한국토양비료학회지 (Korean Journal of Soil Science and Fertilizer)

  • 제49권2호
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  • Pages.144-156
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  • 2016
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  • 0367-6315(pISSN)
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  • 2288-2162(eISSN)
한국토양비료학회 (Korean Society of Soil Science and Fertilizer)
권호 표지
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An Overview of Different Techniques on the Microbial Community Structure, and Functional Diversity of Plant Growth Promoting Bacteria

  • Kim, Kiyoon (Department of Environmental and Biological Chemistry, Chungbuk National University) ;
  • Islam, Rashedul (Department of Environmental and Biological Chemistry, Chungbuk National University) ;
  • Benson, Abitha (Department of Environmental and Biological Chemistry, Chungbuk National University) ;
  • Joe, Manoharan Melvin (Department of Environmental and Biological Chemistry, Chungbuk National University) ;
  • Denver, Walitang (Department of Environmental and Biological Chemistry, Chungbuk National University) ;
  • Chanratan, Mak (Department of Environmental and Biological Chemistry, Chungbuk National University) ;
  • Chatterjee, Poulami (Department of Environmental and Biological Chemistry, Chungbuk National University) ;
  • Kang, Yeongyeong (Department of Environmental and Biological Chemistry, Chungbuk National University) ;
  • Sa, Tongmin (Department of Environmental and Biological Chemistry, Chungbuk National University)
  • 투고 : 2016.02.11
  • 심사 : 2016.04.27
  • 발행 : 2016.04.30
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초록

Soil is a dynamic biological system, in which it is difficult to determine the composition of microbial communities. Knowledge of microbial diversity and function in soils are limited because of the taxonomic and methodological limitations associated with studying the organisms. In this review, approaches to measure microbial diversity in soil were discussed. Research on soil microbes can be categorized as structural diversity, functional diversity and genetic diversity studies, and these include cultivation based and cultivation independent methods. Cultivation independent technique to evaluate soil structural diversity include different techniques such as Phospholipid Fatty Acids (PLFA) and Fatty Acid Methyl Ester (FAME) analysis. Carbon source utilization pattern of soil microorganisms by Community Level Physiological Profiling (CLPP), catabolic responses by Substrate Induced Respiration technique (SIR) and soil microbial enzyme activities are discussed. Genetic diversity of soil microorganisms using molecular techniques such as 16S rDNA analysis Denaturing Gradient Gel Electrophoresis (DGGE) / Temperature Gradient Gel Electrophoresis (TGGE), Terminal Restriction Fragment Length Polymorphism (T-RFLP), Single Strand Conformation Polymorphism (SSCP), Restriction Fragment Length Polymorphism (RFLP) / Amplified Ribosomal DNA Restriction Analysis (ARDRA) and Ribosomal Intergenic Spacer Analysis (RISA) are also discussed. The chapter ends with a final conclusion on the advantages and disadvantages of different techniques and advances in molecular techniques to study the soil microbial diversity.

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참고문헌

  1. Allison, S.D. and J.B.H. Martiny. 2008. Resistance, resilience, and redundancy in microbial communities. Proc. Nat. Acad. Sci. 105:1151-1159.
