Rhizospheric and endophytic bacterial community response to continuous Atractylodes macrocephala cultivation

Rhizospheric and endophytic bacteria play key roles in plant health and soil fertility. Atractylodes macrocephala, a traditional East Asia medicinal herb used to treat gastrointestinal disorders, cancer, and other ailments, experiences reduced growth and increased susceptibility to pathogen under continuous cultivation. We investigated the temporal dynamics of bacterial communities associated with A. macrocephala under continuous cultivation at a grassland site in Lin’an, Zhejiang Province, southeast China (119°25’E, 30°14’N). Using Illumina MiSeq sequencing, we analyzed temporal dynamics of bacterial communities associated with A. macrocephala under continuous cultivation. Continuous cultivation led to a significant shift in the structural and diversity patterns of both rhizospheric and endophytic bacterial communities, particularly in diseased roots. Beneficial genera such as Bacillus and Novosphingobium declined, while pathogenic taxa including Ralstonia and Pseudomonas increased, contributing to disease incidence. However, a two-year fallow period after cultivation helped restore microbial balance, suggesting that fallowing can mitigate continuous cultivation effects. Canonical correspondence analysis revealed that soil pH, hydrolyzable nitrogen, and mercury levels were key factors shaping bacterial community composition. Continuous A. macrocephala cultivation caused root-rot, disrupted endophytic and rhizospheric bacterial communities, and degraded soil fertility. A two-year fallow largely restored microbial communities and soil conditions to near-unplanted levels. Beneficial genera (Bacillus, Novosphingobium) declined under continuous cropping, while disease-associated taxa (Ralstonia, Pseudomonas, mainly P. aeruginosa) increased and may serve as indicators of soil health decline. These results clarify microbes’ roles in plant health and suggest mitigation strategies for continuous A. macrocephala cultivation.