Characterization of Pseudomonas capsici strains from pepper and tomato

Mei Zhao; Ron Gitaitis; Bhabesh Dutta

doi:10.3389/fmicb.2023.1267395

Characterization of Pseudomonas capsici strains from pepper and tomato

Front Microbiol. 2023 Oct 11:14:1267395. doi: 10.3389/fmicb.2023.1267395. eCollection 2023.

Authors

Mei Zhao^{1

2}, Ron Gitaitis², Bhabesh Dutta²

Affiliations

¹ Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China.
² Department of Plant Pathology, University of Georgia, Tifton, GA, United States.

Abstract

Disease outbreaks of bacterial leaf spot and blight of pepper and tomato often occur in both transplant- and field-production systems worldwide. In some cases, the outbreaks are caused by novel bacterial species. Characterization of these novel bacterial species are critical in developing diagnostic assays and identifying management options for pathogen monitoring and sustainable production, respectively. We characterized strains belonging to novel Pseudomonas species that are responsible for outbreaks in pepper and tomato both in transplant-houses and in production fields in Georgia, USA. Phylogenomic analyses and whole genome sequence indices demonstrated that the pepper and tomato strains belonged to P. capsici. The whole-genome comparison revealed that 13 Pseudomonas strains from diverse isolation sources that were curated in NCBI were indeed P. capsici indicating a potential wide-host range for this bacterial species. Our greenhouse-based host-range assay also indicated that P. capsici strains were pathogenic on pepper, tomato, eggplant, cabbage, lettuce, and watermelon corroborating a wide-host-range. A phylogenetic tree inferred from the whole genome sequence data showed that the P. capsici strains from Georgia (pepper and tomato) were genetically diverse, and were closely related to tomato P. capsici strains from Florida. Genomic presence of traditional bacterial virulence factors in P. capsici strains was also determined. Pseudomonascapsici strains encode one set of type I secretion system, two sets of type II secretion systems, one set of type III secretion system, two sets of type V secretion systems, three sets of type VI secretion systems, and various secondary metabolite gene clusters including lipopeptides. In in-vitro assays, it was demonstrated that six out of seven P. capsici strains (pepper and tomato strains from Georgia) were not sensitive to 0.8 mM CuSO₄. When the genomes of copper-tolerant strains were compared with the copper-sensitive strains, it was observed that the former strains encode a cluster of genes related to copper tolerance, which were absent in the genomes of copper-sensitive strains. Considering the ability of P. capsici strains to infect a range of vegetable hosts and possession of a wide range of bacterial virulence factors, secondary metabolites, and copper-tolerance genes, we envision that the management of this pathogen might potentially be a challenge.

Keywords: ANI; Pseudomonas capsici; copper; dDDH; effector; host range.

Grants and funding

The author(s) declare financial support was received for the research, authorship, and/or publication of this article. This work was supported by GACCV AWD0001296901, and the Specialty Crops Research Initiative Awards 2019–51181-30010 and 2022–51181-38242 and from the USDA National Institute of Food and Agriculture. Any opinions, findings, conclusions, or recommendations expressed in this publication are those of the author(s) and do not necessarily reflect the view of the U.S. Department of Agriculture. The University of Georgia is an equal opportunity provider and employer. This study was supported in part by resources and technical expertise from the Georgia Advanced Computing Resource Center, a partnership between the University of Georgia Office of the Vice President for Research and Office of the Vice President for Information Technology.