<br><div> <head profile="http://www.w3.org/1999/xhtml/vocab"> <!--[if IE]><![endif]--> <meta http-equiv="Content-Type" content="text/html; charset=utf-8"/> <link rel="dns-prefetch" href="//scholar.google.com"/> <link rel="dns-prefetch" href="//pnas-movie.glencoesoftware.com"/> <link rel="dns-prefetch" href="//www.google.com"/> <link rel="dns-prefetch" href="//www.google-analytics.com"/> <link rel="dns-prefetch" href="//stats.g.doubleclick.net"/> <meta name="viewport" content="initial-scale=1, maximum-scale=1, width=device-width, user-scalable=yes"/> <link rel="shortcut icon" href="https://www.pnas.org/sites/default/files/images/favicon.ico" type="image/vnd.microsoft.icon"/> <link rel="canonical" href="https://www.pnas.org/content/early/2020/08/18/2008540117"/> <meta name="Generator" content="Drupal 7 (http://drupal.org)"/> <link rel="alternate" type="application/pdf" title="Full Text (PDF)" href="http://www.pnas.org/content/early/2020/08/18/2008540117.full.pdf"/> <link rel="alternate" type="text/plain" title="Full Text (Plain)" href="http://www.pnas.org/content/early/2020/08/18/2008540117.full.txt"/> <link rel="alternate" type="application/vnd.ms-powerpoint" title="Powerpoint" href="http://www.pnas.org/content/early/2020/08/18/2008540117.ppt"/> <meta name="citation_funding_source" content="citation_funder_id=100000057;citation_grant_number=R01GM110444;"/> <meta name="citation_funding_source" content="citation_funder_id=100000104;citation_grant_number=NAI CAN-7 NNA15BB04A;"/> <meta name="type" content="article"/> <meta name="category" content="research-article"/> <meta name="HW.identifier" content="/pnas/early/2020/08/18/2008540117.atom"/> <meta name="HW.pisa" content="pnas;2008540117v1"/> <meta name="DC.Format" content="text/html"/> <meta name="DC.Language" content="en"/> <meta name="DC.Title" content="One gene, multiple ecological strategies: A biofilm regulator is a capacitor for sustainable diversity"/> <meta name="DC.Identifier" content="10.1073/pnas.2008540117"/> <meta name="DC.Date" content="2020-08-19"/> <meta name="DC.Publisher" content="National Academy of Sciences"/> <meta name="DC.Rights" content="Copyright © 2020 the Author(s). Published by PNAS.. https://creativecommons.org/licenses/by-nc-nd/4.0/This open access article is distributed under Creative Commons Attribution-NonCommercial-NoDerivatives License 4.0 (CC BY-NC-ND)."/> <meta name="DC.AccessRights" content="open-access"/> <meta name="DC.Description" content="Many organisms, including bacteria, live in fluctuating environments that require attachment and dispersal. These lifestyle decisions require processing of multiple external signals by several genetic pathways, but how they are integrated is largely unknown. We conducted multiple evolution experiments totaling >20,000 generations with Burkholderia cenocepacia populations grown in a model of the biofilm life cycle and identified parallel mutations in one gene, rpfR , that is a conserved central regulator. Because RpfR has multiple sensor and catalytic domains, different mutations can produce different ecological strategies that can coexist and even increase net growth. This study demonstrates that a single gene may coordinate complex life histories in biofilm-dwelling bacteria and that selection in defined environments can reshape niche breadth by single mutations. Many bacteria cycle between sessile and motile forms in which they must sense and respond to internal and external signals to coordinate appropriate physiology. Maintaining fitness requires genetic networks that have been honed in variable environments to integrate these signals. The identity of the major regulators and how their control mechanisms evolved remain largely unknown in most organisms. During four different evolution experiments with the opportunist betaproteobacterium Burkholderia cenocepacia in a biofilm model, mutations were most frequently selected in the conserved gene rpfR . RpfR uniquely integrates two major signaling systems—quorum sensing