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

Abstract

Abstract In wheat (Triticum aestivum L.)-based cropping systems, rotation crops often provide a yield benefit to the following wheat crop. This has been documented for legume crops and canola (Brassica napus L.). In the present study, we examined bacterial and fungal communities in the rhizosphere of wheat and canola at six paired locations on fall and spring sampling dates using high-throughput sequencing of marker genes (bacterial 16S rRNA gene and fungal internal transcribed spacers). Soil type was the primary driver of both fungal and bacterial communities, with the communities of locations geographically closest, and with the same soil type, clustering together. Season (fall vs spring sampling) had the next strongest effect, followed by the crop species. Differences between the wheat and canola were more evident in the spring than in the fall. However, in contrast, bacterial and fungal species richness and diversity were not related to location or season, and instead were consistently higher in the rhizosphere of canola compared to wheat. Many bacterial groups were shared across both crop species, especially Janthinobacterium and Kaistobacter. Bacterial communities of wheat in the fall were dominated by Actinomycetes and Acidobacteria. But in the spring, these communities shifted to fast growing bacterial copiotrophs, including Pseudomonas, Janthinobacterium, Flavobacterium, Oxalobacteraceae, and Sphingobacteriaceae. Saprotrophic fungi such as Ulocladium, Mortierella, Cryptoccocus, Chaetomium, Penicillium and Trichoderma were also common to, and 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. In conclusion, most of the communities of fungi and bacteria are not “host specific” but colonize the roots of both wheat and canola with differing relative abundance dependent on the season. A much smaller group of taxa were unique to the specific crop. This work provides novel insight into changes in crop rhizosphere communities when canola is introduced into dryland monoculture wheat cropping systems.