Strains of Pseudomonas syringae pv. syringae from pea are phylogenetically and pathogenically diverse

Diversity, Evolution, and Function of Pseudomonas syringae Effectoromes

Pseudomonas syringae is an evolutionarily diverse bacterial species complex and a preeminent model for the study of plant-pathogen interactions due in part to its remarkably broad host range. A critical feature of P. syringae virulence is the employment of suites of type III secreted effector (T3SE) proteins, which vary widely in composition and function. These effectors act on a variety of plant intracellular targets to promote pathogenesis but can also be avirulence factors when detected by host immune complexes. In this review, we survey the phylogenetic diversity (PD) of the P. syringae effectorome, comprising 70 distinct T3SE families identified to date, and highlight how avoidance of host immune detection has shaped effectorome diversity through functional redundancy, diversification, and horizontal transfer. We present emerging avenues for research and novel insights that can be gained via future investigations of plant-pathogen interactions through the fusion of large-scale interaction screens and phylogenomic approaches.

Identification and Genetic Characterization of Pseudomonas syringae pv. syringae from Sweet Cherry in Turkey

Pseudomonas syringae pv. syringae, which causes bacterial canker, is the most polyphagous bacterium in the P. syringae complex because of its broad host range. This pathogen is considered the major bacterial disease in cherry orchards. In this study, several samples were collected from infected sweet cherry (Prunus avium L.) trees in different locations of the Marmara region in Turkey between 2016 and 2018. Sixty-three isolates were identified as P. syringae pv. syringae by pathogenicity, LOPAT, GATTa, and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry tests. Total genomic DNA was extracted to confirm identity, followed by PCR amplification of syrB and cfl genes. Out of 63 isolates, 12 were randomly selected for repetitive element sequence-based PCR and multilocus sequence typing analyses to gain insight into the relationships of those isolates. The cluster analysis of enterobacterial repetitive intergenic consensus-, repetitive extragenic palindromic-, and BOX-A1R-based repetitive extragenic-palindromic-PCR techniques could classify the isolates into two distinct clusters. Phylogenetic analysis was carried out to obtain the relation between isolates and the location. The multilocus sequencing typing analysis of gyrB, rpoDp, rpoDs, and gltA genes allowed a clear allocation of the isolates into two separate main clusters. The relationships among the isolates were also evaluated by constructing a genealogical median-joining network (MJN). The isolates from six locations produced 11 haplotypes that were illustrated in the MJN. The results of this study proved that location could not be an indicator for showing the genetic diversity of P. syringae pv. syringae from cherry orchards. As the genetic variability of Pseudomonads has been demonstrated, this study also showed high diversity among different isolates even within the populations. While more research is recommended, the results of this study contributed to a better understanding of the evolutionary progress of P. syringae pv. syringae and the genetic diversity of sweet cherry isolates.

In silico Analysis of Allium sativum Bioactive Compounds against Effector Protein from Pseudomonas syringae pv. pisi

Allium sativum commonly known as Garlic is a familiar herb, highly studied for its valuable medicinal properties. The main objective involved in the current research is to analyze inhibitor and antibacterial action of bioactive compounds (ligands) present in the methanolic extract of Allium sativum bulbs against phytopathogen protein (receptor) through molecular docking. The effector protein AvrRps4 (4B6X) from phytopathogen Pseudomonas syringae pv. pisi, a protein responsible for Effector triggered immunity (ETI) activation and to subvert host responses in Pea plant was selected as protein target. The docking interactions between opted ligands and target protein, with ampicillin as control was done using PyRx software tool and analysed using Discovery studio 3.1 Visualiser. The outcomes obtained from in silico analysis suggested that the bioactive compound namely Diethyl 3-methyl-5-[(2,2,2-trifluoroacetyl)amino]thiophene-2,4-dicarboxylate bind effectively showing -5.7 binding energy value in comparison with antibiotic ampicillin which showed binding energy -5.8 value. This research study concluded that the bioactive compounds from methanolic extract of Allium sativum bulbs displayed a potential inhibitory activity against effector AvrRps4 protein exhibiting antibacterial properties and may be considered as possible substantial lead molecules in future prospects.

