“Omics” Approaches for Understanding Soil Suppressiveness in Agriculture

Abstract

Disease suppressive soils are instrumental in combating phytopathogens, which cause severe diseases in plants. They provide an eco-friendly way to mitigate biotic stresses in agricultural systems worldwide. Efforts have been made to understand the mechanisms of disease suppressiveness in soil using culture-dependent and culture-independent methods. Omics approaches have provided useful insights into the key markers responsible for imparting antagonism against soil-borne plant pathogens. Specific genera such as Pseudomonas, Bacillus, Streptomyces, Lysobacter, and Trichoderma, along with antibiotics and siderophores, are the key constituents in disease suppressive soils. Disease suppressive potential of a soil is dependent on several factors such as soil pH and soil type, with one of the critical factors being the type of nutrient amendment applied to the soil. While the underlying mechanisms of growth inhibition of specific fungal pathogens such as Fusarium and Rhizoctonia solani in soil ecosystem have been well elucidated, there is restricted knowledge regarding “general-disease suppression”. The mechanisms responsible for imparting broad range suppressiveness can help us develop economically favourable agricultural management practices. In this chapter, we have critically reviewed significant investigations related to specific- and general-disease suppression where omics-based approaches have been adopted to study the microbial community dynamics of disease suppressive soils. Based on the reported studies, we have identified the potential role of diverse markers, compost amendments, and different microbial strains (producing key metabolites) in disease suppressiveness of soil. Thus, we propose that using different molecular and microbial markers, mapping of disease suppressive soils can efficiently be done across the globe. In addition, the effectiveness of synthetic microbial communities, and possibilities of transforming conducive soil by microbiome transfer from suppressive soil may be explored in the context of disease suppressiveness in the future.