Molecular phylogenetic diversity of bacteria and its spatial distribution in composts

Journal of Applied Microbiology

Volumn 103, Issue 4, 2007, Pages 1344-1354

  Guo, Y ^a   Zhu, N ^b   Zhu, S ^a   Deng, C ^a  

^a HUAZHONG AGRICULTURAL UNIVERSITY   (China)

^b SOUTH CHINA UNIVERSITY OF TECHNOLOGY   (China)

Author keywords

16S rRNA gene; Bacteria; Compost; Initial stage; Phylogenetic diversity; Swine manure

Indexed keywords

CLONING; COMPOSTING; FERTILIZERS; GENES; MANURES; PILES; RNA; SPATIAL DISTRIBUTION;

16S RDNA SEQUENCE; 16S RRNA GENE; COMPOST; GRADIENT EFFECT; INITIAL STAGE; MICROBIAL COMMUNITIES; MICROBIAL DIVERSITY; PHYLOGENETIC DIVERSITY; SWINE MANURE; UNIQUE SEQUENCE;

BACTERIA;

DNA;

BACTERIUM; BIODIVERSITY; COMPOST; DNA FINGERPRINTING; MICROBIAL COMMUNITY; MOLECULAR ANALYSIS; PHYLOGENETICS; SPATIAL DISTRIBUTION; TEMPERATURE EFFECT;

AEROCOCCUS; ARTICLE; BACTERIAL GENE; BACTERIAL STRAIN; BACTERIUM CULTURE; CLOSTRIDIUM; COMPOSTING; DNA ISOLATION; DNA SEQUENCE; FIRMICUTES; GENE AMPLIFICATION; GENETIC SCREENING; GENETIC VARIABILITY; LACTOSPHAERA PASTEURII; MANURE; MEGASPHAERA; MICROBIAL DIVERSITY; MOLECULAR CLONING; MOLECULAR PHYLOGENY; NUCLEOTIDE SEQUENCE; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; SOIL MICROFLORA; STENOTROPHOMONAS; SWINE; UNINDEXED SEQUENCE;

AEROCOCCUS; BACTERIA (MICROORGANISMS); CLOSTRIDIUM SP.; FIRMICUTES; MEGASPHAERA; STENOTROPHOMONAS SP.; SUIDAE; TRICHOCOCCUS PASTEURII;

EID: 34848852624     PISSN: 13645072     EISSN: 13652672     Source Type: Journal    
DOI: 10.1111/j.1365-2672.2007.03367.x     Document Type: Article

References (62)

