Management and environmental drivers of soil-borne pathogens in smallholder systems of western Kenya

This study aimed to assess the role of agroecological practices, including diversified cropping systems and organic nutrient inputs, in influencing the abundance of lesion nematodes (LN) and Fusarium pathogens within smallholder systems in western Kenya (Fig. 1). We collected soils from smallholder farms utilizing different cropping systems and nutrient management strategies across five sites in western Kenya. For each soil sample we evaluated a suite of physical and chemical properties and assessed these against the results of simple visual assays that allowed us to measure potential infestation by Fusarium pathogens and LN. We hypothesized that: 1) farms relying on agroecological practices such as organic nutrient inputs (e.g., manure, compost) exhibit reduced Fusarium and LN pressure and improved soil health compared to farms relying on conventional inorganic fertilizers; 2), diversified cropping systems experience lower pest pressure than simpler cropping systems, based on just one or two crops; and 3), site-specific environmental variables, such as soil properties and elevation further explain the variability in Fusarium and LN pressure. We used baiting protocols to assess the abundance of Fusarium and LN in soils collected from 35 smallholder farms. Our findings indicate that agroecological practices such as diversified cropping systems and organic amendments influence soil-borne pathogens and important soil health parameters. For example, organic inputs reduced lesion nematode pressure by 56% compared to inorganic systems, while diversified systems supported higher soil carbon and available phosphorus. These results highlight the importance of agroecological management in maintaining soil health and regulating soil-borne pathogens to improve smallholder productivity.