Arbuscular mycorrhizal fungi mediate rare taxa and network complexity in rhizospheric and endophytic bacterial communities of Allium schoenoprasum L

Arbuscular mycorrhizal fungi (AMF) play a crucial role in enhancing plant growth and regulating rhizospheric microbial composition. However, their influence on rare bacterial taxa in both the rhizospheric and endophytic environments of Allium schoenoprasum L. remains largely unknown. To address this gap, we conducted a randomized experiment with four treatment groups: three inoculated with 30 g of Rhizophagus irregularis, Diversispora epigaea, or Funneliformis mosseae, and one uninoculated control group with sterilized inoculum (20 replicates each), using real-time quantitative PCR and Illumina MiSeq sequencing to analyze microbial communities. Results showed that AMF-inoculated plants exhibited significantly superior phenotypic traits compared to the control, with plant heights of 26.05 ± 2.88 cm (R. irregularis), 28.63 ± 2.09 cm (D. epigaea), and 24.92 ± 2.86 cm (F. mosseae) versus 8.59 ± 1.60 cm in the control, alongside significant differences in other traits. Among AMF treatments, R. irregularis strain notably promoted growth effectively with a high infection rate but lower infection intensity than D. epigaea and F. mosseae strains. Rhizospheric communities had more unique amplified sequence variants among rare bacterial taxa, while endophytic communities showed increased abundances of key taxa. Furthermore, inoculation with AMF leads to alterations in the expression of functional genes associated with the carbon, nitrogen, and phosphorus cycles. Specifically, the expression of the cbbLR and phoD genes was significantly elevated, while the expression of the amoA gene remained stable. Additionally, the complexity of the rhizospheric bacterial network was notably greater compared to the endophytic environment. These findings highlight the different roles of AMF in shaping microbial communities and promoting plant health.