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Spatial Heterogeneity of Bacteria: Evidence from Hot Composts by Culture-independent Analysis

  • Guo, Yan ;
  • Zhang, Jinliang ;
  • Deng, Changyan ;
  • Zhu, Nengwu
  • Received : 2011.09.26
  • Accepted : 2012.04.03
  • Published : 2012.07.01

Abstract

The phylogenetic diversity of the bacteria in hot composting samples collected from three spatial locations was investigated by molecular tools in order to determine the influence of gradient effect on bacterial communities during the thermophilic phase of composting swine manure with rice straw. Total microbial DNA was extracted and bacterial near full-length 16S rRNA genes were subsequently amplified, cloned, restriction fragment length polymorphism-screened and sequenced. The superstratum sample had the highest microbial diversity among the three samples which was possibly related to the surrounding conditions of the sample resulting from the location. The results showed that the sequences related to Bacillus sp. were most common in the composts. In superstratum sample, 45 clones (33%) and 36 clones (27%) were affiliated with the Bacillus sp. and Clostridium sp., respectively; 74 clones (58%) were affiliated with the Clostridium sp. in the middle-level sample; 52 clones (40%) and 29 clones (23%) were affiliated with the Clostridium sp. and Bacillus sp. in substrate sample, respectively. It indicated that the microbial diversity and community in the samples were different for each sampling site, and different locations of the same pile often contained distinct and different microbial communities.

