Canola alters rhizosphere and root microbiomes of following wheat crops

Crop rotation is a critical management tool to diversify and enhance the sustainability of cropping systems. Although it is well established that rotating crops can break disease cycles, reduce reliance on synthetic fertilizers, and improve soil health, the legacy effects of specific rotation crops on plant-associated microbial communities are poorly understood. In this work, we used a long-term crop rotation experiment that included winter wheat ( Triticum aestivum L.), winter triticale ( X Triticosecale Wittmack ) or canola ( Brassica napus L.; either winter or spring) as rotation crops. A continuous annual spring wheat monoculture treatment was also included. Rhizosphere and root microbiomes of spring wheat following each crop were characterized using bacterial and fungal amplicon sequencing (16S and ITS1 regions, respectively). Additionally, the abundance of soil and rhizosphere microbiota was quantified using phospholipid fatty acid analysis (PLFA). Although sampling year was often the strongest driver of microbial community composition and diversity within each plant compartment (r 2 = 0.17 and 0.09 for rhizosphere and root communities), the previous crop species resulted in legacies in both rhizosphere and root communities (r 2 = 0.07 and 0.08 for rhizosphere and root communities). Core wheat rhizosphere taxa were reduced in spring wheat following canola, such as Rhizobium, Mucilaginibacter, Sphingomonas, Burkholderia and Oxalobacteraceae. Notably, many Actinobacteria (eg. Streptomyces ) were relatively enriched in wheat roots following canola versus other crops, which may be related to reduced soil moisture recharge. Similarly, among fungi we observed reductions in relative abundances of arbuscular mycorrhizal taxa (Glomeromycota) as well as enrichment of potential root pathogens (e.g., Waitea ) following canola. Taken together, these results suggest that interactions among soil environmental characteristics and plant-associated microbiomes should be carefully considered when designing diverse crop rotation strategies. • A previous crop of canola reduced the abundance of AMF fungi in following wheat crop. • Core wheat rhizosphere copiotrophic bacteria were reduced after canola. • Actinobacteria were enriched in wheat roots following canola.