  2. Amann, R., W. Ludwig, and K.H. Schleifer. 1995. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59:143-169.
  3. Ananyeva, N.D., E.A. Susyan, and E.G. Gavrilenko. 2011. Determination of the soil microbial biomass carbon using the method of substrate-induced respiration. Eur. Soil Sci. 44(11):1215-1221. https://doi.org/10.1134/S1064229311030021
  4. Banning, N.C., B.M. Lalor, W.R. Cookson, A.H. Grigg, and D.V. Murphy. 2012. Analysis of soil microbial community level physiological profiles in native and post-mining rehabilitation forest: Which substrates discriminate?. Appl. Soil Ecol. 56:27-34. https://doi.org/10.1016/j.apsoil.2012.01.009
  5. Ben-David, E.A., E. Zaady, Y. Sher, and A. Nejidat. 2011. Assessment of the spatial distribution of soil microbial communities in patchy arid and semi-arid landscapes of the Negev Desert using combined PLFA and DGGE analyses. FEMS. Microbiol. Ecol. 76(3):492-503. https://doi.org/10.1111/j.1574-6941.2011.01075.x
  6. Boschker, H.T.S. and J.J. Middelburg. 2002. Stable isotopes and biomarkers in microbial ecology. FEMS. Microbiol. Ecol. 40(2):85-95. https://doi.org/10.1111/j.1574-6941.2002.tb00940.x
  7. Bouasria, A., T. Mustafa, F. De Bello, L. Zinger, G. Lemperiere, R.A. Geremia, and P. Choler. 2012. Changes in root-associated microbial communities are determined by speciesspecific plant growth responses to stress and disturbance. Euro. J. Soil Biol. 52:59-66. https://doi.org/10.1016/j.ejsobi.2012.06.003
  8. Cerrone, F., J.M. Poyatos, M. Molina-Munoz, C. Cortes-Lorenzo, J. Gonzalez-Lopez, and B. Rodelas. 2012. Prevalence of Nitrosomonas cluster 7 populations in the ammoniaoxidizing community of a submerged membrane bioreactor treating urban wastewater under different operation conditions. Bioproc. Biosyst. Eng. 36(7):901-910. https://doi.org/10.1007/s00449-012-0823-0
  9. Chandna, P., S. Mallik, and R.C. Kuhad. 2013. Assessment of bacterial diversity in agricultural by-product compost by sequencing of cultivated isolates and amplified rDNA restriction analysis. Appl. Microbiol. Biotech. 97(15):6991-7003. https://doi.org/10.1007/s00253-012-4434-0
  10. Chaudhary, D.R., J. Saxena, N. Lorenz, L.K. Dick, and R.P. Dick. 2012. Microbial Profiles of Rhizosphere and Bulk Soil Microbial Communities of Biofuel Crops Switch-grass (Panicum virgatum L.) and Jatropha (Jatropha curcas L.). Appl. Environ. Soil Sci. 3:1-6.
  11. Cho, J.C. and J.M. Tiedje. 2001. Bacterial species determination from DNA-DNA hybridization by using genome fragments and DNA microarrays. Appl. Environ. Microbiol. 67:3677-3682. https://doi.org/10.1128/AEM.67.8.3677-3682.2001
  12. Cotta, S.R., A.C.F. Dias, I.E. Marriel, F.D. Andreote, L. Seldin, and J.D. Van Elsas. 2014. Different effects of transgenic maize and nontransgenic maize on nitrogentransforming archaea and bacteria in tropical soils. Appl. Environ. Microbiol. 80(20):6437-6445. https://doi.org/10.1128/AEM.01778-14
  13. Crecchio, C., M. Curci, M.D.R. Pizzigallo, P. Ricciuti, and P. Ruggiero. 2004. Effects of municipal solid waste compost amendments on soil enzyme activities and bacterial genetic diversity. Soil Biol. Biochem. 36:1595-1605. https://doi.org/10.1016/j.soilbio.2004.07.016
  14. Cresswell, N. and E.M.H. Wellington. 1992. Detection of genetic exchange in the terrestrial environment, p. 59-82. In: E.M.H. Wellington and J.D. Van Elsas (ed.). Genetic interactions among microorganisms in the natural environment. Pergamon Press, Oxford, UK. pp. 59-82.
  15. Degens, B.P., L.A. Schipper, G.P. Sparling, and L.C. Duncan. 2001. Is the microbial community in a soil with reduced catabolic diversity resistant to stress or disturbance? Soil Biol. Biochem. 33:1143-1153. https://doi.org/10.1016/S0038-0717(01)00018-9
  16. Dick, R.P., D.P. Breakwell, and R.F. Turco. 1996. Soil enzyme activities and biodiversity measurements as integrative microbiological indicators, p. 247-271. In: J.W. Doran and A.J. Jones (ed.). Methods for assessing soil quality. Soil Science Society of America Special publication (SSSA), Madison, Wisconsin. pp. 49-50.
