Host genome and bacterial taxa shape the Arabidopsis seed microbiome

Plant-microbiome interactions are crucial in shaping plant growth, stress resilience, and disease resistance. Among these, the seed microbiome plays a pivotal role in early plant development and ecological adaptation. However, little is known about the factors that determine the abundance and functions of the seed microbiome, as well as the role of the host genome in shaping the microbial diversity across different ecotypes. In this study, we investigated the diversity of the Arabidopsis seed microbiomes that originate from multiple geographical locations. High-throughput sequencing identified key bacterial taxa that govern Arabidopsis seed microbiota diversity. Distinct compositions of bacterial taxa were identified in Arabidopsis accessions sharing geographical location and similar soil features. Genome-wide association studies (GWAS) revealed that both the abundance of key taxa and common functional traits are associated with specific host genetic loci such as the RNA-binding protein RPB47B, mutants of which showed altered physiological properties related to soil properties and microbial diversity. Overall, our study establishes that geographical, soil and genetic host factors shape the Arabidopsis seed microbiome.