Changes in the actinomycetal communities during continuous thermophilic composting as revealed by denaturing gradient gel electrophoresis and quantitative PCR

Bioresource Technology

Volumn 102, Issue 2, 2011, Pages 1383-1388

  Xiao, Yong ^a   Zeng, Guang Ming ^a   Yang, Zhao Hui ^a   Ma, Yan He ^b   Huang, Cui ^a   Xu, Zheng Yong ^a   Huang, Jing ^a   Fan, Chang Zheng ^a  

^a HUNAN UNIVERSITY   (China)

^b INSTITUTE OF MICROBIOLOGY   (China)

Author keywords

Actinomycetal community; Continuous thermophilic composting; DGGE; Quantitative PCR

Indexed keywords

16S RDNA; ACTINOMYCETAL COMMUNITY; CONTINUOUS THERMOPHILIC COMPOSTING; COPY NUMBER; DENATURING GRADIENT GEL ELECTROPHORESIS; DGGE; DRY WEIGHT; POST-PEAK; QUANTITATIVE PCR;

COMPOSTING; ELECTROPHORESIS; GELS; TEMPERATURE CONTROL;

POLYMERASE CHAIN REACTION;

DNA 16S;

BIODEGRADATION; CELLULOSE; COMPOSTING; ELECTROKINESIS; FUNGUS; LIGNIN; MICROBIAL COMMUNITY; POLYMERASE CHAIN REACTION; QUANTITATIVE ANALYSIS;

ACTINOBACTERIA; ARTICLE; BACTERIAL GROWTH; BIODIVERSITY; COMPOSTING; CONTINUOUS THERMOPHILIC COMPOSTING; CONTROLLED STUDY; COPY NUMBER VARIATION; DENATURING GRADIENT GEL ELECTROPHORESIS; DRY WEIGHT; GENE DOSAGE; HIGH TEMPERATURE PROCEDURES; INVERSE POLYMERASE CHAIN REACTION; MICROBIAL COMMUNITY; MICROBIAL DEGRADATION; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS;

ACTINOBACTERIA; DENATURING GRADIENT GEL ELECTROPHORESIS; GENES, BACTERIAL; MOLECULAR SEQUENCE DATA; PHYLOGENY; POLYMERASE CHAIN REACTION; RNA, RIBOSOMAL, 16S; SOIL; SOIL MICROBIOLOGY; TEMPERATURE;

ACTINOBACTERIA (CLASS);

EID: 78650716111     PISSN: 09608524     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.biortech.2010.09.034     Document Type: Article

References (34)

