Root and rhizosphere fungi associated with the yield of diverse Brassica napus genotypes

The plant microbiome is a key driver of plant health and agroecosystem functioning. This study used internal transcribed spacer (ITS) amplicon sequencing to examine the dynamics of root-associated fungal microbiomes in genetically-diverse Brassica napus genotypes following highly resolved sampling across growth stages at multiple sites in Saskatchewan, Canada. Across all samples including individual B. napus genotypes, sampling times and sites (n = 936 for both roots and rhizosphere), genotype was associated with only 2% of variance in fungal community structure, which was mostly driven by site-year (67% of variance for root and 79% for rhizosphere). Within a single site, this influence increased to between 4 and 16% of root and 5–13% of rhizosphere community variance, indicating genotype-specific adaptation to site conditions across the growing season. A single amplicon sequence variant (ASV) of Olpidium brassicae accounted for over 88% of the root fungal ASVs at two of the three sites. Despite O. brassicae dominance, a diverse fungal core microbiome consisting of 38 ASVs was detected in all genotypes of each site-year. We also identified 13 ASVs that were highly associated with B. napus yield; common between the rhizosphere and root, Gibberella baccata was negatively correlated with yield while Nectria ramulariae and a Tetracladium sp. were positively correlated with yield. The presence of a diverse core microbiome, dominated by O. brassicae, and identification of taxa associated with B. napus yield performance across a variety of environments reveal strategic targets for better understanding the role of the root microbiome in B. napus production.