  17. Dijkman, N.A., H.T.S. Boschker, L.J. Stal, and J.C. Kromkamp. 2010. Composition and heterogeneity of the microbial community in a coastal microbial mat as revealed by the analysis of pigments and phospholipid-derived fatty acids. J. Sea Res. 63(1):62-70. https://doi.org/10.1016/j.seares.2009.10.002
  18. Dungait, J.A.J., S.J. Kemmitt, L. Michallon, S. Guo, Q. Wen, P.C. Brookes, and R.P. Evershed. 2011. Variable responses of the soil microbial biomass to trace concentrations of 13C-labelled glucose, using 13C-PLFA analysis. Eur. J. Soil Sci. 62(1):117-126. https://doi.org/10.1111/j.1365-2389.2010.01321.x
  19. Fang, H., Y. Han, Y. Yin, X. Pan, and Y. Yu. 2014. Variations in dissipation rate, microbial function and antibiotic resistance due to repeated introductions of manure containing sulfadiazine and chlortetracycline to soil. Chemosphere 96: 51-56. https://doi.org/10.1016/j.chemosphere.2013.07.016
  20. Fisher, M.M., and E.W. Triplett. 1999. Automated approach for ribosomal intergenic spacer analysis of microbial diversity and its application to freshwater bacterial communities. Appl. Environ. Microbiol. 65:4630-4636.
  21. Florez, R.V.A., L.C. Carvalhais, and P.M. Schenk. 2013. Culture-independent molecular tools for soil and rhizosphere microbiology. Diversity 5(3):581-612. https://doi.org/10.3390/d5030581
  22. Frac, M., K. Oszust, and J. Lipiec. 2012. Community Level Physiological Profiles (CLPP), Characterization and Microbial Activity of Soil Amended with Dairy Sewage Sludge. Sensors 12(12):3253-3268. https://doi.org/10.3390/s120303253
  23. Gannoun, H., N.B. Othman, H. Bouallagui, and H. Moktar. 2007. Mesophilic and Thermophilic Anaerobic Co-digestion of Olive Mill Wastewaters and Abattoir Wastewaters in an Upflow Anaerobic Filter. Ind. Eng. Chem. Res. 46(21): 6737-6743. https://doi.org/10.1021/ie061676r
  24. Gao, G., D. Yin, S. Chen, F. Xia, J. Yang, Q. Li, and W. Wang. 2012. Effect of biocontrol agent Pseudomonas fluorescens 2P24 on soil fungal community in cucumber rhizosphere using T-RFLP and DGGE. PloS One 7(2): e31806. https://doi.org/10.1371/journal.pone.0031806
  25. Garland, J. and A. Mills. 1991. Classification and characterization of heterotrophic microbial communities on the basis of patterns of community-level sole-carbon-source utilization. Appl. Environ. Microbiol. 57:2351-2359.
  26. Giebler, J., L.Y. Wick, H. Harms, and A. Chatzinotas. 2014. Evaluating T-RFLP protocols to sensitively analyze the genetic diversity and community changes of soil alkane degrading bacteria. Eur. J. Soil Biol. 65:107-113. https://doi.org/10.1016/j.ejsobi.2014.10.006
  27. Greene, E.A. and G. Voordouw. 2003. Analysis of environmental microbial communities by reverse sample genome probing. J. Microbiol. Methods 5:211-219.
