Comparative Genomics of Multiple Strains of Pseudomonas cannabina pv. alisalensis, a Potential Model Pathogen of Both Monocots and Dicots

Sarris, Panagiotis F.; Trantas, Emmanouil; Baltrus, David A.; Bull, Carolee T.; Wechter, W. Patrick; Yan, Shuangchun; Ververidis, Filippos; Almeida, Nalvo F.; Jones, Corbin D.; Dangl, Jeffery L.; Panopoulos, Nickolas J.; Vinatzer, Boris A.; Goumas, Dimitrios E.

doi:10.1371/journal.pone.0059366

Cited by 35 publications

(25 citation statements)

References 67 publications

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“…In this regard, other studies have outlined the close phylogenetic relationships between such strains with the strains of P. avellanae species [18,20,47]. A further and relevant confirmation of the strong relationships between members of the P.…”

Section: Discussionmentioning

confidence: 63%

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A Genomic Redefinition of Pseudomonas avellanae species

et al. 2013

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The circumscription of bacterial species is a complex task. So far, DNA-DNA hybridization (DDH), 16S rRNA gene sequencing, and multiocus sequence typing analysis (MLSA) are currently the preferred techniques for their genetic determination. However, the average nucleotide identity (ANI) analysis of conserved and shared genes between two bacterial strains based on the pair-wise genome comparisons, with support of the tetranucleotide frequency correlation coefficients (TETRA) value, has recently been proposed as a reliable substitute for DDH. The species demarcation boundary has been set to a value of 95-96% of the ANI identity, with further confirmation through the assessment of the corresponding TETRA value. In this study, we performed a genome-wide MLSA of 14 phytopathogenic pseudomonads genomes, and assessed the ANI and TETRA values of 27 genomes, representing seven out of the nine genomospecies of Pseudomonas spp. sensu Gardan et alii, and their phylogenetic relationships using maximum likelihood and Bayesian approaches. The results demonstrate the existence of a well demarcated genomic cluster that includes strains classified as P. avellanae, P. syringae pv. theae, P. s. pv. actinidiae and one P. s. pv. morsprunorum strain all belonging to the single species P. avellanae. In addition, when compared with P. avellanae, five strains of P. s. pv. tomato, including the model strain DC3000, and one P. s. pv. lachrymans strain, appear as very closely related to P. avellanae, with ANI values of nearly 96% as confirmed by the TETRA analysis. Conversely, one representative strain, previously classified as P. avellanae and isolated in central Italy, is a genuine member of the P. syringae species complex and can be defined as P. s. pv. avellanae. Currently. The core and pan genomes of P. avellanae species consist of 3,995 and 5,410 putative protein-coding genes, respectively.

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Section: Discussionmentioning

confidence: 63%

“…avellanae as a distinct bacterial species [12,13,14,15], several other relevant studies aimed at comparing phytopathogenic bacteria and/or inferring evolutionary relationships among them, have followed the MLSA analysis of Wang et al [11] and refer to two P. s. pv. avellanae phylogroups [16,17,18,19,20]. …”

Section: Introductionmentioning

confidence: 99%

A Genomic Redefinition of Pseudomonas avellanae species

et al. 2013

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“…; Sarris et al . ) that can affect infection success. It is unknown whether genomic variation among closely related Pseudomonas spp.…”

Section: Discussionmentioning

confidence: 99%

Diversity and abundance of phyllosphere bacteria are linked to insect herbivory

et al. 2014

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Simultaneous or sequential attack by herbivores and microbes is common in plants. Many seed plants exhibit a defence trade-off against chewing herbivorous insects and leaf-colonizing ('phyllosphere') bacteria, which arises from cross-talk between the phytohormones jasmonic acid (JA, induced by many herbivores) and salicylic acid (SA, induced by many bacteria). This cross-talk may promote reciprocal susceptibility in plants between phyllosphere bacteria and insect herbivores. In a population of native bittercress (Cardamine cordifolia, Brassicaceae), we tested whether simulating prior damage with JA or SA treatment induced resistance or susceptibility (respectively) to chewing herbivores. In parallel, we conducted culture-dependent surveys of phyllosphere bacteria to test the hypothesis that damage by chewing herbivores correlates positively with bacterial abundance in leaves. Finally, we tested whether bacterial infection induced susceptibility to herbivory by a major chewing herbivore of bittercress, Scaptomyza nigrita (Drosophilidae). Overall, our results suggest that reciprocal susceptibility to herbivory and microbial attack occurs in bittercress. We found that JA treatment reduced and SA treatment increased S. nigrita herbivory in bittercress in the field. Bacterial abundance was higher in herbivore-damaged vs. undamaged leaves (especially Pseudomonas syringae). However, Pedobacter spp. and Pseudomonas fluorescens infections were negatively associated with herbivory. Experimental Pseudomonas spp. infections increased S. nigrita herbivory in bittercress. Thus, plant defence signalling trade-offs can have important ecological consequences in nature that may be reflected in a positive correlation between herbivory and phyllosphere bacterial abundance and diversity. Importantly, the strength and direction of this association varies within and among prevalent bacterial groups.

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“…alisalensis strains, one orthologous to the T6SS-II cluster of strain DC3000, while the other is more closely related to T6SS-I from P. aeruginosa PAO1. The absence of orthologs of Tse effectors in these strains hints to significant differences in the biological function of these systems (Sarris et al, 2013). Two T6SS islands were equally found in Pseudomonas mendocina, homologous to HSI-I and HSI-II from PAO1, while Pseudomonas entomophila carries one HSI-II-like locus (Sarris & Scoulica, 2011).…”

Section: Multiplicity Of T6sss In Pseudomonadsmentioning

confidence: 99%

Ribosomally encoded antibacterial proteins and peptides fromPseudomonas

2014

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Members of the Pseudomonas genus produce diverse secondary metabolites affecting other bacteria, fungi or predating nematodes and protozoa but are also equipped with the capacity to secrete different types of ribosomally encoded toxic peptides and proteins, ranging from small microcins to large tailocins. Studies with the human pathogen Pseudomonas aeruginosa have revealed that effector proteins of type VI secretion systems are part of the antibacterial armamentarium deployed by pseudomonads. A novel class of antibacterial proteins with structural similarity to plant lectins was discovered by studying antagonism among plant-associated Pseudomonas strains. A genomic perspective on pseudomonad bacteriocinogeny shows that the modular architecture of S pyocins of P. aeruginosa is retained in a large diversified group of bacteriocins, most of which target DNA or RNA. Similar modularity is present in as yet poorly characterized Rhs (recombination hot spot) proteins and CDI (contact-dependent inhibition) proteins. Well-delimited domains for receptor recognition or cytotoxicity enable the design of chimeric toxins with novel functionalities, which has been applied successfully for S and R pyocins. Little is known regarding how these antibacterials are released and ultimately reach their targets. Other remaining issues concern the identification of environmental triggers activating these systems and assessment of their ecological impact in niches populated by pseudomonads.

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Comparative Genomics of Multiple Strains of Pseudomonas cannabina pv. alisalensis, a Potential Model Pathogen of Both Monocots and Dicots

Cited by 35 publications

References 67 publications

A Genomic Redefinition of Pseudomonas avellanae species

A Genomic Redefinition of Pseudomonas avellanae species

Diversity and abundance of phyllosphere bacteria are linked to insect herbivory

Ribosomally encoded antibacterial proteins and peptides fromPseudomonas

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