Canola alters rhizosphere and root microbiome of following wheat crops

Authors: Schlatter, Daniel; Yin, Chuntao; Hansen, Jeremy; SCHILLINGER, WILLIAM - Washington State University; Paulitz, Timothy

Submitted to: Applied Soil Ecology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/6/2025
Publication Date: 12/20/2025
Citation: Schlatter, D.C., Yin, C., Hansen, J.C., Schillinger, W.F., Paulitz, T.C. 2025. Canola alters rhizosphere and root microbiome of following wheat crops. Applied Soil Ecology. 218. Article 106694. https://doi.org/10.1016/j.apsoil.2025.106694.
DOI: https://doi.org/10.1016/j.apsoil.2025.106694

Interpretive Summary: Crop rotation has been an important agricultural management tactic used for centuries to increase crop yields. However, there is little knowledge of how crop species can generate microbial legacies in subsequent crops in ways that may impact plant health. USDA scientists conducted a multiyear crop rotation experiment in a dryland wheat cropping system in Washington State and examined the impact of integrating canola as a rotation crop versus other cereals (winter wheat, winter triticale) on rhizosphere and root microbiomes of spring wheat. Microbial taxa associated with water stress, as well as potential plant pathogens, were enriched in roots following canola versus other species. Further, beneficial fungi (mycorrhizae) were depleted following canola. Together, this study provides important knowledge on how interactions between plant-associated microbial legacies, soil environmental characteristics, and crop rotational strategies interact to drive variation in crop yields.

Technical Abstract: 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 multi-year crop rotation experiment that included winter wheat, winter triticale, or winter canola as rotation crops integrated into a continuous spring wheat monoculture. 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 PLFA. Although sampling year and plant compartment were the strongest drivers of microbial community composition and diversity, the identity of the previous crop resulted in legacies in both rhizosphere and root communities. 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 (eg. Waitea) following canola. Taken together, these results suggest that interactions among soil environmental characteristics and plant-associated microbiomes should be carefully considered when designing crop rotation strategies to promote crop yields.