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Genomic and phenotypic biology of a novel WH1 isolated from rice in China: Insights into pathogenicity and virulence factors. | LitMetric

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

Front Microbiol

College of Life Sciences, Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, Anhui Normal University, Wuhu, Anhui, China.

Published: October 2022

AI Article Synopsis

  • Soft rot is a significant bacterial disease impacting rice and other plants globally, and this study focused on a newly identified strain, WH1, which was highly pathogenic despite being isolated from healthy rice roots.
  • Genome sequencing revealed WH1's complete structure and its close genetic relationship with another strain (EC2), emphasizing its unique pathogenic characteristics, such as specific enzymes and secretion systems that aid in virulence.
  • Pathogenicity testing confirmed WH1's severe impact on various vegetables and its ability to inhibit rice seed germination, indicating that it produces distinct phytotoxins compared to similar strains, suggesting a possible evolutionary path for its virulence.

Article Abstract

Soft rot caused by 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 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 , a potential biocontrol bacterium against 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 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 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 strains from rice, producing a new type of rice foot rot pathogen. These findings highlight the emergence of a new type of strain with high virulence, causing soft rot in rice and other plants.

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Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9650423PMC
http://dx.doi.org/10.3389/fmicb.2022.997486DOI Listing

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