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Student-led experimental evolution reveals novel biofilm regulators of adaptation to multiple niches

https://doi.org/10.1101/2025.06.06.658356

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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yEvo: A modular eukaryotic genetics and evolution research experience for high school students

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Parallel genetic adaptation across environments differing in mode of growth or resource availability

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Structural insights into the regulatory mechanism of the Pseudomonas aeruginosa YfiBNR system

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Identification of a protein required for disulfide bond formation in vivo

inferredcites →https://doi.org/10.1016/j.bbrc.2015.03.160openalex-snapshot

Crystal structures of YfiR from Pseudomonas aeruginosa in two redox states

inferredcites →https://doi.org/10.1016/j.bbrc.2018.10.190openalex-snapshot

Structural analysis of activating mutants of YfiB from Pseudomonas aeruginosa PAO1

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Symmetric competition causes population oscillations in an individual-based model of forest dynamics

inferredcites →https://doi.org/10.1016/j.febslet.2014.11.002openalex-snapshot

Formation and dimerization of the phosphodiesterase active site of the Pseudomonas aeruginosa MorA, a bi‐functional c‐di‐GMP regulator

inferredcites →https://doi.org/10.1016/j.jbc.2024.105659openalex-snapshot

The dual GGDEF/EAL domain enzyme PA0285 is a Pseudomonas species housekeeping phosphodiesterase regulating early attachment and biofilm architecture

inferredcites →https://doi.org/10.1016/j.scib.2021.03.003openalex-snapshot

A novel copper-sensing two-component system for inducing Dsb gene expression in bacteria

inferredcites →https://doi.org/10.1016/j.tim.2014.03.007openalex-snapshot

Getting Wrinkly Spreaders to demonstrate evolution in schools

inferredcites →https://doi.org/10.1016/j.tim.2016.02.019openalex-snapshot

Studying Bacterial Multispecies Biofilms: Where to Start?

inferredcites →https://doi.org/10.1016/j.tim.2022.02.005openalex-snapshot

Population genetics, biofilm recalcitrance, and antibiotic resistance evolution

inferredcites →https://doi.org/10.1016/j.ygeno.2014.09.007openalex-snapshot

Parallel evolution of small colony variants in Burkholderia cenocepacia biofilms

inferredcites →https://doi.org/10.1038/27900openalex-snapshot

Adaptive radiation in a heterogeneous environment

inferredcites →https://doi.org/10.1038/ismej.2010.136openalex-snapshot

Ecological succession in long-term experimentally evolved biofilms produces synergistic communities

inferredcites →https://doi.org/10.1038/nature12155openalex-snapshot

Psl trails guide exploration and microcolony formation in Pseudomonas aeruginosa biofilms

inferredcites →https://doi.org/10.1038/ng.3148openalex-snapshot

Convergent evolution and adaptation of Pseudomonas aeruginosa within patients with cystic fibrosis

inferredcites →https://doi.org/10.1038/nmeth.2019openalex-snapshot

Fiji: an open-source platform for biological-image analysis

inferredcites →https://doi.org/10.1038/nrmicro.2016.190openalex-snapshot

Cyclic di-GMP: second messenger extraordinaire

inferredcites →https://doi.org/10.1038/nrmicro.2016.84openalex-snapshot

Spatial structure, cooperation and competition in biofilms

inferredcites →https://doi.org/10.1038/nrmicro1838openalex-snapshot

Physiological heterogeneity in biofilms

inferredcites →https://doi.org/10.1038/nrmicro821openalex-snapshot

Bacterial biofilms: from the Natural environment to infectious diseases

inferredcites →https://doi.org/10.1038/s41522-020-00173-5openalex-snapshot

The upper respiratory tract microbiome of indigenous Orang Asli in north-eastern Peninsular Malaysia

inferredcites →https://doi.org/10.1038/s41522-020-00178-0openalex-snapshot

Exposure of Salmonella biofilms to antibiotic concentrations rapidly selects resistance with collateral tradeoffs

inferredcites →https://doi.org/10.1038/s41522-021-00260-1openalex-snapshot

Bacteroidales species in the human gut are a reservoir of antibiotic resistance genes regulated by invertible promoters

inferredcites →https://doi.org/10.1038/s41522-022-00323-xopenalex-snapshot

Biofilm cultivation facilitates coexistence and adaptive evolution in an industrial bacterial community

inferredcites →https://doi.org/10.1038/s41564-020-00817-4openalex-snapshot

Quantitative image analysis of microbial communities with BiofilmQ

inferredcites →https://doi.org/10.1038/s41579-019-0158-9openalex-snapshot

Bacteria and archaea on Earth and their abundance in biofilms

inferredcites →https://doi.org/10.1046/j.1365-2958.1998.00797.xopenalex-snapshot

Initiation of biofilm formation in Pseudomonas fluorescens WCS365 proceeds via multiple, convergent signalling pathways: a genetic analysis

