Comparative Genomics of Plant-Associated Pseudomonas spp.: Insights into Diversity and Inheritance of Traits Involved in Multitrophic Interactions

Abstract

We provide here a comparative genome analysis of ten strains within the Pseudomonas fluorescens group including seven new genomic sequences. These strains exhibit a diverse spectrum of traits involved in biological control and other multitrophic interactions with plants, microbes, and insects. Multilocus sequence analysis placed the strains in three sub-clades, which was reinforced by high levels of synteny, size of core genomes, and relatedness of orthologous genes between strains within a sub-clade. The heterogeneity of the P. fluorescens group was reflected in the large size of its pan-genome, which makes up approximately 54% of the pan-genome of the genus as a whole, and a core genome representing only 45–52% of the genome of any individual strain. We discovered genes for traits that were not known previously in the strains, including genes for the biosynthesis of the siderophores achromobactin and pseudomonine and the antibiotic 2-hexyl-5-propyl-alkylresorcinol; novel bacteriocins; type II, III, and VI secretion systems; and insect toxins. Certain gene clusters, such as those for two type III secretion systems, are present only in specific sub-clades, suggesting vertical inheritance. Almost all of the genes associated with multitrophic interactions map to genomic regions present in only a subset of the strains or unique to a specific strain. To explore the evolutionary origin of these genes, we mapped their distributions relative to the locations of mobile genetic elements and repetitive extragenic palindromic (REP) elements in each genome. The mobile genetic elements and many strain-specific genes fall into regions devoid of REP elements (i.e., REP deserts) and regions displaying atypical tri-nucleotide composition, possibly indicating relatively recent acquisition of these loci. Collectively, the results of this study highlight the enormous heterogeneity of the P. fluorescens group and the importance of the variable genome in tailoring individual strains to their specific lifestyles and functional repertoire.

Heavy metal tolerant Pseudomonas protegens isolates from agricultural well water in northeastern Algeria with plant growth promoting, insecticidal and antifungal activities

“…The isolates S4LiBe and S5LiBe are very similar (99.8% 16SrRNA gene similarity) to each other and are very closely related (99.4 to 99.7%) to the P. protegens strains CHA0 T and Pf-5 [44]. However, a definite phylogenetic clarification would need further analysis based on concatenated alignments of several household genes [30,42], because 16S rRNA analysis alone cannot conclusively resolve very closely related species, like in the Pseudomonas fluorescens cluster.…”

“…have been broadly studied for their roles in plant growth promotion and biological control [16,17,21,25,30,46,59]. Plant growth promoting activities of Pseudomonas spp.…”

Insect pathogenicity in plant-beneficial pseudomonads: phylogenetic distribution and comparative genomics

“…All these features make fluorescent pseudomonads interesting organisms for use as biofertilizers and biopesticides in sustainable agriculture and several products have been commercialized . On top of plant-beneficial activity, genomics has revealed unexpected and broader ecological versatility for these bacteria (Paulsen et al, 2005;Loper et al, 2012). Three of the best-characterized biocontrol strains, Pseudomonas protegens strains CHA0 and Pf-5 and Pseudomonas chlororaphis PCL1391, were shown to have potent insecticidal activity (Péchy-Tarr et al, 2008;Ruffner et al, 2013).…”

“…A survey by Ruffner et al (2015) revealed that sub-clade 2 strains (Loper et al, 2012) neither harbor fit genes nor have ability to kill G. mellonella larvae. In contrast, all tested P. protegens and P. chlororaphis strains, which represent the sub-clade 1 (Loper et al, 2012), have both the toxin and injectable activity. Accordingly, Pseudomonas sp.…”

Evolutionary history predicts the stability of cooperation in microbial communities

“…40). Although classified as P. fluorescens, recent comparative genomics studies indicate that they belong to at least three species 41 . Forty-eight communities were assembled from the eight genotypes, covering a richness of one (each of the eight genotypes in monoculture with two replicates each), two (16 combinations), four (12 combinations) and eight genotypes (4 replicates), according to a previously published design 19 .…”