Agriculture needs to develop novel strategies and practices to meet the increasing global food demand, in an ecological and economical sustainable framework. The plant-associated microbiota is gaining increasing attention as part of these strategies since it strongly contributes to plant health, nutrition, and resilience to environmental perturbations. However, plant domestication has brought to the reduction of the plant abilities to recruit a beneficial microbiota. It is becoming clear that successful use of the plant microbiota requires a multifaceted approach where microbiologist, geneticists, plant scientists, agronomists, and computational biologists can develop ways and solutions to modify both the plant microbiota and plant's ability to recruit it, directed to increase crop performances. Here, while briefly reviewing the state-of-the-art in plant microbiota research, we focus the attention on the need to discover, understand and use the microbiota associated with wild relatives of crops and with neglected crops, which harbour the microbiota biodiversity needed for developing efficient bioinoculant solutions. In particular, we emphasize the convergence of in situ plant biodiversity preservation with microbiome preservation, which provides added value to nature and habitat conservation, as living collections of microbiome biodiversity. The heuristic value of bioinoculants (viz., synthetic communities) and the need of proper computational models to predict the outcome of their applications is also discussed toward a systems-biology-guided synthetic microbiota development.
