Farming practices affect soil's suppressiveness towards phytopathogens

Abstract

Organic farming enhances soil health by beneficially modulating the structure and function of rhizospheric microbiome. While organic farms are known to exhibit suppression against specific plant diseases, the phenomenon of “general disease suppressiveness” is relatively less studied. The systemic interactions between abiotic and biotic factors in organically managed fields, rendering soils suppressive against various phytopathogens, have been less studied. The present study aimed to characterize soils from three farmers' fields in North-Western Himalayan region of India, for their pathogen suppression potential, and understanding the relationship between edaphic factors and biological control against a range of phytopathogens. Culture-dependent assays revealed that organically managed fields exhibited better suppressiveness compared to conventional fields, against the tested phytopathogens. The fungal fraction of the soil microbiome showed significant suppression of Ralstonia solanacearum in apple (p = 0.02) and chili (p = 0.003) fields. Similarly, the fungal fraction of soils showed significant suppression (p < 0.05) of Fusarium solani, Sclerotium rolfsii, and Verticillium dahliae in apple and tomato fields. The soil microbiome's bacterial fraction showed significant (p < 0.05) suppression of Fusarium fujikuroi. Activities of enzymes related to biocontrol, viz. lipase, chitinase, protease and cellulase, and siderophore production were higher in soil from the organic fields than in the conventionally managed fields (p < 0.05). Soil cellulase activity was found to be the lowest among all biocontrol activities in organic apple field soil (0.22 IU/mL) compared to the control soil (0.04 IU/mL). Significantly high siderophore production was detected in the organic soils (93.13 ± 0.32 % siderophore units), and the adjacent soils under natural vegetation (control) (92.81 ± 0.45 % siderophore units), versus conventional soils (89.90 ± 0.79 % siderophore units) from the apple, chili, and tomato fields. Available micronutrients Cu, Fe, and Mn were negatively associated with pathogen suppression. Available Cu was negatively associated with Rhizoctonia solani suppression in apple fields (r = −0.99, p = 0.02) and Fusarium udum in tomato/chili fields (r = −0.91, p = 0.02). From PCA analysis, it was observed that the soil micronutrient availability was a dominant attribute affected by conventional farming practices. The role of mineral nutrients and other biocontrol parameters, such as enzymes and molecular markers, was demonstrated in pathogen suppression in the rhizosphere under different farming practices, emphasizing on the significance of biotic and abiotic factors for the sustainable management of soil-borne pathogens. Adopting sustainable practices and nutrient management will improve the control of soil-borne pathogens in arable land.