Identification of a Pseudomonas amygdali isolate from Hibiscus rosa-sinensis

Authors: GONZALEZ-TOBON, JULIANA - Cornell University; DIAZ, ALLISON - Cornell University; Helmann, Tyler; DAUGHTREY, MARGERY - Cornell University; Stodghill, Paul; Filiatrault, Melanie

Submitted to: International Journal of Systematic and Evolutionary Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/2/2023
Publication Date: 3/6/2023
Citation: Gonzalez-Tobon, J., Diaz, A., Helmann, T.C., Daughtrey, M., Stodghill, P., Filiatrault, M.J. 2023. Identification of a Pseudomonas amygdali isolate from Hibiscus rosa-sinensis. International Journal of Systematic and Evolutionary Microbiology. 115:110600. https://doi.org/10.1016/j.ygeno.2023.110600.
DOI: https://doi.org/10.1016/j.ygeno.2023.110600

Interpretive Summary: Hibiscus rosa-sinensis, commonly known as the ¨Chinese hibiscus¨, is a shrub native to China but widely cultivated. It is the most common garden Hibiscus in tropical and semi-tropical regions. Pseudomonas and Xanthomonas are common bacterial pathogens of ornamental plants, including Hibiscus. We isolated a bacterial strain causing leaf spot from Hibiscus plants and performed experiments to establish the identity and ability to cause disease in other plants. Using whole genome sequencing we identified the bacterium as Pseudomonas amygdali. The genome was compared with the genomes of other Pseudomonas species. Analysis of the whole genome in comparison with several other Pseudomonas amygdali strains identified some conserved factors that the bacterium uses to cause disease and also revealed differences in the genomic content among the strains. These results provide a better understanding of the disease-causing mechanisms of the Pseudomonas species.

Technical Abstract: During the summer of 2019, leaf spots and crinkling symptoms were found on hibiscus (Hibiscus rosa-sinensis). An isolate that presented mild fluorescence when growing on King’s B medium (KB) was identified. Initial identification using partial 16s rRNA and multi locus sequence typing (MLST) with four housekeeping genes (gltA, gyrB, gap, and rpoD), identified the isolate as a member of the genus Pseudomonas. To determine the species, whole genome sequencing using Nanopore and Illumina sequencing technologies was performed. The genomic sequence of the pathogen shared highest homology to two pathovars of Pseudomonas amygdali: pv. tabaci (ANI=99.04%, DNA Homology=80.3%) and pv. lachrymans (ANI=98.96%, DNA Homology=77.19%). Additionally, the genome content and structure were compared against widely known Pseudomonas syringae pathovars: tomato DC3000 and syringae B728a. Several pathogenicity islands containing known effectors from other Pseudomonas were identified, in addition to one that seems to be unique to the Pseudomonas amygdali strain isolated from hibiscus . The genome of the Pseudomonas strain from hibiscus contains unique gene clusters encoding putative secondary metabolites, including a siderophore, a NAGGN, and a furan cluster. Pathogenicity assays showed that the strain caused disease in tomato and a hypersensitivity response in tobacco. The genomic information is being used to better understand the pathogenicity of this pathogen and closely related Pseudomonads that infect floriculture crops.