  28. Guida, M., P.L. Cannavacciuolo, M. Cesarano, M. Borra, E. Biffali, R. D'Alessandro, and B. De Felice. 2014. Microbial diversity of landslide soils assessed by RFLP and SSCP fingerprints. J. Appl. Genetics 55(3):403-415. https://doi.org/10.1007/s13353-014-0208-y
  29. Gupta, R., N. Mathimaran, A. Wiemken, T. Boller, V.S. Bisaria, and S. Sharma. 2014. Non-target effects of bioinoculants on rhizospheric microbial communities of Cajanus cajan. Appl. Soil Ecol. 76:26-33. https://doi.org/10.1016/j.apsoil.2013.12.001
  30. Haack, S.K., H. Garchow, D.A. Odelson, L.J. Forney, and M.J. Klug. 1994. Accuracy, reproducibility, and interpretation of Fatty Acid methyl ester profiles of model bacterial communities. Appl. Environ. Microbiol. 60(7):2483-2493.
  31. Heuer, H. and K. Smalla. 1997. Application of denaturing gradient gel electrophoresis and temperature gradient gel electrophoresis for studying soil microbial communities, p. 353-373. In: J.D. Van Elsas, J.T. Trevors, E.M.H. Wellington (ed.). Modern soil microbiology. Marcel Dekker, New York, pp. 353-373.
  32. Hu, J., X. Lin, J. Wang, J. Dai, R. Chen, J. Zhang, and M.H. Wong. 2010. Microbial functional diversity, metabolic quotient, and invertase activity of a sandy loam soil as affected by long-term application of organic amendment and mineral fertilizer. J. Soils Sediments 11(2):271-280. https://doi.org/10.1007/s11368-010-0308-1
  33. Ibekwe, A.M. and A.C. Kennedy. 1999. Fatty acid methyl ester (FAME) profiles as a tool to investigate community structure of two agricultural soils. Plant Soil. 206:151-161.
  34. Ingham, R.E., J.A. Trofymow, E.R. Ingham, and D.C. Coleman. 1985. Interactions of bacteria, fungi, and their nematode grazers: effects on nutrient cycling and plant growth. Ecol. Monograph 55:119-140. https://doi.org/10.2307/1942528
  35. Janniche, G.S., H. Spliid, and H.J. Albrechtsen. 2012. Microbial Community-Level Physiological Profiles (CLPP) and herbicide mineralization potential in groundwater affected by agricultural land use. J. Contam. Hydrol. 140-141:45-55. https://doi.org/10.1016/j.jconhyd.2012.08.008
  36. Jose, P.A. and S.R.D. Jebakumar. 2012. Phylogenetic diversity of actinomycetes cultured from coastal multipond solar saltern in Tuticorin, India. Aquat. Biosyst. 8(1):23. https://doi.org/10.1186/2046-9063-8-23
  37. Kaplan, H., S. Ratering, T. Hanauer, P. Felix-Henningsen, and S. Schnell. 2013. Impact of trace metal contamination and in situ remediation on microbial diversity and respiratory activity of heavily polluted Kastanozems. Biol. Fert. Soils. 50(5):735-744.
  38. Kaur, A., A. Chaudhary, A. Kaur, R. Choudhary, and R. Kaushik. 2005. Phospholipid fatty acid -A bioindicator of environment monitoring and assessment in soil ecosystem. Current Sci. 89(7):1103-1112.
  39. Kim, S.J., J. Song, O. Kweon, R.D. Holland, D.W. Kim, J. Kim, L.R. Yu, and C.E. Cerniglia. 2012. Functional Robustness of a Polycyclic Aromatic Hydrocarbon Metabolic Network Examined in a nidA Aromatic Ring-Hydroxylating Oxygenase Mutant of Mycobacterium vanbaalenii PYR-1. Appl. Environ. Microbiol. 78(10):3715-3723. https://doi.org/10.1128/AEM.07798-11
  40. Kirk, J.L., L.A. Beaudette, M. Hart, P. Moutoglis, J.N. Klironomos, H. Lee, and J.T. Trevors. 2004. Methods of studying soil microbial diversity. J. Microbiol. Methods. 58: 169-188. https://doi.org/10.1016/j.mimet.2004.04.006
  41. Klindworth, A., E. Pruesse, T. Schweer, J. Peplies, C. Quast, M. Horn, and F.O. Glockner. 2013. Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nucleic Acids Res. 41(1):e1. https://doi.org/10.1093/nar/gks808
  42. Lee, D.H., Y.G. Zo, and S.J. Kim.1996. Non-radioactive method to study genetic profiles of natural bacterial communities by PCR single strand conformation polymorphism. Appl. Environ. Microbiol. 62:3112-3120.