inferredcites →https://doi.org/10.1046/j.1365-2958.2003.03670.xopenalex-snapshot

Biofilm formation at the air–liquid interface by the Pseudomonas fluorescens SBW25 wrinkly spreader requires an acetylated form of cellulose

inferredcites →https://doi.org/10.1073/pnas.0602138103openalex-snapshot

Genetic adaptation by Pseudomonas aeruginosa to the airways of cystic fibrosis patients

inferredcites →https://doi.org/10.1073/pnas.1207025110openalex-snapshot

Tangled bank of experimentally evolved Burkholderia biofilms reflects selection during chronic infections

inferredcites →https://doi.org/10.1073/pnas.2008540117openalex-snapshot

One gene, multiple ecological strategies: A biofilm regulator is a capacitor for sustainable diversity

inferredcites →https://doi.org/10.1073/pnas.2117633119openalex-snapshot

The Wsp system of Pseudomonas aeruginosa links surface sensing and cell envelope stress

inferredcites →https://doi.org/10.1073/pnas.90.3.1038openalex-snapshot

A pathway for disulfide bond formation in vivo.

inferredcites →https://doi.org/10.1074/jbc.m003850200openalex-snapshot

Disulfide Bonds Are Generated by Quinone Reduction

inferredcites →https://doi.org/10.1074/jbc.m311391200openalex-snapshot

In Vivo Substrate Specificity of Periplasmic Disulfide Oxidoreductases

inferredcites →https://doi.org/10.1074/jbc.m411774200openalex-snapshot

The Nonconsecutive Disulfide Bond of Escherichia coli Phytase (AppA) Renders It Dependent on the Protein-disulfide Isomerase, DsbC

inferredcites →https://doi.org/10.1086/282258openalex-snapshot

Theory of Fitness in a Heterogeneous Environment. II. Developmental Flexibility and Niche Selection

inferredcites →https://doi.org/10.1093/femsle/fnx109openalex-snapshot

Adaptive radiation of Pseudomonas fluorescens SBW25 in experimental microcosms provides an understanding of the evolutionary ecology and molecular biology of A-L interface biofilm formation

inferredcites →https://doi.org/10.1093/genetics/161.1.33openalex-snapshot

Adaptive Divergence in Experimental Populations of Pseudomonas fluorescens . I. Genetic and Phenotypic Bases of Wrinkly Spreader Fitness

inferredcites →https://doi.org/10.1093/molbev/msab248openalex-snapshot

Polygenic Adaptation and Clonal Interference Enable Sustained Diversity in Experimental Pseudomonas aeruginosa Populations

inferredcites →https://doi.org/10.1099/mic.0.2006/002824-0openalex-snapshot

The structure–function relationship of WspR, a Pseudomonas fluorescens response regulator with a GGDEF output domain

inferredcites →https://doi.org/10.1111/1462-2920.15763openalex-snapshot

Mutations in surface‐sensing receptor WspA lock the Wsp signal transduction system into a constitutively active state

inferredcites →https://doi.org/10.1111/evo.12581openalex-snapshot

Character displacement and the evolution of niche complementarity in a model biofilm community

inferredcites →https://doi.org/10.1111/j.1461-0248.2006.00955.xopenalex-snapshot

The effect of population structure on the adaptive radiation of microbial populations evolving in spatially structured environments

inferredcites →https://doi.org/10.1111/j.1574-6968.2001.tb10772.xopenalex-snapshot

Triclosan: a widely used biocide and its link to antibiotics

inferredcites →https://doi.org/10.1111/j.1574-6976.2002.tb00597.xopenalex-snapshot

O-antigen structural variation: mechanisms and possible roles in animal/plant–microbe interactions

inferredcites →https://doi.org/10.1111/mmi.12013openalex-snapshot

Surface sensing and lateral subcellular localization of WspA , the receptor in a chemosensory‐like system leading to c‐di‐ GMP production

inferredcites →https://doi.org/10.1128/aem.00039-22openalex-snapshot

The c-di-GMP Phosphodiesterase PipA (PA0285) Regulates Autoaggregation and Pf4 Bacteriophage Production in Pseudomonas aeruginosa PAO1

inferredcites →https://doi.org/10.1128/aem.00299-14openalex-snapshot

Deletion Mutant Library for Investigation of Functional Outputs of Cyclic Diguanylate Metabolism in Pseudomonas aeruginosa PA14

inferredcites →https://doi.org/10.1128/aem.00414-12openalex-snapshot

Fluorescence-Based Reporter for Gauging Cyclic Di-GMP Levels in Pseudomonas aeruginosa

inferredcites →https://doi.org/10.1128/aem.01194-19openalex-snapshot

Diguanylate Cyclases and Phosphodiesterases Required for Basal-Level c-di-GMP in Pseudomonas aeruginosa as Revealed by Systematic Phylogenetic and Transcriptomic Analyses

inferredcites →https://doi.org/10.1128/aem.01306-21openalex-snapshot

Evolutionary Divergence of the Wsp Signal Transduction Systems in Beta- and Gammaproteobacteria

