Bacterial Community Structure During Yard Trimmings Composting
A long-term objective of our group is to understand how various composting parameters affect microbial community structure in composts. In this study, we used terminal restriction fragment length polymorphisms (T-RFLP) of PCR-amplified 16S rRNA genes to analyze bacterial community structure during the composting of yard trimmings. Community DNA was isolated from samples collected on days 0, 8, 29, 64, and 136 from a compost windrow (consisting of leaves, grass, and brush in a 4:2:1 ratio) at a large-scale municipal facility. The DNA was PCR-amplified using fluorescently labeled primers targeted to bacterial domain 16S rRNA genes. The products were restriction-digested with Hhal, Mspl,and Rsal to give fingerprints of the bacterial communities. Terminal restriction fragment (TRF) sizes obtained with the three digestions were compared to the three fragments determined by computer-simulated amplification and restriction digestions of complete 16S rRNA gene sequences. T-RFLP patterns indicated extensive bacterial diversity in all of the composts. A large percentage of the observed TRFs corresponded to sizes predicted for bacteria by computer-simulated digestion. Comparison of fragment sizes from three digestions to those predicted by computer-simulated digestions indicated a substantial shift from a bacterial community containing primarily Gram-negative α, β, and γ Proteobacteria (day 0) to communities containing many members of the Gram-positive Bacillus-Clostridium group (days 8, 29, and 64) and members of the CFB and Actinobacteria (days 29 and 64). Bacterial species identified on days 8, 29, and 64 included those previously isolated from thermophilic composts by cultivation such as Bacillus and Pseudomonas spp. as well as many not previously described in composts. Abundant TRFs corresponding to E. coli and other Gram-negative γ Proteobacteria, decreased dramatically after the first 8 days of composting. The day-136 composts contained a diverse group of bacteria including many fragment sizes consistent with known Pantoea and Pseudomonas biocontrol agents as well as Xanthomonas and Bacillus species. The greatest diversity of bacteria was observed in the stabilized day 64 and 136 composts where 115 and 111 TRFs corresponding to members of 7 and 6 different phylogenetic groups, respectively, were observed.
KeywordsBacterial Community Fragment Size Terminal Restriction Fragment Length Polymorphism Bacterial Community Structure Vibrio Species
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- Amman RI, Ludwig W, Schleifer KH (1995) Phylogenetic identification and in situ detection of microbial cells without cultivation. Microbiol Rev 59: 143 - 169Google Scholar
- Epstein E (1997) The science of composting. Technomic Publishing Co, Lancaster, PA pgs 53 - 76Google Scholar
- Klappenbach J, Dunbar JM, Schmidt TM (2000) rRNA gene copy number predicts ecological strategies in bacteria. Appl Environ Microbiol 66: 1328 - 1333Google Scholar
- LaMontagne ML, Michel, FC Jr. and Reddy CA. Evaluation of DNA extraction and purification methods for obtaining PCR amplifiable DNA from compost for community analysis. J Microbiol Meth (in press).Google Scholar
- Michel FC Jr., Forney LJ, Huang AJF, Drew S, Czuprenski M, Lindeberg JD, Reddy CA (1996) Effects of turning frequency, leaves to grass mix ratio, and windrow vs. pile configurations on the composting of yard trimmings. Compost Sci Util 4 (1): 26 - 43Google Scholar
- Reddy CA, Michel FC Jr (2000) Fate of xenobiotics during composting. Proceedings of the International Symposium of Microbial Ecology. Halifax NS August 20-25, 1998: pp 485 - 491Google Scholar
- Tsai YL, Olson BH (1991) Rapid method for direct extraction of DNA from soil and sediments Appl Environ Microbiol 57: 1070 - 1074Google Scholar