ABSTRACT To analyze the bacterial communities in lime concretion black soil upon the incorporation of crop residues for two years in wheat-maize system, total DNA was directly extracted and PCR-amplified with the F357GC and R518 primers targeting the 16S rRNA genes of V3 region. The amplified fragments were analyzed by perpendicular DGGE. Analyzing of species richness index S and Shannon diversity index H revealed that there was a high diversity of soil bacterial community compositions among all treatments after incorporation of crop residues and fertilizing under field conditions. Eleven DGGE bands recovered were re-amplified, sequenced. Phylogenetic analysis of the representative DGGE fingerprints identified four groups of the prokaryotic communities in the soil by returning wheat residues and fertilizing under field conditions. The bacterial communities belonged to gamma proteobacterium, Cupriavidus sp, halophilic eubacterium, Acidobacterium sp, Sorangium sp, delta proteobacterium, Streptococcus sp and Streptococcus agalactiae were main bacterial communities. Principal Component Analysis (PCA) showed that there were the differences in DNA profiles among the six treatments. It showed that wheat residue returning, maize residue returning and fertilizing all can improve bacterial diversity in varying degrees. As far as improvement of bacterial diversity was concerned, wheat residue returning was higher than fertilizing, and fertilizing higher than maize residue returning.
Cite this paper
S. Tao, Q. Xia, L. Zhu, J. Chen, Y. Wang and B. Qin, "Analysis of the Bacterial Communities in Lime Concretion Black Soil upon the Incorporation of Crop Residues," Open Journal of Soil Science, Vol. 2 No. 3, 2012, pp. 312-319. doi: 10.4236/ojss.2012.23037.
 C.L. Neely, M.H. Beare, W. L. Hargrove, D. C. Coleman, “Relationships between fungal and bacterial substrate-induced respiration, biomass and plant residue decomposition,” Soil Biology and Biochemistry, Vol.23, No.3, 1991, pp. 947-954.
 G. Muyzer, E. C. De Waal, A. G. Uitterlinden, “Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified gene coding for 16S rRNA,” Applied and Environmental Microbiology, Vol.59, No.3, 1993, pp. 695-700.
 C. R. Woese, “Bacterial evolution,” Microbiol. Rev. Vol.51, No.2, 1987, pp. 221–271.
 S. Kim-Jong, M..Sakai, A. Hosoda, T. Matsuguchi, J. S. Kim, Application of DGGE analysis to the study of bacterial community structure in plant roots and in nonrhizosphere soil. Soil Science and Plant Nutrition, Vol.45, No.2, 1999, pp. 493-497.
 A.E. McCaig, L. Glover, J. I. Posser, “Molecular analysis of bacterial community structure and diversity in unimproved and improved upland grassland pastures,” Applied and Environmental Microbiology, Vol.65, No.4, 1999, pp. 1721-1730.
 G. Muyzer, “DGGE/TGGE: a method for identifying genes from natural ecosystems,” Current Opinion Microbioogy, Vol.2, No.3, 1999, pp. 317-322.
 U. Nübel, F. Garcia-Pichel, M. Kühl, G. Muyzer, “ Quantifying microbial diversity: morphotypes, 16S rRNA genes, and carotinoids of oxygenic phototrophs in microbial mats,” Applied and Environmental Microbiology, Vol.65, No.2, 1999, pp. 422-430.
 R. I. Amann, W. Ludwig, K. H. Schileifer, “Phylogenetic identi?cation and in situ detection of individual microbial cells without cultivation,” Microbiology and Molecular Biology Reviews, Vol.59, No.1, pp. 143-169.
 J. M. Neefs, R. De Wachter, “A proposal for the secondary structure of a variable area of eukaryotic small ribosomal subunit RNA involving the existence of a pseudoknot,” Nucleic Acids Research Vol.18, No.19, 1990, pp. 5695-5704. doi:10.1093/nar/18.19.5695
 J. Bloem, A. M. Breure, “Bioindicators/biomonitors-principles, assessment, concepts”. In: B. A. Markert, A. M. Breure, H.G.. Zechmeister Ed., Microbial indicators, Elsevier, Amsterdam, The Netherlands. 2003, pp. 259-282pp.
 O. Dilly, J. Bloem, A. Vos, J. C. Munch, “Bacterial diversity in agricultural soils during litter decomposition.” Applied and Environmental Microbiology, Vol.70, No.1, 2004, pp.468-474. doi:10.1128/AEM.70.1.468-474.2004
 B. S. Grif?ths, K. Ritz, R. Wheatly, H. L. Kuan, B. Boag, S. Christensen, F. Ekelund, S. J. S?rensen, S. Muller, J. Bloem, “An examination of the biodiversity-ecosystem function relationship in arable soil microbial communities,” Soil Biology and Biochemistry, Vol.33, No.12-13, 2001, pp. 1713--1722.
