Korean Journal of Microbiology (미생물학회지)

The Microbiological Society of Korea (한국미생물학회)
권호 표지
DOI QR코드

DOI QR Code

Phylogenetic characteristics of bacterial populations and isolation of aromatic compounds utilizing bacteria from humus layer of oak forest

상수리림 부식층으로부터 방향족 화합물 분해세균의 분리 및 세균군집의 계통학적 특성

  • Han, Song-Ih (Department of Microbial and Nanomaterials, Mokwon University)
  • 한송이 (목원대학교 미생물나노소재학과)
  • Received : 2016.05.09
  • Accepted : 2016.05.16
  • Published : 2016.06.30
Download PDF
⟨ Previous Next ⟩

Abstract

In this study, we isolated aromatic compounds (lignin polymers) utilizing bacteria in humus layer of oak forest and investigated phylogenetic characteristics and correlation with major bacterial populations in the humus layer by pyrosequencing. Forty-two isolates using aromatic compounds such as p-anisic acid, benzoic acid, ferulic acid and p-coumaric acid were isolated and phylogentic analyses based on 16S rRNA gene sequences showed that the isolates belonged to the genus Rhizobium, Sphingomonas, Burkhorlderia, and Pseudomonas. Among these, Burkhorlderia species which belong to Betaproteobacteria class occupied 83% among the isolates. The bacterial populations in humus layer of oak forest were characterized by next generation pyrosequencing based on 16S rRNA gene sequences. The humus sample produced 7,862 reads, 1,821 OTUs and 6.76 variability index with 97% of significance level, respectively. Bacterial populations consist of 22 phyla and Betaproteobacteria were the major phylum consisting of 15 genera including Burkholderia, Polaromonas, Ralstoria, Zoogloea, and Variovorax. Approximately fifty percentage of them was Burkholderia. Burkholderia as the majority of population in the humus was considered to play a role in degrading lignin in humus layer of oak forest.

본 연구에서는 상수리림 부식층으로부터 방향족 화합물(리그닌 polymers) 분해세균을 분리하여 계통학적 특성을 밝히고, pyrosequencing 계통분석을 통해 부식층 내 주요 세균군집과의 상관관계를 검토하고자 하였다. 방향족 화합물(p-anisic acid, benzoic acid, ferulic acid 및 p-coumaric acid)을 이용하는 세균 42균주를 분리하여 16S rRNA 계통해석한 결과, Rhizobium, Sphingomonas, Burkhorlderia, Pseudomonas 계통군으로 확인되었다. 이들 방향족화합물 분해세균 중 Burkhorlderia 계통군은 전체 분리균주의 83%로 높은 비율을 차지하였다. 차세대 염기서열 분석법(pyrosequencing)을 이용하여 부식층시료로부터 7,862개의 16S rRNA 유전자 염기서열을 얻었으며, 유의성 97% 수준에서 1,821 OTUs와 다양성 지수 6.76가 확인되었다. 상수리림 부식층 내 세균군집은 총 22개 문(phylum)으로 구성되었으며, 주요 세균군집으로 확인된 ${\beta}$-proteobacteria 계통군은 Burkholderia, Polaromonas, Ralstoria, Zoogloea, Variovorax를 포함하는 15개 속으로 세분류 되었다. 이들 세균 중 약 50%가 Burkholderia 속으로 확인되었다. 상수리림 부식층 내 우점군집으로 밝혀진 Burkholderia 계통군은 산림 생태계에서 리그닌 분해 대사 과정에 중요한 미생물생태학적 역할을 수행하는 것으로 판단되었다.

