Quantitative divergence of the bacterial root microbiota in Arabidopsis thaliana relatives

All plants carry distinctive bacterial communities on and inside organs such as roots and leaves, collectively called the plant microbiota. How this microbiota diversifies in related plant species is unknown. We investigated the diversity of the bacterial root microbiota in the Brassicaceae family, including three Arabidopsis thaliana ecotypes, its sister species Arabidopsis halleri and Arabidopsis lyrata, and Cardamine hirsuta. We show that differences in root microbiota profiles between these hosts are largely quantitative and that host phylogenetic distance alone cannot explain the observed microbiota diversification. Our work also reveals a largely conserved and taxonomically narrow root microbiota, which comprises stable community members belonging to the Actinomycetales, Burkholderiales, and Flavobacteriales.