Which soil health indicators best track diversification benefits in tropical agroecosystems?

Soil degradation, biodiversity loss, and declining yields threaten smallholder farming in tropical regions under increasing climate pressures. Soil degradation in Mesoamerican maize-based systems is accelerated under continuous monocropping and residue burning. Crop diversification via legume integration and intercropping can regenerate soil functions, but impacts vary across contexts and sensitive indicators for monitoring of soil health effects are lacking. This study evaluated how diversified maize systems influence soil health and productivity and identified the most responsive and accessible soil health indicators. An on-farm trial in Chiapas, Mexico, compared three diversified cropping systems: (1) maize-pigeon pea single-row intercrop, (2) maize-pigeon pea double-row intercrop, and (3) maize-bean rotation, with a (4) conventional maize monoculture with residue burning (control). Four years post-implementation, we measured soil macrofauna, microbial communities (16S and ITS metabarcoding), enzyme activity, substrate-induced respiration rates (SIR), particulate organic matter (POM), permanganate oxidizable carbon (POXC), potentially mineralizable nitrogen (PMN), aggregate stability, and bulk density. Compared to the control, diversified systems significantly improved maize yield (271%), residue cover (210%), macrofauna abundance (253%), and fungal richness (52%), while enhancing aggregate stability (18%) and microbial activity (SIR rates 34% higher). POM, POXC, and PMN were the most sensitive physicochemical indicators, where sensitivity is expressed as responsiveness relative to variability. Macrofauna metrics and enzyme activity showed high responsiveness but greater variability. For smallholder contexts, we recommend a practical, low-cost core set of indicators: soil cover, POM, POXC, PMN, and macrofauna; SIR provides additional sensitivity when resources permit.