and the motile–sessile switch mediated by cyclic-di-GMP—by two domains that sense, respond to, and control the synthesis of the autoinducer cis-2-dodecenoic acid (BDSF). The BDSF response in turn regulates the activity of diguanylate cyclase and phosphodiesterase domains acting on cyclic-di-GMP. Parallel adaptive substitutions evolved in each of these domains to produce unique life history strategies by regulating cyclic-di-GMP levels, global transcriptional responses, biofilm production, and polysaccharide composition. These phenotypes translated into distinct ecology and biofilm structures that enabled mutants to coexist and produce more biomass than expected from their constituents grown alone. This study shows that when bacterial populations are selected in environments challenging the limits of their plasticity, the evolved mutations not only alter genes at the nexus of signaling networks but also reveal the scope of their regulatory functions. RNA sequencing data have been deposited in the National Center for Biotechnology Information (NCBI) BioProject database under accession no. [PRJNA607303][1]. [1]: https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA607303"/> <meta name="DC.Contributor" content="Eisha Mhatre"/> <meta name="DC.Contributor" content="Daniel J. Snyder"/> <meta name="DC.Contributor" content="Emily Sileo"/> <meta name="DC.Contributor" content="Caroline B. Turner"/> <meta name="DC.Contributor" content="Sean W. Buskirk"/> <meta name="DC.Contributor" content="Nicolas L. Fernandez"/> <meta name="DC.Contributor" content="Matthew B. Neiditch"/> <meta name="DC.Contributor" content="Christopher M. Waters"/> <meta name="DC.Contributor" content="Vaughn S. Cooper"/> <meta name="article:published_time" content="2020-08-19"/> <meta name="article:section" content="Biological Sciences"/> <meta name="citation_title" content="One gene, multiple ecological strategies: A biofilm regulator is a capacitor for sustainable diversity"/> <meta name="citation_abstract" lang="en" content="<p>Many bacteria cycle between sessile and motile forms in which they must sense and respond to internal and external signals to coordinate appropriate physiology. Maintaining fitness requires genetic networks that have been honed in variable environments to integrate these signals. The identity of the major regulators and how their control mechanisms evolved remain largely unknown in most organisms. During four different evolution experiments with the opportunist betaproteobacterium <i>Burkholderia cenocepacia</i> in a biofilm model, mutations were most frequently selected in the conserved gene <i>rpfR</i>. RpfR uniquely integrates two major signaling systems—quorum sensing and the motile–sessile switch mediated by cyclic-di-GMP—by two domains that sense, respond to, and control the synthesis of the autoinducer cis-2-dodecenoic acid (BDSF). The BDSF response in turn regulates the activity of diguanylate cyclase and phosphodiesterase domains acting on cyclic-di-GMP. Parallel adaptive substitutions evolved in each of these domains to produce unique life history strategies by regulating cyclic-di-GMP levels, global transcriptional responses, biofilm production, and polysaccharide composition. These phenotypes translated into distinct ecology and biofilm structures that enabled mutants to coexist and produce more biomass than expected from their constituents grown alone. This study shows that when bacterial populations are selected in environments challenging the limits of their plasticity, the evolved mutations not only alter genes at the nexus of signaling networks but also reveal the scope of their regulatory functions.