1. Abd-El-Haleem, D., Moawad, H., Zaki, E.A. Zaki, S. (2002) Molecular characterization of phenol-degrading bacteria isolated from different Egyptian ecosystems. Microb Ecol 43, 217 224.
2. Amann, R.I., Ludwig, W. Schleifer, K.H. (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 59, 143 169.
3. Bathe, S. (2004) Conjugal transfer of plasmid pNB2 to activated sludge bacteria leads to 3-chloroaniline degradation in enrichment cultures. Lett Appl Microbiol 38, 527 531.
4. Beffa, T., Blanc, M., Lyon, P.-F., Vogt, G., Marchiani, M., Fischer, J.L. Aragno, M. (1996a) Isolation of Thermus strains from hot composts (60 to 80°C). Appl Environ Microbiol 62, 1723 1727.
5. Beffa, T., Blanc, M., Marilley, L., Fischer, J.L., Lyon, P.-F. Aragno, M. (1996b) Taxonomic and metabolic microbial diversity during composting. In The Science of Composting ed. de Bertoldi, M., Sequi, P., Lemmes, B. Papi, T. pp. 149 161. Glasgow : Blackie Academic and Professional.
6. 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.
7. Clark, C.S., Buckingham, C.O., Bone, D.H. Clark, R.H. (1977) Laboratory scale composting: techniques. Environ Enngn Di ASCE 103, 47 59.
8. Collins, M.D., Lawson, P.A., Willems, A., Cordoba, J.J., Fernandez-Garayzabal, J., Garcia, P., Cai, J., Hippe, H., et al. (1994) The phylogeny of the genus Clostridium: proposal of five new genera and eleven new species combinations. Int J Syst Bacteriol 44, 812 826.
9. Dees, P.M. Ghiorse, W.C. (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. Dojka, M.A., Hugenholtz, P., Haack, S.K. Pace, N.R. (1998) Microbial diversity in a hydrocarbon- and chlorinated-solvent contaminated aquifer undergoing intrinsic bioremediation. Appl Environ Microbiol 64, 3869 3877.
11. Ekinci, K. (2001) Theoretical and experimental studies on the effects of aeration strategies on the composting process. PhD Thesis, The Ohio State University, Columbus, Ohio.
12. Fergus, C.L. (1964) Thermophilic and thermotolerant molds and actinomycetes of mushroom compost during peak heating. Mycologia 56, 267 284.
13. Fisher, M.M. Triplett, E.W. (1999) Automated approach for ribosomal intergenic spacer analysis of microbial diversity and its application to freshwater bacterial communities. Appl Environ Microbiol 65, 4630 4636.
14. Franke-Whittle, I.H., Klammer, S.H. Insam, H. (2005) Design and application of an oligonucleotide microarray for the investigation of compost microbial communities. J Microb Methods 62, 37 56.
15. Gloueke, C.G. Diaz, L.F. (1996) Historical review of composting and its role in municipal waste management. In The Science of Composting ed. de Bertoldi, M., Sequi, P., Lemmes, B. Papi, T. pp. 3 14. Glasgow : Blackie Academic and Professional.
16. Greenwood, S.J., Keith, I.R., Despres, B.M. Cawthorn, R.J. (2005) Genetic characterization of the lobster pathogen Aerococcus viridans var. homari by 16S rRNA gene sequence and RAPD. Dis Aquat Organ 63, 237 246.
17. Holben, W.E. (1994) Isolation and purification of bacterial DNA from soil. In Methods of Soil Analysis, Part 2. Microbiological and Biochemical Properties ed. Weaver, R.W., Angle, S., Bottomley, P., Bezdicek, D., Smith, S., Tabatabai, A. Wollum, A. pp. 727 751. Madison, WI : Soil Science Society of America.
18. Huang, L.-N., Zhou, H., Zhu, S. Qu, L.-H. (2004) Phylogenetic diversity of bacteria in the leachate of a full-scale recirculating landfill. FEMS Microbiol Ecol 50, 175 183.
19. Hugenholtz, P., Goebel, B.M. Pace, N.R. (1998) Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. J Bacteriol 180, 4765 4774.
20. Imbeah, M. (1998) Composting piggery waste: a review. Bioresour Technol 63, 197 203.
21. 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, 766 777.
