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http://dx.doi.org/10.4014/jmb.0807.455

Fungal Diversity in Composting Process of Pig Manure and Mushroom Cultural Waste Based on Partial Sequence of Large Subunit rRNA  

Cho, Kye-Man (Research Institute of Agricultural Science, Sunchon National University)
Kwon, Eun-Ju (Research Institute of Agricultural Science, Sunchon National University)
Kim, Sung-Kyum (Department of Agricultural Chemistry, Sunchon National University)
Kambiranda, Devaiah M (Division of Applied Life Science (BK21 Program), Gyeongsang National University)
Math, Reukaradhya K (Division of Applied Life Science (BK21 Program), Gyeongsang National University)
Lee, Young-Han (Division of Plant Environmental Research, Gyeongsangnam-do Agricultural Research and Extension Service)
Kim, Jung-Ho (Department of Agricultural Chemistry, Sunchon National University)
Yun, Han-Dae (Division of Applied Life Science (BK21 Program), Gyeongsang National University)
Kim, Hoon (Department of Agricultural Chemistry, Sunchon National University)
Publication Information
Journal of Microbiology and Biotechnology / v.19, no.8, 2009 , pp. 743-748 More about this Journal
Abstract
Fungal diversity during composting was investigated by culture-independent rDNA sequence analysis. Composting was carried out with pig manure and mushroom cultural waste using a field-scale composter (Hazaka system), and samples were collected at various stages. Based on partial sequence analysis of large subunit (LSU) ribosomal RNA (rRNA) and sequence identity values, a total of 12 different fungal species were found at six sampling sites; Geotrichum sp., Debaryomyces hansenii, Monographella nivalis, Acremonium strictum, Acremonium alternatum, Cladosporium sphaerospermum, Myriangium durosai, Pleurotus eryngii, Malassezia globosa, Malassezia restricta, Rhodotorula glutinis, and Fusarium sporotrichioides. Geotrichum sp. of the class Saccharomycetes was the most predominant fungal species throughout the composting process (185 out of a total of 236 identified clones, or 78.4%), followed by Acremonium strictum (7.6%), Monographella nivalis (5.1%), and Pleurotus eryngii (3.8%). The prevalence of Geotrichum sp. was the lowest (61.1%) at the beginning of composting, and then gradually increased to 92.5% after 10 days of composting.
Keywords
Fungal diversity; composting; LSU (26S) rRNA; Geotrichum sp.;
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1 McGinnis, S. and T. L. Madden. 2004. BLAST: At the core of a powerful and diverse set of sequence analysis tools. Nucleic Acids Res. 32: W20-25   DOI   ScienceOn
2 Schloss, P. D., A. G. Hay, D. B. Wilson, and L. P. Walker. 2003. Tracking temporal changes of bacterial community fingerprints during the initial stages of composting. FEMS Microbiol. Ecol. 46: 1-9   DOI   ScienceOn
3 Schulze, K. L. 1962. Continuous thermophilic composting. Appl. Microbiol. 10: 108-122   PUBMED   ScienceOn
4 Walker, L. P., T. D. Nock, J. M. Gossett, and J. S. VanderGheynst. 1999. Managing moisture limitations on microbial activity in high-solids aerobic decomposition: Pilot-scale experimentation. Process Biochem. 34: 601-612   DOI   ScienceOn
5 Anderson, I. C., C. D. Campbell, and J. I. Prosser. 2003. Potential bias of fungal 18S rDNA and internal transcribed spacer polymerase chain reaction primers for estimating fungal biodiversity in soil. Environ. Microbiol. 5: 36-46   DOI   ScienceOn
6 Clark, C. S., C. O. Buckingham, D. H. Bone, and R. H. Clark. 1977. Laboratory scale composting: Techniques. J. Environ. Eng. Div. 103: 47-59
