Soil-borne diseases pose a significant threat to global agriculture, impacting crop yields and soil health. Microbiomes in the vicinity of plant roots (rhizosphere) are critical in maintaining plant health, supplying nutrients, and tolerance against abiotic stress. In some soils, in situ microbiomes can suppress the impact of soil-borne pathogens. The understanding of the mechanistic effects of soil disease suppression will help in developing cropping systems with disease-suppressive capacities through the (i) development of suppressive communities, (ii) modification of host genetics/immunity to support disease suppression and/or (iii) development of synthetic communities conferring stable disease suppression. The use of omics technologies, including genomics, transcriptomics, proteomics, and metabolomics, has shown a greater promise to disentangle microbiome-mediated functions related to plant health.
As a part of the CSIRO Microbiome for One System Health (MOSH) rhizosphere project, we developed multi-omics datasets, including rhizosphere metagenomics, metabolomics, and host transcriptomics, from disease-suppressive and non-disease-suppressive soils for Rhizoctonia solani AG8 in wheat from South Australian cropping soils. For the first time, we profiled small RNAs from rhizosphere soils and presented preliminary evidence on how these molecules may communicate with plants. We also used a cross-cutting tool such as Hi-C genomics to improve our understanding of metagenomics binning in soil samples. Briefly, we generated more than 2.5 TB of omics dataset and analysed it to advance our knowledge on mechanisms of soil disease suppression by elucidating microbial communities, plant responses, and biochemical pathways involved in disease suppression. This presentation will provide an overview of key findings and discuss how integrating these approaches can enhance our understanding of soil disease suppression.
Keywords: MOSH, Omics, Rhizosphere, Small RNAs, Soil disease suppression