Divergent responses of host-specific and generalist soil-borne pathogens to long-term cropping systems under mild saline-alkaline conditions

Soil-borne fungal pathogens pose serious threats to agricultural productivity, with their community structure influenced by cropping systems. Mild salinity-alkalinity stress, increasingly prevalent in the agricultural regions in northern China, can exacerbate the impact of pathogens on crops. However, the host specificity of soil-borne fungal pathogens in various cropping systems, particularly in mildly saline-alkaline soils, remains largely unknown, which impedes the design for sustainable agricultural practices. Here, we hypothesized that reducing host density in crop rotation systems could mitigate the abundance of host-specific pathogens under mild salinity-alkalinity conditions. In a thirteen-year field experiment conducted in a mildly saline-alkaline environment, we examined soil-borne fungal pathogen communities and their host specificity in three different cropping systems: maize monoculture (M), maize-wheat rotation (MW), and maize-wheat-soybean rotation (MWS) systems. Using amplicon sequencing and literature review, we determined the effects of host density and soil nutrient availability on pathogen abundance. We found that soil-borne fungal communities were significantly affected by cropping systems under mild salinity-alkalinity stress. Host-specific pathogens were diluted by 68.9%–90.0% upon the reduction in host density. Specifically, the relative abundance of maize pathogens such as Ustilago maydis was lower in soils from MWS and MW than in M, mainly related to the reduced availability of soil nutrients. The relative abundance of wheat pathogens such as Bipolaris sp. in the soil from MWS was lower than that from MW but higher than that from M, correlating with the reduced host density. The relative abundance of generalist pathogens in the soil from MW was higher than M, associated with soil nutrient availability. Our work suggests the differential responses of host-specific and generalist soil-borne fungal pathogens to different long-term cropping systems. Host-specific pathogens could be reduced by reducing host density in our study. Furthermore, we highlight the potential effects of host density and soil nutrient availability in mitigating pathogen abundance. This study highlights distinct responses of host-specific and generalist soil-borne pathogens to cropping systems under mild salinity-alkalinity stress. Regulating host planting density and managing soil nutrient availability could support the development of more sustainable disease management strategies in saline-alkaline farmland.