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Volumn 23, Issue 3, 2008, Pages 237-243

Archaeal diversity of upland rice field soils assessed by the terminal restriction fragment length polymorphism method combined with real time quantitative-pcr and a clone library analysis

Author keywords

Quenching fluorescence dye; Real time quantitative PCR; Soil Archaea; T RFLP

Indexed keywords

ARCHAEA; CRENARCHAEOTA;

EID: 70349928983     PISSN: 13426311     EISSN: 13426311     Source Type: Journal    
DOI: 10.1264/jsme2.23.237     Document Type: Article
Times cited : (23)

References (37)
  • 2
    • 0000947903 scopus 로고
    • Non-parametric estimation of the number of classes in a population
    • Chao, A. 1984. Non-parametric estimation of the number of classes in a population. Scand. J. Stat. 11:783-791.
    • (1984) Scand. J. Stat. , vol.11 , pp. 783-791
    • Chao, A.1
  • 3
    • 17644372762 scopus 로고    scopus 로고
    • Semi-automated genetic analyses of soil microbial communities: Comparison of T-RFLP and RISA based on descriptive and discriminative statistical approaches
    • Hartmann, M., B. Frey, R. Kölliker, and F. Widmer. 2005. Semi-automated genetic analyses of soil microbial communities: comparison of T-RFLP and RISA based on descriptive and discriminative statistical approaches. J. Microbiol. Methods 61:349-360.
    • (2005) J. Microbiol. Methods. , vol.61 , pp. 349-360
    • Hartmann, M.1    Frey, B.2    Kölliker, R.3    Widmer, F.4
  • 4
    • 38049134986 scopus 로고    scopus 로고
    • Reliability for detecting composition and changes of microbial communities by T-RFLP genetic profiling
    • Hartmann, M., and F. Widmer. 2008. Reliability for detecting composition and changes of microbial communities by T-RFLP genetic profiling. FEMS Microbiol. Ecol. 63:249-260.
    • (2008) FEMS Microbiol. Ecol. , vol.63 , pp. 249-260
    • Hartmann, M.1    Widmer, F.2
  • 7
    • 68949114543 scopus 로고    scopus 로고
    • Evaluation of the effects of different additives in improving the DNA extraction yield and quality from andosol
    • Ikeda, S., H. Tsurumaru, S. Wakai, C. Noritake, K. Fujishiro, M. Akasaka, and K. Ando. 2008. Evaluation of the effects of different additives in improving the DNA extraction yield and quality from andosol. Microbes Environ. 23:159-166.
    • (2008) Microbes Environ. , vol.23 , pp. 159-166
    • Ikeda, S.1    Tsurumaru, H.2    Wakai, S.3    Noritake, C.4    Fujishiro, K.5    Akasaka, M.6    Ando, K.7
  • 8
    • 0035432220 scopus 로고    scopus 로고
    • Optimization of annealing temperature to reduce bias caused by a primer mismatch in multitemplate PCR
    • Ishii, K., and M. Fukui. 2001. Optimization of annealing temperature to reduce bias caused by a primer mismatch in multitemplate PCR. Appl. Environ. Microbiol. 67:3753-3755.
    • (2001) Appl. Environ. Microbiol. , vol.67 , pp. 3753-3755
    • Ishii, K.1    Fukui, M.2
  • 9
    • 0027745825 scopus 로고
    • Effect of PCR conditions on the formation of heteroduplex and single-stranded DNA products in the amplification of bacterial ribosomal DNA spacer regions
    • Jensen, M.A., and N. Straus. 1993. Effect of PCR conditions on the formation of heteroduplex and single-stranded DNA products in the amplification of bacterial ribosomal DNA spacer regions. PCR Methods Appl. 3:186-194.
    • (1993) PCR Methods Appl. , vol.3 , pp. 186-194
    • Jensen, M.A.1    Straus, N.2
  • 10
    • 58149397103 scopus 로고    scopus 로고
    • Evaluation of quenching probe (QProbe)- PCR assay for quantification of the koi herpes virus (KHV)
