AiM  Vol.6 No.2 , February 2016
A Simple Evaluation System for Microbial Property in Soil and Manure
Abstract: Analyses of microbial properties in soil and manure had always included the problem that there was no available standard method to evaluate microbial property. The one of the major problems was the vast diversity and the enormous population of soil microorganisms [1], the other was an existence of numerically dominant unculturable microorganisms which comprise 99% of soil habitat [2]. We evaluated whether our newly developed method, by which taxonomies and their number of each bacterial groups were estimated, could be used as evaluation method of microbial properties of soils and manures. In the forest soil, β-Proteobacteria, which included Burkholderia sp., Ralstonia sp., and Alcaligenes sp., was numerically dominant bacteria (3.64 × 106 MPN g-1 dry soil), followed by γ-Proteobacteria (1.32 × 106 MPN), δ-Proteobacteria (0.006 × 106 MPN), and the other gram negative bacteria (0.006 × 106 MPN). In the commercial manure, Actinobacteria, which included Streptoverticillium salmonis, Mycrococcus sp., Streptomyces bikiniensis, and Microbacterium ulmi, was numerically dominant bacterial group (30.8 × 106 MPN), followed by α-Proteobacteria (26.0 × 106 MPN), β-Proteobacteria (17.1 × 106 MPN), δ-Proteobacteria (11.2 × 106 MPN), the other Firmicutes (1.71 × 106 MPN), γ-Proteobacteria (0.5 × 106 MPN), and the other gram negative bacteria (0.05 × 106 MPN). In the upland field, the other Firmicutes, which included Paenibacillus sp., was numerically dominant bacteria (4.41 × 106 MPN), followed by Actinobacteria (2.14 × 106 MPN), Bacillus sp. (2.14 × 106 MPN), and γ-Proteobacteria (0.35 × 106 MPN). Although the precision of the affiliations became lower because of higher diversity of samples and the number of some Antinobacteria and Firmicutes might be underestimated by the used PCR condition, the method was found suitable as a candidate of a new evaluation system of soil and manure.
Cite this paper: Horinishi, N. , Matsumoto, K. and Watanabe, K. (2016) A Simple Evaluation System for Microbial Property in Soil and Manure. Advances in Microbiology, 6, 88-97. doi: 10.4236/aim.2016.62009.

[1]   Torsvik, V., Goksoyr, J. and Daae, F.L. (1990) High Diversity in DNA of Soil Bacteria. Applied and Environmental Microbiology, 56, 782-787.

[2]   Amann, R.I., Ludwig, W. and Schleifer, K.H. (1995) Phylogenetic Identification and in Situ Detection of Individual Microbial Cells without Cultivation. Microbiological Reviews, 59, 143-169.

[3]   Muyzer, G., Waal, E.C.D. and Uitterlinden, A.G. (1993) Profiling of Complex Microbial Populations by Denaturing Gradient Gel Electrophoresis Analysis of Polymerase Chain Reaction-Amplified Genes Coding for 16S rRNA. Applied and Environmental Microbiology, 59, 695-700.

[4]   Suzuki, M.T. and Giovannoni, S.J. (1996) Bias Caused by Template Annealing in the Amplification of Mixtures of 16S rRNA Genes by PCR. Applied and Environmental Microbiology, 62, 625-630.

[5]   Ishii, K. and Fukui, M. (2001) Optimization of Annealing Temperature to Reduce Bias Caused by a Primer Mismatch in Multitemplate PCR. Applied and Environmental Microbiology, 67, 3753-3755.

[6]   Neilson, J.W., Jordan, F.L. and Maier, R.M. (2013) Analysis of Artifacts Suggests DGGE Should Not Be Used for Quantitative Diversity Analysis. Journal of Microbiological Method, 92, 256-263.

[7]   Direito, S.O.L., Zaura, E., Little, M., Ehrenfreund, P. and Roling, W.F.M. (2014) Systematic Evaluation of Bias in Microbial Community Profiles Induced by Whole Genome Amplification. Environmental Microbiology, 16, 643-657.

[8]   Griffiths, R.I., Whiteley, A.S., O’Donnell, A.G. and Bailey, M.J. (2000) Rapid Method for Coextraction of DNA and RNA from Natural Environments for Analysis of Ribosomal DNA- and rRNA-Based Microbial Community Composition. Applied and Environmental Microbiology, 66, 5488-5491.

[9]   Duineveld, B.M., Kowalchuk, G.A., Keijzer, A., van Elsas, J.D. and van Veen, J.A. (2001) Analysis of Bacterial Communities in the Rhizosphere of Chrysanthemum via Denaturing Gradient Gel Electrophoresis of PCR-Amplified 16S rRNA as Well as DNA Fragments Coding for 16S rRNA. Applied and Environmental Microbiology, 67, 172-178.

[10]   Sun, H.Y., Deng, S.P. and Raun, W.R. (2004) Bacterial Community Structure and Diversity in a Century-Old Manure-Treated Agroecosystem. Applied and Environmental Microbiology, 70, 5868-5874.

[11]   Huang, J., Sheng, X., He, L., Huang, Z., Wang, Q. and Zhang, Z. (2013) Characterization of Depth-Related Changes in Bacterial Community Compositions and Functions of a Paddy Soil Profile. FEMS Microbiology Letters, 347, 33-42.

[12]   Nikolausz, M., Sipos, R., Revesz, S., Szekely, A. and Marialigeti, K. (2005) Observation of Bias Associated with Re-Amplification of DNA Isolated from Denaturing Gradient Gels. FEMS Microbiological Letters, 244, 385-390.

