Linking the genome to the phenotype: Streptomyces anulatus DEF39 treatment on seeds protects wheat from mild water stress and DON accumulation caused by F. graminearum

Fusarium Head Blight (FHB) is a major disease of wheat causing direct production losses and accumulation of trichothecenes that are toxic to humans and animals. The most important mycotoxin is deoxynivalenol (DON). Strain DEF39, a Streptomyces anulatus wheat endophyte, shows the ability to protect wheat spikes from F. graminearum infection by >60% and to reduce DON accumulation in spikes by >50% during field trials when applied as a seed coating. According our results, DEF39 seed treatment leads to whole plant colonization. Interestingly, when mild water stress is applied to wheat, DEF39 colonized plants showed different physiological responses compared to the untreated control, maintaining a higher leaf gas exchange rate. To decipher the possible mechanisms of action of the strain, the genome of DEF39 was assembled using a hybrid strategy combining Nanopore long and Illumina short reads. Two contigs were produced, one linear chromosome (8.8 Mb) with inverted repeats at the edges and one linear plasmid (0.2 Mb). Functional analysis identified a putative role for the plasmid and provided evidence for an indirect effect type of interaction of the strain on the protection of the plant. Comparative genomic analysis within the species S. anulatus diversity leads to the identification of DEF39 specific genes likely involved in the endophytic behaviour, in the ability to colonize wheat plants, and in modulating the plant stress response.