Microbially mediated ecological resilience in the root-soil continuum underlies Achyranthes bidentata adaptation to continuous cropping

Under long-term continuous cropping, Achyranthes bidentata sustained higher yield and quality by maintaining a stable microbial community that fosters positive plant–soil feedback and demonstrates ecological resilience. Our study elucidates how long-term monoculture alters microbial communities across the soil–root continuum. Bacterial diversity increased in both the rhizosphere and endosphere, while fungal diversity decreased in the rhizoplane and endosphere, illustrating a pronounced ecological divergence between bacterial and fungal communities. Bacteria exhibited niche expansion, shifting from K-strategists to r-strategists, adopting more competitive resource-acquisition strategies. In contrast, fungi became increasingly resource-specialized: symbiotic taxa dominated root compartments, while pathogenic taxa accumulated in the rhizoplane and endosphere. Community assembly shifted from stochastic processes to environmental filtering, particularly in the endosphere, reflecting intensified selection pressures over time. Network analysis pinpointed keystone taxa, most notably Pseudomonas spp., that may stabilize microbial networks and sustain ecosystem functions under monoculture stress. Soil sterilization decreased A. bidentata biomass accumulation by 43 % and reduced bioactive compounds by 25.71 % (β-ecdysterone), 28.57 % (25R-inokosterone), and 25 % (25S-inokosterone) (P < 0.05). Exogenous inoculation with the plant growth-promoting rhizobacteria strain Pseudomonas aeruginosa enhanced root fresh weight by 33.88 % compared to the non-inoculated control without significantly altering ecdysteroid profiles. These findings provide valuable insights into microbial adaptations to monoculture, offering strategies for managing soil microbiomes to improve crop resilience and sustainable agroecosystem management.