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Assessment of Korean Paddy Soil Microbial Community Structure by Use of Quantitative Real-time PCR Assays
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 Title & Authors
Assessment of Korean Paddy Soil Microbial Community Structure by Use of Quantitative Real-time PCR Assays
Choe, Myeong-Eun; Lee, In-Jung; Shin, Jae-Ho;
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BACKGROUND: In order to develop effective assessment method for Korean paddy soil microbial community structure, reliable genomic DNA extraction method from paddy soil and quantitative real-time PCR (qRT-PCR) method are needed to establish METHODS AND RESULTS: Out of six conventional soil genomic DNA extraction methods, anion exchange resin purification method was turn to be the most reliable. Various PCR primers for distinguishing five bacterial phylum (-Proteobacteria, -Proteobacteria, Actinobacteria, Bacteroidetes, Firmicutes), all bacteria, and all fungi were tested. Various qRT-PCR temperature conditions were also tested by repeating experiment. Finally, both genomic DNA extraction and qRT-PCR methods for paddy soil were well established. CONCLUSION: Quantitative real-time PCR (qRT-PCR) method to assess paddy soil microbial community was established.
Paddy soil microbial community;Quantitative real-time PCR;
 Cited by
영월한반도습지의 어류군집 특성,한상진;이광열;윤영진;최재윤;김준철;최재석;

한국환경생태학회지, 2014. vol.28. 4, pp.424-431 crossref(new window)
Borneman, J., Hartin, R.J., 2000, PCR primers that amplify fungal rRNA genes from environmental samples, Appl Environ Microbiol. 66, 4356-4360. crossref(new window)

Buckley, D.H., Schmidt, T.M., 2001, The Structure of Microbial Communities in Soil and the Lasting Impact of Cultivation, Microbial Ecology. 42, 11-21.

Christensen, H., Hansen, M., Sorensen, J., 1999, Counting and size classification of active soil bacteria by fluorescence in situ hybridization with an rRNA oligonucleotide probe, Appl Environ Microbiol. 65, 1753-1761.

Dandie, C.E., Miller, M.N., Burton, D.L., Zebarth, B.J., Trevors, J.T., Goyer, C., 2007, Nitric oxide reductase-targeted real-time PCR quantification of denitrifier populations in soil, Appl Environ Microbiol. 73, 4250-4258. crossref(new window)

Fierer, N., Jackson, J.A., Vilgalys, R., Jackson, R.B., 2005, Assessment of soil microbial community structure by use of taxon-specific quantitative PCR assays, Applied and Environmental Microbiology. 71, 4117-4120. crossref(new window)

Grosskopf, R., Janssen, P.H., Liesack, W., 1998, Diversity and structure of the methanogenic community in anoxic rice paddy soil microcosms as examined by cultivation and direct 16S rRNA gene sequence retrieval, Appl Environ Microbiol. 64, 960-969.

Hawksworth, D.L., 2001, The magnitude of fungal diversity: the 1.5 million species estimate revisited, Mycological Research. 105, 1422-1432. crossref(new window)

Kabir, S., Rajendran, N., Amemiya, T., Itoh, K., 2003, Quantitative measurement of fungal DNA extracted by three different methods using real-time polymerase chain reaction, Journal of Bioscience and Bioengineering. 96, 337-343. crossref(new window)

Kolb, S., Knief, C., Stubner, S., Conrad, R., 2003, Quantitative detection of methanotrophs in soil by novel pmoA-targeted real-time PCR assays, Applied and Environmental Microbiology. 69, 2423-2429. crossref(new window)

Lane, D.J., 1991, 16S/23S rRNA sequencing, Nucleic Acid Techniques in Bacterial Systematics.

Marchesi, J.R., Sato, T., Weightman, A.J., Martin, T.A., Fry, J.C., Hiom, S.J., Wade, W.G., 1998, Design and evaluation of useful bacterium-specific PCR primers that amplify genes coding for bacterial 16S rRNA, Applied and Environmental Microbiology. 64, 795-799.