</p>"/> <meta name="citation_abstract" lang="en" scheme="executive-summary" content="<h3>Significance</h3> <p>Many organisms, including bacteria, live in fluctuating environments that require attachment and dispersal. These lifestyle decisions require processing of multiple external signals by several genetic pathways, but how they are integrated is largely unknown. We conducted multiple evolution experiments totaling &gt;20,000 generations with <i>Burkholderia cenocepacia</i> populations grown in a model of the biofilm life cycle and identified parallel mutations in one gene, <i>rpfR</i>, that is a conserved central regulator. Because RpfR has multiple sensor and catalytic domains, different mutations can produce different ecological strategies that can coexist and even increase net growth. This study demonstrates that a single gene may coordinate complex life histories in biofilm-dwelling bacteria and that selection in defined environments can reshape niche breadth by single mutations.</p>"/> <meta name="citation_journal_title" content="Proceedings of the National Academy of Sciences"/> <meta name="citation_publisher" content="National Academy of Sciences"/> <meta name="citation_publication_date" content="2020/08/19"/> <meta name="citation_mjid" content="pnas;2008540117v1"/> <meta name="citation_id" content="2008540117v1"/> <meta name="citation_public_url" content="https://www.pnas.org/content/early/2020/08/18/2008540117"/> <meta name="citation_abstract_html_url" content="https://www.pnas.org/content/early/2020/08/18/2008540117.abstract"/> <meta name="citation_full_html_url" content="https://www.pnas.org/content/early/2020/08/18/2008540117.full"/> <meta name="citation_pdf_url" content="https://www.pnas.org/content/pnas/early/2020/08/18/2008540117.full.pdf"/> <meta name="citation_issn" content="0027-8424"/> <meta name="citation_issn" content="1091-6490"/> <meta name="citation_journal_abbrev" content="PNAS"/> <meta name="citation_doi" content="10.1073/pnas.2008540117"/> <meta name="citation_num_pages" content="11"/> <meta name="citation_article_type" content="Research Article"/> <meta name="citation_section" content="Biological Sciences"/> <meta name="citation_access" content="all"/> <meta name="citation_author" content="Eisha Mhatre"/> <meta name="citation_author_institution" content="University of Pittsburgh School of Medicine"/> <meta name="citation_author_institution" content="Center for Evolutionary Biology and Medicine"/> <meta name="citation_author_institution" content="University of Pittsburgh"/> <meta name="citation_author_orcid" content="https://orcid.org/0000-0001-7203-2632"/> <meta name="citation_author" content="Daniel J. Snyder"/> <meta name="citation_author_institution" content="University of Pittsburgh School of Medicine"/> <meta name="citation_author_institution" content="Center for Evolutionary Biology and Medicine"/> <meta name="citation_author_institution" content="University of Pittsburgh"/> <meta name="citation_author" content="Emily Sileo"/> <meta name="citation_author_institution" content="University of Pittsburgh School of Medicine"/> <meta name="citation_author_orcid" content="https://orcid.org/0000-0003-3032-7373"/> <meta name="citation_author" content="Caroline B. Turner"/> <meta name="citation_author_institution" content="University of Pittsburgh School of Medicine"/> <meta name="citation_author_institution" content="Center for Evolutionary Biology and Medicine"/> <meta name="citation_author_institution" content="University of Pittsburgh"/> <meta name="citation_author" content="Sean W. 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Yan;citation_title=Bow-tie signaling in c-di-GMP: Machine learning in a simple biochemical network;citation_pages=e1005677;citation_volume=13;citation_year=2017;citation_doi=10.1371/journal.pcbi.1005677"/> <meta name="citation_reference" content="citation_journal_title=Environ. Microbiol.;citation_author=L. Townsley;citation_author=F. H. Yildiz;citation_title=Temperature affects c-di-GMP signalling and biofilm formation in Vibrio cholerae;citation_pages=4290-4305;citation_volume=17;citation_year=2015"/> <meta name="citation_reference" content="citation_journal_title=Nucleic Acids Res.;citation_author=T. N. Dalia;citation_title=Enhancing multiplex genome editing by natural transformation (MuGENT) via inactivation of