    • Kamimura, S., T. Hagi, S. Kurata, K. Takatsu, H. Sogo, T. Hoshino, and K. Nakamura. 2007. Evaluation of quenching probe (QProbe)- PCR assay for quantification of the koi herpes virus (KHV). Microbes Environ. 22:223-231.
    • (2007) Microbes Environ , vol.22 , pp. 223-231
    • Kamimura, S.1    Hagi, T.2    Kurata, S.3    Takatsu, K.4    Sogo, H.5    Hoshino, T.6    Nakamura, K.7
  • 11
    • 0344629203 scopus 로고    scopus 로고
    • Bias and artifacts in multitemplate polymerase chain reactions (PCR)
    • Kanagawa, T. 2003. Bias and artifacts in multitemplate polymerase chain reactions (PCR). J. Biosci. Bioeng. 96:317-323.
    • (2003) J. Biosci. Bioeng. , vol.96 , pp. 317-323
    • Kanagawa, T.1
  • 12
    • 0037728487 scopus 로고    scopus 로고
    • Variation between observed and true terminal restriction fragment length is dependent on true T-RF length and purine content
    • Kaplan, C.W., and C.L. Kitts. 2003. Variation between observed and true terminal restriction fragment length is dependent on true T-RF length and purine content. J. Microbiol. Methods 54:121-125.
    • (2003) J. Microbiol. Methods. , vol.54 , pp. 121-125
    • Kaplan, C.W.1    Kitts, C.L.2
  • 13
    • 0035869965 scopus 로고    scopus 로고
    • Fluorescent quenching-based quantitative detection of specific DNA/RNA using a BODIPY FL- labeled probe or primer
    • Kurata, S., T. Kanagawa, K. Yamada, M. Torimura, T. Yokomaku, Y. Kamagata, and R. Kurane. 2001. Fluorescent quenching-based quantitative detection of specific DNA/RNA using a BODIPY FL- labeled probe or primer. Nucleic Acids Res. 29:e34.
    • (2001) Nucleic Acids Res , vol.29
    • Kurata, S.1    Kanagawa, T.2    Yamada, K.3    Torimura, M.4    Yokomaku, T.5    Kamagata, Y.6    Kurane, R.7
  • 17
    • 0030661563 scopus 로고    scopus 로고
    • Characterization of microbial diversity by determining teminal restraiction fragment length polymorphism of genes encoding 16S rRNA
    • Liu, W.-T., T.L. Marsh, H. Cheng, and L.J. Forney, 1997. Characterization of microbial diversity by determining teminal restraiction fragment length polymorphism of genes encoding 16S rRNA. Appl. Environ. Microbiol. 63:4516-4522.
    • (1997) Appl. Environ. Microbiol. , vol.63 , pp. 4516-4522
    • Liu, W.-T.1    Marsh, T.L.2    Cheng, H.3    Forney, L.J.4
  • 18
    • 0037225001 scopus 로고    scopus 로고
    • Evaluation of PCR amplification bias by terminal restriction fragment length polymorphism analysis of small-subunit rRNA and mcrA genes by using defined template mixtures of methanogenic pure cultures and soil DNA extracts
    • Lueders, T., and M.W. Friedrich. 2003. Evaluation of PCR amplification bias by terminal restriction fragment length polymorphism analysis of small-subunit rRNA and mcrA genes by using defined template mixtures of methanogenic pure cultures and soil DNA extracts. Appl. Environ. Microbiol. 69:320-326.
    • (2003) Appl. Environ. Microbiol. , vol.69 , pp. 320-326
    • Lueders, T.1    Friedrich, M.W.2
  • 19
    • 0029967167 scopus 로고    scopus 로고
    • DNA rehybridization during PCR: The 'Cot effect' and its consequences
    • Mathieu-Daude, F., J. Welsh, T. Vogt, and M. McClelland. 1996. DNA rehybridization during PCR: the 'Cot effect' and its consequences. Nucleic Acids Res. 24:2080-2086.
    • (1996) Nucleic Acids Res , vol.24 , pp. 2080-2086
    • Mathieu-Daude, F.1    Welsh, J.2    Vogt, T.3    McClelland, M.4
  • 20
    • 51149111950 scopus 로고    scopus 로고
    • Distribution of cold-adapted ammonia-oxidizing microorganisms in the deep-ocean of the Northeastern Japan Sea