Muyzer, G., de Waal, E.C., Uitterlinden, A.G., 1993, Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA, Appl Environ Microbiol. 59, 695-700.

Nakatsu, C.H., Torsvik, V., Ovreas, L., 2000, Soil Community Analysis Using DGGE of 16S rDNA Polymerase Chain Reaction Products, Soil Sci. Soc. Am. J. 64, 1382-1388. crossref(new window)

NIAST, 2000, Method of soil and plant analysis . National Institute of Agricultural Science and Technology (NIAST), Suwan, Korea.

Okano, Y., Hristova, K.R., Leutenegger, C.M., Jackson, L.E., Denison, R.F., Gebreyesus, B., Lebauer, D., Scow, K.M., 2004, Application of real-time PCR to study effects of ammonium on population size of ammonia-oxidizing bacteria in soil, Applied and Environmental Microbiology. 70, 1008-1016. crossref(new window)

Overmann, J., Coolen, M.J.L., Tuschak, C., 1999, Specific detection of different phylogenetic groups of chemocline bacteria based on PCR and denaturing gradient gel electrophoresis of 16S rRNA gene fragments, Arch Microbiol. 172, 83-94. crossref(new window)

Paul, E.A., Clark, F.E., 1989, Soil Microbiology and Biochemistry. Academic Press, San Diego, CA.

Raeymaekers, L., 2000, Basic principles of quantitative PCR, Molecular Biotechnology. 15, 115-122. crossref(new window)

Rhee, S.K., Liu, X., Wu, L., Chong, S.C., Wan, X., Zhou, J., 2004, Detection of genes involved in biodegradation and biotransformation in microbial communities by using 50-mer oligonucleotide microarrays, Appl Environ Microbiol. 70, 4303-4317. crossref(new window)

Rubio, M.B., Hermosa, M.R., Keck, E., Monte, E., 2005, Specific PCR assays for the detection and quantification of DNA from the biocontrol strain Trichoderma harzianum 2413 in soil, Microb Ecol. 49, 25-33. crossref(new window)

Schollenberger, C.J., 1927, A Rapid Approximate Method for Determining Soil Organic Matter, Soil Science. 24, 65-68. crossref(new window)

Stach, J.E.M., Maldonado, L.A., Ward, A.C., Goodfellow, M., Bull, A.T., 2003, New primers for the class Actinobacteria: application to marine and terrestrial environments, Environ Microbiol. 5, 828-841. crossref(new window)

Straatsma, G., Ayer, F., Egli, S., 2001, Species richness, abundance, and phenology of fungal fruit bodies over 21 years in a Swiss forest plot, Mycological Research. 105, 515-523. crossref(new window)

Stubner, S., 2002, Enumeration of 16S rDNA of Desulfotomaculum lineage 1 in rice field soil by real-time PCR with SybrGreen (TM) detection, J Microbiol Meth. 50, 155-164. crossref(new window)

Torsvik, V., Ovreas, L., 2002, Microbial diversity and function in soil: from genes to ecosystems, Current Opinion in Microbiology. 5, 240-245. crossref(new window)

Torsvik, V., Ovreas, L., Thingstad, T.F., 2002, Prokaryotic diversity-Magnitude, dynamics, and controlling factors, Science. 296, 1064-1066. crossref(new window)

Torsvik, V., Salte, K., Sorheim, R., Goksoyr, J., 1990, Comparison of phenotypic diversity and DNA heterogeneity in a population of soil bacteria, Appl Environ Microbiol. 56, 776-781.

Vazquez-Marrufo, G., Vazquez-Garciduenas, M.S., Gomez-Luna, B.E., Olalde-Portugal, V., 2002, DNA isolation from forest soil suitable for PCR assays of fungal and plant rRNA genes, Plant Molecular Biology Reporter. 20, 379-390. crossref(new window)

Yeates, C., Gillings, M.R., Davison, A.D., Altavilla, N., Veal, D.A., 1998, Methods for microbial DNA extraction from soil for PCR amplification, Biol Proced Online. 1, 40-47. crossref(new window)