Exploring the Holobiont concept through a Plant Evolutionary Experiment study

The evolutionary processes underlying interactions between hosts and their associated microbes is a black box on which biologists have long attempted to shed light. A limiting factor has been knowledge of the precise molecular events, which are now increasingly possible to elucidate with the advent of next-generation sequencing technologies. The Big Data era have revolutionized evolutionary studies through sequencing of thousands of genomes allowing tracing genomic changes. Coupled to these technologies experimental evolution transformed evolution from a predictive to a functional science by opening a window on evolutionary changes in real-time. The challenge that now awaits evolutionary science is in identifying the trajectories simultaneously driving evolution in hosts and microbes. In this context, HoloE2Plant will validate the holobiont concept by looking at the simultaneous evolution of the host and its microbiome. This will be possible thanks to an experimental coevolution approach applied to fast-cycling Brassica rapa plants and Synthetic Microbial Communities (SynComs). SynComs will be selected from bacterial and fungal collections previously established from wild B. rapa populations. This ambitious project is timely and feasible thanks to the combination of high-throughput sequencing, cutting-edge modelling methods for microbial functional network reconstruction and a novel co-evolutionary quantitative genetic approach that will be developed here. Experimental evolution will be carried out in presence/absence of the fungal pathogen Rhizoctonia solani and the genetic bases underlying microbial-plant interactions and associated with disease resistance will be identified. HoloE2Plant will contribute to validating the holobiont concept and will provide unique methods to identify rapid evolutionary changes in holobionts; these theoretical advances will set the stage for future applied projects aiming at designing microbial consortia with biocontrol properties.