006) FEMS Microbiol Ecol , vol.56 , pp. 482-493
    • Mahmood, S.1    Freitag, T.E.2    Prosser, J.I.3
  • 10
    • 84924757791 scopus 로고    scopus 로고
    • Evaluation of revised polymerase chain reaction primers for more inclusive quantification of ammonia-oxidizing archaea and bacteria
    • Meinhardt, K.A., Bertagnolli, A., Pannu, M.W., Strand, S.E., Brown, S.L., and Stahl, D.A. (2015) Evaluation of revised polymerase chain reaction primers for more inclusive quantification of ammonia-oxidizing archaea and bacteria. Environ Microbiol Rep 7: 354–363.
    • (2015) Environ Microbiol Rep , vol.7 , pp. 354-363
    • Meinhardt, K.A.1    Bertagnolli, A.2    Pannu, M.W.3    Strand, S.E.4    Brown, S.L.5    Stahl, D.A.6
  • 11
    • 79955517284 scopus 로고    scopus 로고
    • Diversity and environmental distribution of ammonia-oxidizing bacteria
    • In, Ward, B.B., Arp, D., Klotz, M.G., (eds)., Washington, DC, American Society of Microbiology
    • Norton, J.M. (2011) Diversity and environmental distribution of ammonia-oxidizing bacteria. In Nitrification. Ward, B.B., Arp, D., and Klotz, M.G. (eds). Washington, DC: American Society of Microbiology, pp. 39–55.
    • (2011) Nitrification , pp. 39-55
    • Norton, J.M.1
  • 12
    • 0036167265 scopus 로고    scopus 로고
    • Diversity of ammonia monooxygenase operon in autotrophic ammonia-oxidizing bacteria
    • Norton, J.M., Alzerreca, J.J., Suwa, Y., and Klotz, M.G. (2002) Diversity of ammonia monooxygenase operon in autotrophic ammonia-oxidizing bacteria. Arch Microbiol 177: 139–149.
    • (2002) Arch Microbiol , vol.177 , pp. 139-149
    • Norton, J.M.1    Alzerreca, J.J.2    Suwa, Y.3    Klotz, M.G.4
  • 13
    • 79953211860 scopus 로고    scopus 로고
    • Preferential ligation during TA-cloning of multitemplate PCR products–a factor causing bias in microbial community structure analysis
    • Palatinszky, M., Nikolausz, M., Sváb, D., and Márialigeti, K. (2011) Preferential ligation during TA-cloning of multitemplate PCR products–a factor causing bias in microbial community structure analysis. J Microbiol Methods 85: 131–136.
    • (2011) J Microbiol Methods , vol.85 , pp. 131-136
    • Palatinszky, M.1    Nikolausz, M.2    Sváb, D.3    Márialigeti, K.4
  • 14
    • 0030814870 scopus 로고    scopus 로고
    • The ammonia monooxygenase structural gene amoA as a functional marker: molecular fine-scale analysis of natural ammonia-oxidizing populations
    • Rotthauwe, J.H., Witzel, K.P., and Liesack, W. (1997) The ammonia monooxygenase structural gene amoA as a functional marker: molecular fine-scale analysis of natural ammonia-oxidizing populations. Appl Environ Microbiol 63: 4704–4712.
    • (1997) Appl Environ Microbiol , vol.63 , pp. 4704-4712
    • Rotthauwe, J.H.1    Witzel, K.P.2    Liesack, W.3
  • 15
    • 84941140948 scopus 로고    scopus 로고
    • rrnDB: improved tools for interpreting rRNA gene abundance in bacteria and archaea and a new foundation for future development
    • Stoddard, S.F., Smith, B.J., Hein, R., Roller, B.R.K., and Schmidt, T.M. (2014) rrnDB: improved tools for interpreting rRNA gene abundance in bacteria and archaea and a new foundation for future development. Nucleic Acids Res 43: D593–D598.
    • (2014) Nucleic Acids Res , vol.43 , pp. D593-D598
    • Stoddard, S.F.1    Smith, B.J.2    Hein, R.3    Roller, B.R.K.4    Schmidt, T.M.5
  • 16
    • 67650492058 scopus 로고    scopus 로고
    • Ammonia-oxidizing bacteria and archaea in groundwater treatment and drinking water distribution systems
    • van der Wielen, P.W.J.J., Voost, S., and van der Kooij, D. (2009) Ammonia-oxidizing bacteria and archaea in groundwater treatment and drinking water distribution systems. Appl Environ Microbiol 75: 4687–4695.
    • (2009) Appl Environ Microbiol , vol.75 , pp. 4687-4695
    • van der Wielen, P.W.J.J.1    Voost, S.2    van der Kooij, D.3
  • 17
    • 84924173491 scopus 로고    scopus 로고
    • High-throughput metagenomic technologies for complex microbial community analysis: open and closed formats
    • Zhou, J., He, Z., Yang, Y., Deng, Y., Tringe, S.G., and Alvarez-Cohen, L. (2015) High-throughput metagenomic technologies for complex microbial community analysis: open and closed formats. MBio 6. DOI: 10.1128/mBio.02288-14
    • (2015) MBio , vol.6
    • Zhou, J.1    He, Z.2    Yang, Y.3    Deng, Y.4    Tringe, S.G.5    Alvarez-Cohen, L.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.