A conserved cross-feeding mechanism mediates microbial niche adaptation on leaf

This project contain genomics and transcriptomics data associated with the manuscript titled 'A conserved cross-feeding mechanism mediates microbial niche adaptation on leaf' Microbial homeostasis are crucial for host health and ecosystem functioning, yet the molecular and ecological mechanisms driving community assembly and stability remain elusive. Here, we uncover a conserved cross-kingdom metabolic mutualism that promotes microbial coexistence in the leaf microbiome. Using a continental-scale microbiome survey of natural Arabidopsis thaliana populations, we identified a mutualistic relationship between two eukaryotic hub microbes: the yeast Dioszegia hungarica and the obligate oomycete parasite Albugo laibachii. We show that D. hungarica facilitates A. laibachii colonization by supplying thiamine via a dedicated membrane permease, alleviating the parasite's dependency on external thiamine. Genomics and transcriptomics analyses of Dioszegia populations reveal that natural selection has acted on the regulation of thiamine production and transport in D. hungarica, thereby shaping this mutualistic interaction. In planta assays further demonstrated that this cross-feeding mechanism not only enhances A. laibachii's colonization but also benefits D. hungarica by promoting its persistence on leaves. Our study provides insight into the evolution of nutrient cross-feeding and how it mediates microbial coexistence and microbiome stability. Targeting microbial nutrient flows offers new strategies to engineer microbiomes and enhance plant resilience in natural and agricultural systems.