  43. Lisboa, B.B., C. Bayer, L.M.P. Passaglia, F.A.D.O. Camargo, A. Beneduzi, A. Ambrosini, and L.K. Vargas. 2015. Soil fungistasis against Fusarium graminearum under different crop management systems. Rev. Bras. Cienc. Solo, 39(1): 69-77. https://doi.org/10.1590/01000683rbcs20150683
  44. Liu, W.T., T.L. Marsh, H. Cheng, and L.J. Forney. 1997. Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA. Appl. Environ. Microbiol. 63(11): 4516-22.
  45. Marshall, I.P.G., D.R.V. Berggren, M.F. Azizian, L.C. Burow, L. Semprini, and A.M. Spormann. 2012. The Hydrogenase Chip: a tiling oligonucleotide DNA microarray technique for characterizing hydrogen-producing and -consuming microbes in microbial communities. Int. J. Syst. Evol. Microbiol. 6(4):814-26.
  46. Mayr, C.A.W. and N.B. Hendriksen. 1999. Community level physiological profile of soil bacteria unaffected by extraction method. J. Microbiol. Methods. 36:29-33. https://doi.org/10.1016/S0167-7012(99)00008-1
  47. Mazinani, Z. and A. Asgharzadeh. 2014. Genetic diversity of Azotobacter strains isolated from soils by amplified ribosomal DNA restriction analysis. T. Sitologiia I. Genetika. 48(5): 26-35.
  48. Miller, K.M., T.J. Ming, A.D. Schulze, and R.E. Withler. 1999. Denaturing Gradient Gel Electrophoresis (DGGE): a rapid and sensitive technique to screen nucleotide sequence variation in populations. BioTechniques. 27:1016-1030.
  49. Mnif, S., A. Zayen, F. Karray, V. Bru-Adan, S. Loukil, J.J. Godon, M. Chamkha, and S. Sayadi. 2012. Microbial population changes in anaerobic membrane bioreactor treating landfill leachate monitored by single-strand conformation polymorphism analysis of 16S rDNA gene fragments. Int. Biodet. Biodeg. 73:50-59. https://doi.org/10.1016/j.ibiod.2012.04.014
  50. Moter, A. and U.B. Gobel. 2000. Fluorescence in situ hybridization (FISH) for direct visualization of microorganisms. J. Microbial. Methods. 41(2):85-112. https://doi.org/10.1016/S0167-7012(00)00152-4
  51. Muyzer, G. 1999. DGGE/TGGE a method for identifying genes from natural ecosystems. Curr. Opin. Microbiol. 2: 317-322. https://doi.org/10.1016/S1369-5274(99)80055-1
  52. Muyzer, G., E.C. De Waal, and A.G. Uitterlinden. 1993. Profiling of complex bacterial populations by denaturing gradient gel electro-phoresis analyses of polymerase chain reaction-amplified genes for 16S rRNA. Appl. Environ. Microbiol. 59:695-700.
