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

Abstract

Background Without effective chemical treatments, there is an increased interest on biological control of plant diseases. Trichoderma and Bacillus species 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. Plant-associated microbiomes are complex, and there is a limited knowledge of the mechanisms that maintain and stimulate specific plant-associated microbial communities. In this study, we tested the hypothesis that the introduction of the biological control agents (BCAs) Bacillus subtilis PTA-271 (Bs PTA-271) and Trichoderma atroviride SC1 (Ta SC1) produce distinctive modifications in the composition and co-occurrence network structure of the grapevine rhizosphere microbial community, as well as grapevine induced defenses. Results 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. Conclusions The findings of this research emphasize the complex relationships among microorganisms in the rhizosphere, and point to the impact of biocontrol treatments on fungal and bacterial rhizosphere microbiomes. It highlights 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. In the future, it is crucial to conduct additional studies to explore these microbial interactions in greater detail, with the goal of developing more precise and efficient biocontrol strategies for agriculture.