Advanced SearchSearch Tips
Phylogenetic characteristics of bacterial populations and isolation of aromatic compounds utilizing bacteria from humus layer of oak forest
facebook(new window)  Pirnt(new window) E-mail(new window) Excel Download
 Title & Authors
Phylogenetic characteristics of bacterial populations and isolation of aromatic compounds utilizing bacteria from humus layer of oak forest
Han, Song-Ih;
  PDF(new window)
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.
Burkholderia;aromatic compounds;humus;phylogenetics;
 Cited by
Alexander, M. 1985. Introduction to soil microbiology. 2nd. John Wiley & Sons.

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. crossref(new window)

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. crossref(new window)

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.

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. crossref(new window)

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. crossref(new window)

Han, S.I. 2015. Phylogenetic characterization of bacterial populations in different layers of oak forest soil. Korean J. Microbiol. 51, 133-140. crossref(new window)

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.

Haritash, A.K. and Kaushik, C.P. 2009. Biodegradation aspects of polycyclic aromatic hydrocarbons (PAHs). J. Hazard Mater. 169, 1-15. crossref(new window)

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. crossref(new window)

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. crossref(new window)

Kirk, T.K. and Farrell, R.L. 1987. Enzymatic "combustion": the microbial degradation of lignin. Annu. Rev. Microbiol. 41, 465-505. crossref(new window)

Lee, K.J., Han, S.S., Kim, J.H., and Kim, E.S. 1996. Forest ecology (in Korean). Hyang Moon Sa, Seoul, Korea.

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.

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.

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. crossref(new window)

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.

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.

Quince, C., Lanzen, A., Davenport, R.J., and Turnbaugh, P.J. 2011. Removing noise from pyrosequenced amplicons. BMC Bioinformatics 12, 38. crossref(new window)

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. crossref(new window)

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. crossref(new window)

Song, Y.J. 2009. Characterization of aromatic hydrocarbon degrading bacteria isolated from pine litter. Korean J. Microbiol. Biotechnol. 37, 333-339.

Stevenson, F.J. 1994. Humus chemistry: Genesis, composition, reactions, 2nd ed. John Wiley and Sons, New York, N.Y., USA.

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.

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.

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. crossref(new window)

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.

Wackett, L.P. and Ellis, L.B. 1999. Predicting biodegradation. Environ. Microbiol. 1, 119-124. crossref(new window)

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. crossref(new window)

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.