Coffee is one of the most valuable agricultural commodities worldwide, second only to oil in terms of international trade. Coffea arabica L. is a widely cultivated and economically important crop that is responsible for about 90% of the global production of coffee. In this study, we selected five C. arabica cultivation sites at different altitudes to clarify the effects of altitude on rhizospheric soil physical–chemical characteristics and microbial communities. The samples collected at low altitudes were more nutrient-deficient and acidic than the soil samples collected at medium–high altitudes. The Proteobacteria-to-Acidobacteria ratio increased from lower altitudes to medium–high altitudes. Additionally, although Ascomycota was the dominant fungal phylum, it was unaffected by the altitude. Furthermore, the alpha richness and diversity of the bacterial and fungal communities were higher at medium–high altitudes than at low altitudes. Moreover, the redundancy analysis indicated that microbial phyla were closely associated with pH. These findings suggest that C. arabica should be cultivated at medium–high altitudes, which is conducive to sustainable management and the production of high-quality C. arabica beans.

The color of coffee fruits is influenced by several factors, including cultivar, ripening stage, and metabolite composition. However, the metabolic accumulation of pigments and the molecular mechanisms underlying peel coloration during the ripening process of Coffea arabica L. remain relatively understudied. In this study, UPLC-MS/MS-based metabolomics and RNA sequencing (RNA-seq)-based transcriptomics were integrated to investigate the accumulation of anthocyanins and carotenoids in the peel of Coffea arabica at different ripening stages: green peel (GP), green-yellow peel (GYRP), red peel (RP), and red-purple peel (RPP). This integration aimed at elucidating the molecular mechanisms associated with these changes. A total of ten anthocyanins, six carotenoids, and thirty-five xanthophylls were identified throughout the ripening process. The results demonstrated a gradual decrease in the total carotenoid content in the peel with fruit maturation, while anthocyanin content increased significantly. Notably, the accumulation of specific anthocyanins was closely associated with the transition of peel colors from green to red. Integrated metabolomics and transcriptomics analyses identified the GYRP stage as critical for this color transition. A weighted gene co-expression network analysis (WGCNA) revealed that enzyme-coding genes such as 3AT, BZ1, and lcyE, along with transcription factors including MYB, NAC, and bHLH, which interact with PHD and SET TR, may regulate the biosynthesis of anthocyanins and carotenoids, thereby influencing peel pigmentation. These findings provide valuable insights into the molecular mechanisms underlying the accumulation of anthocyanins and carotenoids in Coffea arabica peel during fruit maturation.

The plant microbiome plays a role in pathogen defense, but its role in different resistant varieties and ecological niches remains unclear. This study used 16S rRNA and ITS sequencing to investigate microbial communities and interactions in disease-resistant (PT) and susceptible (Bourbon) coffee varieties of five ecological niches: leaves, fruits, roots, rhizosphere soil, and non-rhizosphere soil. We found that the microbial communities differed significantly between the two varieties. The resistant variety was enriched in beneficial bacteria from the Actinobacteriota phylum and a stable, modular microbial network dominated by saprotrophic fungi. In contrast, the susceptible variety had a higher abundance of opportunistic pathogens and stress-indicator fungi, including Neurospora spp., which were more prominent in the rhizosphere and non-rhizosphere soils. These networks were fragile and dominated by pathotrophic fungi, reflecting ecological imbalance. Our findings show that plant disease resistance is influenced not only by host genetics but also by co-evolutionary interactions with the microbiome. These insights provide a foundation for developing targeted biocontrol strategies to manage plant-associated microbial communities.

Cymbopogon citratus (DC.) Stapf (lemongrass), a globally significant medicinal and aromatic plant, is widely used in food and pharmaceutical industries owing to its bioactive essential oil. However, conventional whole‐plant extraction methods face challenges such as inconsistent oil quality and suboptimal stability. To elucidate the effects of cultivation environments and plant tissues on oil quality, this study categorized lemongrass plants into shaded and natural light exposure groups. Essential oils were extracted from leaves and stems using steam distillation, followed by compositional analysis using Headspace Solid‐Phase Microextraction (HS‐SPME) coupled with Gas Chromatography–Mass Spectrometry (GC–MS). The investigation focused on how varying radiation intensities influenced physicochemical properties and volatile components of essential oils from various plant parts. Results demonstrated that both physicochemical properties and volatile compositions of lemongrass essential oils exhibited minimal sensitivity to variations in radiation intensity treatments. Leaf‐derived essential oil exhibited a significantly higher yield than stem oil by 54.48%, but their refractive indices and chromatic aberration values did not differ substantially. Leaf oil contained markedly elevated levels of heterocyclic compounds, ethers, and aldehydes than those in stem oil by 14.61%, 10.83%, and 1.57%, respectively, while hydrocarbons were lower by 6.1%. The primary volatile constituents characterizing lemongrass quality—geraniol and citral (specifically 2,6‐octadienal, 3,7‐dimethyl‐, (E)‐)—were significantly more abundant in the leaves than in the stems by 8.64% and 7.20%, respectively ( p < 0.01). Therefore, lemongrass essential oil extracted from leaves cultivated under natural light conditions demonstrated the highest oil yield and superior quality attributes. The integration of natural light cultivation with selective leaf harvesting proposes a promising strategy to enhance lemongrass oil quality. This methodology establishes a theoretical basis for advancing downstream processing techniques and developing high‐value products derived from lemongrass essential oil.