Exploring the drivers of Xanthomonas population dynamics on tomato and pepper

Abstract

Bacterial leaf spot (BLS), caused by four species of Xanthomonas; X. euvesicatoria, X. vesicatoria, X. perforans, and X. gardneri, is an endemic disease of tomato and pepper in Southeastern United States and can result in total crop loss and there are no clear management strategies for this disease. Host resistance is considered as most important and effective method of control of BLS disease. There are some resistant cultivars of peppers against BLS which but the occurrence of the pathogenic races overcoming the resistance genes in tomato resulted in no such resistant cultivars in tomato. Although chemical control based on copper bactericides has been used extensively since decades, occurrence of copper-resistant bacterial pathogens are reducing the efficacy of copper-based bactericides. As majority of antibiotics and heavy metal resistance genes are encoded in plasmids, frequent plasmid transfer among the strains plays an important role in spreading the resistance in field. Recently we found two copper resistant strains of X. perforans without these copper resistance plasmids and integration of copper resistance genes in the chromosome. The goal of this project was to identify the pathogen population diversity of BLS Xanthomonas in Alabama using culture dependent and culture independent (shotgun metagenomics) techniques. Moreover, we also studied the chromosomal copper resistance dynamics in X. perforans population and their transfer potential both in planta and in-vitro studies. Sequencing and phylogenetic classification of 8 representative strains from the collection of 150 strains of BLS Xanthomonas from different places of Alabama suggest the presence of two novel sequence clusters within X. perforans. Culture-independent study of diversity using shotgun metagenomics from tomato, pepper and weed samples showed X. perforans and X. euvesicatoria as a dominant pathogen in tomato and pepper respectively. Shotgun metagenomics also showed the co-infection by multiple species/genera in the field at a given time and provided strain-level resolution showing the presence of two or more lineages of X. perforans in tomato samples. The result further suggest that shotgun metagenomics can be used for higher resolution of pathogen population structure in diversity studies. We also found copper tolerant X. perforans strains Xp 2010 and GEV 904 contained chromosomal encoded copper resistance genes in the genomic island. We further studied the structure of this island and investigate its transfer potential under in-planta and in-vitro conditions. Failure to obtain transconjugants/transductants under both conditions indicates that either the conditions we used for the transfer were not conducive or the transfer frequency is very low. Overall, these study of the pathogen population dynamics helps in providing the insight of bacterial population situation in Alabama. Thus, protective measures can be taken before the outbreak of pathogen in a large scale. The long-term goal of this research is to improve our understanding about pathogen population in Alabama and pathogen dynamics in both host and non-host. This study will help the farmers and large-scale growers to select more resistant/tolerant cultivars and look forward for resistant breeding program based on pathogen population information.