Temporal dynamics of the microbial community in goji fruits over the main picking periods in Qaidam basin and its correlation with host metabolic profiles

Endophytes play an important role in regulating plant metabolites and enhancing resistance. However, their temporal dynamics in goji fruits across the main picking periods and the correlation with host metabolites remain largely unexplored. In this study, high-throughput sequencing and widely targeted metabolomics was used to analyze endophyte community and metabolic changes across picking periods of goji fruits. We found that α-diversity of endophytic fungi in goji fruits from the first picking period was higher than in those from the later picking periods, and also higher in fruits from younger trees than in those from older trees. A notable enrichment in the relative abundance of dominant endophytic fungal taxa was observed in goji fruits from the later picking periods, in contrast to the depletion of most non-dominant taxa. According to β‑diversity analysis, the fungal communities in goji fruits from the first picking period were clearly separated from those from later periods. Screened key biomarkers including Chaetomiaceae, Cladosporium , Saccharomycetales, and Pichia , along with dominant classes of endophytic bacteria, were significantly correlated with certain phenolic acids, flavonoids, alkaloids, and coumarins in goji fruits across picking periods. This study reveals distinct temporal dynamics of endophytic fungal communities in goji fruits across picking periods and provides valuable insights into their potential association with host metabolite accumulation.