ArticleProceedings of the National Academy of Sciences of the United States of America2014
Strain-specific parallel evolution drives short-term diversification during Pseudomonas aeruginosa biofilm formation.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 67 papers.
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Who cites it
67 citing papers in PubMed, 100 citations in OpenAlex.
- Intermittent antibiotic exposure of Escherichia coli biofilms drives resistance in catheter-associated infection models.NPJ biofilms and microbiomes · 2026Article
- Mutations in filamentous bacteriophages spark eco-evolutionary feedbacks in Pseudomonas aeruginosa.The ISME journal · 2026Article
- Filamentous bacteriophages: impact on prokaryotic virulence, eukaryotic immunity, and implications for phage therapy.Frontiers in immunology · 2026Review
- Competition between Pseudomonas species constrains ecological diversification in polymicrobial biofilms.NPJ biofilms and microbiomes · 2025Article
- Filamentous cheater phages drive bacterial and phage populations to lower fitness.bioRxiv : the preprint server for biology · 2025Article
- Crosstalk between inovirus core gene and accessory toxin-antitoxin system mediates polylysogeny.Nature communications · 2025Article
- Control of lysogeny and antiphage defense by a prophage-encoded kinase-phosphatase module.Nature communications · 2024Article
- Review
- VIBES: a workflow for annotating and visualizing viral sequences integrated into bacterial genomes.NAR genomics and bioinformatics · 2024Article
- Targeted deletion of Pf prophages from diverseJournal of bacteriology · 2024Article
- Filamentous prophage Pf4 promotes genetic exchange in Pseudomonas aeruginosa.The ISME journal · 2024Article
- Divergent molecular strategies drive evolutionary adaptation to competitive fitness in biofilm formation.The ISME journal · 2024Article
- Secondary messenger signalling influences Pseudomonas aeruginosa adaptation to sinus and lung environments.The ISME journal · 2024Article
- Inhibition of PQS signaling by the Pf bacteriophage protein PfsE enhances viral replication in Pseudomonas aeruginosa.Molecular microbiology · 2024Article
- Targeted deletion of Pf prophages from diversebioRxiv : the preprint server for biology · 2023Article
- VIBES: A Workflow for Annotating and Visualizing Viral Sequences Integrated into Bacterial Genomes.bioRxiv : the preprint server for biology · 2023Article
- Article
- Tripartite interactions between filamentous Pf4 bacteriophage, Pseudomonas aeruginosa, and bacterivorous nematodes.PLoS pathogens · 2023Article
- Alkyl-quinolone-dependent quorum sensing controls prophage-mediated autolysis inFrontiers in cellular and infection microbiology · 2023Article
- Pf4 Phage Variant Infection Reduces Virulence-Associated Traits inMicrobiology spectrum · 2022Article
7 more citing papers are in PubMed but not listed here.
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Authors and funding
8 authors at 4 institutions in 3 countries.
Funding
Abstract
Generation of genetic diversity is a prerequisite for bacterial evolution and adaptation. Short-term diversification and selection within populations is, however, largely uncharacterised, as existing studies typically focus on fixed substitutions. Here, we use whole-genome deep-sequencing to capture the spectrum of mutations arising during biofilm development for two Pseudomonas aeruginosa strains. This approach identified single nucleotide variants with frequencies from 0.5% to 98.0% and showed that the clinical strain 18A exhibits greater genetic diversification than the type strain PA01, despite its lower per base mutation rate. Mutations were found to be strain specific: the mucoid strain 18A experienced mutations in alginate production genes and a c-di-GMP regulator gene; while PA01 acquired mutations in PilT and PilY1, possibly in response to a rapid expansion of a lytic Pf4 bacteriophage, which may use type IV pili for infection. The Pf4 population diversified with an evolutionary rate of 2.43 × 10(-3) substitutions per site per day, which is comparable to single-stranded RNA viruses. Extensive within-strain parallel evolution, often involving identical nucleotides, was also observed indicating that mutation supply is not limiting, which was contrasted by an almost complete lack of noncoding and synonymous mutations. Taken together, these results suggest that the majority of the P. aeruginosa genome is constrained by negative selection, with strong positive selection acting on an accessory subset of genes that facilitate adaptation to the biofilm lifecycle. Long-term bacterial evolution is known to proceed via few, nonsynonymous, positively selected mutations, and here we show that similar dynamics govern short-term, within-population bacterial diversification.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.