Biocontrol agents establishment and their impact on rhizosphere microbiome and induced grapevine defenses is highly soil-dependent

Abstract

AbstractWithout effective chemical treatments, there is an increased interest on biological control of plant diseases.TrichodermaandBacillusspecies have shown biocontrol potential against several grapevine diseases. However, few studies have investigated the impact of introducing beneficial microorganisms in rhizosphere, on the indigenous soil existent microbiome. In this study, we conducted a greenhouse-based experiment to explore the effect of the two most well characterized BCAs in grapevine,Trichoderma atrovirideSC1 (Ta SC1) andBacillus subtilisPTA-271 (Bs PTA-271), on the grapevine rhizosphere bacterial and fungal microbiome, and on plant defense expression, using high-throughput amplicon sequencing, and quantitative real-time PCR, respectively. Additionally, we quantified both Ta SC1 and Bs PTA-271 in rhizosphere overtime using droplet digital PCR. Our results demonstrated that, the fungal microbiome is more affected by factors such as soil type, BCA treatment, and sampling time than bacterial microbiome. Specifically, Ta SC1 application produced a negative impact on fungal diversity, while applications of BCAs did not affect bacterial diversity. Interestingly, the survival and establishment of both BCAs showed opposite trends depending on the soil type, indicating that the physicochemical properties of soils have a role on BCA establishment. Fungal co-occurrence networks were less complex than bacterial networks, but highly impacted by Ta SC1 application. Soils treated with Ta SC1, presented more complex and stable co-occurrence networks, with a higher number of positive correlations. Induced grapevine defenses also differed according to the soil, being more affected by BCA inoculation on sandy soil. The findings of this research emphasize the complex relationships among microorganisms in the rhizosphere, and highlight the significance of taking into account various factors like soil type, sampling time, and BCA treatment, and their influence on the structure and dynamics of microbial communities.