ssDNA exonucleases;citation_pages=7527-7537;citation_volume=45;citation_year=2017;citation_pmid=28575400;citation_doi=10.1093/nar/gkx496"/> <meta name="citation_reference" content="citation_journal_title=J. Bacteriol.;citation_author=K. M. Dahlstrom;citation_title=A multimodal strategy used by a large c-di-GMP network;citation_pages=e00703-e00717;citation_volume=200;citation_year=2018"/> <meta name="citation_reference" content="citation_journal_title=mBio;citation_author=Y. Luo;citation_title=A hierarchical cascade of second messengers regulates Pseudomonas aeruginosa surface behaviors;citation_pages=e02456-14;citation_volume=6;citation_year=2015;citation_pmid=25626906;citation_doi=10.1128/mBio.02456-14"/> <meta name="citation_reference" content="citation_journal_title=Environmental Microbiology (Print);citation_journal_abbrev=Environmental Microbiology (Print);citation_author=L. Vial;citation_author=A. Chapalain;citation_author=M.-C. Groleau;citation_author=E. Déziel;citation_title=The various lifestyles of the Burkholderia cepacia complex species: a tribute to adaptation.;citation_pages=1-12;citation_volume=13;citation_year=2011;citation_issue=1;citation_pmid=20880095;citation_doi=10.1111/j.1462-2920.2010.02343.x"/> <meta name="citation_reference" content="citation_journal_title=Front. Microbiol.;citation_author=A. M. Richter;citation_title=Key players and individualists of cyclic-di-GMP signaling in Burkholderia cenocepacia;citation_pages=3286;citation_volume=9;citation_year=2019"/> <meta name="citation_reference" content="citation_journal_title=Molecular microbiology;citation_journal_abbrev=Mol Microbiol;citation_author=B. Huber;citation_title=Genetic analysis of functions involved in the late stages of biofilm development in Burkholderia cepacia H111.;citation_pages=411-426;citation_volume=46;citation_year=2002;citation_issue=2;citation_pmid=12406218;citation_doi=10.1046/j.1365-2958.2002.03182.x"/> <meta name="citation_reference" content="citation_journal_title=Proc. Natl. Acad. Sci. U.S.A.;citation_author=Y. Deng;citation_title=Cis-2-dodecenoic acid receptor RpfR links quorum-sensing signal perception with regulation of virulence through cyclic dimeric guanosine monophosphate turnover;citation_volume=109;citation_year=2012;citation_pmid=22949660;citation_doi=10.1073/pnas.1205037109"/> <meta name="citation_reference" content="citation_journal_title=PLoS Biol.;citation_author=E. J. Waldron;citation_title=Structural basis of DSF recognition by its receptor RpfR and its regulatory interaction with the DSF synthase RpfF;citation_pages=e3000123;citation_volume=17;citation_year=2019"/> <meta name="citation_reference" content="citation_journal_title=Proc. Natl. Acad. Sci. U.S.A.;citation_author=C. Yang;citation_title=Burkholderia cenocepacia integrates cis-2-dodecenoic acid and cyclic dimeric guanosine monophosphate signals to control virulence;citation_volume=114;citation_year=2017;citation_pmid=29158389;citation_doi=10.1073/pnas.1709048114"/> <meta name="citation_reference" content="citation_journal_abbrev=PLoS ONE;citation_author=N. Schmid;citation_title=The AHL- and BDSF-Dependent Quorum Sensing Systems Control Specific and Overlapping Sets of Genes in Burkholderia cenocepacia H111.;citation_pages=e49966-e49966;citation_volume=7;citation_year=2012;citation_issue=11;citation_pmid=23185499;citation_doi=10.1371/journal.pone.0049966"/> <meta name="citation_reference" content="citation_journal_title=Proc. Natl. Acad. Sci. U.S.A.;citation_author=C. C. Traverse;citation_author=L. M. Mayo-Smith;citation_author=S. R. Poltak;citation_author=V. S. Cooper;citation_title=Tangled bank of experimentally evolved Burkholderia biofilms reflects selection during chronic infections;citation_volume=110;citation_year=2013;citation_pmid=23271804;citation_doi=10.1073/pnas.1207025110"/> <meta name="citation_reference" content="citation_journal_title=mSphere;citation_author=V. S. Cooper;citation_title=Experimental evolution as a high-throughput screen for genetic