Thiamine cross-feeding drives microbial coexistence in the leaf microbiome

Abstract Microbiome 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 association that promotes their coexistence in the leaf microbiome. Using a continental-scale microbiome survey, we identified an asymmetric 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 indicate that natural selection has acted on thiamine production in Dioszegia , shaping this metabolic complementation. In planta assays further suggest that Albugo presence supports Dioszegia persistence under glasshouse conditions. 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.