Molecular Epidemiology of Xanthomonas perforans Outbreaks in Tomato Plants from Transplant to Field as Determined by Single-Nucleotide Polymorphism Analysis

Abstract

Outbreaks of bacterial spot on tomato (BST) caused by Xanthomonas perforans are a major concern for sustainable crop production. BST is a common occurrence in tomato transplants grown for field production. We hypothesized that BST outbreaks in commercial fields originate from X. perforans strains inadvertently introduced from commercial transplant facilities. To test this hypothesis, we used a genome-wide single-nucleotide polymorphism (SNP) analysis to characterize X. perforans strains recovered from tomato transplant facilities and fields in commercial production areas. X. perforans strains were isolated from symptomatic transplants prior to roguing at two commercial transplant growers. Then, the same groups of transplants were tracked to commercial fields to recover X. perforans strains from diseased plants prior to harvest. Whole-genome sequencing was carried out on 84 strains isolated from transplant and field plants from Florida and South Carolina. SNPs were called using three reference strains that represented the genetic variation of the sampled strains. Field strains showing genetic similarity to transplant strains had a difference of 2 to 210 SNPs. Transplant and field strains clustered together by grower within each phylogenomic group, consistent with expectations. The range of genetic divergence among strains isolated from field plants was similar to the range obtained from strains on transplants. Using the range of genetic variation observed in transplants, we estimate that 60% to 100% of field strains were an extension of the transplant strain population. Our results stress the importance of BST management to reduce X. perforans movement from transplant to field and to minimize subsequent disease outbreaks.IMPORTANCE Current management of Xanthomonas perforans on tomato plants mainly relies on the frequent application of pesticides. However, the lack of effective pesticides and the development of strain tolerance to certain bactericides limit the ability to control outbreaks in production fields. Better knowledge of probable sources of X. perforans inoculum during tomato production is required to refine management strategies. Tomato plants are typically established in the field using transplants. This study aimed to determine if strains from field epidemics were coming from transplant facilities or resulted from local field outbreaks. The overall goal was to identify potential sources of inoculum and subsequently develop strategies to reduce carryover from transplant production to the field. Our results indicate that tomato producers should shift disease management efforts to transplant facilities to reduce disease in the field. Improved transplant health should reduce the likelihood of bacterial spot outbreaks and subsequently reduce pesticide usage in the field.

Keywords: DAPC; PCA; SNP; bacterial spot; cgMLST; ecology; epidemics; genome; seedlings; tracking.

FIG 1

Maximum likelihood phylogenetic tree of 103 Xanthomonas perforans strains based on 11,007 concatenated SNPs. Tree was rooted with X. perforans 91-118. All strains were isolated from Florida except strains appended to orange-colored branches, which were isolated from South Carolina (SC). 2012 strains were previously examined by Schwartz et al. (18). Green squares, purple circles, and red triangles refer to field, transplant, and reference strains, respectively. Branches are color-coded for the grower location or source of strain. Numbers on branches indicate bootstrap support.

FIG 2

Maximum likelihood phylogenetic tree of group 2 (A) and 3 (B) strains of Xanthomonas perforans strains based on 947 and 423 concatenated SNPs using Xp2010 and Xp17-12 as a reference strain. All strains were isolated from Florida except strains appended to orange-colored branches, which were isolated from South Carolina (SC). 2012 strains were previously examined by Schwartz et al. (18). Green squares, purple circles, and red triangles refer to field, transplant, and reference strains, respectively. Trees were rooted with the corresponding reference strain. Branches are color-coded for the grower location. Numbers on branches indicate bootstrap support.

FIG 3

Principal-component analysis of strains based on cgMLST of 1,356 genes. (A) Strains isolated from field versus transplants. (B) Location of strain isolation.