[13]   Santegoeds, C.M., Ferdelman, T.G., Muyzer, G. and Beer, D.D. (1998) Structural and Functional Dynamics of Sulfate-Reducing Populations in Bacterial Biofilms. Applied and Environmental Microbiology, 64, 3731-3739.

[14]   Watanabe, T., Asakawa, S., Nakamura, A., Nagaoka, K. and Kimura, M. (2004) DGGE Method for Analyzing 16S rDNA of Methanogenic Archaeal Community in Paddy Field Soil. FEMS Microbiology Letters, 232, 153-163.

[15]   Chu, H., Fujii, T., Morimoto, S., Lin, X., Yagi, K., Hu, J. and Jiabao, Z. (2007) Community Structure of Ammonia-Oxidizing Bacteria under Long-Term Application of Mineral Fertilizer and Organic Manure in a Sandy Loam Soil. Applied and Environmental Microbiology, 73, 485-491.

[16]   Tsai, Y.L. and Olson, B.H. (1991) Rapid Method for Direct Extraction of DNA from Soil and Sediments. Applied and Environmental Microbiology, 57, 1070-1074.

[17]   Watanabe, K. and Okuda, M. (2003) Method and System for Searching for Relationships between Base Sequences in Genes. Japanese Patent 3431135, (2006) US Patent 7,006,924.

[18]   Watanabe, K. and Koga, N. (2009) Use of a Microchip Electrophoresis System for Estimation of Bacterial Phylogeny and Analysis of NO3- Reducing Bacterial Flora in Field Soils. Bioscience Biotechnology and Biochemistry, 73, 479-488.

[19]   Watanabe, K., Okuda, M. and Koga, N. (2008) A Newly Developed System Based on Multiple Enzyme Restriction Fragment Length Polymorphism—An Application to Proteolytic Bacterial Flora Analysis. Soil Science and Plant Nutrition, 54, 204-215.

[20]   Watanabe, K., Horinishi, N. and Matumoto, K. (2015) Antibiotic-Resistant Bacterial Group in Field Soil Evaluated by a Newly Developed Method Based on Restriction Fragment Length Polymorphism Analysis. Advances in Microbiology, 5, 807-816.

[21]   Watanabe, K., Horinishi, N., Matumoto, K., Tanaka, A. and Yakushido, K. (2015) Bacterial Groups Concerned with Maturing Process in Manure Production Analyzed by a Method Based on Restriction Fragment Length Polymorphism Analysis. Advances in Microbiology, 5, 832-841.

[22]   Bochner, B. (1989) “Breathprints” at the Microbial Level. ASM News, 55, 536-539.

[23]   Weidner, S., Arnold, W. and Puhler, A. (1996) Diversity of Uncultured Microorganisms Associated with the Seagrass Halophila stipulacea Estimated by Restriction Fragment Length Polymorphism Analysis of PCR-Amplified 16S rRNA Genes. Applied and Environmental Microbiology, 62, 766-771.

[24]   Cole, J.R., Chai, B., Farris, R., Wang, Q., Kulam-Syed-Mohideen, A.S., McGarrell, D.M., Bandela, A.M., Cardenas, E., Garrity, G.M. and Tiedje, J.M. (2007) The Ribosomal Database Project (RDP-II): Introducing myRDP Space and Quality Controlled Public Data. Nucleic Acids Research, 35, D169-D172.

[25]   Nei, M. and Li, W.H. (1979) Mathematical Model for Studying Genetic Variation in Terms of Restriction Endonucleases. Proceedings of the National Academy of Sciences of the United States of America, 76, 5269-5273.

[26]   Blodgett, R. (2010) FDA, Bacterial Analytical Manual, Appendix 2 Most Probable Number from Serial Dilutions. ucm109656.htm

[27]   Tsai, S.H., Selvam, A., Chang, Y.P. and Yang, S.S. (2009) Soil Bacterial Community Composition across Different Topographic Sites Characterized by 16S rRNA Gene Clones in the Fushan Forest of Taiwan. Botanical Studies, 50, 57-68.

[28]   Naether, A., Foesel, B.U., Naegele, V., Wust, P.K., Weinert, J., Bonkowski, M., Alt, F., Oelmann, Y., Polle, A., Lohaus, G., Gockel, S., Hemp, A., Kalko, E.K.V., Linsenmair, K.E., Pfeiffer, S., Renner, S., Schoning, I., Weisser, W.W., Wells, K., Fischer, M., Overmann, J. and Friedricha, M.W. (2012) Environmental Factors Affect Acidobacterial Communities below the Subgroup Level in Grassland and Forest Soils. Applied and Environmental Microbiology, 78, 7398-7406.

[29]   Gardener, B.B.M. (2004) Ecology of Bacillus and Paenibacillus spp. in Agricultural Systems. Phytopathology, 94, 1252-1258.

[30]   Tang, H., Xiao, C., Ma, J., Yu, M., Li, Y., Wang, G. and Zhang, L. (2009) Prokaryotic Diversity in Continuous Cropping and Rotational Cropping Soybean Soil. FEMS Microbiology Letters, 298, 267-273.

[31]   Bae, J.W., Kim, J.J., Jeon, C.O., Kim, K., Song, J.J., Lee, S.G., Poo, H., Jung, C.M., Park, Y.H. and Sung, M.H. (2003) Application of Denaturing Gradient Gel Electrophoresis to Estimate the Diversity of Commensal Thermophiles. Journal of Microbiology and Biotechnology, 13, 1008-1012.