22. Janssen, P.H., Evers, S., Rainey, F.A., Weiss, N., Ludwig, W., Harfoot, C.G. Schink, B. (1995) Lactosphaera gen. nov., a new genus of lactic acid bacteria, and transfer of Ruminococcus pasteurii Schink 1984 to Lactosphaera pasteurii comb. nov. Int J Syst Bacteriol 45, 565 571.
23. Juteau, P., Tremblay, D., Villemur, R., Bisaillon, J.-G. Beaudet, R. (2005) Analysis of the bacterial community inhabiting an aerobic thermophilic sequencing batch reactor (AT-SBR) treating swine waste. Appl Microbiol Biotechnol 66, 115 122.
24. Kimura, M. (1980) A simple method for estimating evolutionary rate of bas substitutions through comparative studies of nucleotide sequences. J Mol Evol 16, 111 120.
25. Kowalchuk, G.A., Naoumenko, Z.S., Derikx, P.J.L., Felske, A., Stephen, J.R. Arkhipchenko, I.A. (1999) Molecular analysis of ammonia-oxidizing bacteria of the L subdivision of the class Proteobacteria in compost and composted materials. Appl Environ Microbiol 65, 396 403.
26. Lane, D.J. (1991) 16S/23S rRNA sequencing. In Nucleic Acid Techniques in Bacterial Systematics ed. Stackebrandt, E. Goodfellow, M. pp. 115 175. New York : Wiley.
27. Leser, T.D., Amenuvor, J.Z., Jensen, T.K., Lindecrona, R.H., Boye, M. Moller, K. (2002) Culture-independent analysis of gut bacteria: the pig gastrointestinal tract microbiota revisited. Appl Environ Microbiol 68, 673 690.
28. Miller, F.C. (1989) Matric water potential as an ecological determinant in compost, a substrate dense system. Microb Ecol 18, 59 71.
29. Miller, F.C. (1996) Composting of municipal solid waste and its components. In Microbiology of Solid Waste ed. Palmisano, A.C. Barlaz, M.A. pp. 115 154. Boca Raton, FL : CRC Press.
30. Millner, P.D. (1982) Thermophilic and thermotolerant actinomycetes in sewage-sludge compost. Dev Ind Microbiol 23, 61 78.
31. Mukai, T., Arihara, K., Ikeda, A., Nomura, K., Suzuki, F. Ohori, H. (2003) Lactobacillus kitasatonis sp. nov., from chicken intestine. Int J Syst Evol Microbiol 53, 2055 2059.
32. Ntougias, S., Zervakis, G.I., Kavroulakis, N., Ehaliotis, C. Papadopoulou, K.K. (2004) Bacterial diversity in spent mushroom compost assessed by amplified rDNA restriction analysis and sequencing of cultivated isolates. Syst Appl Microbiol 27, 746 754.
33. Ozutsumi, Y., Tajima, K., Takenaka, A. Itabashi, H. (2005) The effect of protozoa on the composition of rumen bacteria in cattle using 16S rRNA gene clone libraries. Biosci Biotechnol Biochem 69, 499 506.
34. Paster, B.J., Boches, S.K., Galvin, J.L., Ericson, R.E., Lau, C.N., Levanos, V.A., Sahasrabudhe, A. Dewhirst, F.E. (2001) Bacterial diversity in human subgingival plaque. J Bacteriol 183, 3770 3783.
35. Peters, S., Koschinsky, S., Schwieger, F. Tebbe, C.C. (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.
36. Ryckeboer, J., Mergaert, J., Vaes, K., Klammer, S., De Clercq, D., Coosemans, J., Insam, H. Swings, J. (2003) A survey of bacteria and fungi occurring during composting and self-heating processes. Ann Microbiol 53, 349 410.
37. Rynk, R., Kamp, M., Willson, G., Singley, M., Richard, T., Kolega, J. Gouin, F. (1991) On-farm Composting Handbook. Ithaca, NY : North-East Regional Agricultural Engineering Service.
38. Saitou, N. Nei, M. (1987) The neighbor-joining method: a method for constructing phylogenetic trees. Mol Biol Evol 4, 406 425.
39. Sambrook, J., Fritsch, E.F. Maniatis, T. (1989) Molecular Cloning: A Laboratory Manual, 2nd edn. New York : Cold Spring Harbor Laboratory Press.
40. Schloss, P.D., Hay, A.G., Wilson, D.B. Walker, L.P. (2003) Tracking temporal changes of bacterial community fingerprints during the initial stages of composting. FEMS Microbiol Ecol 46, 1 9.
