A vitamin cross-feeding mechanism mediates microbial niche adaptation on leaves

Microbial homeostasis is crucial for host health and ecosystem function, yet the molecular and ecological mechanisms underlying community assembly and stability remain elusive. Here, we uncover a conserved yeast-oomycete metabolic mutualism that promotes their coexistence in the leaf microbiome. Using a continental-scale microbiome survey, we identified a mutualistic interaction between two eukaryotic hub microbes: the yeast Dioszegia hungarica and the obligate oomycete Albugo laibachii. We show that Dioszegia facilitates Albugo colonization by supplying thiamine via a dedicated membrane permease, alleviating Albugo’s auxotrophy. Genomic and transcriptomic analyses reveal that natural selection has acted on thiamine production in D. hungarica, shaping this mutualistic interaction. In planta assays further demonstrate that cross-feeding enhances Albugo colonization and promotes Dioszegia persistence. Our study illustrates how the evolution of nutrient cross-feeding mediates microbial coexistence and microbiome stability. Targeting microbial nutrient flows offers new strategies for engineering microbiomes and enhancing plant resilience in natural and agricultural systems.