Keywords

References

  1. Alexander, M. 1985. Introduction to soil microbiology. 2nd. John Wiley & Sons.
  2. Baboshin, M., Akimov, V., Baskunov, B., Born, T.L., Khan, S.U., and Golovleva, L. 2008. Conversion of polycyclic aromatic hydrocarbons by Sphingomonas sp. VKM B-2434. Biodegradation 19, 567-576. https://doi.org/10.1007/s10532-007-9162-2
  3. Basu, A., Apte, S.K., and Phale, P.S. 2006. Preferential utilization of aromatic compounds over glucose by Pseudomonas putida CSV86. Appl. Environ. Microbiol. 72, 2226-2230. https://doi.org/10.1128/AEM.72.3.2226-2230.2006
  4. Cole, J.R., Wang, Q., Cardenas, E., Fish, J., Chai, B., Farris, R.J., Kulam-Syed-Mohideen, A.S., McGarrell, D.M., Marsh, T., Garrity, G.M., et al. 2009. The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res. 37, 141-145.
  5. Hackl, E., Pfeffer, M., Donat, C., Bachmann, G., and Zechmeister-Boltenstern, S. 2005. Composition of the microbial communities in 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
  6. 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
  7. Han, S.I. 2015. Phylogenetic characterization of bacterial populations in different layers of oak forest soil. Korean J. Microbiol. 51, 133-140. https://doi.org/10.7845/kjm.2015.5017
  8. Han, S.I., Cho, M.H., and Whang, K.S. 2008. Comparison of phylogenetic characteristics of bacterial populations in a quercus and pine humus forest soil. Korean J. Microbiol. 44, 237-243.
  9. Haritash, A.K. and Kaushik, C.P. 2009. Biodegradation aspects of polycyclic aromatic hydrocarbons (PAHs). J. Hazard Mater. 169, 1-15. https://doi.org/10.1016/j.jhazmat.2009.03.137
  10. Kato, H., Mori, H., Maruyama, F., Toyoda, A., Oshima, K., Endo, R., Fuchu, G., Miyakoshi, M., Dozono, A., Ohtsubo, Y., et al. 2015. Time-series metagenomic analysis reveals robustness of soil microbiome against chemical disturbance. DNA Res. 22, 413-424. https://doi.org/10.1093/dnares/dsv023
  11. Kim, Y.G., Son, H.J., Kim, K.K., Kim, H.S., and Lee, Y.G. 2002. Isolation of a lignolytic bacterium for degradation and utilization of lignocellulose. J. Life Sci. 12, 392-398. https://doi.org/10.5352/JLS.2002.12.4.392
  12. Kirk, T.K. and Farrell, R.L. 1987. Enzymatic "combustion": the microbial degradation of lignin. Annu. Rev. Microbiol. 41, 465-505. https://doi.org/10.1146/annurev.mi.41.100187.002341
  13. Lee, K.J., Han, S.S., Kim, J.H., and Kim, E.S. 1996. Forest ecology (in Korean). Hyang Moon Sa, Seoul, Korea.
  14. Monties, B. 1988. Preparation of dioxane lignin fractions by acidolysis, pp. 31-35. In Wood, W.A. and Kellogg, S.T. (eds.). Methods in Enzymology, Vol. 161. Academy press, New York, USA.
  15. 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.
  16. Otsuka, Y., Muramatus, Y., Nakagawa, Y., Matsuda, M., Nakamura, M., and Murata, H. 2011. Burkholderia oxyphila sp. nov., isolated from acidic forest soil that catabolizes (+)-catechin and its putative aromatic derivatives. Int. J. Syst. Evol. Microbiol. 61, 249-254. https://doi.org/10.1099/ijs.0.017368-0
  17. Park, J.W. 2016. Metagenome analysis of plant detritus from the Torrya nucifera reveals a novel lignocellulose degrading community. Master's thesis. Chung-Ang University.
