Contrasting patterns of microbial dominance in the <i>Arabidopsis thaliana</i> phyllosphere

Abstract

<i>Sphingomonas</i> is one of the most abundant bacterial genera in the phyllosphere of wild <i>Arabidopsis thaliana</i>, but relative to <i>Pseudomonas</i>, the ecology of <i>Sphingomonas</i> and its interaction with plants is poorly described. We analyzed the genomic features of over 400 <i>Sphingomonas</i> isolates collected from local <i>A. thaliana</i> populations, which revealed much higher intergenomic diversity than for the considerably more uniform <i>Pseudomonas</i> isolates found in the same host populations. Variation in <i>Sphingomonas</i> plasmid complements and additional genomic features suggest high adaptability of this genus, and the widespread presence of protein secretion systems hints at frequent biotic interactions. While some of the isolates showed plant-protective phenotypes in lab tests, this was a rare trait. To begin to understand the extent of strain sharing across alternate hosts, we employed amplicon sequencing and a bulk-culturing metagenomics approach on both <i>A. thaliana</i> and neighboring plants. Our data reveal that both <i>Sphingomonas</i> and <i>Pseudomonas</i> thrive on other diverse plant hosts, but that <i>Sphingomonas</i> is a poor competitor in dying or dead leaves.