1. Aslanidis C., de Jong P.J. Ligation-independent cloning of PCR products (LIC-POR). Nucleic Acids Res. 1990, 18:6069-6074.
2. Birnboim H.C., Doly J. A rapid alkaline extraction procedure for screening recombinant plasmid DNA. Nucleic Acids Res. 1979, 7:1513-1523.
3. Chakravorty S., Helb D., Burday M., Connell N., Alland D. A detailed analysis of 16S ribosomal RNA gene segments for the diagnosis of pathogenic bacteria. J. Microbiol. Methods 2007, 69:330-339.
4. Chun J., Kimt S.B., Oh Y.K., Seongt C.-N., Lee D.-H., Bae K.S., Lee K.-J., Kang S.-O., Hah Y.C., Goodfellow M. Amycolatopsis thermoflava sp. nov., a novel soil actinomycete from Hainan Island, China. Int. J. Syst. Bacteriol. 1999, 49:1369-1373.
5. Crawford J.H. Composting of agricultural wastes-a review. Process Biochem. 1983, 18:14-18.
6. Cross T. Thermophilic actinomycetes. J. Appl. Bact. 1968, 31:36-53.
7. El-Tarabily K.A., Sykes M.L., Kurtbke I.D., Hardy G.E.St.J., Barbosa A.M., Dekker R.F.H. Synergistic effects of a cellulase-producing Micromonospora carbonacea and an antibiotic-producing Streptomyces violascens on the suppression of Phytophthora cinnamomi root rot of Banksia grandis. Can. J. Bot. 1996, 74:618-624.
8. Farrelly V., Rainey F.A., Stackebrandt E. Effect of genome size and rrn gene copy number on PCR amplification of 16S rRNA genes from a mixture of bacterial species. Appl. Environ. Microbiol. 1995, 61:2798-2801.
9. Fergus C.L. The cellulolytic activity of thermophilic fungi and actinomycetes. Mycologia 1960, 60:120-129.
10. Fleuri L.F., Sato H.H. Beta-1,3 glucanases and chitinases: application in the yeast cell lysis and fungi inhibition. Ciênc. Agrotec. 2008, 32:1224-1231.
11. Godden B., Ball A.S., Helvenstein P., McCarthy A.J., Penninckx M.J. Towards elucidation of the lignin degradation pathway in actinomycetes. J. Gen. Microbiol. 1992, 138:2441-2448.
12. Goodfellow M., Kim S.B., Minnikin D.E., Whitehead D., Zhou Z.-H., Mattinson-Rose A.D. Amycolatopsis sacchari sp. nov., a moderately thermophilic actinomycete isolated from vegetable matter. Int. J. Syst. Evol. Microbiol. 2001, 51:187-193.
13. Jin X., Xu L.-H., Mao P.-H., Hseu T.-H., Jiang C.-L. Description of Saccharomonospora xinjiangensis sp. nov. based on chemical and molecular classification. Int. J. Syst. Bacteriol. 1998, 48:1095-1099.
14. Kindaichi T., Kawano Y., Ito T., Satoh H., Okabe S. Population dynamics and in situ kinetics of nitrifying bacteria in autotrophic nitrifying biofilms as determined by real-time quantitative PCR. Biotech. Bioeng. 2006, 94:1111-1121.
15. Larney F.J., Yanke L.J., Miller J.J., McAllister T.A. Fate of coliform bacteria in composted beef cattle feedlot manure. J. Environ. Qual. 2003, 32:1508-1515.
16. Li Y., Irwin D.C., Wilson D.B. Processivity, substrate binding, and mechanism of cellulose hydrolysis by Thermobifida fusca Cel9A. Appl. Environ. Microbiol. 2007, 73:3165-3172.
17. Lim J., Do H., Shin S.G., Hwang S. Primer and probe sets for group-specific quantification of the genera Nitrosomonas and Nitrosospira using real-time PCR. Biotech. Bioeng. 2008, 99:1374-1383.
18. Mayhew L.E., Swanner E.D., Martin A.P., Templeton A.S. Phylogenetic relationships and functional genes: distribution of a manganese-oxidizing gene (mnxG) in Bacillus species. Appl. Environ. Microbiol. 2008, 74:7265-7271.
19. McCaig A.E., Glover L.A., Prosser J.I. Molecular analysis of bacterial community structure and diversity in unimproved and improved upland grass pastures. Appl. Environ. Microbio1. 1999, 65:1721-1730.
20. Murray A.E., Hollibaugh J.T., Orrego C.N. Phylogenetic compositions of bacterioplankton from two california estuaries compared by denaturing gradient gel electrophoresis of 16s rDNA fragments. Appl. Environ. Microbiol. 1996, 62:2676-2680.
21. Muyzer, G., Brinkhoff, T., Ulrich, N., Santegoeds, C., Schäfer, H., Wawer, C., 1998. Denaturing gradient gel electrophoresis (DGGE) in microbial ecology. Mol. Microbial Ecol. Manual 3.4.4, 1-27.
22. Nakamura Y., Satoh H., Kindaichi T., Okabe S. Community structure, abundance, and in situ activity of nitrifying bacteria in river sediments as determined by the combined use of molecular techniques and microelectrodes. Environ. Sci. Technol. 2006, 40:1532-1539.
23. Otsuka S., Sudian I., Komori A., Isobe K., Deguchi S., Nishiyama M., Shimizu H., Senoo K. Community structure of soil bacteria in a tropical rainforest several years after fire. Microbes Environ. 2008, 23:49-56.
24. Ramírezy P., Coha J.M. Enzymatic degradation of cellulose for thermophilic actinomycete: isolation, characterization and cellulolytic activity determination. Rev. Peru. Biol. 2003, 10:67-77.
25. Ryckeboer J., Mergaert J., Vaes K., Klammer S., De Clercq D., Coosemans J., Insam H., Swings J. A survey of bacteria and fungi occurring during composting and self-heating processes. Ann. Microbiol. 2003, 53:349-410.
26. Schulze K.L. Continuous thermophilic composting. Appl. Environ. Microbiol. 1962, 10:108-122.
27. Strom P.F. Effect of temperature on bacterial species diversity in thermophilic solid-waste composting. Appl. Environ. Microbiol. 1985, 50:899-905.
28. Suler D.J., Finstein M.S. Effect of temperature, aeration, and moisture on CO2 formation in bench-scale, continuously thermophilic composting of solid waste. Appl. Environ. Microbiol. 1977, 33:345-350.
29. Tuomela M., Vikman M., Hatakka A., Itävaara M. Biodegradation of lignin in a compost environment: a review. Bioresour. Technol. 2000, 7:169-183.
30. Wong J.W.C., Li S.W.Y., Wong M.H. Coal fly ash as a composting material for sewage sludge: effects on microbial activities. Environ. Technol. 1995, 16:527-537.
31. Xiao Y., Zeng G.M., Yang Z.H., Shi W.J., Huang C., Fan C.Z., Xu Z.Y. Continuous thermophilic composting (CTC) for rapid biodegradation and maturation of organic municipal solid waste. Bioresour. Technol. 2009, 100:4807-4813.
32. Xiao Y., Zeng G.M., Yang Z.H., Liu Y.S., Ma Y.H., Yang L., Wang R.J., Xu Z.Y. Coexistence of nitrifiers, denitrifiers and Anammox bacteria in a sequencing batch biofilm reactor as revealed by PCR-DGGE. J. Appl. Microbiol. 2009, 106:96-505.
33. Yang Z.H., Xiao Y., Zeng G.M., Xu Z.Y., Liu Y.S. Comparison of methods for total community DNA extraction and purification from compost. Appl. Microbiol. Biotechnol. 2007, 74:918-925.
34. Yoon J.-H., Kim I.-G., Shin Y.-K., Park Y.-H. Proposal of the genus Thermoactinomyces sensu stricto and three new genera, Laceyella, Thermoflavimicrobium and Seinonella, on the basis of phenotypic, phylogenetic and chemotaxonomic analyses. Int. J. Syst. Evol. Microbiol. 2005, 55:395-400.