Bacterial Community Structure During Yard Trimmings Composting

  • F. C. MichelJr
  • T. J. Marsh
  • C. A. Reddy
Conference paper


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.


Bacterial Community Fragment Size Terminal Restriction Fragment Length Polymorphism Bacterial Community Structure Vibrio Species 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. Amman RI, Ludwig W, Schleifer KH (1995) Phylogenetic identification and in situ detection of microbial cells without cultivation. Microbiol Rev 59: 143 - 169Google Scholar
  2. Beffa T, Blanc M, Aragno M (1996a) Obligately and facultatively autotrophic, sulfur-and hydrogen-oxidizing thermophilic bacteria isolated from hot composts. Arch Microbiol 165: 34 - 40CrossRefGoogle Scholar
  3. Beffa T, Blanc M, Lyon PF, Vogt G, Marchiani M, Lott-Fischer J and Aragno M (1996b) Isolation of Thermus strains from hot composts (60° to 80° C.). Appl. Environ. Microbiol. 62 (5) 1723 - 1727.PubMedGoogle Scholar
  4. Blanc M, Marilley L, Beffa T, Aragno M (1997) Rapid identification of heterotrophic, thermophilic, spore-forming bacteria isolated from hot composts. Int J Syst Bacteriol 47: 1246 - 1248PubMedCrossRefGoogle Scholar
  5. Dunbar J, Ticknor LO, Kuske CR (2001) Phylogenetic specificity and reproducibility and new method for analysis of terminal restriction fragment profiles of 16S rRNA genes from bacterial communities. Appl Environ Microbiol 67: 190 - 197PubMedCrossRefGoogle Scholar
  6. Epstein E (1997) The science of composting. Technomic Publishing Co, Lancaster, PA pgs 53 - 76Google Scholar
  7. Einstein M (1975) The microbiology of municipal solid waste composting. Adv App] Microbiol 19: 113 - 151CrossRefGoogle Scholar
  8. Hoitink HAJ, Boehm MJ (1999) Biocontrol within the context of soil microbial communities: substrate-dependent phenomenon. Annu Rev Phytopathol 37: 427 - 446PubMedCrossRefGoogle Scholar
  9. Klamer M, Baath E (1998) Microbial community dynamics during composting of straw material studied using phospholipid fatty acid analysis. FEMS Microbiol Ecol 27: 9 - 20CrossRefGoogle Scholar
  10. Klappenbach J, Dunbar JM, Schmidt TM (2000) rRNA gene copy number predicts ecological strategies in bacteria. Appl Environ Microbiol 66: 1328 - 1333Google Scholar
  11. Laine MM, Jorgensen KS (1997) Effective and safe composting of chlorphenol-contaminated soil in pilot scale. Environ Sci Technol 31: 371 - 378CrossRefGoogle Scholar
  12. 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
  13. Liu WT, Marsh TL, Cheng H, Forney U (1997) Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of 16S ribosomal DNA. Appl Environ Microbiol 63: 4516 - 4522PubMedGoogle Scholar
  14. Maidak BL, Cole JR, Lilburn TG, Parker CT Jr, Saxman PR, Stredwick JM, Garrity GM, Li B, Olsen GJ, Pramanik S, Schmidt TM, Tiedje JM (2000) The RDP (ribosomal database project) continues. Nucleic Acids Res 28: 173 - 174PubMedCrossRefGoogle Scholar
  15. Marsh TL, Saxman PR, Cole JR, Tiedje JM (2000) Terminal restriction fragment length polymorphism analysis program, a web based research tool for microbial community analysis. Appl Environ Microbiol 66: 3615 - 3620CrossRefGoogle Scholar
  16. Michel FC Jr., Reddy CA, Forney U (1995) Microbial degradation and humification of 2,4 dichlorophenoxy acetic acid during the composting of yard trimmings. Appl Environ Microbiol 61: 2566 - 2571PubMedGoogle Scholar
  17. 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
  18. Muyzer GE, De Waal C, Uitterlinden AG (1993) Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl Environ Microbiol 59: 695 - 700PubMedGoogle Scholar
  19. Peters S., Koschinsky S, Schwieger F, Tebbe CC (2000) Succession of microbial communities during hot composting as detected by PCR—single-strand-conformation polymorphism-based genetic profiles of small-subunit rRNA genes. Appl Environ Microbiol 66: 930 - 936PubMedCrossRefGoogle Scholar
  20. 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
  21. Strom PF (1985a) Effect of temperature on bacterial species diversity during thermophilic solid waste composting. Appl Environ Microbiol 50: 899 - 905PubMedGoogle Scholar
  22. Strom PF (1985b) Identification of thermophilic bacteria in solid-waste composting. Appl Environ Microbiol 50: 906 - 913PubMedGoogle Scholar
  23. Tebbe CC, Schwieger F (1998) A new approach to utilize PCR-single-strand-conformation polymorphism for 16S rRNA gene-based microbial community analysis. Appl Environ Microbiol 64: 4870 - 4876PubMedGoogle Scholar
  24. Tsai YL, Olson BH (1991) Rapid method for direct extraction of DNA from soil and sediments Appl Environ Microbiol 57: 1070 - 1074Google Scholar
  25. Zhou J, Burns MA, Tiedje JM (1996) DNA recovery from soils of diverse composition. Appl Environ Microbiol 62: 316 - 322PubMedGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2002

Authors and Affiliations

  • F. C. MichelJr
    • 1
  • T. J. Marsh
    • 2
  • C. A. Reddy
    • 2
  1. 1.Department of Food, Agricultural and Biological EngineeringOhio State University-OARDCWoosterUSA
  2. 2.NSF Center for Microbial Ecology and Department of MicrobiologyMichigan State UniversityEast LansingUSA

Personalised recommendations