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

Applied Microbiology and Biotechnology

Volumn 66, Issue 4, 2005, Pages 457-463

  Schloss, Patrick D ^a,b   Hay, Anthony G ^c   Wilson, David B ^c   Gossett, James M ^d   Walker, Larry P ^a  

^a Department of Biological and Environmental Engineering   (United States)

^b UNIVERSITY OF WISCONSIN MADISON   (United States)

^c Department of Obstetrics Gynecology   (United States)

^d Cornell University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPETITION; COMPOSTING; ECOLOGY; POPULATION STATISTICS; PROBES; RNA;

LOW-G+C GRAM-POSITIVE BACTERIA (LGC-GPB); TAXON-SPECIFIC GENE TARGETS;

BACTERIA;

BACTERIAL RNA; RIBOSOME RNA;

BACTERIUM; COMPOST; POPULATION DYNAMICS;

ARTICLE; BACILLUS; BACTERIAL GENETICS; COMPOST; GENE PROBE; GENE TARGETING; GRAM POSITIVE BACTERIUM; HYBRIDIZATION; NONHUMAN; PH; PHYLOGENY; PSEUDOMONAS; TAXON; TEMPERATURE; TIME;

BASE COMPOSITION; BASE SEQUENCE; COLONY COUNT, MICROBIAL; DNA, BACTERIAL; GENES, BACTERIAL; GRAM-POSITIVE BACTERIA; OLIGONUCLEOTIDE PROBES; PSEUDOMONAS; RNA, BACTERIAL; RNA, RIBOSOMAL, 16S; SOIL MICROBIOLOGY;

BACTERIA (MICROORGANISMS); FIRMICUTES; POSIBACTERIA; PSEUDOMONAS;

EID: 12144257237     PISSN: 01757598     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00253-004-1727-y     Document Type: Article

References (41)

1. Alm EW, Oerther DB, Larsen N, Stahl DA, Raskin L (1996) The oligonucleotide probe database. Appl Environ Microbiol 62:3557-3559
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 56:1919-1925
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, Dordrecht
4. Ausubel FM, Brent R, Kingston RE, Moore DD, Seidman JG, Smith JA, Struhl K (1987) Current protocols in molecular biology. Wiley-Interscience, New York
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 28:141-149
6. Buckley DH, Schmidt TM (2001) The structure of microbial communities in soil and the lasting impact of cultivation. Microb Ecol 42:11-21
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 415:312-315
8. Choi MH, Park YH (1998) The influence of yeast on thermophilic composting of food waste. Lett Appl Microbiol 26:175-178
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 35:207-216
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 64:4994-4999
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 65:1516-1523
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 26:141-149
13. Haug RT (1993) The practical handbook of compost engineering. Lewis, Boca Raton
14. Higgins CW, Walker LP (2001) Validation of a new model for aerobic organic solids decomposition: simulations with substrate specific kinetics. Process Biochem 36:875-884
15. Howeler M, Ghiorse WC, Walker LP (2003) A quantitative analysis of DNA extraction and purification from compost. J Microbiol Methods 54:37-45
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 89:768-777
17. Kaiser J (1995) Modelling composting as a microbial ecosystem: a simulation approach. Ecol Model 91:25-37
18. Malik M, Kain J, Pettigrew C, Ogram A (1994) Purification and molecular analysis of microbial DNA from compost. J Microbiol Methods 20:183-196
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 22:186-196
20. Nakasaki K, Shoda M, Kubota H (1985) Effect of temperature on composting of sewage sludge. Appl Environ Microbiol 500:1526-1530
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 91:159-165
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 66:930-936
23. Polz MF, Cavanaugh CM (1998) Bias in template-to-product ratios in multitemplate PCR. Appl Environ Microbiol 64:3724-3730
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 60:1241-1248
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 58:3012-3019
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 148:3651-3660
27. Schloss PD, Walker LP (2000) Measurement of the process performance and variability in inoculated composting reactors using ANOVA and power analysis. Process Biochem 35:931-942
28. Schloss P, Walker L (2001) Assessment and improvement of process variable reproducibility in composting reactors. Trans ASAE 44:1022-1030
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 35:675-687
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 46:1-9
31. Schloss PD, Hay AG, Wilson DB, Walker LP (2003b) Molecular assessment of inoculum efficacy and process reproducibility in composting using ARISA. Trans ASAE 46:919-927
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 50:215-223
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 54:1079-1084
34. Strom PF (1985) Effect of temperature on bacterial species diversity in thermophilic solid waste composting. Appl Environ Microbiol 50:899-905
35. Strom PF (1985) Identification of thermophilic bacteria in solid-waste composting. Appl Environ Microbiol 50:906-913
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 62:625-630
37. VanderGheynst JS, Gossett JM, Walker LP (1997a) High-solids aerobic decomposition: pilot-scale reactor development and experimentation. Process Biochem 32:361-375
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 47:642-651
39. VanderGheynst JS, Walker LP, Parlange J-Y (1997c) Energy transport in a high-solids aerobic degradation process: mathematical modeling and analysis. Biotechnol Prog 13:238-248
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 32:3713-3718
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 34:601-612