DOI QR코드

DOI QR Code

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

상수리나무림의 토양 층위별 세균군집의 계통학적 특성

  • Han, Song-Ih (Department of Microbial & Nanomaterials, Mokwon University)
  • 한송이 (목원대학교 미생물나노소재학과)
  • Received : 2015.04.24
  • Accepted : 2015.06.19
  • Published : 2015.06.30

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.

상수리림 산림토양 각 층위 내 물리 화학적, 미생물학적 환경변수간 상관관계를 확인한 결과, 낙엽 분해 층(F)과 부식층(H)은 각 환경변수와 높은 상관관계를 갖는 특징을 나타내었다. 특히, F층에서는 pH가 C 그리고 N과 높은 상관관계를 나타내었고, 부식층(H)에서는 각종 유기산이 토양 세균 밀도와 높은 상관관계를 나타내었다. 상수리림 산림토양의 층위별 세균군집 구조의 계통해석을 위해 각 층위의 계절별 시료로부터 DNA를 직접 추출하고 DGGE 분석한 결과 낙엽층(L)의 경우 43 bands, F층은 42 bands, H층은 43 bands 그리고 근권 토양층(A)은 47 bands로 총 175 bands가 상수리림 산림토양의 DGGE 주요 bands로 선발되었다. 확보된 총 175 DGGE 주요 bands의 16S rRNA 유전자 염기서열 정보를 바탕으로 세균군집의 계통 해석한 결과, 7개 phylum에 32개 order로 세 분류되었다. 각 order에 속하는 염기서열을 heat map 분석하고 상수리림 산림토양의 각 층위을 clustering 한 결과 F층과 H층이 L층 그리고 A층과 서로 다른 cluster를 형성하는 것이 확인되었다. 또한, 산림토양의 각 층위에 존재하는 세균군집 중 약 50%가 ${\alpha}$-proteobacteria로 우점계통군으로 나타났다. 특히, Rhizobiales, Burkholderiales, 그리고 Actinobacteriales 목은 모든 계절과 모든 층위에서 보여지는 세균군집으로 확인되어 상수리림 산림토양에서 대표적인 토착세균 군집임이 확인되었다.

Keywords

References

  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. https://doi.org/10.1016/j.soilbio.2004.08.023
  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. https://doi.org/10.1128/AEM.70.9.5057-5065.2004
  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. https://doi.org/10.1128/AEM.72.3.1719-1728.2006
  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. https://doi.org/10.1016/S0168-6496(03)00212-5
  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. https://doi.org/10.1007/s00248-005-5130-8
  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. https://doi.org/10.1016/S1369-5274(99)80055-1
  17. 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.
  18. NIAST. 1988. Methods of soil chemical analysis. National institute of agricultural science and technology, RDA, Suwon, Korea.
  19. 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.
  20. 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. https://doi.org/10.1099/ijs.0.63936-0
  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. https://doi.org/10.1016/j.soilbio.2004.12.007
  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. https://doi.org/10.1111/j.1574-6941.2009.00733.x
  25. Zhang, L. and Xu, Z. 2008. Assessing bacterial diversity in soil. J. Soils Sediments 8, 379-388. https://doi.org/10.1007/s11368-008-0043-z

Cited by

  1. Phylogenetic characteristics of bacterial populations and isolation of aromatic compounds utilizing bacteria from humus layer of oak forest vol.52, pp.2, 2016, https://doi.org/10.7845/kjm.2016.6028
  2. Diversity and physiological properties of soil actinobacteria in Ulleung Island vol.53, pp.4, 2015, https://doi.org/10.7845/kjm.2017.7057
  3. 침엽수림과 혼효림에서 토양특성과 토양세균 군집이 산양삼 초기 생육특성에 미치는 영향 vol.28, pp.3, 2020, https://doi.org/10.7783/kjmcs.2020.28.3.183