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Comparative Analysis of Bacterial Diversity in the Intestinal Tract of Earthworm (Eisenia fetida) using DGGE and Pyrosequencing  

Kim, Eun-Sung (Division of Biological Science and Technology, Yonsei University)
Hong, Sung-Wook (Division of Biological Science and Technology, Yonsei University)
Chung, Kun-Sub (Division of Biological Science and Technology, Yonsei University)
Publication Information
Microbiology and Biotechnology Letters / v.39, no.4, 2011 , pp. 374-381 More about this Journal
Abstract
The beneficial effects of Eisenia fetida on soil properties have been attributed to their interaction with soil microorganisms. The bacterial diversity of the intestinal tract of E. fetida was investigated by culture-dependent and culture-independent methods including denaturing gradient gel electrophoresis (DGGE) and pyrosequencing analyses. In a pure culture, Lysinibacillus fusiformis (51%), Bacillus cereus (30%), Enterobacter aerogenes (21%), and L. sphaericus (15%) were identified as the dominant microorganisms. In the DGGE analyses, B. cereus (15.1%), Enterobacter sp. (13.6%), an uncultured bacterium (13.1%), and B. stearothermophilus (7.8%) were identified as the dominant microorganisms. In the pyrosequencing analyses, Microbacterium soli (26%), B. cereus (10%), M. esteraromaticum (6%), and Frigoribacterium sp. (6%) were identified as the dominant microorganisms. The other strains identified were Aeromonas sp., Pseudomonas sp., Borrelia sp., Cellulosimicrobium sp., Klebsiella sp., and Leifsonia sp. The results illustrate that culture independent methods are better able to detect unculturable microorganisms and a wider range of species, as opposed to isolation by culture dependent methods.
Keywords
Bacterial diversity; pure culture; DGGE; pyrosequencing;
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1 Shin, K. H., H. Yi, J. S. Chun, C. J. Cha, I. S. Kim, and H. G. Hur. 2004. Analysis of the anaerobic bacterial community in the Earthworm (Eisenia fetida) intestine. Agric. Chem. Biotechnol. 47: 147-152.
2 Song, E. Y., J. K. Noh, Y. M. Yoon, Y. S. Choi, S. S. Park, E. K. Ra, and K. S. Han. 2006. ABO genotyping by pyrosequencing analysis. Korean J. Blood Transfusion. 17: 106- 115.
3 Walter, J., G. W. Tannock, A. Tilsala-Timisjarvi, S. Rodtong, D. M. Loach, K. Munro, and T. Alatossava. 2000. Detection and identification of gastrointestinal Lactobacillus species by using denaturing gradient gel electrophoresis and species specific PCR primers. Appl. Environ. Microbiol. 66: 297- 303.   DOI   ScienceOn
4 Kim, M. N. and H. J. Bang. 2006. Comparison of culturedependent and DGGE based methods the analysis of marine bacterial community. Kor. J. Environ. Biol. 24: 307-313.
5 Kim, T. S., H. S. Kim, S. D. Kwon, and H. D. Park. 2010. Analysis of bacterial community composition in waste water treatment bioreactors using 16 rRNA gene-based pyrosequencing. Kor. J. Microbiol. 46: 352-358.
6 Knapp, B. A., J. Seeber, S. M. Podmirseg, E. Meyer, and H. Insam. 2008. Application of denaturing gradient gel electrophoresis for analysing the gut microflora of Lumbricus rubellus Hoffmeister under different feeding conditions. Bull. Entomol. Res. 98: 271-279.
7 Kwon, K. R. and J. C. Seo. 2004. Genetical identification of Korean wild ginseng and american wild ginseng by using pyrosequencing method. Kor. J. Herbology 19: 45-50.
8 Miller, K. M, T. J. Ming, A. D. Schulze, and R. E. Withler. 1999. Denaturing gradient gel electrophoresis (DGGE): a rapid and sensitive technique to screen nucleotide sequence variation in populations. Biotechniques 27: 1016-1018.
