Visualizing the Effect of Cultivation Regimes on Carotenoid Metabolism and Its Interplay with Endophytic Bacterial Communities in <i>Crocus sativus</i> L

As the demand for saffron expands, it is urgent to find suitable local cultivation regimes to improve saffron quality. Two-segment cultivation was proposed in the Yangtze River Delta of China. However, the soil- and water-free cultivation method may alter the grown microenvironment, thereby affecting the endophytic bacterial communities and its interactions with bioactive compounds. Herein, a comprehensive strategy based on nontargeted spatial metabolomics and high-throughput sequencing was established. Mass spectrometry imaging results showed that the crocins accumulated in the stigma part of saffron with the two-segment cultivation method. Flavor components like safranal and picrocrocin accumulated in the stigma and style part of saffron with a traditional outdoor cultivation method. Additionally, <i>Citrobacter</i> showed a positive correlation with the contents of crocin, which might be attributed to the elevated gene expression of <i>ALDH</i>, <i>UGT74AD1</i>, and <i>UGT91P3</i>. The strategy established might provide a valuable foundation for understanding cultivation regimes in nontraditional saffron-growing regions.