 K. Westergaard, A. K. Müller, S. Christensen, J. Bloem, S. J. S?rensen,, “Effects of tylosin as a disturbance on the soil microbial community,” Soil Biology and Biochemistry, Vol.33, No.15, 2001, pp. 2061--2071.
 J.B. Hughes, J. J. Hellmann, T. H. Ricketts, B. J. M. Bohannan, “Counting the uncountable: statistical approaches to estimating microbial diversity,” Applied and Environmental Microbiology, Vol.67, No.10, 2001, pp. 4399-4406. doi:10.1128/AEM.67.10.4399-4406.2001
 J. Zhou, M. A. Bruns, J. M. Tiedje, “ DNA recovery from soils of diverse composition,” Applied and Environmental Microbiology, Vol.62, No.2, 1996, pp. 316-322.
 C. A. Eichner, R. W. Erb, K. N. Timmis, I. Wagner-D?bler, “Thermal gradient gel electrophoresis analysis of bioprotection from pollutant shocks in the activated sludge microbial community,” Applied and Environmental Microbiology, Vol.65, No.1, 1999, pp. 102-109
 J. Logemann, J. Schell, L. Willmitzer, “Improved method for the isolation of RNA from plant tissues,” Analytical Biochemistry, Vol.163, No.1, 1987, pp. 16-20.
 L. D. Stetzenbach, M. V. Yates, Ed., Dictionary of Environmental Microbiology, Academic Press, London, 2003.
 S.G. Fischer, L. S. Lerman, “DNA fragments differing by single basepair substitutions are separated in denaturing gradient gels: correspondence with melting theory,” Proceeding of the National Academy Sciences of the United States of Amercia, Vol.80, No.6, 1983, pp.1579-1583.
 M. Kimura, C. C. Tun, “Microscopic observation of the decomposition process of leaf sheath of rice straw and colonizing microorganisms during the cultivation period of paddy rice,” Soil Science and Plant Nutrition, Vol.45, No.2, 1999, pp.427-437
 D. M. Ward, M. M. Bateson, R. Weller, A. L .Ruff-Roberts, “Ribosomal RNA analysis of microorganisms as they occur in nature,” Advances in Microbial Ecology, Vol.12, 1992, pp.219 – 286.
 S. J. Giovannoni, T. B. Britschgi, C. L. Moyer, K. G. Field, “Genetic diversity in Sargasso Sea bacterioplankton,’ Nature (London) Vol.345, No.3, 1990, pp. 60-63. doi:10.1038/345060a0
 D. M. Ward, R. Weller, M. M. Bateson, “16S rRNA sequences reveal numerous uncultured microorganisms in a natural community,” Nature (London) Vol.345, No.3, 1990, pp. 63-65. doi:10.1038/345063a0
 K. Smalla, N. Cresswell, L. C. Mendonca-Hagler, A. Wolters, J. D. Van Elsas, “Rapid DNA extraction protocol from soil for polymerase chain reaction-mediated amplification,” Journal Applied Microbiology, Vol.74, No.1, 1993, pp. 78-85.
 Y. L. Tsai, B. H. Olson, “Rapid method for separation of bacterial DNA from humic substances in sediments for polymerase chain reaction,” Applied and Environmental Microbiology, Vol.58, No.7, 1992, pp. 2292-2295.
 C. C. Tebbe, W. Vahjen, “Interference of humic acids and DNA extracted directly from soil in detection and transformation of recombinant DNA from bacteria and yeast,” Applied and Environmental Microbiology, Vol.59, No.8, 1993, pp.2657--2665.
 R. J. Steffan, R. M. Atlas, “DNA amplification to enhance detection of genetically engineered bacteria in environmental samples,” Applied and Environmental Microbiology, Vol.54, No.9, 1988, pp.2185-2191.
 N. Fromin, J. Hamelin, S. Tarnawski, D. Roesti, K. Jourdain-Miserez, N. Forestier, S. Teyssier-Cuvelle, F. Gillet, M. Aragno, P. Rossi, “Statistical analysis of denaturing gel electrophoresis (DGE) fingerprinting patterns,” Environmental Microbiology, Vol. 4, No.11, 2002, pp.634-643. doi:10.1046/j.1462-2920.2002.00358.x
 H. Sekiguchi, M. Watanabe, T. Nakahara, B. Xu, H. Uchiyama, “Succession of bacterial community structure along the Changjiang river determined by denaturing gradient gel electrophoresis and clone library analysis,” Applied and Environmental Microbiology, Vol.68, No.10, 2002, pp.5142-5150. doi:10.1128/AEM.68.10.5142