Transcriptomics reveal core activities of the plant growth-promoting bacterium Delftia acidovorans RAY209 during interaction with canola and soybean roots

Abstract

The plant growth-promoting rhizobacterium Delftia acidovorans RAY209 is capable of establishing strong root attachment during early plant development at 7 days post-inoculation. The transcriptional response of RAY209 was measured using RNA-seq during early (day 2) and sustained (day 7) root colonization of canola plants, capturing RAY209 differentiation from a medium-suspended cell state to a strongly root-attached cell state. Transcriptomic data was collected in an identical manner during RAY209 interaction with soybean roots to explore the putative root colonization response to this globally relevant crop. Analysis indicated there is an increased number of significantly differentially expressed genes between medium-suspended and root-attached cells during early soybean root colonization relative to sustained colonization, while the opposite temporal pattern was observed for canola root colonization. Regardless of the plant host, root-attached RAY209 cells exhibited the least amount of differential gene expression between early and sustained root colonization. Root-attached cells of either canola or soybean roots expressed high levels of a fasciclin gene homolog encoding an adhesion protein, as well as genes encoding hydrolases, multiple biosynthetic processes, and membrane transport. Notably, while RAY209 ABC transporter genes of similar function were transcribed during attachment to either canola or soybean roots, several transporter genes were uniquely differentially expressed during colonization of the respective plant hosts. In turn, both canola and soybean plants expressed genes encoding pectin lyase and hydrolases – enzymes with purported function in remodelling extracellular matrices in response to RAY209 colonization. RAY209 exhibited both a core regulatory response and a planthost-specific regulatory response to root colonization, indicating that RAY209 specifically adjusts its cellular activities to adapt to the canola and soybean root environments. This transcriptomic data defines the basic RAY209 response as both a canola and soybean commercial crop and seed inoculant.

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

“…Root colonization is often associated with PGPR and has been studied in D. acidovorans RAY209 [ 48 ]. Of 50 RAY209 genes previously found to have altered transcription during colonization of canola or soybean roots [ 49 ], 17 were detected in all 61 Delftia genomes and 29 were detected in at least 60 genomes (Fig. S3).…”

“…Separating DA2 for comparison showed that the four genomes in clade DA2 were on average 96 % identical to members of the 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. DA1 clade, and 94 % identical to members of the DLT clade, indicating DA2 may be forming a new species.…”

Phosphate-Solubilizing Pseudomonas sp. Strain WS32 Rhizosphere Colonization-Induced Expression Changes in Wheat Roots

“…The ABC transporter family is a class of superfamily transmembrane proteins that are widely present in organisms and play important roles in secondary metabolite transport and accumulation in plants ( Badri et al, 2009 ; Yan et al, 2017 ; Qu et al, 2020 ). Suchan et al (2020) found that ABC transporter-related genes were upregulated according to the transcriptome of soybean inoculated with Delftia acidovorans RAY209. The results of the present study showed that the expression levels of ABC transporter genes and phospholipase genes related to membrane synthesis were differentially expressed in wheat roots, which may be caused by the strain WS32 bacteria inducing ABC transporters to release energy through the hydrolysis of ATP and transport of nutrients across the membrane into wheat cells, thus inducing changes in membrane transporter activity and synthesis-related genes.…”

Genotype by microbiome interactions have large effects on growth in Lotus japonicus

“…On the other hand, Ralstonia and Delftia bacteria were enriched as sensitive microbes to the interaction effects among G, C, and E. Ralstonia is a significant plant pathogen (Alvarez et al, 2019). In addition, several strains belonging to Delftia have been reported as plant growth-promoting rhizobacteria (Suchan et al, 2020). Bacteria under the direct influence of G factors were enriched in Pseudomonas and Sphingobium ; nevertheless, their frequency was not correlated (Supplemental Figures S13 and S14).…”