Effects of a resistance gene affecting fungal pathogen infection on the microbiome of crop residue: the case of the Leptosphaeria maculans-Brassica napus pathosystem

Oilseed rape residues are a crucial determinant of the epidemiology of stem canker, as they support the sexual reproduction of the fungal pathogen Leptosphaeria maculans. The goal of this study was to characterize the impact of a resistance gene affecting L. maculans infection on the residue microbial communities and to identify microorganisms interacting with this pathogen during the residue degradation. To this end, we used near-isogenic lines to obtain healthy and infected host plants. The microbiome associated with the two types of plant residues was characterized by metabarcoding. A combination of Linear Discriminant Analysis and Ecological Network Analysis was used to compare the microbial communities and to identify microorganisms interacting with L. maculans. The structuration of fungal communities was different between the two lines at harvest but not at the following dates, suggesting that the presence/absence of the resistance gene influences the stem basis microbiome when the plant is still alive, but does not necessary induce a differential colonization of residues by fungi. Direct interactions with other members of the communities involved many fungal and bacterial ASV (amplicon sequence variants). L. maculans appeared as having a weak role in networks, while one ASV affiliated to Plenodomus biglobosus (synonym Leptosphaeria biglobosa) belonging to the Leptosphaeria species complex was considered a keystone taxa in the networks at harvest. This approach might be used to identify and promote beneficial microorganisms against residue-borne pathogens, and more broadly, to decipher the complex interactions between multi-species pathosystem and other microbial components in crop residues.