Genomic and phenotypic biology of a novel Dickeya zeae WH1 isolated from rice in China: Insights into pathogenicity and virulence factors

Abstract

Soft rot caused by Dickeya zeae is an important bacterial disease affecting rice and other plants worldwide. In this study, Nanopore and Illumina sequencing platforms were used to sequence the high-quality complete genome of a novel D. zeae strain WH1 (size: 4.68 Mb; depth: 322.37x for Nanopore, 243.51x for Illumina; GC content: 53.59%), which was isolated from healthy rice root surface together with Paenibacillus polymyxa, a potential biocontrol bacterium against D. zeae strain WH1. However, the pure WH1 culture presented severe pathogenicity. Multilocus sequence analysis (MLSA) indicated that strains WH1, EC1, and EC2 isolated from rice were grouped into a clade differentiated from other D. zeae strains. The average nucleotide identity (ANI) and DNA-DNA hybridization (DDH) analyses demonstrated that WH1 was phylogenetically closest to EC2. Furthermore, the pathogenicity determinants and virulence factors of WH1 were mainly analyzed through genomic comparison with complete genomes of other D. zeae strains with high virulence (EC1, EC2, MS1, and MS2). The results revealed that plant cell wall-degrading extracellular enzymes (PCWDEs), flagellar and chemotaxis, and quorum sensing were highly conserved in all analyzed genomes, which were confirmed through phenotypic assays. Besides, WH1 harbored type I, II, III, and VI secretion systems (T1SS, T2SS, T3SS, and T6SS), but lost T4SS and T5SS. Like strains MS1 and MS2 isolated from bananas, WH1 harbored genes encoding both capsule polysaccharide (CPS) and exopolysaccharide (EPS) biosynthesis. The results of pathogenicity assays demonstrated that WH1 produced severe soft rot symptoms on potato tubers, carrots, radishes, and Chinese cabbage. Meanwhile, WH1 also produced phytotoxin(s) to inhibit rice seed germination with an 87% inhibitory rate in laboratory conditions. More importantly, we confirmed that phytotoxin(s) produced by WH1 are different from zeamines produced by EC1. Comparative genomics analyses and phenotypic and pathogenicity assays suggested that WH1 likely evolved through a pathway different from the other D. zeae strains from rice, producing a new type of rice foot rot pathogen. These findings highlight the emergence of a new type of D. zeae strain with high virulence, causing soft rot in rice and other plants.

Unravelling the aetiology of Dickeya zeae using polyphasic approaches for bacterial stalk rot in maize

“…Tan et al. (2022) stated that the 16S rRNA gene sequence is insufficient to assign the taxonomy of the bacterium and they used a joint phylogenetic tree based on MLSA to characterize the D. zeae strains WH1, EC1 and EC2 isolated from rice, which grouped them into a clade differentiated from other D. zeae strains.…”

“…The 16S rRNA gene showed 99.78%-99.93% homology with D. zeae in BLAST analysis and, in phylogenetic tree, placed the isolates in the same cluster as the DZ-E4-2 (KJ438951) strain of D. zeae reported byMartinez-Cisneros et al (2014). Several researchers have also successfully employed the 16S rRNA gene to identify Dickeya at species level(Balamurugan et al, 2020;Guan et al, 2019;Martinez-Cisneros et al, 2014).Phylogenetic analyses based on a single gene are not generally recommended for species identification because the effects of gene duplication or loss, horizontal gene transfer and recombination can interfere with the accurate reconstruction of an organism's evolutionary history(Marrero et al, 2013) Tan et al (2022). stated that the 16S rRNA gene sequence is insufficient to assign the taxonomy of the bacterium and they used a joint phylogenetic tree based on MLSA to characterize the D. zeae strains WH1, EC1 and EC2 isolated from rice, which grouped them into a clade differentiated from other D. zeae strains.…”

Alkaline phosphatase LapA regulates quorum sensing–mediated virulence and biofilm formation in Pseudomonas aeruginosa PAO1 under phosphate depletion stress

“…AHL signal molecules produced by P. aeruginosa were extracted and measured according to the methods described previously by our group with slight modifications ( 53 ). Briefly, AHL production was determined by inoculating 200 µL of overnight culture into 200 mL of PP or LB medium.…”