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.

土壤退化、土壤生物多样性丧失与作物产量下滑，正威胁着全球范围内的小农耕作体系，尤其在农民面临日益加剧气候压力的热带地区。
在中美洲的玉米种植体系中，连作与秸秆焚烧会加剧土壤退化。通过整合豆科作物与间作实现的耕作体系多样化，常被推广以恢复土壤功能，但不同情境下其对土壤健康的影响差异显著，且有关指标响应性的实证证据仍较为匮乏。
本研究聚焦多样化玉米种植体系对土壤健康与作物产量的影响，旨在明确哪些土壤健康指标对管理措施变化响应最为灵敏、精度最高且便于农户获取使用。
研究在墨西哥恰帕斯州开展了田间试验，对比了四种种植体系：(1) 玉米-木豆单行间作、(2) 玉米-木豆双行间作、(3) 玉米-菜豆轮作，以及(4) 采用年度秸秆焚烧的常规玉米单作体系。所有多样化种植处理均设置了一行果树作为侵蚀控制的活体屏障。
试验于2023年8月采集土壤与产量数据，此时距处理措施实施已过去四年（2019-2023年）。测定指标包括土壤大型动物（soil macrofauna）丰度与多样性、细菌与真菌群落（通过16S与ITS元条形码测序评估）、酶活性、底物诱导呼吸速率（substrate-induced respiration rates, SIR）、颗粒态有机质（particulate organic matter, POM）、高锰酸盐可氧化碳（permanganate oxidizable carbon, POXC）、潜在矿化氮（potentially mineralizable nitrogen, PMN）、团聚体稳定性与容重。
未采用秸秆焚烧的多样化种植体系显著提升了玉米产量、秸秆覆盖度、土壤大型动物丰度与真菌丰富度。多样化种植体系可改善团聚体稳定性与微生物活性，其中双行间作模式下的土壤表现尤为突出。
在所测定的变量中，颗粒态有机质（POM）、高锰酸盐可氧化碳（POXC）与潜在矿化氮（PMN）是最为灵敏的理化指标。与其他生物学指标相比，土壤大型动物相关参数（尤其是丰度与分类丰富度）及酶活性灵敏度较高，但变异性也更强。底物诱导呼吸速率（SIR）在检测管理措施引发的微生物功能潜力变化时，展现出较高的灵敏度与可重复性。
本研究表明，保留秸秆的耕作体系多样化可显著改善土壤有机质动态、养分循环、土壤结构与水分调控能力，以及生物群落多样性，进而提升热带坡地种植体系的生产力。
本研究结果显示，结合颗粒态有机质（POM）、高锰酸盐可氧化碳（POXC）、潜在矿化氮（PMN）、土壤大型动物群落与底物诱导呼吸速率（SIR）等指标，可有效监测土壤健康变化，并助力再生耕作策略的落地，使小农耕作在资源受限的条件下更具生产力与可持续性。