Management and environmental drivers of soilborne pathogens in smallholder systems of western Kenya

Soilborne pathogens limit productivity, exert chronic stress and may cause severe diseases in many crops, especially in smallholder systems. Despite the damage they cause, there is limited knowledge of the agroecological drivers that determine their abundance in sub-Saharan Africa. In this study, we assessed how farming practices (e.g. cropping systems, and organic input strategies) along with soil and environmental properties, influence the presence and relative abundance of Fusarium and lesion nematodes (Pratylenchus spp.) across multiple locations in western Kenya. Common farming practices in the region include maize monocultures, maize-legume intercrops, maize in rotation with legumes and vegetables, and perennial-based horticultural systems. Fertilization strategies typically involve organic, inorganic or combined nutrient inputs. 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 soilborne 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 soilborne pathogens to improve smallholder productivity.