Characterization and spatial distribution of bacterial communities within passively aerated cattle manure composting piles

Bioresource Technology

Volumn 101, Issue 24, 2010, Pages 9631-9637

  Maeda, Koki ^a   Hanajima, Dai ^a   Morioka, Riki ^a   Osada, Takashi ^b  

^a NATIONAL AGRICULTURAL RESEARCH CENTER FOR HOKKAIDO REGION   (Japan)

^b NATIONAL INSTITUTE OF LIVESTOCK AND GRASSLAND SCIENCE   (Japan)

Author keywords

16S rRNA; Bacterial community; Compost; DGGE

Indexed keywords

16S RRNA; 16S RRNA SEQUENCES; BACILLUS SPECIES; BACTERIAL COMMUNITY; CATTLE MANURE COMPOST; CATTLE MANURES; CLOSTRIDIUM SPECIES; COMPOST; COMPOSTING PILES; DGGE; MESOPHILIC BACTERIA; MICROBIAL COMMUNITIES; PROTEOBACTERIA; SPATIAL DISTRIBUTION; SURFACE ZONES;

BACTERIOLOGY; COMPOSTING; MANURES; PILES; RNA; SIZE DISTRIBUTION;

BACTERIA;

RNA 16S;

AERATION; CARBON; CATTLE; COMPOST; GENETIC ANALYSIS; MANURE; MICROBIAL COMMUNITY; NITROGEN; POLYMERASE CHAIN REACTION; RNA; SPATIAL DISTRIBUTION; TAXONOMY; THERMOPHILIC BACTERIUM;

ALPHAPROTEOBACTERIA; ARTICLE; BACILLI; BACILLUS; BACTEROIDETES; CATTLE; CHROMATIUM; CLOSTRIDIALES; CLOSTRIDIUM; COMAMONAS; COMPOST; CYTOPHAGA; DESULFOTOMACULUM; FLAVOBACTERIACEAE; FLAVOBACTERIUM; GAMMAPROTEOBACTERIA; MANURE; MESOPHILIC BACTERIUM; MESORHIZOBIUM; MICROBIAL COMMUNITY; NONHUMAN; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; PRINCIPAL COMPONENT ANALYSIS; PRIORITY JOURNAL; PROTEOBACTERIA; RNA SEQUENCE; THERMOPHILIC BACTERIUM;

AEROBIOSIS; ANIMALS; BACILLUS; CATTLE; CLOSTRIDIUM; DENATURING GRADIENT GEL ELECTROPHORESIS; HYDROGEN-ION CONCENTRATION; MANURE; MOLECULAR SEQUENCE DATA; PRINCIPAL COMPONENT ANALYSIS; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; SOIL; SURFACE PROPERTIES; TEMPERATURE;

BACILLUS (BACTERIUM); BACTERIA (MICROORGANISMS); BACTEROIDETES; BOS; CLOSTRIDIUM; GAMMAPROTEOBACTERIA;

EID: 77956169948     PISSN: 09608524     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.biortech.2010.07.057     Document Type: Article

References (50)

