Community Succession and Diversity Variation of Endophytic and Rhizosphere Soil Bacteria Across Gastrodia elata Seed Formation Stages

The Gastrodia elata Blume (GE) life cycle is unique, since its successful germination and growth rely on symbiosis with specific fungi (e.g., Armillaria mellea). However, the community succession, tissue specificity and functional potential of endophytic and rhizosphere bacterial communities during the seed formation stage of GE remain unclear. Here, we used high-throughput 16S rRNA gene sequencing to systematically explore the composition, diversity, and dynamic succession of bacterial communities across different stages of seed formation and among various tissues. Our results revealed that the endophytic community remained relatively stable across most developmental stages and tissue types (ANOSIM R = 0.4568, p = 0.001), with significant compositional shifts only occurring at the fruiting stage in specific tissues (stems and seeds). In contrast, the rhizosphere soil bacterial community showed stronger developmental succession (ANOSIM R = 0.7037, p = 0.001), with progressive divergence and the strongest segregation observed between the initial planting and fruiting stages. Alpha diversity peaked at the flowering stage for endophytic bacteria (Shannon index) and at the bud formation stage for rhizosphere soil bacteria, with persistent core taxa (Bacteroides in endophytic bacteria, Pseudarthrobacter in rhizosphere soil bacteria) dominating across stages. Functional predictions revealed stable core metabolic pathways, with stage-specific enrichments of glycolysis or gluconeogenesis at late developmental stages. These results provide novel ecological insights into the spatiotemporal dynamics of bacterial communities across different stages of GE seed formation, highlighting the distinct ecological strategies of endophytic and rhizosphere soil bacteria during the reproductive development of the plant.