Applied Microbiology and Biotechnology

, Volume 66, Issue 4, pp 457–463 | Cite as

Quantifying bacterial population dynamics in compost using 16S rRNA gene probes

  • Patrick D. Schloss
  • Anthony G. Hay
  • David B. Wilson
  • James M. Gossett
  • Larry P. Walker
Environmental Biotechnology

Abstract

Composting provides a dynamic setting for studying ecological topics such as succession, competition, and community stability in a relatively short period of time. This study used hierarchical small sub-unit-based rRNA gene probes to quantify the change in the relative abundance of phylogenetic groups common to compost in laboratory scale reactors. Bacterial 16S rRNA gene targets accounted for only 37% of all small subunit (SSU) rRNA genes initially, but increased to a maximum of 83% of the total at 84 h. The sum of rRNA genes detected using probes specific to Pseudomonas and low-G+C Gram-positive rRNA genes represented between 16% and 87% of the total. The lack of hybridization to the taxon-specific probes was most pronounced between 36 h and 60 h, when the pH was between 4.6 and 4.8. During this period the relative abundance of taxon-specific gene targets accounted for only 17–33% of the total bacterial rRNA gene targets. Pseudomonas-type 16S rRNA genes were the most abundant of the groups measured until 72 h. Those genes had their highest relative abundance at 12 h (78% of bacterial rRNA genes; 30% of all rRNA genes), after which time their relative abundance began to decline as the temperature increased. Prior to 72 h, 16S rRNA genes from low-G+C Gram-positive bacteria (LGC-GPB) represented less than 7% of the bacterial rRNA genes. However, by 84 h the relative abundance of LGC-GPB and Bacillus rRNA genes had increased to 60% and 18% of the bacterial rRNA gene targets, respectively (50% and 15% of all rRNA genes, respectively).