7 Hansgate, A. M., P. D. Schloss, A. G. Hay, and L. P. Walker. 2005. Molecular characterization of fungal community dynamics in the initial stages of composting. FEMS Microbiol. Ecol. 51: 209-214   DOI   ScienceOn
8 Higgins, C. W. and L. P. Walker. 2001. Validation of a new model for aerobic organic solids decomposition: Simulations with substrate specific kinetics. Process Biochem. 36: 875-884   DOI   ScienceOn
9 Ishii, K., M. Fukui, and S. Takii. 2000. Microbial succession during a composting process as evaluated by denaturing gradient gel electrophoresis analysis. J. Appl. Microbiol. 89: 768-777   DOI   ScienceOn
10 Kim, M.-C., J.-H. Ahn, H.-C. Shin, T. Kim, T.-H. Ryu, D.-H. Kim, H.-G. Song, G. H. Lee, and J.-O. Ka. 2008. Molecular analysis of bacterial community structures in paddy soils for environmental risk assessment with two varieties of genetically modified rice, Iksan 483 and Milyang 204. J. Microbiol. Biotechnol. 18: 207-218   PUBMED   ScienceOn
11 Liew, P. W. Y. and B. C. Jong. 2008. Application of rDNA-PCR amplification and DGGE fingerprinting for detection of microbial diversity in a Malaysian crude oil. J. Microbiol. Biotechnol. 18: 815-820   PUBMED   ScienceOn
12 Ranjard, L., F. Poly, J. C. Lata, C. Mougel, J. Thioulouse, and S. Nazaret. 2001. Characterization of bacterial and fungal soil communities by automated ribosomal intergenic spacer analysis fingerprints: Biological and methodological variability. Appl. Environ. Microbiol. 67: 4479-4487   DOI   ScienceOn
13 Wong, J. W., K. F. Mak, N. W. Chan, A. Lam, M. Fang, L. X. Zhou, Q. T. Wu, and X. D. Liao. 2001. Co-composting of soybean residues and leaves in Hong Kong. Bioresour. Technol. 76: 99-106   DOI   ScienceOn
14 Guillamon, J. M., J. Sabate, E. Barrio, J. Cano, and A. Querol. 1998. Rapid identification of wine yeast species based on RFLP analysis of the ribosomal internal transcribed spacer (ITS) region. Arch. Microbiol. 169: 387-392   DOI   ScienceOn
15 Kurtzman, C. P. and C. J. Robnett. 1998. Identification and phylogeny of ascomycetous yeasts from analysis of nuclear large subunit (26S) ribosomal DNA partial sequences. Antonie van Leeuwenhoek 73: 331-373   DOI   ScienceOn
16 Bailey, K. L. and L. G. Lazarovits. 2003. Suppressing soil-borne diseases with residue management and organic amendments. Soil Tillage Res. 72: 169-180   DOI   ScienceOn
17 Schloss, P. D., A. G. Hay, D. B. Wilson, and L. P. Walker. 2003. Molecular assessment of inoculum efficacy and process reproducibility in composting using ARISA. Trans. ASAE 46: 919-927   ScienceOn
18 Tiquia, S. M. and N. F. Y. Tam. 2000. Co-composting of spent pig litter and sludge with forced aeration. Bioresour. Technol. 72: 1-7   DOI   ScienceOn
19 Unmar, G. and R. Mohee. 2008. Assessing the effect of biodegradable and degradable plastics on the composting of green wastes and compost quality. Bioresour. Technol. 99: 6738- 6744   DOI   ScienceOn
20 Peters, S., S. Koschinsky, F. Schwieger, and C. C. Tebbe. 2000. Succession of microbial communities during hot composting as detected by PCR-single- trand-conformation polymorphism based genetic profiles of small-subunit rRNA enes. Appl. Environ. Microbiol. 66: 930-936   DOI   ScienceOn
21 Nakasaki, K., S. Hiraoka, and H. Nakada. 1998. A new operation for producing disease-suppressive compost from grass clippings. Appl. Environ. Microbiol. 64: 4015-4020   PUBMED   ScienceOn
