Applicability of soil health assessment dominated by biological indicators in facility agriculture

The minimum data set (MDS) is widely used for soil health index (SHI) assessment, with the selection of indicators being crucial. However, biological indicators are less frequently used compared to physical and chemical indicators. This study aimed to establish a biologically-centered MDS for assessing soil health in tomato facility agriculture in Ningbo. Using biochemical, microbiological, and nematode data from 60 continuous cropping soils, we identified key indicators for the MDS. Principal component analysis revealed a strong correlation between the MDS and the total data set (TDS), with the final MDS including available phosphorus, electrical conductivity, β-glucosidase, urease, bacterial Chao1 index, bacterial Shannon index, Ralstonia solanacearum, nematode Shannon index, structure index, and channel index. Random forest modeling showed that the predicted SHI had a high fit with the MDS-SHI, with bacterial and nematode Shannon indices being the most influential predictors, emphasizing the critical role of biological communities in maintaining soil health. Furthermore, the study identified three distinct phases in soil health during long-term continuous cropping: healthy (0–10 years), sub-healthy (11–15 years), and recovery (16–20 years), demonstrating the soil's potential for self-recovery. By incorporating biodiversity as a core component, this biologically-focused MDS provides a more comprehensive and precise method for evaluating soil health in facility agriculture. The findings suggest that this MDS could inform future research and applications in similar agricultural systems. Moreover, the results highlight the vital role of biodiversity in agroecosystem stability, suggesting that future soil health assessments should place greater emphasis on biological indicators to better capture the complexity of soil functions. [Display omitted] •Biological indicators are more responsive to the current state of facility soil health than physical and chemical indicators.•Microbial and nematode community diversity are important predictors in facility soil health assessment.•Facility soils have the capacity for self-recovery following long-term continuous cropping, which can enhance soil health.•Biodiversity plays a key role in predicting soil health and maintaining agroecosystem stability.