Divergent microbial strategies under saline–alkali stress: a comparative study of bacterial and fungal communities in four agro-pastoral habitats

Introduction Microorganisms regulate nutrient cycling and ecosystem stability in saline–alkali ecosystems. However, their adaptation mechanisms and metabolic functions to saline–alkali stress in agro-pastoral ecotones remain unclear. Methods We characterized bacterial and fungal communities in four typical saline–alkali habitats in the agro-pastoral ecotone of the Loess Plateau [saline–alkali flat (SAF), natural grassland, maize cropland, and shrubland] via Illumina MiSeq sequencing. We analyzed community compositions, α-diversity, co-occurrence network characteristics, and functional group differences, using Mantel tests, redundancy analysis (RDA), and partial least squares path to examine environmental drivers of microbial structure and function. Results Saline–alkali stress significantly altered soil physicochemical properties ( P < 0.05), with SAF exhibiting higher pH, EC, Na + , and low available nutrients. Bacteria α-diversity differed significantly among habitats ( P < 0.05), suggestive of sensitivity to saline–alkali stress. Under such stress, bacterial co-occurrence networks simplified with intensified interspecific competition, whereas fungal networks maintained high modularity (0.77–0.81) and were dominated by positive correlations (>93%), reflecting a synergistic coexistence. Functionally, saline–alkali stress inhibited bacterial chemoheterotrophy, aerobic ammonia oxidation, and nitrification. Saline–alkali stress also promoted fermentation, phototrophy, and nitrate reduction and jointly drove microbial functional expression, with pH, available phosphorus, and soil organic carbon (SOC) identified as key drivers ( P < 0.05). Conclusion We identified adaptive strategies and functional differentiation of bacterial and fungal communities under saline–alkali stress. These findings provide important insights for the sustainable management and ecological restoration of saline–alkali lands in agro-pastoral ecotones.