Keywords

Spatial Heterogeneity;16S rRNA Gene;Swine Manure;Composting

References

  1. Alfreider, A., C. Vogt and W. Babel. 2002. Microbial diversity in an in situ reactor system treating monochlorobenzene contaminated groundwater as revealed by 16S ribosomal DNA analysis. Syst. Appl. Microbiol. 25:232-240. https://doi.org/10.1078/0723-2020-00111
  2. Arbeli, Z. and C. L. Fuentes. 2007. Improved purification and PCR amplification of DNA from environmental samples. FEMS Microbiol. Lett. 272:269-275. https://doi.org/10.1111/j.1574-6968.2007.00764.x
  3. Barns, S. M., R. E. Fundyga, M. W. Jeffries and N. R. Pace. 1994. Remarkable archaeal diversity detected in a Yellowstone National Park hot spring environment. Proc. Natl. Acad. Sci. USA. 91:1609-1613. https://doi.org/10.1073/pnas.91.5.1609
  4. Blanc, M., L. Marilley, T. Beffa and M. Aragno. 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. https://doi.org/10.1111/j.1574-6941.1999.tb00569.x
  5. Bosshard, P. P., R. Zbinden and M. Altwegg. 2002. Turicibacter sanguinis gen. nov., sp. nov., a novel anaerobic, Gram-positive bacterium. Int. J. Syst. Evol. Microbiol. 52:1263-1266. https://doi.org/10.1099/ijs.0.02056-0
  6. Dees, P. M. and W. C. Ghiorse. 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. https://doi.org/10.1111/j.1574-6941.2001.tb00805.x
  7. DeLong, E. F. 1992. Archaea in coastal marine environments. Proc. Natl. Acad. Sci. USA. 89:5685-5689. https://doi.org/10.1073/pnas.89.12.5685
  8. Dojka, M. A., P. Hugenholtz, S. K. Haack and N. R. Pace. 1998. Microbial diversity in a hydrocarbon- and chlorinated-solvent contaminated aquifer undergoing intrinsic bioremediation. Appl. Environ. Microbiol. 64:3869-3877.
  9. Eckburg, P. B., E. M. Bik, C. N. Bernstein, E. Purdom, L. Dethlefsen, M. Sargent, S. R. Gill, K. E. Nelson and D. A. Relman. 2005. Diversity of the human intestinal microbial flora. Science 308:1635-1638. https://doi.org/10.1126/science.1110591
  10. Egert, M., B. Wagner, T. Lemke, A. Brune and M. W. Friedrich. 2003. Microbial community structure in midgut and hindgut of the humus-feeding larva of Pachnoda ephippiata (Coleoptera: Scarabaeidae). Appl. Environ. Microbiol. 69:6659-6668. https://doi.org/10.1128/AEM.69.11.6659-6668.2003
  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, USA.
  12. Frey, J. C., J. M. Rothman, A. N. Pell, J. B. Nizeyi, M. R. Cranfield and E. R. Angert. 2006. Fecal bacterial diversity in a wild gorilla. Appl. Environ. Microbiol. 72:3788-3792. https://doi.org/10.1128/AEM.72.5.3788-3792.2006
  13. Gagne, A., M. Chicoine, A. Morin and A. Houde. 2001. Phenotypic and genotypic characterization of esterase-producing Ureibacillus thermosphaericus isolated from an aerobic digestor of swine waste. Can J. Microbiol. 47:908-1015. https://doi.org/10.1139/w01-096
  14. Gill, S. R., M. Pop, R. T. Deboy, P. B. Eckburg, P. J. Turnbaugh, B. S. Samuel, J. I. Gordon, D. A. Relman, C. M. Fraser-Liggett and K. E. Nelson. 2006. Metagenomic analysis of the human distal gut microbiome. Science 312:1355-1359. https://doi.org/10.1126/science.1124234
  15. Giovannoni, S. J., T. B. Britschgi, C. L. Moyer and K. G. Field. 1990. Genetic diversity in Sargasso Sea bacterioplankton. Nature 345:60-63. https://doi.org/10.1038/345060a0
  16. Guo, Y., N. Zhu, S. Zhu and C. Deng. 2007. Molecular phylogenetic diversity of bacteria and its spatial distribution in composts. J. Appl. Microbiol. 103:1344-1354. https://doi.org/10.1111/j.1365-2672.2007.03367.x
  17. Hassen, A., K. Belguith, N. Jedidi and A. Cherif. 2001. Microbial characterization during composting of municipal solid waste. Bioresour. Technol. 80:217-225. https://doi.org/10.1016/S0960-8524(01)00065-7
  18. Heuer, H., M. Krsek, P. Baker, K. Smalla and E. M. H. Wellington. 1997. Analysis of actinomycete communities by specific amplification of genes encoding 16S rRNA and gel-electrophoretic separation in denaturing gradients. Appl. Environ. Microbiol. 63:3233-3241.
  19. Hiraishi, A., T. Narihiro and Y. Yamanaka. 2003. Microbial community dynamics during start-up operation of flowerpot-using fed-batch reactors for composting of household biowaste. Environ. Microbiol. 5:765-776. https://doi.org/10.1046/j.1462-2920.2003.00473.x