41. Schloss, P.D., Hay, A.G., Wilson, D.B., Gossett, J.M. Walker, L.P. (2005) Quantifying bacterial population dynamics in compost using 16S rRNA gene probes. Appl Microbiol Biotechnol 66, 457 463.
42. Schulze, K.L. (1961) Relationship between moisture content and activity of finished compost. Compost Sci 2, 32 34.
43. Schulze, K.L. (1962) Continuous thermophilic composting. Appl Microbiol 10, 129 140.
44. Snell, J.R. (1957) Some engineering aspects of high rate composting. Proc ASCE 83, 1178.
45. Stackebrandt, E., Kramer, I., Swiderski, J. Hippe, H. (1999) Phylogenetic basis for a taxonomic dissection of the genus Clostridium. FEMS Immunol Med Microbiol 24, 253 258.
46. Strom, P.F. (1985a) Effect of temperature on bacterial species diversity in thermophilic solid waste composting. Appl Environ Microbiol 50, 899 905.
47. Strom, P.F. (1985b) Identification of thermophilic bacteria in solid waste composting. Appl Environ Microbiol 50, 906 913.
48. Swofford, D.L. (1999) PAUP: Phylogenetic Analysis Using Parsimony, Version 4.0. Champaign, IL : Illinois Natural History Survey.
49. Tiquia, S.M. Michel, F.C. Jr. (2002) Bacterial diversity in livestock manure composts as characterized by terminal restriction fragment length polymorphisms (T-RFLP) of PCR-amplified 16S rRNA gene sequences. In Microbiology of Composting ed. Insam, H., Riddech, N. Klammer, S. pp. 641 682. Berlin Heidelberg, New York : Springer.
50. Tiquia, S.M., Ichida, J.M., Keener, H.M., Elwell, D.L., Burtt, E.H. Jr. Michel, F.C. Jr. (2005) Bacterial community profiles on feathers during composting as determined by terminal restriction fragment length polymorphism analysis of 16S rDNA genes. Appl Microbiol Biotechnol 67, 412 419.
51. Torsvik, V., Sorheim, R. Goksoyr, J. (1996) Total diversity in soil and sediment communities: a review. J Ind Microbiol 17, 170 178.
52. Van Dyke, M.I. McCarthy, A.J. (2002) Molecular biological detection and characterization of Clostridium populations in municipal landfill sites. Appl Environ Microbiol 68, 2049 2053.
53. Wang, R.F., Cao, W.W. Cerniglia, C.E. (1997) Phylogenetic analysis and identification of Shigella spp. by molecular probes. Mol Cell Probes 11, 427 432.
54. Ward, D.M., Bateson, M.M., Weller, R. Ruff-Roberts, A.L. (1992) Ribosomal RNA analysis of microorganisms as they occur in nature. Adv Microb Ecol 12, 219 226.
55. Whitehead, T.R. Cotta, M.A. (2004) Isolation and identification of hyper-ammonia producing bacteria from swine manure storage pits. Curr Microbiol 48, 20 26.
56. Wiley, J.S. Pearce, G.W. (1957) A preliminary study of high-rate composting. Trans ASCE 122, 1009 1032.
57. Woese, C.R. Fox, G.E. (1977) Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc Natl Acad Sci USA 11, 5088 5090.
58. Zhao, H.X., Yang, D.C., Woese, C.R. Bryant, M.P. (1990) Assignment of Clostridium bryantii to Syntrophospora bryantii gen. nov., comb. nov. on the basis of a 16S rRNA sequence analysis of its crotonate-grown pure culture. Int J Syst Bacteriol 40, 40 44.
59. Zhu, N. (2003) Plan and design of pig farm and the facility and process control of aerobic composting of swine manure. PhD Thesis, Huazhong Agricultural University, Wuhan, China.
60. Zhu, N. (2005) Temporal-spatial distribution of pile temperature of aerated static bin composting system. J South China Univ Technol 33, 19 23.
61. Zhu, N., Deng, C., Xiong, Y. Tang, W. (2003) Design and operational effect of time/temperature-based aeration control system for aerobic composting. Trans CSAE 19, 282 286.
62. Zhu, N., Deng, C., Xiong, Y. Qian, H. (2004) Performance characteristics of three aeration systems in the swine manure composting. Bioresour Technol 95, 319 326.