Conversion of maize cropping to alfalfa alters spatial stratification of aggregate microbiomes and enhances carbon sequestration in Mollisols

Abstract The conversion of crops to pastures has the potential to mitigate soil organic carbon (SOC) losses associated with long-term intensive cropping. Despite increasing evidence of pasture-induced SOC accumulation, microbial mechanisms governing the spatial sequestration of SOC within aggregate fractions throughout the soil profile of Mollisols under long-term monoculture remain largely unknown. Given the vigorous and deep rooting system of alfalfa, we investigated how the initial conversion of a > 50-year maize monoculture to alfalfa pasture influences SOC sequestration within aggregate fractions across the soil profile and associated microbial communities over the growing season. Alfalfa establishment significantly increased SOC in the mineral-associated aggregate fraction ( P < 0.05), with the most pronounced accumulation at 40–50 cm depth ( P < 0.01). Correspondingly, alfalfa cultivation markedly shifted microbial community composition. At the flowering stage, copiotrophic taxa such as Subgroup 10 and nitrogen-cycling groups including Nitrospira were enriched across aggregate fractions. At maturity, oligotrophic taxa including Pseudoxanthomonas , Massilia , and Moraxellaceae became more abundant. Notably, alfalfa-driven shifts in microbial community assembly were consistent across aggregate fractions. These findings demonstrate that conversion from maize to alfalfa promotes SOC accumulation in mineral-associated aggregates of deep soil layers. The enrichment of plant species-specific microbial taxa across aggregates suggests enhanced transformation and stabilization of fresh plant-derived carbon inputs.