    • Nakagawa, T., K. Mori, C. Kato, R. Takahashi, and T. Tokuyama. 2007. Distribution of cold-adapted ammonia-oxidizing microorganisms in the deep-ocean of the Northeastern Japan Sea. Microbes Environ. 22:365-372.
    • (2007) Microbes Environ , vol.22 , pp. 365-372
    • Nakagawa, T.1    Mori, K.2    Kato, C.3    Takahashi, R.4    Tokuyama, T.5
  • 21
    • 0034547801 scopus 로고    scopus 로고
    • An evaluation of terminal-restriction fragment length polymorphism (T-RFLP) analysis for the study of microbial community structure and dynamics
    • Osborn, A.M., E.R. Moore, and K.N. Timmis. 2000. An evaluation of terminal-restriction fragment length polymorphism (T-RFLP) analysis for the study of microbial community structure and dynamics. Environ. Microbiol. 2:39-50.
    • (2000) Environ. Microbiol. , vol.2 , pp. 39-50
    • Osborn, A.M.1    Moore, E.R.2    Timmis, K.N.3
  • 22
    • 33847298917 scopus 로고    scopus 로고
    • Variations in T-RFLP profiles with differing chemistries of fluorescent dyes used for labeling the PCR primers
    • Pandey, J., K. Ganesan, and R.K. Jain. 2007. Variations in T-RFLP profiles with differing chemistries of fluorescent dyes used for labeling the PCR primers. J. Microbiol. Methods 68:633-638.
    • (2007) J. Microbiol. Methods. , vol.68 , pp. 633-638
    • Pandey, J.1    Ganesan, K.2    Jain, R.K.3
  • 23
    • 0031711754 scopus 로고    scopus 로고
    • Bias in template-to-product ratios in multitemplate PCR
    • Polz, M.F., and C.M. Cavanaugh. 1998. Bias in template-to-product ratios in multitemplate PCR. Appl. Environ. Microbiol. 64:3724-3730.
    • (1998) Appl. Environ. Microbiol. , vol.64 , pp. 3724-3730
    • Polz, M.F.1    Cavanaugh, C.M.2
  • 25
    • 4644260588 scopus 로고    scopus 로고
    • Ecology and microbial structures of archaeal/bacterial strings-of-pearls communities and archaeal relatives thriving in cold sulfidic springs
    • Rudolph, C., C. Moissl, R. Henneberger, and R. Huber. 2004. Ecology and microbial structures of archaeal/bacterial strings-of-pearls communities and archaeal relatives thriving in cold sulfidic springs. FEMS Microbiol. Ecol. 50:1-11.
    • (2004) FEMS Microbiol. Ecol. , vol.50 , pp. 1-11
    • Rudolph, C.1    Moissl, C.2    Henneberger, R.3    Huber, R.4
  • 26
    • 52649180148 scopus 로고    scopus 로고
    • Broad distribution and phylogeny of anaerobic endophytes of cluster XIVa clostridia in plant species including crops
    • Saito, A., M. Kawahara, S. Ikeda, M. Ishimine, S. Akao, and K. Minamisawa. 2008. Broad distribution and phylogeny of anaerobic endophytes of cluster XIVa clostridia in plant species including crops. Microbes Environ. 23:73-80.
    • (2008) Microbes Environ , vol.23 , pp. 73-80
    • Saito, A.1    Kawahara, M.2    Ikeda, S.3    Ishimine, M.4    Akao, S.5    Minamisawa, K.6
  • 27
    • 0031680049 scopus 로고    scopus 로고
    • Genomic analysis reveals chromosomal variation in natural populations of the uncultured psychrophilic archaeon Cenarchaeum symbiosum
    • Schleper, C., E.F. DeLong, C.M. Preston, R.A. Feldman, K.Y. Wu, and R.V. Swanson. 1998. Genomic analysis reveals chromosomal variation in natural populations of the uncultured psychrophilic archaeon Cenarchaeum symbiosum. J. Bacteriol. 180:5003-5009.
    • (1998) J. Bacteriol. , vol.180 , pp. 5003-5009
    • Schleper, C.1    Delong, E.F.2    Preston, C.M.3    Feldman, R.A.4    Wu, K.Y.5    Swanson, R.V.6
  • 29
    • 0003341851 scopus 로고
    • Development and application of nucleic acid probes