9 Miwa, H., I. Ahmed, A. Yokota, and T. Fujiwara. 2009. Lysinibacillus parviboronicapiens sp. nov., a low-boroncontaining bacterium isolated from soil. Int. J. Syst. Evol. Microbiol. 59: 1427-1432.   DOI   ScienceOn
10 Parle, J. N. 1963. Microorganisms in the intestines of earthworms. J. Gen. Microbiol. 31: 1-11.   DOI
11 Rondon, M. R., R. M. Goodman, and J. Handelsman. 1999. The Earth's bounty: assessing and accessing soil microbial diversity. Trends Biotechnol. 17: 403-409.   DOI   ScienceOn
12 Park, J. S., C. J. Sim, and K. D. An. 2009. Community structure of bacteria associated with two marine sponges from Jeju Island based on 16S rDNA-DGGE profiles. Kor. J. Microbiol. 45: 170-176.
13 Parthasarathi, K., L. S. Ranganathan, V. Anandi, and J. Zeyer. 2007. Diversity of microflora in the gut and casts of tropical composting earthworms reared on different substrates. J. Environ. Biol. 28: 87-97.
14 Petrosino, J. F., S. Highlander, R. A. Luna, A. G. Richard, and J. Versalovic. 2009. Metagenomic pyrosequencing and microbial identification. Clin. Chem. 55: 856-866.   DOI   ScienceOn
15 Schleifer, K. H. and O. Kandler. 1972. Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol. Rev. 36: 407-477.
16 Droege, M. and H. Brendon. 2008. The genome sequencer $FLX^{TM}$ System-longer reads, more applications, straight forward bioinformatics and more complete data sets. J. Biotechnol. 136: 3-10.   DOI   ScienceOn
17 Edwards, C. A. and K. E. Fletcher. 1988. Interactions between earthworms and microorganisms in organic-matter breakdown. Agric. Ecosyst. Environ. 24: 235-247.   DOI
18 Farnleitner, A. H., F. Zibuschka, M. M. Burtscher, G. Lindner, G. R. L. Mach. 2004. Eubacterial 16S-rDNA amplicon profiling: a rapid technique for comparsion and differentiation of heterotrophic plate count communities from drinking water. Int. J. Food Microbiol. 92: 333-375.   DOI   ScienceOn
19 Hong, S. W., J. S. Lee, and K. S. Chung. 2011. Effect of enzyme producing microorganisms on the biomass of epigeic earthworms (Eisenia fetida) in vermicompost. Bioresour. Technol. 102: 6344-6347.   DOI   ScienceOn
20 Fisher, S. G. and L. S. Lerman. 1983. DNA fragments differing by single base-pair substitutions are separated in denaturing gradient gels: correspondence with melting theory. Proc. Natl. Acad. Sci. USA 80: 1579-1583.   DOI   ScienceOn
21 Ihssen, J., M. A. Horn, C. Matthies, A. Gössner, A. Schramm, and H. L. Drake. 2003. $N_{2}O$-Producing microorganisms in the gut of the earthworm Aporrectodea caliginosa are indicative of ingested soil bacteria. Appl. Environ. Microbiol. 69: 1655-1661.   DOI   ScienceOn
22 Kathrin, F., D. Hanhn, W. Honerlage, and J. Zeyer. 1997. Effect of passage through the gut of the earthworm Lumbricus terrestris L. on Bacillus megaterium studied by whole cell hybridization. Soil Biol. Biochem. 29: 1149-1152.   DOI   ScienceOn
23 Kim, H. J., K. H. Shin, C. J. Cha, and H. G. Hur. 2004. Analysis of aerobic and culturable bacterial community structures in earthworm (Eisenia fetida) intestine. Agric. Chem. Biotechnol. 47: 137-142.
24 Byzov, B. A., T. Nechitailo, B. K. Bumazhkin, A. V. Kurakov, P. N. Golyshin, and D. G. Zvyagintsev. 2009. Culturable microorganisms from the digestive tract of earthworm. Mikrobiolgiia. 78: 404-413.
25 Ahmed, I., A. Yokota, A. Yamazoe, and T. Fujiwara. 2007. Proposal of Lysinibacillus boronitolerans gen. nov. sp. nov., and transfer of Bacillus fusiformis to Lysinibacillus fusiformis comb. nov. and Bacillus sphaericus to Lysinibacillus sphaericus comb. nov. Int. J. Syst. Evol. Microbiol. 57: 1117- 1125.   DOI   ScienceOn