A PCR-based method for the screening of bacterial strains with antifungal activity in suppressive soybean rhizosphere

Selection and evaluation of microbial strains for their antifungal activity in natural environments is time- and energy-consuming. We have adapted a PCR-based method to avoid these inconveniences. Soils that are naturally suppressive to plant disease were chosen as a source of antibiotic-producing bacteria. The screening was performed by means of PCR amplification using degenerate primers corresponding to peptide synthetase genes. Amplification fragments were obtained using template DNA from the rhizosphere of three different soybean fields. In order to assay their potential utility in pathogen control, several Bacillus strains were analysed for their in vitro antifungal activity by testing growth inhibition of Sclerotinia sclerotiorum. Four Bacillus sp. isolates gave a positive amplification signal, and three of them had an inhibitory effect on S. sclerotiorum growth, whereas two strains that failed to give an amplification signal did not inhibit fungal growth. These results show that PCR-based techniques could be useful to assess the presence of strains with potential use as biocontrol agents.