  53. Nannipieri, P., J. Ascher, M.T. Ceccherini, L. Landi, G. Pietramellara, and G. Renella. 2003. Microbial diversity and soil functions. Eur. J. Soil Biol. 54:655-670. https://doi.org/10.1046/j.1351-0754.2003.0556.x
  54. Newman, M.M., M.R. Liles, and J.W. Feminella. 2015. Litter Breakdown and Microbial Succession on Two Submerged Leaf Species in a Small Forested Stream. PloS One. 10(6): e0130801. https://doi.org/10.1371/journal.pone.0130801
  55. Ogram, A. 2000. Soil molecular microbial ecology at age 20: methodological challenges for the future. Soil Biol. Biochem. 32:1499-1504. https://doi.org/10.1016/S0038-0717(00)00088-2
  56. Ollivier, J., S. Yang, C. Dorfer, G. Welzl, P. Kuhn, T. Scholter, D. Wagner, and M. Schloter. 2013. Bacterial community structure in soils of the Tibetan Plateau affected by discontinuous permafrost or seasonal freezing. Biol. Fert. Soils. 50(3):555-559. https://doi.org/10.1007/s00374-013-0869-4
  57. Orita, M., Y. Suzuki, T. Sekiya, and K. Hayashi. 1989. A rapid and sensitive detection of point mutations and genetic polymorphisms using polymerase chain reaction. Genomics. 5:874-879. https://doi.org/10.1016/0888-7543(89)90129-8
  58. Pan, Q., F. Wang, Y. Zhang, M. Cai, J. He, and H. Yang. 2013. Denaturing gradient gel electrophoresis fingerprinting of soil bacteria in the vicinity of the Chinese Great Wall Station, King George Island, Antarctica. J. Environ. Sci. 25(8):1649-1655. https://doi.org/10.1016/S1001-0742(12)60229-0
  59. Parkin, T.B. 1987. Soil microsites as a source of denitrification variability. Soil Sci. Soc. Am. J. 51:1194-1199. https://doi.org/10.2136/sssaj1987.03615995005100050019x
  60. Pinton, R., Z. Varanini, and P. Nannipieri. 2001. The Rhizosphere: Biochemistry and Organic Substances at the Soil-Plant Interface. Marcel Dekker, New York.
  61. Pisa, G., G.S. Magnani, H. Weber, E.M. Souza, H. Faoro, R. A. Monteiro, E. Daros, V. Baura, J.P. Bespalhok, F.O. Pedros, and L.M. Cruz. 2011. Diversity of 16S rRNA genes from bacteria of sugarcane rhizosphere soil. Braz. J. Med. Biol. Res. 44(12):1215-21. https://doi.org/10.1590/S0100-879X2011007500148
  62. Pratt, B., R. Riesen, and C.G. Johnston. 2012. PLFA Analyses of Microbial Communities Associated with PAH-Contaminated Riverbank Sediment. Microb. Ecol. 64(3):680-691. https://doi.org/10.1007/s00248-012-0060-8
  63. Preston-Matham, J., L. Boddy, and P.F. Randerson. 2002. Analysis of microbial community functional diversity using sole-carbon-source utilization profiles-a critique. FEMS Microbiol. Ecol. 42:1-14.
  64. Rosello-Mora, R. and R. Amann. 2001. The species concept for prokaryotes. FEMS Microbiol. Rev. 25:39-67. https://doi.org/10.1111/j.1574-6976.2001.tb00571.x
  65. Sanchez-Castro, I., N. Ferrol, and J.M. Barea. 2012. Analyzing the community composition of arbuscular mycorrhizal fungi colonizing the roots of representative shrub land species in a Mediterranean ecosystem. J. Arid Environ. 80:1-9. https://doi.org/10.1016/j.jaridenv.2011.12.010
  66. Shannon, C. and W. Weaver. 1949. The mathematical theory of communication. 10th ed., University of Illinois Press, Urbana, Illinois, USA.
