A Review on Soil and Phytomicrobiome for Plant Disease Management

Pests and pathogens significantly reduce crop yields and cost the global economy USD 540 billion annually. The phytomicrobiome is becoming a cornerstone of a comprehensive rethink of agricultural management practices, with microbiome-assisted plant breeding focusing on three principles: minimal soil disturbance, continuous soil cover with crops, cover crops, or a mulch of crop residues, and crop rotation. Plant diseases, phytomicrobiomes, and agricultural practices can all affect plant health. Conservational agricultural practices like minimum tillage and no-tillage have been implemented to reduce anthropogenic activity and preserve microbial diversity. Mulching is a common practice in agriculture to stop moisture loss, maintain soil temperature, control weed growth, and stop soil erosion. Monoculture farming is the practice of cultivating a single crop continuously over several growing seasons on the same field. Intercropping systems encourage the growth of beneficial fungi, such as mycorrhiza, endophytes, saprophytes, decomposers, and bioprotective fungi, and can benefit forest ecosystems by creating disease-suppressive soils. By combining conservation tillage and crop rotation, farmers can reduce disease pressure by disrupting the life cycles of soil-borne pathogens linked to particular crops or genotypes. Composed manure and plant residues can control plant pathogens like Pythium, but the effect is thought to be due to microbial competition or plant host resistance. Green manure can control plant diseases brought on by pathogens in Rhizoctonia, Verticillium, Sclerotinia, Phythophthora, Pythium, Aphanomyces, and Macrophomina, but manure-derived fertilizers may contain antibiotic resistance genes and mobilomes, which could pose risks to both human and animal health. Climate change impacts crop yields by reducing crop physiology and productivity, increasing pathogen diversity, and affecting pathogen genetic traits and speciation. The state of the environment and the availability of suitable hosts significantly impact the ability of these pathogens to survive and spread. However, PGPRs are unpredictable and soil warming can interfere with their effectiveness. Interdisciplinary collaborations between plant biologists, microbiologists, climatologists, and agronomists are required to create effective strategies to reduce the effects of climate change on plant health, crop production, and ecosystem stability.