A comparison of soil health indicators for tracking the benefits of diversification in maize-based smallholder farming systems of Chiapas
Soil degradation, soil biodiversity loss, and declining yields threaten smallholder farming systems around the globe, particularly in tropical regions where farmers face increasing climate pressures. In maize systems of Mesoamerica, continuous monocropping and residue burning accelerate soil degradation. Crop system diversification, via legume integration and intercropping, is often promoted to restore soil function, but impacts on soil health can vary considerably across contexts, and empirical evidence on indicator responsiveness remains limited. This study focused on how diversified maize systems influence soil health and crop yield, and identified which soil health indicators are most responsive to management changes, have the highest precision, and are accessible to farmers. An on-farm trial was conducted in Chiapas, Mexico, comparing three diversified cropping systems: (1) maize–pigeon pea single-row intercrop, (2) maize–pigeon pea double-row intercrop, and (3) maize–bean rotation, with (4) a conventional maize monoculture with annual residue burning. All diversified treatments included a single line of fruit trees established as living barriers for erosion control. Soil and yield data were collected in August 2023, four years (2019-2023) after treatment implementation. Measurements included soil macrofauna abundance and diversity, bacterial and fungal communities (assessed by 16S and ITS metabarcoding), enzymatic activity, substrate-induced respiration rates (SIR), particulate organic matter (POM), permanganate oxidizable carbon (POXC), potentially mineralizable nitrogen (PMN), aggregate stability, and bulk density. Diversified systems without residue burning significantly improved maize yield, residue cover, macrofauna abundance, and fungal richness. The diversified systems enhanced aggregate stability and microbial activity, particularly for soil under double-row intercropping. Among the measured variables, POM, POXC, and PMN were the most sensitive physicochemical indicators. Macrofauna metrics (particularly abundance and taxonomic richness) and enzyme activity showed high sensitivity relative to other biological metrics, but with greater variability. Substrate-induced respiration rates showed high sensitivity and reproducibility in detecting management-induced changes in microbial functional potential. This study demonstrates that cropping system diversification with residue retention substantially improves soil organic matter dynamics, nutrient cycling, soil structure and water regulation, and biological community diversity, leading to enhanced productivity in tropical hillside systems. Our findings suggest that a combination of indicators, including POM, POXC, PMN, macrofauna communities, and SIR, can be used to effectively monitor soil health changes and support regenerative farming strategies that make smallholder farming more productive and sustainable under resource constraints.