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

By J. Loper, Karl A. Hassan, D. Mavrodi, Edward W. Davis, Chee Kent Lim, B. T. Shaffer, Liam D. H. Elbourne, V. Stockwell, Sierra L. Hartney, Katy Breakwell and 25 more. PLoS Genetics, 2012

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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.

Subfields: Plant Science

View Paper: https://www.semanticscholar.org/paper/26f5737961058b2705ade396b2fdc69c7742dd48

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Citations in the corpus

Plant growth promotion induced by phosphate solubilizing endophytic Pseudomonas isolates (2015, background): “Pseudomonas fluorescens Loper et al., 2012 NZ_CM001513.”
Pseudomonas simiae WCS417: star track of a model beneficial rhizobacterium (2020, background): “Many root-associated Pseudomonas sp. strains possess BGCs for the production of antimicrobial compounds, such as cyclic lipopeptide biosurfactants, 2,4- diacetylphloroglucinol, phenazines, hydrogen cyanide, and pyrrolnitrin (Loper et al. 2012).”
Induced systemic resistance by beneficial microbes. (2014, background): “Possible mechanisms of disease suppression include competition for space and (micro)nutrients; hyperparasitism; antagonism via microbial production of secondary metabolites, such as iron-chelating siderophores, antibiotics, and lytic enzymes; and elicitation of ISR (75, 110, 182) (Figure 3).”
Probiotic Pseudomonas communities enhance plant growth and nutrient assimilation via diversity-mediated ecosystem functioning (2017, positive): “All strains have been extensively investigated in relation to their ability to promote plant growth (Loper et al., 2012) and to affect biodiversity-ecosystem functioning in microbial communities (Hu et al., 2016; Jousset, Schmid, Scheu and Eisenhauer, 2011) (for more details see Table S1).”