  67. Sheibani, S., S.F. Yanni, R. Wilhelm, J.K. Whalen, L.G. Whyte, C.W. Greer, and C.A. Madramootoo. 2013. Soil bacteria and archaea found in long-term corn (Zea mays L.) agroecosystems in Quebec, Canada. Can. J. Soil Sci. 93(1): 45-57. https://doi.org/10.4141/cjss2012-040
  68. Shimizu, T. S., K. Ohshima, K. Ohtani, K. Hoshino, K. Honjo, and H. Hayashi. 2001. Sequence heterogeneity of the ten rRNA operons in Clostridium perfringens. Syst. Appl. Microbiol. 24:149-156. https://doi.org/10.1078/0723-2020-00024
  69. Singh, R., D. Sharma, N. Raghav, R.S. Chhokar, and I. Sharma. 2015. Molecular genotyping of herbicide resistance in P. minor: ACCase resistance. Appl. Biochem. Biotech. 175(3):1617-21. https://doi.org/10.1007/s12010-014-1363-7
  70. Smalla, K., G. Wieland, A. Buchner, A. Zock, J. Parzy, S. Kaiser, R. Roskot, H. Heuer, and G. Berg. 2001. Bulk and rhizosphere soil bacterial communities studied by denaturing gradient gel electrophoresis: plant-dependent enrichment and seasonal shifts revealed. Appl. Environ. Microbiol. 67: 4742-4751. https://doi.org/10.1128/AEM.67.10.4742-4751.2001
  71. Smalla, K., M. Oros-Sichler, A. Milling, H. Heuer, S. Baumgarte, R. Becker, G. Neuber, S. Kropf, A.Ulrich, and C.C. Tebbe. 2007. Bacterial diversity of soils assessed by DGGE, T-RFLP and SSCP fingerprints of PCR-amplified 16S rRNA gene fragments: do the different methods provide similar results?. J. Microbiol. Methods. 69(3):470-479. https://doi.org/10.1016/j.mimet.2007.02.014
  72. Smets, W., J.W. Leff, M.A. Bradford, R.L. McCulley, S. Lebeer, and N. Fierer. 2015. A method for simultaneous measurement of soil bacterial abundances and community composition via 16S rRNA gene sequencing. Peer J. Pre. Prints. 3:e1622
  73. Srivastava, A.K., P. Bhargava, A. Kumar, L.C. Rai, and B.A. Neilan. 2009. Molecular characterization and the effect of salinity on cyanobacterial diversity in the rice fields of Eastern Uttar Pradesh, India. Saline Syst. 5:4-9. https://doi.org/10.1186/1746-1448-5-4
  74. Tabacchioni, S., L. Chiarini, A. Bevivino, C. Cantale, and C. Dalmastri. 2000. Bias caused by using different isolation media for assessing the genetic diversity of a natural microbial population. Microb. Ecol. 40(3):169-176.
  75. Tiedje, J.M., S. Asming-Brempong, K. Nusslein, T.L. Marsh, and S.J. Flynn. 1999. Opening the black box of soil microbial diversity. Appl. Soil Ecol. 13:109-122. https://doi.org/10.1016/S0929-1393(99)00026-8
  76. Tipayno, S., C.G. Kim, and T. Sa. 2012. T-RFLP analysis of structural changes in soil bacterial communities in response to metal and metalloid contamination and initial phytoremediation. Appl. Soil Ecol. 61:137-146. https://doi.org/10.1016/j.apsoil.2012.06.001
  77. Tlili, A., M. Marechal, A. Berard, B. Volat, and B. Montuelle. 2011. Enhanced co-tolerance and co-sensitivity from longterm metal exposures of heterotrophic and autotrophic components of fluvial biofilms. Sci. Total Environ. 409(20): 4335-4343. https://doi.org/10.1016/j.scitotenv.2011.07.026
  78. Torsvik, V., L. Ovreas, and T.F. Thingstad. 2002. Prokaryotic diversity -Magnitude, dynamics, and controlling factors. Science. 296:1064-1066. https://doi.org/10.1126/science.1071698
  79. Trevors, J.T.1998. Bacterial biodiversity in soil with an emphasis on chemically-contaminated soils. Water Air Soil Poll. 101:45-67. https://doi.org/10.1023/A:1004953404594
  80. Weber, K.P. and R.L. Legge. 2009. One-dimensional metric for tracking bacterial community divergence using sole carbon source utilization patterns. J. Microbiol. Methods. 79(1):55-61. https://doi.org/10.1016/j.mimet.2009.07.020
  81. Wetzel, K., G. Silva, U. Matczinski, F. Oehl, and T. Fester. 2014. Superior differentiation of arbuscular mycorrhizal fungal communities from till and no-till plots by morphological spore identification when compared to T-RFLP. Soil Biol. Biochem. 72:88-96. https://doi.org/10.1016/j.soilbio.2014.01.033
  82. Whiteley, A.S. and M.J. Bailey. 2000. Bacterial community structure and physiological state within an industrial phenol bioremediation system. Appl. Environ. Microbiol. 66:2400-2407. https://doi.org/10.1128/AEM.66.6.2400-2407.2000
  83. Winding, A. and N.B. Hendriksen. 1997. Biolog substrate utilization assay for metabolic fingerprints of soil bacteria: effects of incubation, p.195-205. In: H. Insam and A. Rangger (ed.). Microbial Communities: Functional versus structural approaches. Springer, Verlag, Berlin.