  20. Holben, W. E. 1994. Isolation and purification of bacterial DNA from soil. In : Methods of soil analysis. Part 2. Microbiogical and Biochemical Properties (Ed. R. W. Weaver, S. Angle and P. Bottomley). pp. 727-751. Soil Science Society of America, Madison, WI, USA.
  21. Hugenholtz, P., B. M. Goebel and N. R. Pace. 1998. Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. J. Bacteriol. 180:4765-4774.
  22. Imbeah, M. 1998. Composting piggery waste: a review. Bioresour. Technol. 63:197-203. https://doi.org/10.1016/S0960-8524(97)00165-X
  23. LaMontagne, M. G., F. C. Michel, P. A. Holden and C. A. Reddy. 2002. Evaluation of extraction and purification methods for obtaining PCR-amplifiable DNA from compost for microbial community analysis. J. Microbiol. Methods 49:255-264. https://doi.org/10.1016/S0167-7012(01)00377-3
  24. Lane, D. J. 1991. 16S⁄23S rRNA sequencing. In: Nucleic Acid Techniques in Bacterial Systematics (Ed. E. Stackebrandt and M. Goodfellow). pp. 115-175. New York: Wiley.
  25. Larsen, N., G. J. Olsen, B. L. Maidak, M. J. McCaughey, R. Overbeek, T. J. Macke, T. L. Marsh and C. R. Woese. 1993. The ribosomal database project. Nucleic Acids Res. 21:3021-3023. https://doi.org/10.1093/nar/21.13.3021
  26. Leser, T. D., J. Z. Amenuvor, T. K. Jensen, R. H. Lindecrona, M. Boye and K. Moller. 2002. Culture-independent analysis of gut bacteria: the pig gastrointestinal tract microbiota revisited. Appl. Environ. Microbiol. 68:673-690. https://doi.org/10.1128/AEM.68.2.673-690.2002
  27. Liu, K., Y. Liu, Z. Lei, C. Li and A. Shi. 2003. Effects of different microorganism consortiums on quality of composting pig-dung. J. Agro-Environ. Sci. 22:311-314.
  28. Muyzer, G., E. C. de Waal and A. G. Uitterlinden. 1993. Profiling of microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction amplified genes coding for 16S rRNA. Appl. Environ. Microbiol. 59:695-700.
  29. Naser, S. M., M. Vancanneyt, C. Snauwaert, G. Vrancken, B. Hoste, L. De Vuyst and J. Swings. 2006. Reclassification of Lactobacillus amylophilus LMG 11400 and NRRL B-4435 as Lactobacillus amylotrophicus sp. nov. Int. J. Syst. Evol. Microbiol. 56:2523-2527. https://doi.org/10.1099/ijs.0.64463-0
  30. Nelson, K. E., S. H. Zinder, I. Hance, P. Burr, D. Odongo, D. Wasawo, A. Odenyo and R. Bishop. 2003. Phylogenetic analysis of the microbial populations in the wild herbivore gastrointestinal tract: insights into an unexplored niche. Environ. Microbiol. 5:1212-1220. https://doi.org/10.1046/j.1462-2920.2003.00526.x
  31. Olsson, C., S. Ahrne, B. Pettersson and G. Molin. 2003. The bacterial flora of fresh and chill-stored pork: analysis by cloning and sequencing of 16S rRNA genes. Int. J. Food Microiol. 83:245-252. https://doi.org/10.1016/S0168-1605(02)00372-0
  32. Ozutsumi, Y., K. Tajima, A. Takenaka and H. Itabashi. 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. https://doi.org/10.1271/bbb.69.499
  33. Pace, N. R. 1996. New perspective on the natural microbial world: molecular microbial ecology. ASM News 62:463-470.
  34. Peters, S., S. Koschinsky, F. Schwieger and C. C. Tebbe. 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. https://doi.org/10.1128/AEM.66.3.930-936.2000
  35. Rawls, J. F., M. A. Mahowald, R. E. Ley and J. I. Gordon. 2006. Reciprocal gut microbiota transplants from zebrafish and mice to germ-free recipients reveal host habitat selection. Cell 127: 423-433. https://doi.org/10.1016/j.cell.2006.08.043
  36. Roeselers, G., T. B. Norris, R. W. Castenholz, S. Rysgaard, R. N. Glud, M. Kühl and G. Muyzer. 2007. Diversity of phototrophic bacteria in microbial mats from Arctic hot springs (Greenland). Environ. Microbiol. 9:26-38. https://doi.org/10.1111/j.1462-2920.2006.01103.x
  37. Sasaki, H., J. Nonaka, K. Otawa, O. Kitazume, R. Asano, T. Sasaki and Y. Nakai. 2009. Analysis of the structure of the bacterial community in the livestock manure-based composting process. Asian-Aust. J. Anim. Sci. 22:113-118. https://doi.org/10.5713/ajas.2009.70658
  38. Schwarza, J. I. K., W. Eckertb and R. Conrad. 2007. Community structure of Archaea and Bacteria in a profundal lake sediment Lake Kinneret (Israel). Syst. Appl. Microbiol. 30:239-254. https://doi.org/10.1016/j.syapm.2006.05.004
  39. Simpson, J. M., J. W. Santo Domingo and D. J. Reasoner. 2004. Assessment of equine fecal contamination: the search for alternative bacterial source-tracking targets. FEMS Microbiol. Ecol. 47:65-75. https://doi.org/10.1016/S0168-6496(03)00250-2