    • E. Stackebrendt, and M. Goodfel- low (ed.) Wiley, Cichester, England
    • Stahl, D.A., and R. Amann. 1991. Development and application of nucleic acid probes. p. 205-248 In E. Stackebrendt, and M. Goodfel- low (ed.), Nucleic acid techniques in bacterial systematics. Wiley, Cichester, England.
    • (1991) Nucleic Acid Techniques in Bacterial Systematics , pp. 205-248
    • Stahl, D.A.1    Amann, R.2
  • 30
    • 0030067991 scopus 로고    scopus 로고
    • Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR
    • Suzuki, M.T., and S.J. Giovannoni. 1996. Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR. Appl. Environ. Microbiol. 62:625-630.
    • (1996) Appl. Environ. Microbiol. , vol.62 , pp. 625-630
    • Suzuki, M.T.1    Giovannoni, S.J.2
  • 31
    • 0031790538 scopus 로고    scopus 로고
    • Kinetic bias in estimates of coastal picoplankton community structure obtained by measurements of small-subunit rRNA gene PCR amplicon length heterogeneity
    • Suzuki, M., M.S. Rappe, and S.J. Giovannoni. 1998. Kinetic bias in estimates of coastal picoplankton community structure obtained by measurements of small-subunit rRNA gene PCR amplicon length heterogeneity. Appl. Environ. Microbiol. 64:4522-11529
    • (1998) Appl. Environ. Microbiol. , vol.64 , pp. 4522-11529
    • Suzuki, M.1    Rappe, M.S.2    Giovannoni, S.J.3
  • 32
    • 0027968068 scopus 로고
    • CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice
    • Thompson, J.D., D.G. Higgins, and T.J. Gibson. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673-4680.
    • (1994) Nucleic Acids Res. , vol.22 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 33
    • 0036566806 scopus 로고    scopus 로고
    • Heteroduplexes in mixed-template amplifications: Formation, consequence and elimination by 'reconditioning PCR'
    • Thompson, J.R., L.A. Marcelino, and M.F. Polz. 2002. Heteroduplexes in mixed-template amplifications: formation, consequence and elimination by 'reconditioning PCR'. Nucleic Acids Res. 30:2083-2088.
    • (2002) Nucleic Acids Res , vol.30 , pp. 2083-2088
    • Thompson, J.R.1    Marcelino, L.A.2    Polz, M.F.3
  • 35
    • 34548293679 scopus 로고    scopus 로고
    • Naïve bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy
    • Wang, Q., G.M. Garrity, J.M. Tiedje, and J.R. Cole. 2007. Naïve bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl. Environ. Microbiol. 73:5261-5267.
    • (2007) Appl. Environ. Microbiol. , vol.73 , pp. 5261-5267
    • Wang, Q.1    Garrity, G.M.2    Tiedje, J.M.3    Cole, J.R.4
  • 36
    • 33644606606 scopus 로고    scopus 로고
    • Fast-GroupII: A web-based bioinformatics platform for analyses of large 16S rDNA libraries
    • Yu, Y., M. Breitbart, P. McNairnie, and F. Rohwer. 2006. Fast- GroupII: A web-based bioinformatics platform for analyses of large 16S rDNA libraries. BMC Bioiform. 7:57
    • (2006) BMC Bioiform. , vol.7 , pp. 57
    • Yu, Y.1    Breitbart, M.2    McNairnie, P.3    Rohwer, F.4
  • 37
    • 70349900215 scopus 로고    scopus 로고
    • Relationships between fungal biomass and nitrous oxide emission in upland rice soils under no tillage and cover cropping systems
    • Zhaorigetu, M. Komatsuzaki, Y. Sato, and H. Ohta. 2008. Relationships between fungal biomass and nitrous oxide emission in upland rice soils under no tillage and cover cropping systems. Microbes Environ. 23:201-208.
    • (2008) Microbes Environ. , vol.23 , pp. 201-208
    • Komatsuzaki, Z.M.1    Sato, Y.2    Ohta, H.3


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