1. Alfreider A., Peters S., Tebbe C., Rangger A., Insam H. Microbial community dynamics during composting of organic matter as determined by 16 S ribosomal DNA analysis. Compost Sci. Util. 2002, 10:303-312.
2. Bae J., Rhee S., Park J., Kim B., Park Y. Isolation of uncultivated anaerobic thermophiles from compost by supplementing cell extract of Geobacillus toebii in enrichment culture medium. Extremophiles 2005, 9:477-485.
3. Boon N., De Windt W., Verstraete W., Top E. Evaluation of nested PCR-DGGE (denaturing gradient gel electrophoresis) with group-specific 16S rRNA primers for the analysis of bacterial communities from different wastewater treatment plants. FEMS Microbiol. Ecol. 2002, 39:101-112.
4. Bremner J.M. Total nitrogen, Inorganic forms of nitrogen. Methods of soil analysis: part 2 1965, 1149-1255. Soil Science Society of America, Madison, WI. C.A. Black (Ed.).
5. Chefetz B., Hatcher P., Hadar Y., Chen Y. Chemical and biological characterization of organic matter during composting of municipal solid waste. J. Environ. Qual. 1996, 25:776-785.
6. Cho K., Lee S., Math R., Islam S., Kambiranda D., Kim J., Yun M., Cho J., Kim J., Lee Y. Culture-independent analysis of microbial succession during composting of swine slurry and mushroom cultural wastes. J. Microbiol. Biotech. 2008, 18:1874-1883.
7. Desai C., Parikh R., Vaishnav T., Shouche Y., Madamwar D. Tracking the influence of long-term chromium pollution on soil bacterial community structures by comparative analyses of 16S rRNA gene phylotypes. Res. Microbiol. 2009, 160:1-9.
8. Fan Z., Li X., Mao D., Zhu G., Wang S., Quan Z. Could nested PCR be applicable for the study of microbial diversity?. World J. Microbiol. Biotechnol. 2009, 25:1447-1452.
9. Farrell M., Jones D. Critical evaluation of municipal solid waste composting and potential compost markets. Bioresour. Tech. 2009, 100:4301-4310.
10. Fernandes L., Zhan W., Patni N., Jui P. Temperature distribution and variation in passively aerated static compost piles. Bioresour. Tech. 1994, 48:257-264.
11. Goberna M., Insam H., Franke-Whittle I. Effect of biowaste sludge maturation on the diversity of thermophilic bacteria and archaea in an anaerobic reactor. Appl. Environ. Microbiol. 2009, 75:2566-2572.
12. Green S., Michel F., Hadar Y., Minz D. Similarity of bacterial communities in sawdust-and straw-amended cow manure composts. FEMS Microbiol. Lett. 2004, 233:115-123.
13. Guo Y., Zhu N., Zhu S., Deng C. Molecular phylogenetic diversity of bacteria and its spatial distribution in composts. J. Appl. Microbiol. 2007, 103:1344-1354.
14. Hanajima D., Haruta S., Hori T., Ishii M., Haga K., Igarashi Y. Bacterial community dynamics during reduction of odorous compounds in aerated pig manure slurry. J. Appl. Microbiol. 2009, 106:118-129.
15. Hansgate A., Schloss P., Hay A., Walker L. Molecular characterization of fungal community dynamics in the initial stages of composting. FEMS Microbiol. Ecol. 2005, 51:209-214.
16. Hao X., Chang C., Larney F.J., Travis G.R. Greenhouse Gas Emissions during Cattle Feedlot Manure Composting. J. Environ. Qual. 2001, 30:376-386.
17. Haruta S., Kondo M., Nakamura K., Aiba H., Ueno S., Ishii M., Igarashi Y. Microbial community changes during organic solid waste treatment analyzed by double gradient-denaturing gel electrophoresis and fluorescence in situ hybridization. Appl. Microbiol. Biotechnol. 2002, 60:224-231.
18. Hatayama K., Shoun H., Ueda Y., Nakamura A. Planifilum fimeticola gen. nov., sp. nov. and Planifilum fulgidum sp. nov., novel members of the family 'Thermoactinomycetaceae' isolated from compost. Int. J. Syst. Evol. Microbiol. 2005, 55:2101-2104.
19. Hatayama K., Shoun H., Ueda Y., Nakamura A. Tuberibacillus calidus gen Nov., sp. nov., isolated from a compost pile and reclassification of. Bacillus naganoensis. Int. J. Syst. Evol. Microbiol. 2006, 56:2545-2551.
20. He Y., Ding Y., Long Y. Two cellulolytic Clostridium species: Clostridium cellulosi sp Nov. and Clostridium cellulofermentans sp. nov. Int. J. Syst. Evol. Microbiol. 1991, 41:306-309.
21. Heyrman J., Rodriguez-Diaz M., Devos J., Felske A., Logan N., De Vos P. Nov., Bacillus arvi sp. nov. and Bacillus humi sp. nov., isolated from soil. Bacillus arenosi sp. Int. J. Syst. Evol. Microbiol. 2005, 55:111-117.
22. Hullar M., Kaplan L., Stahl D. Recurring seasonal dynamics of microbial communities in stream habitats. Appl. Environ. Microbiol. 2006, 72:713-722.
23. Inbar Y., Hadar Y., Chen Y. Recycling of cattle manure: the composting process and characterization of maturity. J. Environ. Qual. 1993, 22:857-863.
24. Ishii K., Fukui M., Takii S. Microbial succession during a composting process as evaluated by denaturing gradient gel electrophoresis analysis. J. Appl. Microbiol. 2000, 89:768-777.
25. Jin F., Yamasato K., Toda K. Clostridium thermocopriae sp Nov., a cellulolytic thermophile from animal feces, compost, soil, and a hot spring in Japan. Int. J. Syst. Evol. Microbiol. 1988, 38:279-281.
