Micro-Environmental Variation in Soil Microbial Biodiversity in Forest Frontier Ecosystems—Implications for Sustainability Assessments

Soil health indicators based on microbial biodiversity are increasingly used in agricultural sustainability assessments. However, little is known about how microbial communities vary within micro-environmental gradients across different land uses, which is crucial for designing field sampling and monitoring protocols. Our objective was to assess how soil microbial communities changed with soil depth and spatial distance across land-use types. We sampled soils in four spatial distances (within 0.1–70 m) and four depths (within 0–40 cm) in forests, grasslands, and horticultural lands, and combined 16S rRNA gene sequencing, DNA quantification and soil chemical characterization to explore micro-environmental variation in microbial biomass, α-β-diversity, and communities’ assembly processes. Depth and spatial distance had differential effects on microbial biodiversity within different land uses. Microbial biomass was most sensitive to depth, α-diversity to spatial distance, and β-diversity to both depth and spatial distance. Deterministic processes dominate microbial communities’ assembly along depth in all land uses, which is a promising result for developing soil quality indicators based on microbial biodiversity. Overall, our results suggest that collecting soil samples separated by at least 12 m is adequate to capture biodiversity changes across land uses. However, collecting randomly within the first 10 cm is recommended for native forests, while systematic sampling within the first 20 cm is advised for grasslands and horticultural lands. Our findings underscore the need for land use-specific sampling frameworks in soil life-based sustainability assessments for meaningful regional comparisons.