Stolons transmit specific bacterial strains across generations in a clonal plant

ABSTRACT The patterns and processes of endophytic microbiota transmission across generations in clonal plants remain poorly understood. While stolons have been hypothesized to act as a transmission pathway, direct evidence, particularly at the strain level, is scarce, and the dynamics of microbial assembly during transmission are uncharacterized. Here, we conducted a multi-level investigation in the clonal plant ground ivy ( Glechoma longituba ), integrating amplicon sequencing of bacterial and fungal communities, and genomic analysis of culturable bacterial isolates. Our results reveal that the stolon network serves as a conduit for vertical transmission. We demonstrate the hereditary succession of specific bacterial strains, providing direct evidence at the genotype level. Furthermore, we identify a spatiotemporal dynamics pattern: endophytic diversity declines systematically along stolon internodes, and the final community structure is affected by host generation and compartment. These findings provide a new framework for understanding the maintenance and transmission of the plant microbiome in clonal systems.