Common and unique rhizosphere microbial communities of wheat and canola in a semiarid Mediterranean environment

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

Submitted to: Soil Biology and Biochemistry
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/12/2019
Publication Date: 12/3/2019
Citation: Schlatter, D.C., Hansen, J.C., Schillinger, W.F., Sullivan, T.S., Paulitz, T.C. 2019. Common and unique rhizosphere microbial communities of wheat and canola in a semiarid Mediterranean environment. Soil Biology and Biochemistry. 144:170-181. https://doi.org/10.1016/j.apsoil.2019.07.010.
DOI: https://doi.org/10.1016/j.apsoil.2019.07.010

Interpretive Summary: The bacterial and fungal communities on the roots of wheat and canola were examined with next-generation sequencing, in order to find what could be causing a yield decrease when wheat is grown after canola. In the fall, wheat roots were dominated by Acidobacteria and Actinobacteria, which are adapted for dry condition. In the spring, wheat roots are dominated by fast growing bacteria like Pseudomonas, Flavobacterium and Oxalobacteraceae. For fungi, potential wheat pathogens like Rhizoctonia and Typhula were more predominate on wheat roots, while Chytridiomycetes were more dominant on canola. In conclusion, most of the communities of fungi and bacteria are not “host specific” but colonize around the roots of both wheat and canola with differing levels of abundance.

Technical Abstract: In wheat cropping systems, rotation crops often provide a benefit yield to the following wheat crop. This has been documented for legume crops and canola. However, in a series of replicated field trials over 6 years NE Washington state, spring wheat grown after winter canola had an average of 17% yield decrease, compared to when grown after winter wheat. Diseases, water use, and nutrient use could not explain this reduction. We examined the bacterial and fungal communities in the rhizosphere of wheat and canola at six locations and two sampling dates for differences that could potentially explain this yield decline. Over 3,700 bacterial and 970 fungal total OTUs were obtained. Soil type was the primary driver of both fungal and bacterial communities, with locations geographically closest to each other clustering together. Season (fall vs spring sampling) had the next strongest effect, followed by the crop. Differences between the two crops were more evident in the spring than the fall. Richness and diversity were consistently higher in the rhizosphere of canola compared to wheat. Pseudomonas, Flavobacterium and Pedobacter were more abundant in the wheat rhizosphere compared to the canola rhizosphere. A few bacterial genera including Opitus and Sporocytophaga were more abundant on canola. Many bacterial groups were highly abundant in the rhizosphere of both crop species, especially Janthinobacterium and Kaistobacter. Bacterial communities on winter wheat in the fall were dominated by Actinomycetes and Acidobacteria. But in the spring, these communities were dominated by fast growing bacteria copiotrophs, including Pseudomonas, Janthinobacterium, Flavobacterium, Oxalobacteraceae, and Sphingobacteriaceae. Saprotrophic fungi such as Ulocladium, Mortierella, Cryptoccocus, Chaetomium, Penicillium and Trichoderma were equally abundant in the rhizosphere of both crops. Potential wheat root pathogens such as Thanatephorus (Rhizoctonia) Ceratobasidium, Oculimacula, Typhula, and Microdochium were more abundant in the wheat rhizosphere compared to canola. OTUs in the Chytridiomycota were more abundant on canola in the spring. In conclusion, most of the communities of fungi and bacteria are not “host specific” but colonize around the roots of both wheat and canola with differing levels of abundance and evenness highly dependent on the season. A much smaller group of taxa were more crop specific.