Abstract
Pseudomonas is a highly diverse genus that includes species that cause disease in both plants and animals. Recently, pathogenic pseudomonads from the Pseudomonas syringae and Pseudomonas fluorescens species complexes have caused significant outbreaks in several agronomically important crops in Turkey, including tomato, citrus, artichoke and melon. We characterized 169 pathogenic Pseudomonas strains associated with recent outbreaks in Turkey via multilocus sequence analysis and whole-genome sequencing, then used comparative and evolutionary genomics to characterize putative virulence mechanisms. Most of the isolates are closely related to other plant pathogens distributed among the primary phylogroups of P. syringae, although there are significant numbers of P. fluorescens isolates, which is a species better known as a rhizosphere-inhabiting plant-growth promoter. We found that all 39 citrus blast pathogens cluster in P. syringae phylogroup 2, although strains isolated from the same host do not cluster monophyletically, with lemon, mandarin orange and sweet orange isolates all being intermixed throughout the phylogroup. In contrast, 20 tomato pith pathogens are found in two independent lineages: one in the P. syringae secondary phylogroups, and the other from the P. fluorescens species complex. These divergent pith necrosis strains lack characteristic virulence factors like the canonical tripartite type III secretion system, large effector repertoires and the ability to synthesize multiple bacterial phytotoxins, suggesting they have alternative molecular mechanisms to cause disease. These findings highlight the complex nature of host specificity among plant pathogenic pseudomonads.
Highlights
Pseudomonas is a highly complex genus that includes hundreds of described species, some of which cause devastating disease in both plants and animals [1,2,3,4,5,6]
The diseases caused by the 169 isolates from Turkey include: 39 citrus blast pathogens from lemon, mandarin orange and sweet orange; 38 bacterial speck pathogens from tomato; 33 knot disease pathogens from oleander, olive, fontanesia, myrtle and pomegranate; 20 pith necrosis pathogens from tomato; 10 bacterial canker pathogens from plum and apricot; 7 halo blight pathogens from bean; 6 bacterial blight pathogens from artichoke and pea; 6 leaf blight pathogens from muskmelon; 4 seedling blight pathogens from watermelon; 2 bacterial leaf spot pathogens from parsley; 2 leaf necrosis pathogens from muskmelon; and 2 uncategorized pathogens (Fig. S1)
We found that common and widespread diseases on the same crop can be caused by distinct lineages of P. syringae, while phenotypically similar diseases on distinct, but closely related, hosts can be caused by a single, closely related clade of pathogens
Summary
Pseudomonas is a highly complex genus that includes hundreds of described species, some of which cause devastating disease in both plants and animals [1,2,3,4,5,6]. P. fluorescens is more commonly known as a biocontrol [12, 13] or commensal bacterium associated with the plant rhizosphere [14, 15], some strains are known to cause important diseases in animals (including humans), plants and fungi [16,17,18,19,20,21,22,23]. This phenotypic diversity is reflected in their genomes, as the P. syringae and P.
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