adaptations;citation_pages=e00121-18;citation_volume=3;citation_year=2018"/> <meta name="citation_reference" content="citation_journal_abbrev=Curr Genomics;citation_author=C. P. Bagowski;citation_author=W. Bruins;citation_author=A. J. W. Te Velthuis;citation_title=The nature of protein domain evolution: shaping the interaction network.;citation_pages=368-376;citation_volume=11;citation_year=2010;citation_issue=5;citation_pmid=21286315;citation_doi=10.2174/138920210791616725"/> <meta name="citation_reference" content="citation_journal_abbrev=ISME J;citation_author=S. R. Poltak;citation_author=V. S. Cooper;citation_title=Ecological succession in long-term experimentally evolved biofilms produces synergistic communities.;citation_pages=369-378;citation_volume=5;citation_year=2011;citation_issue=3;citation_pmid=20811470;citation_doi=10.1038/ismej.2010.136"/> <meta name="citation_reference" content="citation_journal_title=Evolution;citation_author=C. N. Ellis;citation_author=C. C. Traverse;citation_author=L. Mayo-Smith;citation_author=S. W. Buskirk;citation_author=V. S. Cooper;citation_title=Character displacement and the evolution of niche complementarity in a model biofilm community;citation_pages=283-293;citation_volume=69;citation_year=2015;citation_pmid=25494960;citation_doi=10.1111/evo.12581"/> <meta name="citation_reference" content="citation_journal_title=mSystems;citation_author=I. N. Silva;citation_title=Long-term evolution of Burkholderia multivorans during a chronic cystic fibrosis infection reveals shifting forces of selection;citation_pages=e00029-16;citation_volume=1;citation_year=2016;citation_doi=10.1128/mSystems.00029-16"/> <meta name="citation_reference" content="citation_journal_title=Evol. Lett.;citation_author=C. B. Turner;citation_author=C. W. Marshall;citation_author=V. S. Cooper;citation_title=Parallel genetic adaptation across environments differing in mode of growth or resource availability;citation_pages=355-367;citation_volume=2;citation_year=2018"/> <meta name="citation_reference" content="citation_journal_title=Mol. Ecol.;citation_author=C. B. Turner;citation_author=S. W. Buskirk;citation_author=K. B. Harris;citation_author=V. S. Cooper;citation_title=Negative frequency-dependent selection maintains coexisting genotypes during fluctuating selection;citation_pages=138-148;citation_volume=29;citation_year=2020"/> <meta name="citation_reference" content="citation_journal_title=Appl. Environ. Microbiol.;citation_author=C. N. Ellis;citation_author=V. S. Cooper;citation_title=Experimental adaptation of Burkholderia cenocepacia to onion medium reduces host range;citation_volume=76;citation_year=2010;citation_pmid=20154121;citation_doi=10.1128/AEM.01930-09"/> <meta name="citation_reference" content="citation_journal_title=Methods Mol. Biol.;citation_author=C. J. Jones;citation_author=D. J. Wozniak;citation_title=Congo red stain identifies matrix overproduction and is an indirect measurement for c-di-GMP in many species of bacteria;citation_pages=147-156;citation_volume=1657;citation_year=2017"/> <meta name="citation_reference" content="citation_journal_title=J. Bacteriol.;citation_author=K. M. Flynn;citation_title=Evolution of ecological diversity in biofilms of Pseudomonas aeruginosa by altered cyclic diguanylate signaling;citation_volume=198;citation_year=2016;citation_pmid=27021563;citation_doi=10.1128/JB.00048-16"/> <meta name="citation_reference" content="citation_journal_title=EMBO J.;citation_author=S. Lindenberg;citation_author=G. Klauck;citation_author=C. Pesavento;citation_author=E. Klauck;citation_author=R. Hengge;citation_title=The EAL domain protein YciR acts as a trigger enzyme in a c-di-GMP signalling cascade in E. coli biofilm control;citation_volume=32;citation_year=2013;citation_pmid=23708798;citation_doi=10.1038/emboj.2013.120"/> <meta name="citation_reference" content="citation_journal_title=Molecular microbiology;citation_journal_abbrev=Mol