  84. Winsley, T., J.M. Van Dorst, M.V. Brown, and B.C. Ferrari. 2012. Capturing greater 16S rRNA gene sequence diversity within the domain Bacteria. Appl. Environ. Microbiol. 78(16): 5938-5941. https://doi.org/10.1128/AEM.01299-12
  85. Wu, T., D.O. Chellemi, J.H. Graham, K.J. Martin, and E.N. Rosskopf. 2008. Comparison of soil bacterial communities under diverse agricultural land management and crop production practices. Microbial Ecol. 55:293-310. https://doi.org/10.1007/s00248-007-9276-4
  86. Yan, F., A.B. McBratney, and L. Copeland. 2000. Functional substrate biodiversity of cultivated and uncultivated a horizons of vertisols in New South Wales. Geoderma 96: 321-343. https://doi.org/10.1016/S0016-7061(00)00018-5
  87. Ying, Y.X., W.L. Ding, and Y. Li. 2012. Characterization of soil bacterial communities in rhizospheric and nonrhizospheric soil of panax ginseng. Biochem. Genet. 50(11-12):848-859. https://doi.org/10.1007/s10528-012-9525-1
  88. Yu, J., X.F. Zhou, S.J. Yang, W.H. Liu, and X.F. Hu. 2013. Design and application of specific 16S rDNA-targeted primers for assessing endophytic diversity in Dendrobium officinale using nested PCR-DGGE. Appl. Microbiol. Biotech. 97:9825-9836. https://doi.org/10.1007/s00253-013-5294-y
  89. Zak, J. C., M.R. Willig, D.L. Moorhead, and H.G. Wildman. 1994. Functional diversity of microbial communities: a quantitative approach. Soil Biol. Biochem. 26:1101-1108. https://doi.org/10.1016/0038-0717(94)90131-7
  90. Zelles, L. 1999. Fatty acid patterns of phospholipids and lipopolysaccharides in the characterization of microbial communities in soil: a review. Biol. Fert. Soils. 29:111-129. https://doi.org/10.1007/s003740050533
  91. Zhao, B., C.C. Yeo, C.C. Lee, A. Geng, F.T. Chew, and C.L. Poh. 2004. Proteome analysis of gentisate-induced response in Pseudomonas alcaligenes NCIB 9867. Proteomics, 4(7): 2028-2036. https://doi.org/10.1002/pmic.200300730
  92. Zhou, J., S. Kang, C.W. Schadt, and C.T. Garten. 2008. Spatial scaling of functional gene diversity across various microbial taxa. Proceedings of the National Academy of Sciences, 105(22):7768-7773. https://doi.org/10.1073/pnas.0709016105
  93. Zhou, L., H. Li, Y. Zhang, S. Han, and H. Xu. 2013. Development of genus-specific primers for better understanding the diversity and population structure of Sphingomonas in soils. J. Basic Microbiol. 22:1-9.