Crop microbiome responses to pathogen colonisation regulate the host plant defence

Aims: Soil-borne pathogens severely damage the yield and quality of crops worldwide. Plant and soil microbiomes (e.g. in the rhizosphere) intimately interact with the plant, the pathogen and influence outcomes of disease infection. Investigation of how these microbiomes respond to disease infection is critical to develop solutions to control diseases. Methods: Here, we conducted a field experiment and collected healthy and crown rot disease infected (caused by Fusarium pseudograminearum, Fp) wheat plants. We investigated their microbiomes in different compartments, plant immune responses and interactions with the pathogen (Fp) aiming at advancing our knowledge on microbiome-mediated regulation of plant responses to pathogens. Results: We found that Fp colonised wheat plants significantly in terms of relative abundances, accounting for 11.3% and 60.7% of the fungal communities in the rhizosphere and roots, respectively. However, Fp presented with a small fraction of the leaf microbiome, up to 1.2%. Furthermore, Fp-infection led to significant changes in the composition of microbiomes in the rhizosphere and root while had little impact on leaves. We further found that wheat defence signalling pathways, microbiomes and the pathogen intimately correlated with each other in structural equation modelling. As such, we also identified ecological clusters explained changes in the wheat defence signalling pathways. Lastly, microbial co-occurrence network complexity was higher in Fp-infected plants relative to healthy plants, suggesting that Fp-infection may have led to changes in the wheat microbial community structure. Conclusions: We provide novel evidence that soil-borne diseases disrupt belowground plant microbiomes influencing the responses of plant immunity to pathogens.