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Specific enumeration and analysis of the community structure of culturable pseudomonads in agricultural soils under no-till management in Argentina

Agaras, Betina, Wall, Luis G., Valverde, Claudio
Applied soil ecology 2012 v.61 pp. 305-319
agricultural soils, no-tillage, community structure, ribosomal DNA, soil biology, cover crops, probiotics, genes, nucleotide sequences, soil sampling, Pseudomonas, population dynamics, Argentina
Members of the Pseudomonas genus have been isolated and identified worldwide as plant probiotic microorganisms. Little is known about the dynamics of pseudomonads population in extensive agricultural systems under the influence of biotic and abiotic factors. As part of the national consortium BIOSPAS devoted to study soil biology and its relationship with productivity, our lab began to characterize pseudomonad populations in agricultural soils under no-till management. We here report the set up and application of a combination of selective plating and PCR-RFLP analysis of the genus specific gacA and oprF genes, to quantify and study the community structure of culturable pseudomonads in bulk soil and rhizosphere samples. The specificity of both methods has been verified by 16S rDNA and oprF sequencing. The application of selective plating and gacA/oprF PCR-RFLP analyses revealed differences in the amount and predominant type of culturable pseudomonads among geographical locations, among treatments, and between rhizospheric and bulk soil. The results indicate that these simple methods prove useful to systematically monitor pseudomonads structure in bulk and rhizospheric soils along sampling periods covering crop rotations and agricultural practices at different locations.