16S and metagenomic data of A. thaliana across Europe

Microbes in the phyllosphere affect plant health, stress tolerance1 and life history. In different geographic regions, plants are colonized by distinct pathogenic and commensal microbiomes, but the abiotic and biotic factors driving geographic variation are largely unknown. We identified and measured the core leaf microbiome of Arabidopsis thaliana in its native range, from almost 300 populations across Europe. Comparing the distribution of the approximately 500 major bacterial phylotypes, we discovered marked, geography-dependent differences in microbiome composition within A. thaliana and between A. thaliana and other Brassicaceae, with two distinct microbiome types segregating along a latitudinal gradient. The differences in microbiome composition mirror the spatial genetics of A. thaliana, with over 50% of variance in microbiome type explained by host genotype, including a significant association with polymorphisms in the host plant immune regulator ACD6. Microbiome composition is best predicted by drought-associated metrics that are well known to be a major selective agent on A. thaliana populations. The reproducible and predictable associations between specific microbes and water availability raise the possibility that drought not only directly shapes genetic variation in A. thaliana, but also through its effects on the leaf microbiome.