Ammopiptanthus mongolicus is a relict species from the ancient Mediterranean of the Tertiary period and the only strong xerophytic evergreen broad-leaved shrub in the central Asian desert. Foliar endophytic and epiphytic bacteria jointly form phyllosphere microorganisms that influence plant health. This study investigated the dynamic changes in foliar endophytic bacterial communities across four leaf growth stages (Young, Mature, Old1, and Old2). Illumina 16S region (V5–V7) amplicon sequencing was used to analyze community composition, function, construction process, and environmental driving factors. The Old1 and Old2 stages were clearly separated from the Young and Mature stages, which demonstrated closer clustering. Community diversity and evenness first increased from the Young to Mature stages, declined at the Old1 stage, and finally reached maximum values at the Old2 stage; richness increased gradually. Total amplicon sequence variant (ASV) numbers, stage-specific ASVs, and their proportion increased with leaf development, whereas the proportion of shared ASVs between adjacent, interval, and all stages decreased. Dominant genera were Rhodococcus (Young), unclassified_f__Comamonadaceae (Mature), Rhodococcus (Old1), and Bacillus (Old2). Co-occurrence networks became progressively simpler, with reduced inter-node and positive connectivity. Functional predictions revealed that chemoheterotrophy and aerobic chemoheterotrophy decreased initially and then increased, with the lowest values at Old1. N, C/P, N/P, and SOD reached maximum at the Old2 stage. P was maximum at the Mature stage. P, C/P, and N/P were significantly positively correlated with the Young stage, N with the Mature stage, and SOD with the Old2 stage (p < 0.05). These findings enhance understanding of the diversity, composition, function, and plant–endophyte relationships in xerophytic relict species, particularly evergreen desert shrubs.

Morel ( Morchella spp.) is one of the most valuable edible and medicinal fungi globally. Red-stipe disease severely impairs morel quality and yield, although its causative pathogens remain unclear. To investigate changes in morel fruiting bodies during red-stipe disease, this study employed absolute quantification full-length sequencing and metabolomics. Red-stipe disease significantly altered bacterial communities. All α-diversity indices increased except the Pielou evenness index. Absolute abundances of Pseudomonas, Carnobacterium, Stenotrophomonas, and Sphingobacterium were elevated, and they were identified as potential pathogenic candidates. Co-occurrence network complexity was higher in diseased samples than in healthy samples. Metabolomics revealed that red-stipe disease affected metabolite accumulation. A total of 868 metabolites were upregulated, including anabasine, dinoprost, 4-nitrophenyl β-D-glucopyranosiduronic acid, glucotropaeolin, and homocamptothecin. By contrast, 928 metabolites were downregulated, including cimifugin, defibrotide, D-sedoheptulose 7-phosphate, 1-O-feruloyl-β-D-glucose, and geniposide. Differential metabolites were primarily classified as amino acids, peptides and analogs, and carbohydrates and carbohydrate conjugates. They were mainly enriched in the biosynthesis of cofactors, tryptophan metabolism, ABC transporters, D-amino acid metabolism, and nucleotide metabolism KEGG pathways. This study revealed distinct bacterial and metabolic alterations associated with red-stipe disease in morel fruiting bodies. The findings provide foundational data for identifying causative agents and elucidating the metabolic mechanisms underlying nutrient composition changes in diseased morels.