Desert Cucurbit Microbiomes: Spatiotemporal Dynamics and Functional Adaptations

Aridification and climate stress threaten global plant productivity, but the survival strategies of desert plants remain only partly understood. In this study, we examined how the microbiome of Citrullus colocynthis, a hardy desert cucurbit valued for its ecological and medicinal benefits, may influence the plants ability to withstand harsh conditions. Using 16S rRNA amplicon sequencing, shotgun metagenomics, and culture-based methods, we analyzed microbiome changes across two regions of the UAE during the rainy and dry seasons. Leaf and root bacterial communities showed clear seasonal shifts, with greater richness in winter and higher evenness in summer, while soil microbiomes remained stable. Dominant bacterial groups, Actinomycetota and Pseudomonadota, varied seasonally, indicating trade-offs between stress tolerance and metabolic flexibility. Fungal communities (mainly Ascomycota and Basidiomycota) were stable at the phylum level but reorganized by order between seasons; archaeal populations showed little change. Among 24 cultured bacterial isolates, including three potential new species, we identified multiple stress tolerance and plant growth-promoting traits. Genomic data revealed biosynthetic clusters for antimicrobial and stress-protective functions, as well as adaptation genes in Pseudomonas orientalis. These results demonstrate that the dynamic, functionally diverse microbiome of C. colocynthis enhances its resilience to desert stress, offering potential for arid-land agriculture.