Quantitative divergence of the bacterial root microbiota in Arabidopsis thaliana relatives

Abstract

Plants host at the contact zone with soil a distinctive root-associatedbacterial microbiota believed to function in plant nutrition andhealth. We investigated the diversity of the root microbiota withina phylogenetic framework of hosts: three Arabidopsis thaliana eco-types along with its sister species Arabidopsis halleri and Arabidopsis lyrata,as wellas Cardamine hirsuta, which diverged from theformer ~35 Mya. We surveyed their microbiota under controlledenvironmental conditions and of A. thaliana and C. hirsuta in twonatural habitats. Deep 16S rRNA gene profiling of root and corresponding soil samples identified a total of 237 quantifiable bacterialribotypes, of which an average of 73 community members wereenriched in roots. The composition of this root microbiota dependsmore on interactions with the environment than with host species.Interhost species microbiota diversity is largely quantitative and isgreater between the three Arabidopsis species than the threeA. thaliana ecotypes. Host species-specific microbiota were identified at the levels of individual community members, taxonomicgroups, and whole root communities. Most of these signatureswere observed in the phylogenetically distant C. hirsuta. However,the branching order of host phylogeny is incongruent with inter-species root microbiota diversity, indicating that host phylogeneticdistance alone cannot explain root microbiota diversification. Ourwork reveals within 35 My of host divergence a largely conserved and taxonomically narrow root microbiota, which comprisesstable community members belonging to the Actinomycetales,Burkholderiales, and Flavobacteriales.