Dynamics of Fusarium populations responsible for Fusarium Head Blight and microbial communities among key components of the agroecosystem – POPNCO

Fusarium Head Blight (FHB) is a devastating fungal disease of small-grain cereals including wheat resulting in yield loss and grain contamination with mycotoxins. Basic but yet unanswered questions regarding FHB epidemiology and the interactions between the field microbiome and Fusarium spp. (Fspp) remain. These fungi colonize various components of the field during their life cycle including previous crop residues, soil and grains. Although soil and residues constitute the main inoculum source, these components have received much less attention than grains. Studies on Fspp genetic diversity at the intraspecific level also constitute a second research gap. Yet, these knowledge are of paramount importance for the development of efficient control methods, including biocontrol, an environmentally-friendly alternative to chemical pesticides. Actually, the use of biocontrol agents (BCA) to reduce FHB has been intensively examined and, despite some promising results under laboratory or greenhouse conditions, field results are often disappointing. In addition to the aforementioned research gaps, several scientific and technical barriers can also account for such delay in the development of efficient BCA to FHB including the establishment of relevant screening methods and the design and use of appropriate tools for evaluating BCA efficacy.
In this context, this project aims to determine i) the diversity and dynamics of bacterial, fungal and Fspp communities throughout the wheat cycle among the field components colonized by Fspp (i.e. residues, soil after residue decomposition and wheat heads and kernels); ii) the intraspecific variability, both phenotypic and genetic, within the predominant FHB species, that is F. graminearum (Fg); iii) the ability of isolates from the field microbiome to reduce Fspp growth and mycotoxin production using a bottleneck selection process.
To address these objectives, we plan to thoroughly monitor, throughout the wheat cycle, 5 fields during 2 years. Samples from soil, wheat grains and maize residues, will be collected at different time-points over the wheat cycle (just after maize harvest, during the first wheat growth stages, at flowering and harvest). On those samples, the diversity and dynamics of bacterial, fungal and Fspp communities will be determined using a metabarcoding approach. A collection of Fg single-spore isolates from soil, maize residues and kernels will be constituted and genotyped using SNP-based markers in partnership with UR MycSA to study Fg intraspecific diversity at the field scale. Last, a collection of 700 isolates (including both bacteria and fungi) will be generated and screened for their ability to reduce predominant Fspp growth using soil and plant-based media. Mesocosm experiments will finally be set up to determine the ability of a subset of the most active isolates, either alone or in combination, to colonize non-sterilized soil, maize residues and/or wheat grains, to displace predominant Fspp and reduce mycotoxin contamination in wheat grains.
Overall, results of the POPNCO project will help us determine i) which are the main Fspp responsible for FHB and where they are found; ii) the level of intraspecific diversity among Fg within fields and iii) to which degree the soil and residue inoculum source contribute to the disease within a field. These findings are central for the selection of appropriate biocontrol strategies in order to determine the predominant Fspp that should be targeted for BCA selection and the field components and wheat stages during which BCA application is more likely to affect pathogen population or its impact on the plant. In addition, results will contribute to gain a deeper insight into Fspp/field microbiota interactions and identify antagonistic isolates to Fspp to be implemented in biocontrol strategies. Our results may represent a real breakthrough with the findings of isolates or consortia of isolates with great potential as BCA towards Fspp.