Long-term organic matter inputs enhance soil health and reduce soil-borne pathogen pressure in maize-bean rotations in Kenya

In smallholder farming systems across East Africa, soil-borne pathogens lead to significant crop losses, with their impact shaped by various factors such as management practices and soil properties. We conducted our research within an existing long-term (45-year) trial that manipulated synthetic fertilizers (N and P applied vs. no application), manure application (10 Mg ha-1 yr-1 farmyard manure vs. no application), and maize stover management (retained vs. removed) in a full-factorial design within a maize-bean rotation. This study aimed to assess the impact of continuous organic nutrient inputs (farmyard manure and maize stover) and synthetic fertilizers on soil-borne pathogens (Fusarium, Pythium, root knot and lesion nematodes) and their relationships with key soil health parameters (organic matter fractions, aggregate stability, available P, soil pH, bulk density). Our results indicated that the addition of manure led to increases of 37 % in particulate organic matter, 114 % in permanganate oxidizable C, 74 % in aggregate stability, and 24 % in pH, compared to plots that did not receive manure. Similarly, maize residue retention enhanced particulate organic matter by 47 %, permanganate oxidizable C by 11 %, mean weight diameter by 28 %, and pH by 5 %. Manure significantly reduced root knot nematodes by 68 %, Pythium colonies by 39 %, and lesion nematodes by 28 %, but increased Fusarium by 205 %. In contrast, the impacts of synthetic fertilizers on soil health were less pronounced, with significant effects observed only for permanganate oxidizable C (5 % increase), available P (67 % increase), and Pythium (41 % reduction). Additionally, relationships between soil-borne pathogens and soil health variables indicated significant negative associations between particulate organic matter, permanganate oxidizable C, and pH with the abundance of plant parasitic nematodes and Pythium, but a positive association with Fusarium. Pythium and lesion nematodes were positively associated with bulk density. Our findings suggest that both manure and plant residue retention hold great promise for supporting long-term soil health and fertility, which can, in turn, reduce the impact of soil-borne pathogens on crop yields. This is a major challenge for low-income farmers in Kenya who practice continuous cultivation.