Abstract
A detailed description of methods most frequently used for the identification and characterization of beneficial microbial strains is presented in this chapter. The methods include microbiological, biochemical, and molecular approaches. Microbiological and biochemical methods comprise a broad range of techniques that are based on the analysis of phosphate solubilization, nitrogenase activity, indole-3-acetic acid production, bacterial motility, presence of catalase and nitrate reductase enzyme, Gram’s staining of the cell wall, siderophore production, and microbial chemotaxis. The molecular methods involve a range of techniques that are based on the extraction and analysis of microbial DNA. The extracted nucleic acid can be specifically amplified using polymerase chain reaction (PCR), and subsequently cloned and sequenced. The sequencing of conserved genes such as internal transcribed spacer (ITS) region or 16S rRNA in a microbial genome is used extensively in resolving taxonomic identity of microbial strains. These methods are highly sensitive and allow for a high degree of specificity.
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References
Tikhonovich IA, Provorov NA (2011) Microbiology is the basis of sustainable agriculture: an opinion. Ann Appl Biol 159:155–168
Bell T, Newman JA, Silverman BW et al (2005) The contribution of species richness and composition to bacterial services. Nature 436:1157–1160
Hol WHG, de Boer W, Termorshuizen AJ et al (2010) Reduction of rare soil microbes modifies plant-herbivore interactions. Ecol Lett 13:292–301
Bever JD (2003) Soil community feedback and the coexistence of competitors: conceptual frameworks and empirical tests. New Phytol 157:465–473
Reynolds HL, Packer A, Bever JD et al (2003) Grassroots ecology: plant-microbe-soil interactions as drivers of plant community structure and dynamics. Ecology 84:2281–2291
Schmidt V, Jarosch A, Marz P et al (2012) Rapid identification of bacteria in positive blood culture by matrix-assisted laser desorption ionization time-of-flight mass spectrometry. Eur J Clin Microbiol Infect Dis 31:311–317
Islam S, Akanda AM, Prova A et al (2015) Isolation and identification of plant growth promoting rhizobacteria from cucumber rhizosphere and their effect on plant growth promotion and disease suppression. Front Microbiol 6:1360
Bellenger JP, Wichard T, Kustka AB et al (2008) Uptake of molybdenum and vanadium by a nitrogen-fixing soil bacterium using siderophores. Nat Geosci 1:243–246
Braud A, Jézéquel K, Bazot S et al (2009) Enhanced phytoextraction of an agricultural Cr-and Pb-contaminated soil by bioaugmentation with siderophore-producing bacteria. Chemosphere 74:280–286
O’Toole GA, Kolter R (1998) Flagellar and twitching motility are necessary for Pseudomonas aeruginosa biofilm development. Mol Microbiol 30:295–304
Zhulin IB, Tretyakova SE, Ignatov VV (1988) Chemotaxis of Azospirillum brasilense towards compounds typical of plant roots exudates. Folia Microbiol 33:277–280
Yarza P, Yilmaz P, Pruesse E et al (2014) Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences. Nat Rev Microbiol 12:635–645
Nautiyal CS (1999) An efficient microbiological growth medium for screening phosphate solubilizing microorganisms. FEMS Microbiol Lett 170:265–270
Berrios J, Illanes A, Aroca G (2004) Spectrophotometric method for determining Gibberellic acid in fermentation broths. Biotechnol Lett 26:67–70
Cocking EC (2003) Endophytic colonization of plat roots by nitrogen-fixing bacteria. Plant Soil 252:169–175
Gøtterup J, Olsen K, Knøchel S et al (2007) Relationship between nitrate/nitrite reductase activities in meat associated staphylococci and nitrosyl myoglobin formation in a cured meat model system. Int J Food Microbiol 120:303–310
Hague A, Jones GE (2008) Cell motility assays. Cell Biol Toxicol 24:381
O’Toole GA (2011) Microtiter dish biofilm formation assay. J Vis Exp 30:2437
Margie O, Palmer C, Chin-Sang I (2013) C. elegans chemotaxis assay. J Vis Exp 74:e50069
Beveridge TJ (2001) Use of the gram stain in microbiology. Biotech Histochem 76:111–118
Toda T, Hyakumachi M, Suga H et al (1999) Differentiation of Rhizoctonia AG-D isolates from turf grass into subgroups I and II based on rDNA and RAPD analysis. Eur J Plant Pathol 105:835–846
Hayakawa T, Toda T, Ping Q et al (2006) New subgroup of Rhizoctonia AG-D, AG-DIII, obtained from Japanese zoysia grass exhibiting symptoms of a new disease. Plant Dis 90:1389–1394
Hossain MM, Sultana F, Miyazawa M et al (2014) Plant growth-promoting fungus Penicillium spp. GP 15-1 enhance growth and confers protection against damping-off and anthracnose in the cucumber. J Oleo Sci 63:391–400
Spiff ED, Odu CT (1973) Acetylene reduction by Beijerinckia under various partial pressures of oxygen and acetylene. J Gen Microbiol 78:207–209
Acknowledgments
The authors would like to acknowledge the financial assistance from University Grant Commissions through Research Management Committee of Bangabandhu Sheikh Mujibur Rahman Agricultural University, Bangladesh.
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Hossain, M.M., Sultana, F. (2018). Methods for the Characterization of Plant-Growth Promoting Rhizobacteria. In: Medina, C., López-Baena, F. (eds) Host-Pathogen Interactions. Methods in Molecular Biology, vol 1734. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7604-1_24
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DOI: https://doi.org/10.1007/978-1-4939-7604-1_24
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