22 Thompson, J. D., D. G. Higgins, and T. J. Gibson. 1994. CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22: 4673-4680   DOI   ScienceOn
23 Pedro, M. S., S. Haruta, M. Hazaka, R. Shimada, C. Yoshida, K. Hiura, M. Ishii, and Y. Igarashi. 2001. Denaturing gradient gel electrophoresis analyses of microbial community from field scale composter. J. Biosci. Bioeng. 91: 159-165   DOI   PUBMED   ScienceOn
24 Van der Auwera, G., S. Chapelle, and R. De Wachter. 1994. Structure of the large ribosomal subunit RNA of Phytophthora megasperma, and phylogeny of the oomycetes. FEBS Lett. 338: 133-136   DOI   ScienceOn
25 Dees, P. M. and W. C. Ghiorse. 2001. Microbial diversity in hot synthetic compost as revealed by PCR-amplified rRNA sequences from cultivated isolates and extracted DNA. FEMS Microbiol. Ecol. 35: 207-216   DOI   ScienceOn
26 Giannoutsou, E. P., C. Meintanis, and A. D. Karagouni. 2004. Identification of yeast strains isolated from a two-phase decanter system olive oil waste and investigation of their ability for its fermentation. Bioresour. Technol. 93: 301-306   DOI   ScienceOn
27 Strom, P. F. 1985. Effect of temperature on bacterial species diversity in thermophilic solid-waste composting. Appl. Environ. Microbiol. 50: 899-905   PUBMED   ScienceOn
28 Barker, A. V. and G. M. Bryson. 2002. Bioremediation of heavy metals and organic toxicants by composting. Sci. World J. 12: 407-420
29 Saitou, N. and M. Nei. 1987. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4: 406-425   PUBMED   ScienceOn
30 Haug, R. T. 1993. The Practical Handbook of Compost Engineering. Lewis Publishers, Boca Raton, Florida, U.S.A
31 Bridge, P. D., P. J. Roberts, B. M. Spooner, and G. Panchal. 2003. On the unreliability of published DNA sequences. New Phytol. 160: 43-48   DOI   ScienceOn
32 Smit, E., P. Leeflang, B. Glandorf, J. Dirk van Elsas, and K. Wernars. 1999. Analysis of fungal diversity in the wheat rhizosphere by sequencing of cloned PCR-amplified genes encoding 18S rRNA and temperature gradient gel electrophoresis. Appl. Environ. Microbiol. 65: 2614-2621   PUBMED   ScienceOn
33 Esteve-Zarzoso, B., C. Belloch, F. Uruburu, and A. Querol. 1999. Identification of yeasts by RFLP analysis of the 5.8S rRNA gene and the two ribosomal internal transcribed spacers. Int. J. Syst. Bacteriol. 49: 329-337   DOI   ScienceOn
34 Malik, M., J. Kain, C. Pettigrew, and A. Ogram. 1994. Purification and molecular analysis of microbial DNA from compost. J. Microbiol. Methods 20: 183-196   DOI   ScienceOn
35 Anastasi, A., G. C. Varese, S. Voyron, S. Scannerini, and M. V. Filipello. 2004. Characterization of fungal biodiversity in compost and vermicompost. Compost Sci. Util. 12: 185-191   DOI   ScienceOn
36 Singh, A., K. Billingsley, and O. Ward. 2006. Composting: A potentially safe process for disposal of genetically modified organisms. Crit. Rev. Biotechnol. 26: 1-16   DOI   ScienceOn
37 Ntougias, S., G. I. Zervakis, N. Kavroulakis, C. Ehaliotis, and K. K. Papdopoulou. 2004. Bacterial diversity in spent mushroom compost assessed by amplified rDNA restriction analysis and sequencing of cultivated isolates. Syst. Appl. Microbiol. 27: 746-754   DOI   ScienceOn
38 Strom, P. F. 1985. Identification of thermophilic bacteria in solid-waste composting. Appl. Environ. Microbiol. 50: 906- 913   PUBMED   ScienceOn
39 Takaku, H., S. Kodaira, A. Kimoto, M. Nashimoto, and M. Takagi. 2006. Microbial communities in the garbage composting with rice hull as an amendment revealed by culture-dependent and -independent approaches. J. Biosci. Bioeng. 101: 42-50   DOI   ScienceOn