Environmental conditions significantly influence the metabolic composition and quality attributes of fruits. This study investigated the impact of altitude-associated environmental variation on flavonoid profiles and fruit quality parameters by comparing the “Red Face” strawberry variety grown in two distinct locations: high-altitude-associated environmental conditions in Zhaotong and low-altitude conditions in Dandong. Using LC-MS/MS analysis, we identified 163 bioactive flavonoids, comprising 85 flavonols, 37 flavanones, 33 flavones, and 8 flavanonols. The high-altitude environment of Zhaotong significantly enhanced specific flavonoid compounds, with notable increases in neohesperidin (20.4-fold), tamarixetin-3-O-glucoside-7-O-rhamnoside (17.7-fold), isovitexin (9.1-fold), and hesperidin (8.5-fold) compared to Dandong-grown fruits. Conversely, Dandong-grown fruits showed higher levels of chrysoeriol-7-O-glucoside (53.9-fold), 6-hydroxykaempferol-6,7-O-diglucoside (36.3-fold), and eucalyptin (9.7-fold). The tricetin 3’-glucuronide (24.49% vs 15.31%) and quercetin-4’-O-glucuronide (24.15% vs 15.59%), are the major flavonoids identified in Zhaotong strawberries than Dandong-grown fruits. Furthermore, strawberries cultivated in Zhaotong demonstrated superior antioxidant activities and capacity, increased quality parameters, including higher sugar content (15.30°Brix vs 10.96°Brix), increased ascorbic acid (15.73 mg/g vs 8.53 mg/g), and optimal firmness (20.51 N vs 23.16 N) than Dandong strawberries. These findings suggest that high-altitude cultivation conditions positively influence strawberry fruit characteristics, enhancing both bioactive compound profiles and overall fruit quality. This research provides valuable insights for optimizing strawberry cultivation conditions to maximize nutritional and commercial value.

The Defective in Induced Resistance 1 (DIR1) gene, a member of the lipid transferase proteins (LTPs), plays a crucial role in plant defense against pathogens. While previous transcriptomic studies have highlighted the significant expression of citrus LTPs during biotic stress, functional annotations of LTPs in the Citrus genera remain limited. In this study, we cloned the Murraya paniculata DIR1 (MpDIR1(t)) gene and overexpressed it in Arabidopsis thaliana to evaluate its stress response mechanisms against biotic stress. The transgenic Arabidopsis lines showed fewer disease symptoms in response to Pseudomonas syringae (Pst DC3000) compared to wild-type Arabidopsis. Defense and pathogenesis-responsive genes such as PR1, PR4, PR5, and WRKY12 were significantly induced, showing a 2- to 12-fold increase in all transgenic lines compared to the wild type. In addition, the Pst DC3000-infected transgenic Arabidopsis lines demonstrated elevated levels of flavonoids and salicylic acid (SA), along with higher expression of SA-related genes, compared to the wild type. Moreover, all transgenic lines possessed lower reactive oxygen species levels and higher activity of antioxidant defense enzymes such as superoxide dismutase, peroxidase, and catalase under Pst DC3000 stress compared to the wild type. The up-regulation of defense genes, activation of the SA pathway, accumulation of flavonoids, and reinforcement of antioxidant defense mechanisms in transgenic Arabidopsis lines in response to Pst DC3000 underscore the critical role of MpDIR1(t) in fortifying plant immunity. Thus, MpDIR1(t) constitutes a promising candidate gene for improving bacterial disease resistance in commercial citrus cultivars.

To investigate the effects of different Armillaria mellea (A. mellea) sources on Gastrodia elata (GE) yield, quality, and soil microecology, five A. mellea of difference sources (M1–M5) were co-cultivated with Zhaotong GE at two sites. M5 co-cultivation produced the highest yields (fresh weight) at both Xiaocaoba, Yiliang (XCB) and Wanchang, Zhenxiong (ZXWC), reaching 3239 g/m² and 2550 g/m². For quality, M1 resulted in the highest total gastrodin and parishin content at XCB, while M3 was superior at ZXWC. Post-cultivation, soil pH increased across all treatments. Soil nutrients increased with M1 and M2 at XCB, and with M4 at ZXWC. In GE rhizosphere soil samples, Proteobacteria, Acidobacteria, and Actinobacteria were dominant bacterial phyla, with Proteobacteria abundance decreasing. The dominant fungal phyla were Ascomycota, Basidiomycota, and Mucoromycota; Basidiomycota abundance increased in all soils, while Ascomycota increased only with M1 and M2. M3-treated soils had the highest Gram-negative bacteria abundance, and M1-treated soils were enriched with saprotrophic fungi. This study has several limitations. The conclusions were drawn indirectly with the host (GE) as the focus, and the A. mellea were not identified to clarify potential genetic differences. Future research should integrate fungal omics analyses for a more in-depth investigation.

Gastrodia elata is a fully mycoheterotrophic orchid whose tuber development depends on carbon delivered by Armillaria fungi. Its formal inclusion in China’s “medicine and food homology” catalog has intensified demand for cultivated tubers combining high yield with consistent bioactive quality. Here, we tested whether Armillaria mellea strains steer host carbon allocation between biomass accumulation and phenolic glycoside biosynthesis. Using a standardized EPS symbiotic cultivation system (AM1, AM2, AM3; n = 3 biological replicates per strain), we integrated agronomic traits with widely targeted metabolomics and RNA-seq transcriptomics, including weighted gene co-expression network analysis (WGCNA). AM3 produced the highest tuber yield and higher primary carbon status (PCAI), but lower gastrodin/parishin-type phenolic glycosides and lower allocation efficiency (BER), whereas AM1 showed a quality-dominant profile with significantly higher BER. WGCNA highlighted an AM3-associated module enriched in starch-biosynthetic genes, and PCAI was strongly negatively correlated with the weighted Parishin-Gastrodin Index (wPGI) across samples (n = 9), consistent with a carbohydrate-storage versus phenolic-glycoside trade-off. These results indicate that fungal strain identity functions as an external regulator of source–sink dynamics in G. elata, supporting “precision symbiosis” for food-grade versus medicinal-grade production.

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.

Armillaria mellea (A. mellea) serves as a crucial nutritional source for Gastrodia elata (GE) growth, and its origin directly influences the GE quality and yield. This study analyzed GE symbiotic with A. mellea from different sources using metabolomics and transcriptomics. Results demonstrated that Group A exhibited significant differences in metabolites and gene expression compared to other groups. Group A showed significantly higher accumulation of active components like gastrodin and p-hydroxybenzyl alcohol than others, but its yield was lower than Group B. Metabolomic analysis identified 2418 metabolites, while transcriptomic sequencing produced 964,110,904 clean reads, with 14,637 annotated transcripts. KEGG analysis revealed that Group A’s DEGs and DEMs were co-enriched in three key pathways, including flavonoid biosynthesis, phenylpropanoid biosynthesis, and plant hormone signal transduction, such as the positive regulatory roles of key genes (CHS, 4CL, MYC2) on metabolites such as hesperetin, ferulate, and jasmonic acid, respectively. The coordinated upregulation of gene–metabolite interactions in Group A GE may be closely related to the accumulation of major active components, indirectly suggesting the influence of the A. mellea source on metabolic and transcriptional response differences in GE. This study, centered on the host GE, indirectly deduces the association between A. mellea and GE, providing a theoretical basis for screening high-quality “fungus-GE” combinations. Further in-depth research and validation experiments will be conducted in conjunction with fungal omics.