Contrasting nitrogen fertilization and Brassica napus (canola) variety development impact recruitment of the root-associated microbiome

Canola (Brassica napus) is an important broadacre crop, produced under high nitrogen (N) fertilizer application. Modern canola varieties are developed under high N rates but the impacts on root-associated microbiomes of different varieties are unknown. We studied eight canola varieties spanning historical Canadian spring canola development at two sites under high and low N fertility and characterized bacterial and fungal microbiomes in the root and rhizosphere using amplicon sequencing. Environmental conditions and the resulting canola varietal responses strongly affected the root-associated bacterial and fungal microbiomes. Microbes regulated by N fertility in each canola variety were mainly Gammaproteobacteria, Bacteroidia, Actinobacteria, Sordariomycetes, Dothideomycetes, and Agaricomycetes classes. Differentially abundant (DA) microbial taxa showed that N more strongly enriched bacteria in the roots and fungi in the rhizosphere. Each variety had its specific pattern of DA-ASVs responding to soil N availability, and the profile of DA-ASVs in paired canola varieties were also altered by soil N availability, especially bacteria in rhizosphere. The yield was strongly associated with a subset of microbial taxa mainly from Proteobacteria, Actinobacteriota, and Ascomycota. These variety-dependent responses to N and links to yield performance make root-associated microbiome a promising target for improving the agronomic performance of canola by manipulating microorganisms tailored to soil fertility and plant genotype.