Phylogenomic analysis of the genus Delftia reveals distinct major lineages with ecological specializations

Abstract

<i>Delftia</i> is a diverse betaproteobacterial genus with many strains having agricultural and industrial relevance, including plant-growth promotion, bioremediation of hydrocarbon-contaminated soils, and heavy metal immobilization. <i>Delftia</i> spp. are broadly distributed in the environment, and have been isolated from plant hosts as well as healthy and diseased animal hosts, yet the genetic basis of this ecological versatility has not been characterized. Here, we present a phylogenomic comparison of published <i>Delftia</i> genomes and show that the genus is divided into two well-supported clades: one '<i>Delftia acidovorans</i>' clade with isolates from soils and plant rhizospheres, and a second '<i>Delftia lacustris</i> and <i>Delftia tsuruhatensis</i>' clade with isolates from humans and sludge. The pan-genome inferred from 61 <i>Delftia</i> genomes contained over 28 000 genes, of which only 884 were found in all genomes. Analysis of industrially relevant functions highlighted the ecological versatility of <i>Delftia</i> and supported their role as generalists.