Plants’ genetic improvement has been exploited for a long time as an important approach to cope with environmental stresses (both biotic and abiotic) or to improve traits useful for human needs. As a shortcoming of the incessant selection of genomic plant traits, and the considerable number of inputs needed to sustain the selected genotypes, nowadays a negative impact on the biodiversity of the plant-associated microbes can be observed. It is worth noting that these microbes represent an extended plant genome, termed as the hologenome, which can play a pivotal role in plant adaptation to several stresses. In recent years, many researchers have increasingly focused their attention on the isolation, characterization, and preservation of plant-associated microbes (termed as the holobiont). In this context a publicly available repository of grapevine-associated microbes has been established with the aim of preserving the microbial biodiversity and exploit such arsenal to improve viticulture sustainability and resilience. To reach such objective, we attempted the manipulation of the holobiont/hologenome through the development of tailored synthetic microbial communities (SynComs). Specifically, a collection of endophytic bacterial isolates obtained from grapevine woody tissues has been exploited to produce an ad-hoc inoculum comprising potential biological control agents to counteract the esca syndrome. Employing a comprehensive approach that integrates molecular, biochemical, and eco-physiological assessments, we demonstrated that SynCom treatment influenced the trade-off between plant growth and defence features. Plants inoculated with SynComs redirected their energy allocation towards defence pathways, thereby affecting their physiological performance. Our findings suggest that a holistic approach considering both the attributes of the bacteria and their impacts on plant growth and defence mechanisms can unveil the intricate mechanisms underlying plantendophyte interactions. Despite the enormous potential of SynComs, important information is still lacking, and it is crucial to shed light on the ‘dark-side effects’ of SynCom applications with the aim to harness their potential with a refined awareness.
