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.

Wild Polygala crotalarioides is an ethnomedicinal plant traditionally used for neurological health. Endophytic fungi associated with medicinal plants are increasingly recognized as sources of bioactive natural products; however, their diversity and biological activities in wild P. crotalarioides remain poorly understood. We used high-throughput sequencing and culture-dependent methods to explored the diversity, community composition, and bioactivities of endophytic fungi associated with wild P. crotalarioides. Culturable isolates were identified via ITS sequencing and further screened for AChE-inhibitory and antioxidant activities. Our results revealed that a total of 818 fungal OTUs were detected, revealing pronounced tissue-specific community differentiation. Stem tissues harbored the highest fungal diversity, richness, and number of unique OTUs. Ascomycota and Basidiomycota dominated fungal communities across all tissues, while distinct biomarker taxa were enriched in different organs. Functional annotation indicated marked tissue-dependent variation in trophic composition. Among 108 culturable isolates, Penicillium sp. PRP024 and Trichoderma sp. PRP008 exhibited the strongest AChE inhibitory activities (>80%), whereas Fusarium sp. PSP053, Diaporthe sp. PSM027 and Exserohilum sp. PSP042 showed notable antioxidant activities. Wild P. crotalarioides hosts highly diverse and tissue-specific endophytic fungal communities. Several isolates exhibited promising acetylcholinesterase inhibitory and antioxidant activities, highlighting medicinal plant-associated endophytic fungi as potential sources of antioxidative natural products.