Loop-mediated isothermal amplification (LAMP) assay proved the mechanism of biological control against root rot pathogens

Abstract Background The soil-borne fungi, Rhizoctonia solani and Sclerotium rolfsii, are major pathogens of Brassicae crops. This study was performed to clarify the relationship between the accumulation pattern of the genus Trichoderma and disease suppression in frequently inoculated soils with binucleate Rhizoctonia (BNR), Rhizoctonia solani and Sclerotium rolfsii. Results As compared to the control group, five Trichoderma virens strains isolated from soil inoculated with R. solani or BNR significantly reduced the severity of S. rolfsii (85.6–100% covering percentage) and R. solani (95.7–100% covering percentage). Similarly, five T. hamatum strains obtained from soil inoculated with R. solani were shown to be highly suppressive against S. rolfsii (83.9–97.1% covering percentages) and R. solani (60.2–96.2% covering percentages). Four out of five T. hamatum strains obtained from soil infected with S. rolfsii exhibited considerable suppression against S. rolfsii (63.7–91.2% covering percentages), while the SM5 strain did not. The phylogenetic analysis of the TEF and ITS regions of Trichoderma hamatum revealed that most isolates were classified into the same cluster with homology of 99–100%. Five strains of each T. virens and T. hamatum were isolated from the suppressive soil with high antagonistic potentials against R. solani and S. rolfsii. Suppression and antagonistic activity of T. hamatum isolated from soil frequently inoculated with sterile barley grains were negligible, whereas T. hamatum isolated from frequently inoculated soil with BNR and R. solani demonstrated considerable suppression of the pathogens and antagonistic activity. Accumulation and quantification of T. virens and T. hamatum were confirmed using loop-mediated isothermal amplification (LAMP). Conclusion In conclusion, disease suppression in frequently inoculated soil with BNR, R. solani and S. rolfsii was due to Trichoderma spp. accumulated selectively in each replicate of soil inoculation.