cDNA Transcriptome of Arabidopsis Reveals Various Defense Priming Induced by a Broad-Spectrum Biocontrol Agent Burkholderia sp. SSG

Abstract

Burkholderia sp. SSG is a potent biological control agent. Even though its survival on the leaf surface declined rapidly, SSG provided extended, moderate plant protection from a broad spectrum of pathogens. This study used Arabidopsis Col-0 and its mutants, eds16-1, npr1-1, and pad4-1 as model plants and compared treated plants with non-treated controls to elucidate whether SSG triggers plant defense priming. Only eds16-1 leaves with SSG became purplish, suggesting the involvement of salicylic acid (SA) in SSG-induced priming. cDNA sequencing of Col-0 plants and differential gene expression analysis identified 120 and 119 differentially expressed genes (DEGs) at 6- and 24-h post-treatment (hpt) with SSG, respectively. Most of these DEGs encoded responses to biotic and abiotic stimuli or stresses; four DEGs had more than two isoforms. A total of 23 DEGs were shared at 6 and 24 hpt, showing four regulation patterns. Functional categorization of these shared DEGs, and 44 very significantly upregulated DEGs revealed that SSG triggered various defense priming mechanisms, including responses to phosphate or iron deficiency, modulation of defense-linked SA, jasmonic acid, ethylene, and abscisic acid pathways, defense-related gene regulation, and chromatin modification. These data support that SSG is an induced systemic resistance (ISR) trigger conferring plant protection upon pathogen encounter.

Keywords: Arabidopsis; Burkholderia sp.; Oxford Nanopore Technology (ONT) sequencing; biocontrol agent; cDNA transcriptome; defense priming; induced systemic resistance (ISR); leaf endophyte; systemic acquired resistance (SAR).

Figure 1

MA plot based on the EdgeR analysis showing differences in measurements between SSG-treated and control plants at 6 (a) and 24 hpt (b). M, log-fold-change (−log₂ FC) (ratio of gene expression calculated between the control and SSG treated plants). A, Average log CPM, or log2 (counts per million abundances, CPM). Schemes follow the same formatting.

Figure 2

Heatmap of the differentially expressed genes encoding the top 15 significant GO terms. (a) Significant BP terms at 6 hpt. (b) Significant BP terms at 24 hpt. Overlapping genes were orange and not overlapping genes were light blue. Schemes follow the same formatting.

Figure 3

Percentage of differentially expressed genes (DEGs) by SSG for BP (a), CC (b), and MF terms (c) at 6 and 24 hpt. The expressed genes were determined with EdgeR analysis and separated by their regulation type, down or up. GO terms and functional categorization of the genes are generated through TAIR (The Arabidopsis Information Resource). The GO term of interest in the same box of color depicts a similar pattern. Schemes follow the same formatting.

Figure 4

Upregulated DEGs in Arabidopsis Col-0 at 6 and 24 hpt with SSG at FDR < 0.001 determined by EdgeR analysis. Functional categorization of the genes is based on GO annotation on TAIR (The Arabidopsis Information Resource). The DEGs functions involving defense priming are bold.

Figure 5

Responses of Arabidopsis to Burkholderia sp. SSG. Four weeks-old plants were sprayed with SSG at 10⁸ to 10⁹ CFU mL⁻¹ PBS or the control CK, PBS alone. (a) The morphology of Col-0 and its mutants at 10 days post-treatment (dpt). (b) Symptom development on eds16-1 after SSG spray.