26. Kim B., Lee S., Weon H., Kwon S., Go S., Park Y., Schumann P., Fritze D. Ureibacillus suwonensis sp Nov., isolated from cotton waste composts. Int. J. Syst. Evol. Microbiol. 2006, 56:663-666.
27. Kröber M., Bekel T., Diaz N., Goesmann A., Jaenicke S., Krause L., Miller D., Runte K., Viehöver P., Pühler A., Shülter A. Phylogenetic characterization of a biogas plant microbial community integrating clone library 16S-rDNA sequences and metagenome sequence data obtained by 454-pyrosequencing. J. Biotech. 2009, 142:38-49.
28. Lane D. 16S/23S rRNA sequencing. Nucleic Acid Techniques in Bacterial Systematics, 1, 115-176 1991, John Wiley & Sons, Hoboken, NJ. E. Stackebrandt (Ed.).
29. Maeda K., Morioka R., Osada T. Effect of covering composting piles with mature compost on ammonia emission and microbial community structure of composting process. J. Environ. Qual. 2009, 38:598-606.
30. Maeda K., Toyoda S., Shimojima R., Osada T., Hanajima D., Morioka R., Yoshida N. Source of nitrous oxide emissions during the cow manure composting process as revealed by isotopomer analysis of and amoA abundance in betaproteobacterial ammonia-oxidizing bacteria. Appl. Environ. Microbiol. 2010, 76:1532-1555.
31. Miyatake F., Iwabuchi K. Effect of high compost temperature on enzymatic activity and species diversity of culturable bacteria in cattle manure compost. Bioresour. Tech. 2005, 96:1821-1825.
32. Muyzer G., De Waal E., Uitterlinden A. Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl. Environ. Microbiol. 1993, 59:695-700.
33. Nagel M., Andreesen J. Bacillus niacini sp Nov., a nicotinate-metabolizing mesophile isolated from soil. Int. J. Syst. Evol. Microbiol. 1991, 41:134-139.
34. Nakasaki K., Tran L., Idemoto Y., Abe M., Rollon A. Comparison of organic matter degradation and microbial community during thermophilic composting of two different types of anaerobic sludge. Bioresour. Technol. 2009, 100:676-682.
35. Nielsen P., Fritze D., Priest F. Phenetic diversity of alkaliphilic Bacillus strains: proposal for nine new species. Microbiology 1995, 141:1745-1761.
36. Nishiyama T., Ueki A., Kaku N., Ueki K. Clostridium sufflavum sp Nov., isolated from a methanogenic reactor treating cattle waste. Int. J. Syst. Evol. Microbiol. 2009, 59:981-986.
37. Partanen P., Hultman J., Paulin L., Auvinen P., Rmantschuk M. Bacterial diversity at different stages of the composting process. BMC Microbiol. 2010, 10:94.
38. S.A.S.Institute SAS/STAT user's guide 2001, SAS Institute, Cary, NC.
39. Scheldeman P., Rodriguez-Diaz M., Goris J., Pil A., De Clerck E., Herman L., De Vos P., Logan N., Heyndrickx M. Bacillus farraginis sp Nov., Bacillus fortis sp. nov. and Bacillus fordii sp. nov., isolated at dairy farms. Int. J. Syst. Evol. Microbiol. 2004, 54:1355-1364.
40. Steger K., Eklind Y., Olsson J., Sundh I. Microbial community growth and utilization of carbon constituents during thermophilic composting at different oxygen levels. Microb. Ecol. 2005, 50:163-171.
41. Strom P. Effect of temperature on bacterial species diversity in thermophilic solid-waste composting. Appl. Environ. Microbiol. 1985, 50:899-905.
42. Sundberg C., Smrs S., Jonsson H. Low pH as an inhibiting factor in the transition from mesophilic to thermophilic phase in composting. Bioresour. Tech. 2004, 95:145-150.
43. Székely A., Sipos R., Berta B., Vajna B., Hajdú C., Márialigeti K. DGGE and T-RFLP analysis of bacterial succession during mushroom compost production and sequence-aided T-RFLP profile of mature compost. Microb. Ecol. 2009, 57:522-533.
44. Tang J., Kanamori T., Inoue Y., Yasuta T., Yoshida S., Katayama A. Changes in the microbial community structure during thermophilic composting of manure as detected by the quinone profile method. Proc. Biochem. 2004, 39:1999-2006.
45. Tilman D., Cassman K., Matson P., Naylor R., Polasky S. Agricultural sustainability and intensive production practices. Nature 2002, 418:671-677.
46. Tiquia S., Tam N., Hodgkiss I. Changes in chemical properties during composting of spent pig litter at different moisture contents. Agric. Ecosys. Environ. 1998, 67:79-89.
47. Vaz-Moreira I., Faria C., Nobre M., Schumann P., Nunes O., Manaia C. Paenibacillus humicus sp Nov., isolated from poultry litter compost. Int. J. Syst. Evol. Microbiol. 2007, 57:2267-2271.
48. Vuorinen A.H., Saharinen M.H. Evolution of microbiological and chemical parameters during manure and straw co-composting in a drum composting system. Agric. Ecosys. Environ. 1997, 66:19-29.
49. Wang P., Changa C., Watson M., Dick W., Chen Y., Hoitink H. Maturity indices for composted dairy and pig manures. Soil Biol. Biochem. 2004, 36:767-776.
50. Yamada T., Suzuki A., Ueda H., Ueda Y., Miyauchi K., Endo G. Successions of bacterial community in composting cow dung wastes with or without hyperthermophilic pre-treatment. Appl. Microbiol. Biotechnol. 2008, 81:771-781.