Phenology-dependent root bacteria enhance yield of Brassica napus

The plant root microbiome can enhance yield in crops, but whether this effect is due to one yield-promoting bacterial community consisting of key taxa, or multiple configurations of taxa with different traits is unclear. A changing climate and the need to reduce carbon-intensive agricultural inputs has spurred breeding programs to explore holobiont approaches to optimizing crop yields. Here we used an extensive dataset of >1300 Brassica napus (a key oilseed crop) root samples across 4 trials and 16 varieties in a novel, robust analytical pipeline to decipher the beneficial root-associated bacterial communities associated with B. napus yield performance. We found three taxonomically distinct, but phylogenetically similar communities associated with leaf development, anthesis, and seed development that were linked to crop yield performance across multiple years and sites. Here we show B. napus is associated with not one, but several phenology-dependent yield-promoting root bacterial communities that influence seed yield via different, and yet undetermined, mechanisms. Therefore, we need to consider the relationship between B. napus phenology, and holobiont community assembly and function in selecting microbiome associated traits for use in breeding programs. •Crop yield-enhancing root microbiomes contain not one, but multiple groups of key taxa.•Three taxonomically distinct, but phylogenetically similar microbiomes increase B. napus yield.•Yield-promoting bacteria were associated with B. napus phenology across multiple years and sites.