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
The PCR amplification-based analysis of microbial diversity is subject to potential problems. In this study, to minimize the bias toward a 1:1 ratio in multitemplate PCR, a real-time PCR assay was carried out using a quenching fluorescence dye primer and amplification efficiency was monitored. Then...
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| Published in | Microbes and Environments Vol. 23; no. 3; pp. 237 - 243 |
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| Main Authors | , , , |
| Format | Journal Article |
| Language | English |
| Published |
Japan
Japanese Society of Microbial Ecology / Japanese Society of Soil Microbiology / Taiwan Society of Microbial Ecology / Japanese Society of Plant Microbe Interactions / Japanese Society for Extremophiles
01.01.2008
Japan Science and Technology Agency |
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| Online Access | Get full text |
| ISSN | 1342-6311 1347-4405 |
| DOI | 10.1264/jsme2.23.237 |
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| Abstract | The PCR amplification-based analysis of microbial diversity is subject to potential problems. In this study, to minimize the bias toward a 1:1 ratio in multitemplate PCR, a real-time PCR assay was carried out using a quenching fluorescence dye primer and amplification efficiency was monitored. Then terminal-restriction fragment length polymorphism (T-RFLP) profiling was performed using the PCR product with minimized PCR bias. This method was applied to an analysis of the diversity of the archaeal community in an upland rice field under different tillage systems and winter cover cropping. Terminal restriction fragments (T-RFs) of PCR-amplified archaeal 16S rRNA genes were assigned to the gene sequences recovered from the same soil by using an archaeal 16S rRNA gene clone library. Our results indicated that soil archaeal members were not influenced but the relative abundance of archaeal species particularly those belonging to Crenarchaeota which changed between the tillage and non-tillage treatments. |
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| AbstractList | The PCR amplification-based analysis of microbial diversity is subject to potential problems. In this study, to minimize the bias toward a 1:1 ratio in multitemplate PCR, a real-time PCR assay was carried out using a quenching fluorescence dye primer and amplification efficiency was monitored. Then terminal-restriction fragment length polymorphism (T-RFLP) profiling was performed using the PCR product with minimized PCR bias. This method was applied to an analysis of the diversity of the archaeal community in an upland rice field under different tillage systems and winter cover cropping. Terminal restriction fragments (T-RFs) of PCR-amplified archaeal 16S rRNA genes were assigned to the gene sequences recovered from the same soil by using an archaeal 16S rRNA gene clone library. Our results indicated that soil archaeal members were not influenced but the relative abundance of archaeal species particularly those belonging to Crenarchaeota which changed between the tillage and non-tillage treatments. The PCR amplification-based analysis of microbial diversity is subject to potential problems. In this study, to minimize the bias toward a 1:1 ratio in multitemplate PCR, a real-time PCR assay was carried out using a quenching fluorescence dye primer and amplification efficiency was monitored. Then terminal-restriction fragment length polymorphism (T-RFLP) profiling was performed using the PCR product with minimized PCR bias. This method was applied to an analysis of the diversity of the archaeal community in an upland rice field under different tillage systems and winter cover cropping. Terminal restriction fragments (T-RFs) of PCR-amplified archaeal 16S rRNA genes were assigned to the gene sequences recovered from the same soil by using an archaeal 16S rRNA gene clone library. Our results indicated that soil archaeal members were not influenced but the relative abundance of archaeal species particularly those belonging to Crenarchaeota which changed between the tillage and non-tillage treatments.The PCR amplification-based analysis of microbial diversity is subject to potential problems. In this study, to minimize the bias toward a 1:1 ratio in multitemplate PCR, a real-time PCR assay was carried out using a quenching fluorescence dye primer and amplification efficiency was monitored. Then terminal-restriction fragment length polymorphism (T-RFLP) profiling was performed using the PCR product with minimized PCR bias. This method was applied to an analysis of the diversity of the archaeal community in an upland rice field under different tillage systems and winter cover cropping. Terminal restriction fragments (T-RFs) of PCR-amplified archaeal 16S rRNA genes were assigned to the gene sequences recovered from the same soil by using an archaeal 16S rRNA gene clone library. Our results indicated that soil archaeal members were not influenced but the relative abundance of archaeal species particularly those belonging to Crenarchaeota which changed between the tillage and non-tillage treatments. |
| Author | Ohta, Hiroyuki Komatsuzaki, Masakazu Kaneko, Nobuhiro Nishizawa, Tomoyasu |
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| References_xml | – reference: 34) Valenzuela-Encinas, C., I. Neria-González, R. Alcántara-Hernández, J. Enríquez-Aragón, I. Estrada-Alvarado, C. Hernández-Rodríguez, L. Dendooven, and R. Marsch. 2008. Phylogenetic analysis of the archaeal community in an alkaline-saline soil of the former lake Texcoco (Mexico). Extremophiles 12:247-254. – reference: 5) Hatzenpichler, R., E.V. Lebedeva, E. Spieck, K. Stoecker, A. Richter, H. Daims, and M. Wagner. 2008. A moderately thermophilic ammonia-oxidizing crenarchaeote from a hot spring. Proc. Natl. Acad. Sci. USA 105:2134-2139. – reference: 18) 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. – reference: 6) Hoshino-Takada, Y., and A. Hasebe. 2005. DNA extraction from soil. J. Environ. Biotechnol. 5:43-53. – reference: 26) 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. – reference: 7) 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. – reference: 29) Stahl, D.A., and R. Amann. 1991. Development and application of nucleic acid probes. p. 205-248 In E. Stackebrendt, and M. Goodfellow (ed.), Nucleic acid techniques in bacterial systematics. Wiley, Cichester, England. – reference: 2) Chao, A. 1984. Non-parametric estimation of the number of classes in a population. Scand. J. Stat. 11:783-791. – reference: 15) Kvist, T., B.K. Ahring, and P. Westermann. 2007. Archaeal diversity in Icelandic hot springs. 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| Title | 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 |
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