Bacterial endophytes in Arctium lappa seeds were found to play an important role in the metabolism of Arctium lappa lignans

Objective Bacterial endophytes in plant seeds provide multifaceted benefits, such as nutrient acquisition, growth promotion, and pathogen suppression. This study aimed to explore the diversity, functional roles, and metabolic impacts of bacterial endophytes in Arctium lappa L. Methods The diversity of bacterial endophytes in different tissues of A. lappa was analyzed using 16S rRNA sequencing, followed by an isolation and functional characterization of key endophytic strains from A. lappa seeds. Genomic analysis of these key strains was performed to identify β-glucosidase genes involved in arctiin metabolism. Gene expression was validated by quantitative reverse transcription polymerase chain reaction (qRT-PCR), and the metabolic effects of endophytes on A. lappa at different developmental stages were assessed by liquid chromatography–mass spectrometry (LC–MS). Results The analysis of bacterial endophyte diversity revealed the highest richness in root tissues, followed by stem and fruit tissues. Two key endophytic strains, DI4 and ISX2, were successfully isolated from A. lappa seeds. Functional characterization demonstrated their capabilities in nitrogen fixation, phosphate solubilization, siderophore production, and IAA biosynthesis. Genomic analysis indicated a high level of conservation between these two strains and identified β-glucosidase genes (BglX1 and BglX3) involved in the biosynthesis and metabolic pathways of the lignan compound arctiin. qRT-PCR analysis showed significant stage-specific expression differences of BglX1 and BglX3 during A. lappa development. Subsequent ultra-performance liquid chromatography –mass spectrometry (UPLC–MS) analysis further confirmed the different effects of DI4 and ISX2 strains on lignan metabolism during seed germination. Conclusion This study underscores the significant role of endophytes in the growth and development of A. lappa , elucidating the collaborative and adaptive relationship between endophytes and A. lappa in response to environmental conditions. It also suggests potential applications for enhancing the bioactive compounds in medicinal plants.