References

  1. Alm EW, Oerther DB, Larsen N, Stahl DA, Raskin L (1996) The oligonucleotide probe database. Appl Environ Microbiol 62:3557–3559PubMedGoogle Scholar
  2. Amann RI, Binder BJ, Olson RJ, Chisholm SW, Devereux R, Stahl DA (1990) Combination of 16S rRNA targeted oligonucleotide probes with flow-cytometry for analyzing mixed microbial populations. Appl Environ Microbiol 56:1919–1925PubMedGoogle Scholar
  3. Applegate B, Matrubutham U, Sanseverino J, Sayler G (1995) Biodegradation genes as marker genes in microbial ecosystems. In: Molecular microbial ecology manual, vol 6.1.8. Kluwer, DordrechtGoogle Scholar
  4. Ausubel FM, Brent R, Kingston RE, Moore DD, Seidman JG, Smith JA, Struhl K (1987) Current protocols in molecular biology. Wiley-Interscience, New YorkGoogle Scholar
  5. Blanc M, Marilley L, Beffa T, Aragno M (1999) Thermophilic bacterial communities in hot composts as revealed by most probable number counts and molecular (16S rDNA) methods. FEMS Microbiol Ecol 28:141–149CrossRefGoogle Scholar
  6. Buckley DH, Schmidt TM (2001) The structure of microbial communities in soil and the lasting impact of cultivation. Microb Ecol 42:11–21PubMedGoogle Scholar
  7. Chapelle FH, O’Neill K, Bradley PM, Methe BA, Ciufo SA, Knobel LL, Lovley DR (2002) A hydrogen-based subsurface microbial community dominated by methanogens. Nature 415:312–315CrossRefPubMedGoogle Scholar
  8. Choi MH, Park YH (1998) The influence of yeast on thermophilic composting of food waste. Lett Appl Microbiol 26:175–178CrossRefPubMedGoogle Scholar
  9. Dees PM, Ghiorse WC (2001) Microbial diversity in hot synthetic compost as revealed by PCR-amplified rRNA sequences from cultivated isolates and extracted DNA. FEMS Microbiol Ecol 35:207–216CrossRefPubMedGoogle Scholar
  10. DuTeau NM, Rogers JD, Bartholomay CT, Reardon KF (1998) Species-specific oligonucleotides for enumeration of Pseudomonas putida F1, Burkholderia sp. strain JS150, and Bacillus subtilis ATCC 7003 in biodegradation experiments. Appl Environ Microbiol 64:4994–4999PubMedGoogle Scholar
  11. Edgcomb VP, McDonald JH, Devereux R, Smith DW (1999) Estimation of bacterial cell numbers in humic acid-rich salt marsh sediments with probes directed to 16S ribosomal DNA. Appl Environ Microbiol 65:1516–1523PubMedGoogle Scholar
  12. Hansen MC, Tolker-Nielsen T, Givskov M, Molin S (1998) Biased 16S rDNA PCR amplification caused by interference from DNA flanking the template region. FEMS Microbiol Ecol 26:141–149CrossRefGoogle Scholar
  13. Haug RT (1993) The practical handbook of compost engineering. Lewis, Boca RatonGoogle Scholar
  14. Higgins CW, Walker LP (2001) Validation of a new model for aerobic organic solids decomposition: simulations with substrate specific kinetics. Process Biochem 36:875–884CrossRefGoogle Scholar
  15. Howeler M, Ghiorse WC, Walker LP (2003) A quantitative analysis of DNA extraction and purification from compost. J Microbiol Methods 54:37–45CrossRefPubMedGoogle Scholar
  16. Ishii K, Fukui M, Takii S (2000) Microbial succession during a composting process as evaluated by denaturing gradient gel electrophoresis analysis. J Appl Microbiol 89:768–777CrossRefPubMedGoogle Scholar
  17. Kaiser J (1995) Modelling composting as a microbial ecosystem: a simulation approach. Ecol Model 91:25–37CrossRefGoogle Scholar
  18. Malik M, Kain J, Pettigrew C, Ogram A (1994) Purification and molecular analysis of microbial DNA from compost. J Microbiol Methods 20:183–196CrossRefGoogle Scholar
  19. Meier H, Amann R, Ludwig W, Schleifer KH (1999) Specific oligonucleotide probes for in situ detection of a major group of Gram-positive bacteria with low DNA G+C content. Syst Appl Microbiol 22:186–196PubMedGoogle Scholar
  20. Nakasaki K, Shoda M, Kubota H (1985) Effect of temperature on composting of sewage sludge. Appl Environ Microbiol 500:1526–1530Google Scholar
  21. Pedro MS, Haruta S, Hazaka M, Shimada R, Yoshida C, Hiura K, Ishii M, Igarashi Y (2001) Denaturing gradient gel electrophoresis analyses of microbial community from field-scale composter. J Biosci Bioeng 91:159–165CrossRefGoogle Scholar
  22. 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 66:930–936CrossRefPubMedGoogle Scholar
  23. Polz MF, Cavanaugh CM (1998) Bias in template-to-product ratios in multitemplate PCR. Appl Environ Microbiol 64:3724–3730PubMedGoogle Scholar