inferredcites →https://doi.org/10.1128/aem.02430-07openalex-snapshot

Genetic Tools for Select-Agent-Compliant Manipulation of Burkholderia pseudomallei

inferredcites →https://doi.org/10.1128/aem.02924-20openalex-snapshot

Triclosan Tolerance Is Driven by a Conserved Mechanism in Diverse Pseudomonas Species

inferredcites →https://doi.org/10.1128/ecosalplus.esp-0012-2018openalex-snapshot

Disulfide Bond Formation in the Periplasm of Escherichia coli

inferredcites →https://doi.org/10.1128/jb.00048-16openalex-snapshot

Evolution of Ecological Diversity in Biofilms of Pseudomonas aeruginosa by Altered Cyclic Diguanylate Signaling

inferredcites →https://doi.org/10.1128/jb.00698-09openalex-snapshot

Differential Lipopolysaccharide Core Capping Leads to Quantitative and Correlated Modifications of Mechanical and Structural Properties in Pseudomonas aeruginosa Biofilms

inferredcites →https://doi.org/10.1128/jb.01018-15openalex-snapshot

Laboratory Evolution of Microbial Interactions in Bacterial Biofilms

inferredcites →https://doi.org/10.1128/mbio.00932-20openalex-snapshot

Parallel Evolution of Tobramycin Resistance across Species and Environments

inferredcites →https://doi.org/10.1128/mbio.01698-19openalex-snapshot

Pseudomonas aeruginosa Interstrain Dynamics and Selection of Hyperbiofilm Mutants during a Chronic Infection

inferredcites →https://doi.org/10.1128/msphere.01216-20openalex-snapshot

Phenotypic and Genotypic Adaptations in Pseudomonas aeruginosa Biofilms following Long-Term Exposure to an Alginate Oligomer Therapy

inferredcites →https://doi.org/10.1128/msystems.00737-22openalex-snapshot

Identification of Cyclic-di-GMP-Modulating Protein Residues by Bidirectionally Evolving a Social Behavior in Pseudomonas fluorescens

inferredcites →https://doi.org/10.1146/annurev-micro-012120-063427openalex-snapshot

Surface Sensing and Adaptation in Bacteria

inferredcites →https://doi.org/10.1146/annurev.ecolsys.31.1.343openalex-snapshot

Mechanisms of Maintenance of Species Diversity

inferredcites →https://doi.org/10.1146/annurev.micro.58.030603.123654openalex-snapshot

The Ecology and Genetics of Microbial Diversity

inferredcites →https://doi.org/10.1186/s12052-019-0103-4openalex-snapshot

EvolvingSTEM: a microbial evolution-in-action curriculum that enhances learning of evolutionary biology and biotechnology

inferredcites →https://doi.org/10.1371/journal.ppat.1000804openalex-snapshot

YfiBNR Mediates Cyclic di-GMP Dependent Small Colony Variant Formation and Persistence in Pseudomonas aeruginosa

inferredcites →https://doi.org/10.1371/journal.ppat.1002760openalex-snapshot

The YfiBNR Signal Transduction Mechanism Reveals Novel Targets for the Evolution of Persistent Pseudomonas aeruginosa in Cystic Fibrosis Airways

inferredcites →https://doi.org/10.1534/genetics.106.069906openalex-snapshot

Adaptive Divergence in Experimental Populations of Pseudomonas fluorescens. III. Mutational Origins of Wrinkly Spreader Diversity

inferredcites →https://doi.org/10.1534/genetics.109.107110openalex-snapshot

Adaptive Divergence in Experimental Populations ofPseudomonas fluorescens. IV. Genetic Constraints Guide Evolutionary Trajectories in a Parallel Adaptive Radiation

inferredcites →https://doi.org/10.1534/genetics.113.154948openalex-snapshot

Adaptive Divergence in Experimental Populations of Pseudomonas fluorescens . V. Insight into the Niche Specialist Fuzzy Spreader Compels Revision of the Model Pseudomonas Radiation

inferredcites →https://doi.org/10.3389/fevo.2018.00010openalex-snapshot

Negative Frequency-Dependent Selection Is Frequently Confounding

inferredcites →https://doi.org/10.3389/fgene.2015.00018openalex-snapshot

There and back again: consequences of biofilm specialization under selection for dispersal

inferredcites →https://doi.org/10.3389/fmicb.2011.00118openalex-snapshot

Genetic and Functional Diversity of Pseudomonas aeruginosa Lipopolysaccharide

inferredcites →https://doi.org/10.3389/fmicb.2022.949597openalex-snapshot

Phenotypic and integrated analysis of a comprehensive Pseudomonas aeruginosa PAO1 library of mutants lacking cyclic-di-GMP-related genes

inferredcites →https://doi.org/10.7554/elife.47612openalex-snapshot

Evolutionary pathways to antibiotic resistance are dependent upon environmental structure and bacterial lifestyle

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1101/2025.07.18.665463openalex-snapshot

The yEvo Mutation Browser: Enhancing student understanding of experimental evolution and genomics through interactive data visualization

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