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http://dx.doi.org/10.7845/kjm.2015.5017

Phylogenetic characterization of bacterial populations in different layers of oak forest soil  

Han, Song-Ih (Department of Microbial & Nanomaterials, Mokwon University)
Publication Information
Korean Journal of Microbiology / v.51, no.2, 2015 , pp. 133-140 More about this Journal
Abstract
We have examined the correlation between the physicochemical and microbiological environment variables for the different layers of oak forest soil in Mt. Gyeryong, Korea. The result shows that there is a high correlation in the environment variables between the soil parameters of the fermented (F) layer and humus (H) layer. In particular, the pH level in the F layer shows a high correlation with C and N, while the various organic acids of the H layer turns out to be closely correlated with soil bacteria density. As we evaluated phylogenetic characteristics of bacterial populations by DGGE analysis with DNA extracted. Total of 175 bands including 43 bands from litter (L) layer, 42 bands from F layer, 43 bands from H layer and 47 bands from rhizosphere (A) layer were selected as the major DGGE band of oak forest soil. Based on the 16S rRNA gene sequences, 175 DGGE bands were classified into 32 orders in 7 phylum. The heat map was analyzed in order to compare the quantity of the base sequences of each order and based on the clustering of the different layers of oak forest soil, the result confirms that the F layer and H layer belong to a different cluster from that of L layer and A layer. Furthermore, it also showed that approximately 50% of the total microbial population in different layers is ${\alpha}$-proteobacteria, which indicates that they belong to the dominant system group. In particular, Rhizobiales, Burkholderiales and Actinobacteriales were observed in all the seasons and layers of oak forest soil, which confirms that they are the indigenous soil bacterial community in oak forest soil.
Keywords
bacterial populations; DGGE; oak forest soil; phylogeny;
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1 Alexander, M. 1985. Introduction to soil microbiology. John Wiley & Sons, Newyork, USA.
2 Cho, S.J., Park, C.S., and Uhm, D.I. 1997. Soil Science, pp. 321-325. In Hyangmoon Press, Seoul, Korea.
3 Hackl, E., Pfeffer, M., Donat, C., Bachmann, G., and Zechmeister Boltenstern, S. 2005. Composition of the microbial communities n the mineral soil under different types of natural forest. Soil Biol. Biochem. 37, 661-671.   DOI
4 Hackl, E., Zechmeister-Boltenstern, S., Bodrossy, L., and Sessitsch, A. 2004. Comparison of diversities and compositions of bacterial populations inhabiting natural forest soils. Appl. Environ. Microbiol. 70, 5057-5065.   DOI
5 Han, S.I., Cho, M.H., and Whang, K.S. 2008. Comparison of phylogenetic characteristics of bacterial populations in a oak and pine humus forest soil. Kor. J. Microbiol. 44, 237-243.
6 Han, S.I., Kim, Y.J., and Whang, K.S. 2006. Comparison of phylogenetic characteristics of viable but non-culturable (VBNC) bacterial populations in the pine and oak forest soil by 16S rDNA-ARDRA. Kor. J. Microbiol. 42, 116-124.
7 Janssen, P.H. 2006. Identifying the dominant soil bacterial taxa in libraries of 16S rRNA and 16S rRNA genes. Appl. Environ. Microbiol. 72, 1719-1728.   DOI
8 Johnson, J.L. 1994. Similarity analysis of rRNAs, In Gerhardt, P., Murray, R.G.E., Wood, W.A., and Krieg, N.R. (eds.), Methods for general and molecular bacteriology, pp. 683-700. American Society for Microbiology, Washington, DC, USA.
9 Kim, J.W. 1996. Floristic characterization of the temperate oak forests in the Korean Peninsula using high-rank taxa. J. PI. Biol. 39, 149-159.
10 Kim, J.G. and Chang, N.L. 1989. Litter production and decomposition in the Pinus rigida plantation in Mt. Kwan-ak. Korea J. Ecol. 12, 9-20.
11 Koizumi, Y., Kozima, Y., and Fukui, M. 2003. Characterization of depth-related microbial community structure in lake sediment by Denaturing Gradient Gel Electrophoresis of amplified 16S rDNA and reversely transcribed 16S rRNA fragments. FEMS Microbiol. Ecol. 46, 147-157.   DOI
12 Lane, D.J. 1991. 16S/23S rRNA sequencing. In Stackebrandt, E. and Goodfellow, M. (eds.), Nucleic acid techniques in bacterial systematics, pp. 115- 175. John Wiley and Sons, Chichester.
13 Lejon, D.P., Chaussod, R., Ranger, J., and Ranjard, L. 2005. Microbial community structure and density under different tree species in an acid forest soil (Morvan, France). Microb. Ecol. 50, 614-625.   DOI
14 Mun, H.T. and Joo, H.T. 1994. Litter production and decomposition in the Quercus acutissima and Pinus rigida forest soil. Korean J. Ecol. 17, 345-353.
15 Mun, H.T. and Kim, J.H. 1992. Litter fall decomposition, and nutrient dynamics of litter in red pine (Pinus densiflora) and Chinese thuja (Thuja orientalis) stands in the lime stone area. Korean J. Ecol. 15, 147-155.
16 Muyzer, G. 1999. DGGE/TGGE a method for identifying genes from natural ecosystems. Curr. Opin. Microbiol. 2, 317-322.   DOI
17 Rudi, K., Zimonja, M., and Naes, T. 2006. Alignment independent bi-linear multivariate modeling (AIBIMM) for global analyses of 16S rRNA phylogeny. Int. J. Syst. Evol. Microbiol. 56, 1565-1575.   DOI
18 Muyzer, G., de Waal, E.C., and Uitterlinden, A.G. 1993. Profiling of complex microbial populations by denaturing gradient gel eletrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA fragments. Appl. Environ. Microbiol. 59, 695-700.
19 NIAST. 1988. Methods of soil chemical analysis. National institute of agricultural science and technology, RDA, Suwon, Korea.
20 Park, B.K. and Kim, M.R. 1985. The decomposition rate of litter and soil microorganisms in slope directions. Korean J. Ecol. 8, 31-37.
21 Tsai, Y.L. and Olson, B.H. 1991. Rapid method for direct extraction of DNA from soil and sediments. Appl. Environ. Microbiol. 57, 1070-1074.
22 Tsai, S.H., Selvam, A., Chang, Y.P., and Yang, S.S. 2009. Soil bacterial community composition across different topographic sites characterized by 16S rRNA gene clones in the fushan forest of Taiwan. Bot. Stud. 50, 57-68.
23 White, C., Tardif, J.C., Adkins, A., and Staniforth, R. 2005. Functional diversity of microbial communities in the mixed boreal plain forest of central Canada. Soil Biol. Biochem. 37, 1359-1372.   DOI
24 Yarwood, S.A., Myrold, D.D., and Hogberg, M.N. 2009. Termination of below-ground C allocation by tree alters soil fungal and bacterial communities in a boreal forest. FEMS Microbiol. Ecol. 70, 151-162.   DOI
25 Zhang, L. and Xu, Z. 2008. Assessing bacterial diversity in soil. J. Soils Sediments 8, 379-388.   DOI