Diversity of pathogenic Pseudomonas isolated from citrus in Tunisia

The damages observed in Tunisian citrus orchards have prompted studies on the Pseudomonas spp. responsible for blast and black pit. Prospective orchards between 2015 and 2017 showed that the diseases rapidly spread geographically and to new cultivars. A screening of Pseudomonas spp. isolated from symptomatic trees revealed their wide diversity according to phylogenetic analysis of their housekeeping rpoD and cts genes. The majority of strains were affiliated to Pseudomonas syringae pv. syringae (Phylogroup PG02b), previously described in Tunisia. However, they exhibited various BOX-PCR fingerprints and were not clonal. This work demonstrated, for the first time in Tunisia, the involvement of Pseudomonas cerasi (PG02a) and Pseudomonas congelans (PG02c). The latter did not show significant pathogenicity on citrus, but was pathogenic on cantaloupe and active for ice nucleation that could play a role in the disease. A comparative phylogenetic study of citrus pathogens from Iran, Montenegro and Tunisia revealed that P. syringae (PG02b) strains are closely related but again not clonal. Interestingly P. cerasi (PG02a) was isolated in two countries and seems to outspread. However, its role in the diseases is not fully understood and it should be monitored in future studies. The diversity of pathogenic Pseudomonas spp. and the extension of the diseases highlight that they have become complex and synergistic. It opens questions about which factors favor diseases and how to fight against them efficiently and with sustainable means.

Virulence Factors in the Phytopathogen-Host Interactions: An Overview

Phytopathogens are responsible for great losses in agriculture, once they are able to subvert or elude the host defense mechanisms through virulence factors secretion for their dissemination. Herein, it is reviewed phytotoxins that act as virulence factors and are produced by bacterial phytopathogens (Candidatus Liberibacter spp., Erwinia amylovora, Pseudomonas syringae pvs and Xanthomonas spp.) and fungi (Alternaria alternata, Botrytis cinerea, Cochliobolus spp., Fusarium spp., Magnaporthe spp., and Penicillium spp.), which were selected in accordance to their worldwide importance due to the biochemical and economical aspects. In the current review, it is sought to understand the role of virulence factors in the pathogen-host interactions that result in plant diseases.

Zucchini Vein Clearing Disease Is Caused by Several Lineages Within Pseudomonas syringae Species Complex

Zucchini (Cucurbita pepo) is worldwide affected by Pseudomonas syringae, inducing vein clearing, stunting, and necroses during plantlet development. A collection of 58 P. syringae strains isolated from diseased zucchini plantlets was characterized by multilocus sequence analysis (MLSA). A subset of 23 strains responsible for vein clearing of zucchini (VCZ) was evaluated for pathogenicity on zucchini, and their genomes were sequenced. The host range of six VCZ strains was evaluated on 11 cucurbit species. Most VCZ strains belong to clades 2a and 2b-a within phylogroup 2 of P. syringae species complex and are closely related to other strains previously isolated from cucurbits. Genome analyses revealed diversity among VCZ strains within each clade. One main cluster, once referred to by the invalid pathovar name (peponis), gathers VCZ strains presenting a narrow host range including zucchini and squashes. Other VCZ strains present a large host range including zucchini, squashes, cucumber, melons, and in some cases watermelon. The VCZ strain pathogenic features are strongly associated with type III effector repertoires. The presence of avrRpt2 and absence of hopZ5 are associated with a narrow host range, whereas the presence of hopZ5 and absence of avrRpt2 are most generally associated with a large host range. To better detect the different clusters identified with whole genome sequence and pathogenicity analyses, we used a specific-k-mers approach to refine the MLSA scheme. Using this novel MLSA scheme to type P. syringae isolates from diseased cucurbits would give insight into distribution of worldwide strains and origin of epidemics.

Host Range Determinants of Pseudomonas savastanoi Pathovars of Woody Hosts Revealed by Comparative Genomics and Cross-Pathogenicity Tests

The study of host range determinants within the Pseudomonas syringae complex is gaining renewed attention due to its widespread distribution in non-agricultural environments, evidence of large variability in intra-pathovar host range, and the emergence of new epidemic diseases. This requires the establishment of appropriate model pathosystems facilitating integration of phenotypic, genomic and evolutionary data. Pseudomonas savastanoi pv. savastanoi is a model pathogen of the olive tree, and here we report a closed genome of strain NCPPB 3335, plus draft genome sequences of three strains isolated from oleander (pv. nerii), ash (pv. fraxini) and broom plants (pv. retacarpa). We then conducted a comparative genomic analysis of these four new genomes plus 16 publicly available genomes, representing 20 strains of these four P. savastanoi pathovars of woody hosts. Despite overlapping host ranges, cross-pathogenicity tests using four plant hosts clearly separated these pathovars and lead to pathovar reassignment of two strains. Critically, these functional assays were pivotal to reconcile phylogeny with host range and to define pathovar-specific genes repertoires. We report a pan-genome of 7,953 ortholog gene families and a total of 45 type III secretion system effector genes, including 24 core genes, four genes exclusive of pv. retacarpa and several genes encoding pathovar-specific truncations. Noticeably, the four pathovars corresponded with well-defined genetic lineages, with core genome phylogeny and hierarchical clustering of effector genes closely correlating with pathogenic specialization. Knot-inducing pathovars encode genes absent in the canker-inducing pv. fraxini, such as those related to indole acetic acid, cytokinins, rhizobitoxine, and a bacteriophytochrome. Other pathovar-exclusive genes encode type I, type II, type IV, and type VI secretion system proteins, the phytotoxine phevamine A, a siderophore, c-di-GMP-related proteins, methyl chemotaxis proteins, and a broad collection of transcriptional regulators and transporters of eight different superfamilies. Our combination of pathogenicity analyses and genomics tools allowed us to correctly assign strains to pathovars and to propose a repertoire of host range-related genes in the P. syringae complex.

