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ARS Home » Northeast Area » Ithaca, New York » Robert W. Holley Center for Agriculture & Health » Emerging Pests and Pathogens Research » Research » Research Project #441736

Research Project: Advancing Knowledge of the Biology and Etiology of Bacterial Plant Pathogens Towards Management Strategies

Location: Emerging Pests and Pathogens Research

Project Number: 8062-21000-048-000-D
Project Type: In-House Appropriated

Start Date: Feb 26, 2022
End Date: Feb 25, 2027

Objective 1: Identify genomic resources for development of diagnostics and detection tools for emerging and re-emerging bacterial plant pathogens. Sub-objective 1.A: Perform comparative genomics of bacterial pathogens. Sub-objective 1.B: Investigate diversity of soft rot Pectobacteriaceae (SRP). Objective 2: Characterize biology and virulence factors of bacterial plant pathogens and identify their targets in host plants. Sub-objective. 2.A: Discover and characterize genes that contribute to disease and/or host adaptation of bacterial soft rot pathogens. Sub-objective 2.B: Discover and characterize genes involved with interactions between bacterial species. Sub-objective 2.C: Determine the mechanistic basis of socially affected behaviors in bacteria. Sub-objective 2.D: Determine the contribution of AlgU to virulence and factors affecting AlgU activity. Sub-objective 2.E: Characterize the signaling pathways that impact expression of HiVir gene cluster in Pantoea. Objective 3: Investigate sustainable strategies for control of bacterial plant diseases. Sub-objective. 3.A: Investigate the role of antimicrobials in tolerance to bacterial soft rot pathogens. Sub-objective 3.B: Identify genetic markers of soft rot disease tolerance in US Potato Genebank germplasm.

Soft rot bacteria, such as Dickeya, Pectobacterium, and Pantoae are among the most important pathogens of vegetables, fruits, and ornamentals. Bacterial diseases of potato and onion alone cause more than $60M in losses annually in the U.S. Despite the extensive amount of research available on bacterial plant pathogens, there is a lack of understanding about how bacterial plant pathogens enter and move within crop production systems and to what degree these diseases are caused by endemic populations. Furthermore, some bacterial species are endemic and, in some environments, a single bacterial species can be represented by a number of different strains, some of which are pathogens, and some of which are non-pathogens with beneficial biocontrol activities. Therefore, determining which bacteria are responsible for disease and furthermore how certain bacterial strains become pathogenic is an area of research that warrants further study. To address this, we will use genome sequencing methods to characterize populations bacteria present in diseased crops. The patterns that emerge at the intersection of pathogen diversity and geographical location will provide key insights on disease emergence as well as identify diagnostic markers able to distinguish pathogens from non-pathogens. For some plant diseases, such as bacterial soft rot (potato: Dickeya spp. and Pectobacterium spp.; onion: Pantoea spp.) many bacterial species may be involved, with the pathogens being members of a broader community of plant-associated microbes. Little is known about the relationships and interactions of plant pathogens with the host, the microbial community, and the environment and the impact on disease outcome. We will investigate bacterial communication mechanisms involved in pathogen fitness and formation of complex communities in plants to identify factors critical for disease. For many bacterial soft rot diseases there are no effective management options. For example, there are no commercially available potato or onion cultivars with soft rot resistance, thus management options for these pathogens are very limited. Additionally, there is little known about the specific mechanisms involved in host tolerance or susceptibility. To address this, we will first identify and characterize factors that bacteria use to cause disease and then use that information to guide discovery of bacterial control strategies. Second, we will identify and characterize sources of natural resistance in wild crop relatives to provide information for breeders as well as a source germplasm for breeding resistant varieties. All together this research will lead to improved fundamental understanding of bacterial soft rot disease dynamics and reveal vulnerabilities that can be exploited for control of bacterial plant diseases, helping us work towards the goal of sustainable plant disease management.