  40. Stahl, D. A. 1995. Application of phylogenetically based hybridization probes to microbial ecology. Mol. Ecol. 4:535-542. https://doi.org/10.1111/j.1365-294X.1995.tb00254.x
  41. Stahl, D. A., D. J. Lane, G. J. Olsen and N. R. Pace. 1985. Characterization of a Yellowstone hot spring microbial community by 5S rRNA sequences. Appl. Environ. Microbiol. 49:1379-1384.
  42. Stentiford, E. I. 1987. Recent developments in composting. In: Compost, Production, Quality and Use (Ed. M. de Bertoldi, M. Ferranti, P. L'Hermite and F. Zuicconi). Elsevier, London, pp. 52-60.
  43. Stentiford, E. I. 1996. Composting control: principles and practice. Chapman and Hall, London, UK.
  44. Strom, P. F. 1985a. Effect of temperature on bacterial species diversity in thermophilic solid waste composting. Appl. Environ. Microbiol. 50:899-905.
  45. Strom, P. F. 1985b. Identification of thermophilic bacteria in solid waste composting. Appl. Environ. Microbiol. 50:906-913.
  46. Suau, A., R. Bonnet, M. Sutren, J. J. Godon, G. R. Gibson, M. D. Collins and J. Dore. 1999. Direct analysis of genes encoding 16S rRNA from complex communities reveals many novel molecular species within the human gut. Appl. Environ. Microbiol. 65:4799-4807.
  47. Swofford, D. L. 1999. PAUP: Phylogenetic Analysis Using Parsimony, Version 4.0. Champaign, IL: Illinois Natural History Survey.
  48. Tiquia, S. M., J. M. Ichida, H. M. Keener, D. L. Elwell, Jr., E. H. Burtt and F. C. Jr Michel. 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. https://doi.org/10.1007/s00253-004-1788-y
  49. Van Dyke, M. I. and A. J. McCarthy. 2002. Molecular biological detection and characterization of Clostridium populations in municipal landfill sites. Appl. Environ. Microbiol. 68:2049-2053. https://doi.org/10.1128/AEM.68.4.2049-2053.2002
  50. von Wintzingerode, F., U. B. Gbel and E. Stackebrandt. 1997. Determination of microbial diversity in environmental samples: pit-falls of PCR-based rRNA analysis. FEMS Microbiol. Rev. 21:213-229. https://doi.org/10.1111/j.1574-6976.1997.tb00351.x
  51. Wang, X. L., K. H. Shin, H. G. Hur and S. I. Kim. 2005. Enhanced biosynthesis of dihydrodaidzein and dihydrogenistein by a newly isolated bovine rumen anaerobic bacterium. J. Biotechnol. 115:261-269. https://doi.org/10.1016/j.jbiotec.2004.08.014
  52. Ward, D. M., R. Weller and M. M. Bateson. 1990. 16S rRNA sequences reveal numerous uncultured microorganisms in a natural community. Nature 345:63-65. https://doi.org/10.1038/345063a0
  53. Wei, Y. 2000. Efficient and economical composting of sewage sludge for small and mid-scale municipal wastewater treatment plants. Ph.D. thesis. Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences.
  54. Whitehead, T. R. and M. A. Cotta. 2004. Isolation and identification of hyper-ammonia producing bacteria from swine manure storage pits. Curr. Microbiol. 48:20-26. https://doi.org/10.1007/s00284-003-4084-7
  55. Wu, L., F. G. Li, C. Y. Deng, D. Q. Xu, S. W. Jiang and Y. Z. Xiong. 2009. A method for obtaining DNA from compost. Appl. Microbiol. Biotechnol. 84:389-395. https://doi.org/10.1007/s00253-009-2103-8
  56. Yang, Z. H., Y. Xiao, G. M. Zeng, Z. Y. Xu and Y. S. Liu. 2007. Comparision of methods for total commmunity DNA extraction and purification from compost. Appl. Microbiol. Biotechnol. 74:918-925. https://doi.org/10.1007/s00253-006-0704-z
  57. Zhu, N. 2005 Temporal-spatial distribution of pile temperature of aerated static bin composting system. J. South China Univ. Technol. 33:19-23.
  58. Zhu, N. 2006. Composting of high moisture content swine manure with corncob in a pilot scale system. Bioresour. Technol. 97:1870-1875. https://doi.org/10.1016/j.biortech.2005.08.011
  59. Zhu, N. 2007. Effect of low initial C/N ratio on the composting of swine manure with rice straw. Bioresour. Technol. 98:9-13. https://doi.org/10.1016/j.biortech.2005.12.003
  60. Zhu, N., C. Deng, Y. Xiong and H. Qian. 2004. Performance characteristics of three aeration systems in the swine manure composting. Bioresour. Technol. 95:319-326. https://doi.org/10.1016/j.biortech.2004.02.021

Cited by

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Acknowledgement

Supported by : National Natural Science Foundation of China, International Foundation for Science, Natural Science Foundation of Guangdong Province