  18. Pometto, A.L. and Craword, D.L. 1986. Catabolic fate of Streptomyces viridosporus T7A-produced, acid-precipitable polymeric lignin upon incubation with lignolytic 15. Streptomyces species and Phanerochaete chrysosporium. Appl. Environ. Microbiol. 51, 171-179.
  19. Quince, C., Lanzen, A., Davenport, R.J., and Turnbaugh, P.J. 2011. Removing noise from pyrosequenced amplicons. BMC Bioinformatics 12, 38. https://doi.org/10.1186/1471-2105-12-38
  20. Schloss, P.D., Westcott, S.L., Ryabin, T., Hall, J.R., Hartmann, M., Hollister, E.B., Lesniewski, R.A., Oakley, B.B., Parks, D.H., Robinson, C.J., et al. 2009. Introducing mothur: open-source, platform-independent, community supported software for describing and comparing microbial communities. Appl. Environ. Microbiol. 75, 7537-7541. https://doi.org/10.1128/AEM.01541-09
  21. Shannon, P., Markiel, A., Ozier, O., Baliga, N.S., Wang, J.T., Ramage, D., Amin, N., Schwikowski, B., and Ideker, T. 2003. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 13, 2498-2504. https://doi.org/10.1101/gr.1239303
  22. Song, Y.J. 2009. Characterization of aromatic hydrocarbon degrading bacteria isolated from pine litter. Korean J. Microbiol. Biotechnol. 37, 333-339.
  23. Stevenson, F.J. 1994. Humus chemistry: Genesis, composition, reactions, 2nd ed. John Wiley and Sons, New York, N.Y., USA.
  24. Story, S.P., Kline, E.L., Hughes, T.A., Riley, M.B., and Hayasaka, S.S. 2004. Degradation of aromatic hydrocarbons by Sphingomonas paucimobilis EPA505. Arch. Environ. Contam. Toxicol. 47, 168-176.
  25. Sutherland, J.B., Rafii, F., Kahn, A.A., and Cerniglia, C.E. 1995. Mechanisms of polycyclic aromatic hydrocarbon degradation, pp. 269-306. In Young, L.Y. and Cerniglia, C.E. (eds.), Microbial transformation and degradation of toxic organic chemicals. Wiley-Liss, NY, USA.
  26. Takada-Hoshino, Y. and Matsumoto, M. 2004. An improved DNA extraction method using skim milk from soils that strongly absorb DNA. Microbes Environ. 19, 13-19. https://doi.org/10.1264/jsme2.19.13
  27. Vandamme, P., Govan, J.R.W., and LiPuma, J.J. 2007. Diversity and role of Burkholderia spp. Burkholderia: Molecular Microbiology and Genomics, pp. 1-28. In Coenye, T. and Vandamme, P. (eds.). Horizon Bioscience, Wymondham, UK.
  28. Wackett, L.P. and Ellis, L.B. 1999. Predicting biodegradation. Environ. Microbiol. 1, 119-124. https://doi.org/10.1046/j.1462-2920.1999.00029.x
  29. Yanagi, Y., Hamaguchi, S., Tamaki, H., Suzuki, T., Otsuka, H., and Fujitake, N. 2003. Relation of chemical properties of soil humic acids to decolorization by white rot fungus-Coriolus consors. Soil Sci. Plant Nutr. 49, 201-206. https://doi.org/10.1080/00380768.2003.10409998
  30. Yang, H.C. and Whang, K.S. 2003. Phylogenetic characteristics and a quantitative evaluation of aromatic compounds utilizing bacteria in forest soil. J. Inst. Sci. Technol. 12, 67-77.

Cited by

  1. Metagenomic SMRT Sequencing-Based Exploration of Novel Lignocellulose-Degrading Capability in Wood Detritus from Torreya nucifera in Bija Forest on Jeju Island vol.27, pp.9, 2016, https://doi.org/10.4014/jmb.1705.05008
  2. 퇴비사의 효율적인 운영기술에 대한 고찰 vol.23, pp.4, 2017, https://doi.org/10.7464/ksct.2017.23.4.345
  3. Conversion of organic carbon from decayed native and invasive plant litter in Jiuduansha wetland and its implications for SOC formation and sequestration vol.20, pp.2, 2016, https://doi.org/10.1007/s11368-019-02464-7