The microbiome is a key determinant in maintaining animal and plant health. With the increasing evidence of the effect of microbiomes on host phenotypic traits, host-associated microbes have been factored into evolutionary studies by the modern hologenome theory of evolution, considering all living organisms as polygenomic entities (holobionts), on which natural selection and drift can operate. The holobiont/hologenome theory has important implications on evolutionary studies, animal health and agronomy. Nevertheless, we currently lack a tangible proof of the synergic evolution of holobionts to be able to effectively deploy this concept for developing novel and actionable research perspectives. Importantly, identifying the genetic bases behind this interaction under an evolutionary perspective is the first step in categorizing and engineering microbial consortia associated with plant fitness and health. In other words, decrypting the hologenome concept will help to formulate novel bio-sourced strategies to manage crop production by reducing pesticide use. In this context, the overall aim of HoloE2Plant is to provide evidence for the holobiont theory by identifying the genetic signatures that are under rapid evolution in both plant host and microbiota and affecting resistance to pathogens.
To address this main question and bring solutions applicable in the short-term to agriculture HoloE2Plant scientific objectives are:
i) To deeply characterize, by genomic and biochemical methodologies, bacterial and fungal communities isolated from natural Brassica rapa populations. Compared to agricultural lands, non-cultivated habitats harbor a wider diversity of wild plants and by consequence a larger species microbial diversity.
ii) To develop methods to reconstruct Synthetic Microbial Communities (SynComs) by using the genomic and biochemical information obtained from bacteria and fungi. SynComs are microbial assemblages’ representative of the host microbiota. SynComs can be used in agronomy to protect plants or to restore soil microbial biodiversity associated with ecosystems functioning. In HoloE2Plant, the obtained SynComs have a biostimulant and biocontrol properties conferring resistance to the soil-born fungal pathogen Rhizoctonia solani when applied to B. rapa plants.
iii) To use SynComs conferring a different degree of resistance to R. solani, in a cutting-edge experimental evolution study. For this, HoloE2Plant is using fast-cycling B. rapa plants that have the peculiarity to produce seeds in 40 days. These plants are extremely rapid when we compare to a natural Brassica life cycle (6 months). We make co-evolve these fast-cycling plants with SynComs and R. solani over 10 plant cycles. At each cycle, we monitor the impact of the SynComs on plant resistance and other phenotypes and we collect the evolved microbial populations and seeds.
At the end of the experimental evolution, we will be able to compare the genomic evolution of both plants and microbes and study the coevolutionary traits conferring resistance to R. solani.
