ArticlePLoS genetics2012
Comparative genomics of plant-associated Pseudomonas spp.: insights into diversity and inheritance of traits involved in multitrophic interactions.
Article in PLoS genetics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 304 papers, 1 of them a synthesis that pooled it.
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Who cites it
304 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Bacillus drives functional states in synthetic plant root bacterial communities.Genome biology · 2025Pooled it
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- Isolation, biochemical characterization, and antimicrobial activities of EPS-producing bacterial endophytes from Moringa oleifera.Folia microbiologica · 2026Article
- Beyond the Usual Suspects: EmergingInternational journal of molecular sciences · 2026Review
- Plant growth-promoting Pseudomonas strains modulate potato tuberization signalling and development.Journal of experimental botany · 2026Article
- Engineering Pseudomonas protegens as a Targeted Antifungal-Effector Delivery Chassis via Heterologous Type III Secretion System Reconstitution.Microbial biotechnology · 2026Article
- From genome to lifestyle: adaptive strategies ofApplied and environmental microbiology · 2026Article
- Functional characterization of Pseudomonas soli VMAP1 as a biocontrol agent against Xanthomonas vesicatoria in tomato plants.Scientific reports · 2026Article
- Astragalus verus, a miracle in de-desertification or a surprising niche for ecologically adaptable bacteria?BMC plant biology · 2026Article
- Characterization and genetic diversity of pseudomonads population from highbush blueberry in western Canada.Applied microbiology and biotechnology · 2026Article
- Isolation and Genomic Characterization of a Novel Japanese Strain of Pseudomonas protegens and an Evaluation of Its Biocontrol Potential.Microbes and environments · 2026Article
- Lineage-restricted genomic islands drive rhizosphere niche specialization inISME communications · 2026Article
- Predicting Strain-Specific Metabolic Capabilities in the GenusComputational and structural biotechnology journal · 2026Article
- GacA uses two distinct regulatory mechanisms to control the biosynthesis of 2,4-diacetylphloroglucinol inApplied and environmental microbiology · 2025Article
- Fluorescent Pseudomonas spp. from suppressive and conducive soils share genomic and functional traits relevant to Fusarium graminearum disease suppression.BMC genomics · 2025Article
- Integrated genomic and mutagenesis analysis of Pseudomonas argentinensis SA190 reveals mechanisms of plant root colonization and stress resilience.BMC microbiology · 2025Article
- Wild rice-associatedmSystems · 2025Article
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- Native Bacteria Are Effective Biocontrol Agents at a Wide Range of Temperatures ofPlants (Basel, Switzerland) · 2025Article
- Interspecies signaling modulates the biosynthesis of antimicrobial secondary metabolites related to biological control activities ofMicrobiology spectrum · 2025Article
244 more citing papers are in PubMed but not listed here.
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Authors and funding
35 authors.
Funding
No grant is acknowledged in the PubMed record.
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.
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