Ecological Genomics of Pseudomonas syringae
Pseudomonas syringae is well known as a model bacterial phytopathogen in the laboratory, environment, and the field. A focus on understanding mechanisms of virulence in planta has motivated extensive research into genetic, genomic, and evolutionary factor
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Ecological Genomics of Pseudomonas syringae David A. Baltrus, Tory A. Hendry, and Kevin L. Hockett
Pseudomonas syringae is a facultative bacterial phytopathogen of many (if not all) plant species, but strains can also survive and thrive outside of their plant hosts across many different environments (Hirano and Upper 2000). Given an abundance of recent reviews that focus largely on studies of pathogenicity (Block and Alfano 2011; Lindeberg et al. 2012; O’Brien et al. 2011; Studholme 2011), we take this opportunity to summarize and explore what is known about genomic features that influence ecological dynamics for P. syringae inside and outside of plant hosts. Recent sequencing efforts have yielded a wealth of data about genomic diversity throughout this species, but have also given rise to numerous overarching questions about evolutionary dynamics for P. syringae and related bacteria. We view this chapter as an incomplete roadmap that both summarizes current knowledge of the genomic basis for ecological diversity throughout the species and highlights unexplained patterns that arise from comparison across genomes.
D. A. Baltrus (&) T. A. Hendry K. L. Hockett School of Plant Sciences, The University of Arizona, Tucson, AZ 85721-0036, USA e-mail: [email protected]
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Taxonomy
Taxonomic relationships across phytopathogens and other soil-associated microbes often change, with nomenclatural disputes sparking heated disagreements across disciplines. The focus of this chapter will be what is currently referred to as P. syringae but which includes other potential species such as P. savastanoi and P. cannabina (Ramos et al. 2012; Sarris et al. 2013; Young 2010). We reference genome sequences from within these isolates as a point of context for comparison, but support those that would chose to split off species names given appropriate phenotypic contexts. P. syringae as a whole contains upward of 50 different pathovars spanning pathogens of important crops as well as wild plants (O’Brien et al. 2011; Young 2010). In recent years, due to extensive environmental sampling, greater appreciation has been given to environmental isolates that are not known to be virulent on any host (and thus lack pathovar designations) but which phylogenetically cluster within P. syringae (Diallo et al. 2012a; Kniskern et al. 2010; Morris et al. 2010). One clade in particular, referred to below as MLST group 2C, stands out as having shifted its ecological niche compared to closely related phytopathogenic strains. For the moment, we consider these all to be P. syringae isolates and suggest that elucidation of the ecological roles
D. C. Gross et al. (eds.), Genomics of Plant-Associated Bacteria, DOI: 10.1007/978-3-642-55378-3_3, Springer-Verlag Berlin Heidelberg 2014
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for these environmental isolates is an intriguing future research direction. Historically, P. syringae has been classified based on phenotypic responses to the LOPAT test, with positive interactions for levan synthesis and tobacco hypersensitive response an
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