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

Abstract

Delftia 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. Delftia 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 Delftia genomes and show that the genus is divided into two well-supported clades: one 'Delftia acidovorans' clade with isolates from soils and plant rhizospheres, and a second 'Delftia lacustris and Delftia tsuruhatensis' clade with isolates from humans and sludge. The pan-genome inferred from 61 Delftia 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 Delftia and supported their role as generalists.

Keywords: Delftia; gold metabolism; plant-growth promotion.

Fig. 1.

Delftia phylogeny showing two main clades, DA and DLT, and the DA sub-clades, DA1 and DA2. Support values from 1000 bootstrap pseudoreplicates are shown as numbers and as circles coloured according to the ‘bootstrap support’ legend on the left. Branch thickness also indicates support level with thinner branches having lower support. The scale bar at the bottom indicates branch length as the number of substitutions per site. The boxes to the right of the phylogeny show, from the left, (i) habitat of isolation for each strain (colour according to the key on the left), (ii) presence (peach) or absence (grey) of genes shown to be expressed in RAY209 during plant root colonization [49], and (iii) presence (green) or absence (grey) of genes that encode or regulate production of delftibactin and the CzcABC-like heavy metal efflux system.

Fig. 2.

ANI estimates for 61 Delftia genomes. (a) A cluster diagram showing ANI values between each pairwise comparison. (b) Distribution of ANI values for between-clade and within-clade comparisons.

Fig. 3.

Parsimony reconstruction of ancestral habitats for Delftia . The phylogeny is the same as shown in Fig. 1. Circles indicate habitat of isolation for terminal branches and ancestral predictions for internal nodes.