  24. Raskin L, Poulsen LK, Noguera DR, Rittmann BE, Stahl DA (1994) Quantification of methanogenic groups in anaerobic biological reactors by oligonucleotide probe hybridization. Appl Environ Microbiol 60:1241–1248PubMedGoogle Scholar
  25. Romanowski G, Lorenz MG, Sayler G, Wackernagel W (1992) Persistence of free plasmid DNA in soil monitored by various methods, including a transformation assay. Appl Environ Microbiol 58:3012–3019Google Scholar
  26. Salzman NH, De Jong H, Paterson Y, Harmsen HJ, Welling GW, Bos NA (2002) Analysis of 16S libraries of mouse gastrointestinal microflora reveals a large new group of mouse intestinal bacteria. Microbiology 148:3651–3660PubMedGoogle Scholar
  27. Schloss PD, Walker LP (2000) Measurement of the process performance and variability in inoculated composting reactors using ANOVA and power analysis. Process Biochem 35:931–942CrossRefGoogle Scholar
  28. Schloss P, Walker L (2001) Assessment and improvement of process variable reproducibility in composting reactors. Trans ASAE 44:1022–1030Google Scholar
  29. Schloss PD, Chaves B, Walker LP (2000) The use of the analysis of variance to assess the influence of mixing during composting. Process Biochem 35:675–687CrossRefGoogle Scholar
  30. Schloss PD, Hay AG, Wilson DB, Walker LP (2003a) Tracking temporal changes of bacterial community fingerprints during the initial stages of composting. FEMS Microbiol Ecol 46:1–9CrossRefGoogle Scholar
  31. Schloss PD, Hay AG, Wilson DB, Walker LP (2003b) Molecular assessment of inoculum efficacy and process reproducibility in composting using ARISA. Trans ASAE 46:919–927Google Scholar
  32. Shaver YJ, Nagpal ML, Rudner R, Nakamura LK, Fox KF, Fox A (2002) Restriction fragment length polymorphism of rRNA operons for discrimination and intergenic spacer sequences for cataloging of Bacillus subtilis sub-groups. J Microbiol Methods 50:215–223CrossRefPubMedGoogle Scholar
  33. Stahl DA, Flesher B, Mansfield HR, Montgomery L (1988) Use of phylogenetically based hybridization probes for studies of ruminal microbial ecology. Appl Environ Microbiol 54:1079–1084PubMedGoogle Scholar
  34. Strom PF (1985) Effect of temperature on bacterial species diversity in thermophilic solid waste composting. Appl Environ Microbiol 50:899–905PubMedGoogle Scholar
  35. Strom PF (1985) Identification of thermophilic bacteria in solid-waste composting. Appl Environ Microbiol 50:906–913PubMedGoogle Scholar
  36. Suzuki MT, Giovannoni SJ (1996) Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR. Appl Environ Microbiol 62:625–630PubMedGoogle Scholar
  37. VanderGheynst JS, Gossett JM, Walker LP (1997a) High-solids aerobic decomposition: pilot-scale reactor development and experimentation. Process Biochem 32:361–375CrossRefGoogle Scholar
  38. VanderGheynst JS, VanderGheynst GB, Walker LP (1997b) Development and analysis of oxygen sensing probes for in-situ monitoring of solid-state biodegradation processes. J Air Waste Manag Assoc 47:642–651PubMedGoogle Scholar
  39. VanderGheynst JS, Walker LP, Parlange J-Y (1997c) Energy transport in a high-solids aerobic degradation process: mathematical modeling and analysis. Biotechnol Prog 13:238–248CrossRefGoogle Scholar
  40. VanderGheynst JS, Cogan DJ, DeFelice PJ, Gossett JM, Walker LP (1998) Effect of process management on the emission of organosulfur compounds and gaseous antecedents from composting processes. Environ Sci Technol 32:3713–3718CrossRefGoogle Scholar
  41. Walker LP, Nock TD, Gossett JM, VanderGheynst JS (1999) Managing moisture limitations on microbial activity in high-solids aerobic decomposition: pilot-scale experimentation. Process Biochem 34:601–612CrossRefGoogle Scholar

Copyright information

© Springer-Verlag 2004

Authors and Affiliations

  • Patrick D. Schloss
    • 1
  • Anthony G. Hay
    • 3
  • David B. Wilson
    • 4
  • James M. Gossett
    • 5
  • Larry P. Walker
    • 1
  1. 1.Department of Biological and Environmental Engineering, Riley-Robb HallCornell UniversityIthacaUSA
  2. 2.Department of Plant PathologyUniversity of Wisconsin-MadisonMadisonUSA
  3. 3.Department of MicrobiologyCornell UniversityIthacaUSA
  4. 4.Department of Molecular Biology & GeneticsCornell UniversityIthacaUSA
  5. 5.School of Civil and Environmental EngineeringCornell UniversityIthacaUSA

Personalised recommendations