Identification of microbial signatures linked to oilseed rape yield decline at the landscape scale

Abstract Background The plant microbiome plays a vital role in determining host health and productivity. However, we lack real-world comparative understanding of the factors which shape assembly its diverse biota, crucially relationships between microbiota composition health. Here investigated landscape scale rhizosphere microbial processes oilseed rape (OSR), UK’s third most cultivated crop by area world's largest source vegetable oil, suffers from yield decline associated with frequency it is grown rotations. By including 37 conventional farmers’ fields varying OSR rotation frequencies, present an innovative approach to identify signatures characteristic microbiomes are beneficial harmful host. Results We show that linked agricultural systems. demonstrate fundamental differences environmental agronomic drivers protist, bacterial fungal communities root, soil bulk compartments. further discovered fungi, but neither bacteria nor protists, was influenced frequency. there were individual abundant OTUs correlated either or A variety protist pathogens detected roots OSR, several increased relative abundance root compartments as increased. Importantly, pathogen Olpidium brassicae both short rotations significantly low yield. In contrast, endophyte Tetracladium spp. showed reverse associations O. , suggesting they benefits also identified novel clades highly connected within could play composition. Conclusions at scale, governed interplay complex biota modulated Our comprehensive study has dysbiosis microbiome, systems, be used strategies promote