Background and aimsIn recent years, soil microbes have been recognized as essential partners of Biological Soil Crust (BSC) organisms, such as mosses and lichens. Together, these organisms contribute significantly to ecosystem functions and services. However, the influence of different BSC types on microbial habitats and the subsequent impact on microbial regulation of soil functions, particularly in degraded mining ecosystems, remains largely unexplored.MethodsThis study investigated soil microbial diversity and community composition using high-throughput sequencing. To assess soil multifunctionality, five soil variables related to nutrient pools-soil organic matter, total nitrogen, total phosphorus, ammonium nitrogen, and nitrate nitrogen-were measured and calculated.ResultsOur results indicated that as BSC succession progressed, both individual soil functions and overall multifunctionality increased concurrently with an expansion of bacterial niche breadth. Compared to earlier successional stages, bacterial generalists in later stages exhibited significantly greater abundance, diversity, and metabolic functions. These generalists were positively correlated with both individual soil functions and multifunctionality. The complexity of interactions between bacterial generalists and soil functionality increased in later successional stages, characterized by predominantly positive relationships, in contrast to the earlier stages with numerous negative interactions. Moreover, the overlap in species between bacterial generalists and neutral microbes exceeded 80%. Structural equation modeling revealed that in later successional stages, factors such as BSC coverage, thickness, micro-topographic slope and height, soil moisture, and soil bulk density positively influenced the role of bacterial generalists in regulating both individual soil functions and multifunctionality.ConclusionThese findings collectively suggest that as succession advances, BSCs enhance nutrient and moisture input by increasing microtopographic roughness, thereby shifting bacterial niche expansion from a survival-oriented strategy to an active role in promoting soil nutrient accumulation. Our results underscore the critical role of well-developed BSCs in the ecological restoration of rare earth tailings soils and provide novel insights into BSC ecology in similarly degraded mining environments.