Phylogenetic Relationships of Pseudomonas syringae pv. syringae Isolates Associated with Bacterial Inflorescence Rot in Grapevine

Pseudomonas syringae pv. syringae causes extensive yield losses in wine-grape production in some Australian cool-climate vineyards. Putative P. syringae pv. syringae isolates from infected grapevines within a range of vineyards were genotyped using RNA polymerase β-subunit (rpoB) and multilocus sequence typing (MLST) using primers for glyceraldehyde-3-phosphate dehydrogenase (gapA), citrate synthase (gltA), DNA gyrase B (gyrB), and σ factor 70 (rpoD). The isolates were also evaluated for pathogenicity by inoculation of detached grapevine leaves. The isolates were grouped by MLST data into two well-supported clades, each containing a mixture of pathogenic and nonpathogenic grapevine isolates, indicating that P. syringae pv. syringae in Australian vineyards is genetically diverse. Each clade also contained P. syringae pv. syringae from nongrape hosts pathogenic to grapevine, demonstrating a lack of host specificity and possible potential for cross-infection of grape and other horticultural crops. Furthermore, the isolation of pathogenic P. syringae pv. syringae isolates from grapevine sucker shoots suggests that sucker shoots may allow overwintering of the pathogen. The vineyard quarantine status of P. syringae pv. syringae may need to be reconsidered, due to its easy dispersal through pruning equipment.

Genomics-Based Exploration of Virulence Determinants and Host-Specific Adaptations of Pseudomonas syringae Strains Isolated from Grasses

The Pseudomonas syringae species complex has recently been named the number one plant pathogen, due to its economic and environmental impacts, as well as for its role in scientific research. The bacterium has been repeatedly reported to cause outbreaks on bean, cucumber, stone fruit, kiwi and olive tree, as well as on other crop and non-crop plants. It also serves as a model organism for research on the Type III secretion system (T3SS) and plant-pathogen interactions. While most of the current work on this pathogen is either carried out on one of three model strains found on dicot plants with completely sequenced genomes or on isolates obtained from recent outbreaks, not much is known about strains isolated from grasses (Poaceae). Here, we use comparative genomics in order to identify putative virulence-associated genes and other Poaceae-specific adaptations in several newly available genome sequences of strains isolated from grass species. All strains possess only a small number of known Type III effectors, therefore pointing to the importance of non-Type III secreted virulence factors. The implications of this finding are discussed.

A Pseudomonas syringae diversity survey reveals a differentiated phylotype of the pathovar syringae associated with the mango host and mangotoxin production

Pseudomonas syringae pv. syringae, the causal agent of bacterial apical necrosis (BAN) in mango crops, has been isolated in different mango-producing areas worldwide. An extensive collection of 87 P. syringae pv. syringae strains isolated from mango trees affected by BAN from different countries, but mainly from Southern Spain, were initially examined by repetitive sequence-based polymerase chain reaction (rep-PCR) to analyze the genetic diversity with an epidemiological aim. rep-PCR was powerful in assessing intrapathovar distribution and also allowing clustering of the P. syringae pv. syringae strains isolated from mango, depending on the isolation area. A clear pattern of clustering was observed for all the P. syringae pv. syringae strains isolated from mango distinct from strains from other hosts, including strains for the same geographical regions as the mango isolates. For this reason, a representative group of 51 P. syringae pv. syringae strains isolated from mango and other hosts, as well as some P. syringae strains from other pathovars, were further characterized to determine their possible genetic, phenotypic, and phylogenetic relationships. Similar to the rep-PCR results, the randomly amplified polymorphic DNA PCR (RAPD-PCR) and catabolic diversity analysis using the Biolog GN2 profile grouped 90% of the mango isolates together in a unique cluster. Interestingly, the majority of P. syringae pv. syringae strains isolated from mango produced mangotoxin. The analysis of the phylogenetic distribution using the multilocus sequence typing analysis strongly supports the existence of a differentiated phylotype of the pathovar syringae mainly associated with the mango host and characterized by the mangotoxin production.