Early soil health responses to crop diversification and manure application vary across tropical agroecological zones

Soil degradation severely limits agricultural productivity and food security across sub-Saharan Africa, particularly due to declining soil functions related to nutrient cycling, organic matter turnover, and water retention. Addressing this challenge requires management practices that can regenerate and sustain these functions, as well as sensitive indicators to track progress. In this study, we evaluated the effects of crop diversification, legume integration, manure application, and their impacts on soil health across four sites representing contrasting agroecological settings in Kenya. All sites contained long-term experiments that were recently redesigned from maize monoculture to include more diversified systems, such as maize-legume rotations, maize-fodder relay, and improved
intercropping. We assessed soil health indicators linked to carbon (C) cycling (permanganate oxidizable C, POXC; particulate organic matter, POM), nutrient availability (potentially mineralizable nitrogen, PMN, available N and P, pH), and substrate-induced respiration rates (SIR). Within one year of implementation, crop diversification had improved soil health indicators relative to a degraded control soil, although the magnitude of improvement
varied by site. Sandy soils exhibited stronger increases in soil health indicators compared to clay soils.
Legume integration had a stronger influence on substrate-induced respiration than manure inputs (evenness decreased from ∼ 2.0 to ∼ 1.3 in legume systems), contributing to more specialized respiration patterns linked to labile C, likely root derived substrates. Manure application generally improved available P and PMN, though effects
varied by site and cropping system. Mineral N fertilizer application contributed to soil acidification (pH decreased by 0.3–0.6 units) despite recent liming but had limited effects on other soil health indicators. Microbial activity was driven primarily by cropping treatments rather than site, whereas other soil health parameters were sensitive to both treatment and site differences. Our findings highlight that integrating legumes and applying organic amendments can initiate rapid improvements in key soil properties and functions, but agroecological context and crop type strongly modulate these outcomes.