Microbiol;citation_author=H. Weber;citation_author=C. Pesavento;citation_author=A. Possling;citation_author=G. Tischendorf;citation_author=R. Hengge;citation_title=Cyclic-di-GMP-mediated signalling within the sigma network of Escherichia coli.;citation_pages=1014-1034;citation_volume=62;citation_year=2006;citation_issue=4;citation_pmid=17010156;citation_doi=10.1111/j.1365-2958.2006.05440.x"/> <meta name="citation_reference" content="citation_journal_title=J. Roy. Statist. Soc. Ser. B;citation_author=Y. Benjamini;citation_author=Y. Hochberg;citation_title=Controlling the false discovery rate: A practical and powerful approach to multiple testing;citation_pages=289-300;citation_volume=57;citation_year=1995"/> <meta name="citation_reference" content="citation_journal_title=Appl. Environ. Microbiol.;citation_author=D.-G. Ha;citation_author=M. E. Richman;citation_author=G. A. O’Toole;citation_title=Deletion mutant library for investigation of functional outputs of cyclic diguanylate metabolism in Pseudomonas aeruginosa PA14;citation_volume=80;citation_year=2014;citation_pmid=24657857;citation_doi=10.1128/AEM.00299-14"/> <meta name="citation_reference" content="citation_journal_abbrev=Am Nat;citation_author=A. Ross-Gillespie;citation_author=A. Gardner;citation_author=S. A. West;citation_author=A. S. Griffin;citation_title=Frequency dependence and cooperation: theory and a test with bacteria.;citation_pages=331-342;citation_volume=170;citation_year=2007;citation_issue=3;citation_pmid=17879185;citation_doi=10.1086/519860"/> <meta name="citation_reference" content="citation_journal_title=Appl. Environ. Microbiol.;citation_author=A. S. Ferreira;citation_title=Functional analysis of Burkholderia cepacia genes bceD and bceF, encoding a phosphotyrosine phosphatase and a tyrosine autokinase, respectively: Role in exopolysaccharide biosynthesis and biofilm formation;citation_volume=73;citation_year=2007;citation_pmid=17114319;citation_doi=10.1128/AEM.01450-06"/> <meta name="citation_reference" content="citation_journal_title=Molecular microbiology;citation_journal_abbrev=Mol Microbiol;citation_author=M. Fazli;citation_title=The CRP/FNR family protein Bcam1349 is a c-di-GMP effector that regulates biofilm formation in the respiratory pathogen Burkholderia cenocepacia.;citation_pages=327-341;citation_volume=82;citation_year=2011;citation_issue=2;citation_pmid=21883527;citation_doi=10.1111/j.1365-2958.2011.07814.x"/> <meta name="citation_reference" content="citation_journal_title=MicrobiologyOpen;citation_author=M. Fazli;citation_title=Regulation of Burkholderia cenocepacia biofilm formation by RpoN and the c-di-GMP effector BerB;citation_pages=e00480;citation_volume=6;citation_year=2017"/> <meta name="citation_reference" content="citation_journal_title=PLoS One;citation_author=B. Cuzzi;citation_title=Versatility of the Burkholderia cepacia complex for the biosynthesis of exopolysaccharides: A comparative structural investigation;citation_pages=e94372;citation_volume=9;citation_year=2014"/> <meta name="citation_reference" content="citation_journal_title=Int. J. Mol. Sci.;citation_author=B. Bellich;citation_title=Burkholderiacenocepacia H111 produces a water-insoluble exopolysaccharide in biofilm: Structural determination and molecular modelling;citation_pages=1702;citation_volume=21;citation_year=2020"/> <meta name="citation_reference" content="citation_journal_title=J. Bacteriol.;citation_author=B. S. Tseng;citation_title=Quorum sensing influences Burkholderia thailandensis biofilm development and matrix production;citation_volume=198;citation_year=2016;citation_pmid=27068594;citation_doi=10.1128/JB.00047-16"/> <meta name="citation_reference" content="citation_journal_title=MicrobiologyOpen;citation_author=M. Fazli;citation_author=Y. McCarthy;citation_author=M. Givskov;citation_author=R. P. Ryan;citation_author=T. Tolker-Nielsen;citation_title=The exopolysaccharide gene cluster Bcam1330-Bcam1341 is involved in Burkholderia cenocepacia biofilm formation, and its expression is regulated by c-di-GMP and Bcam1349;citation_pages=105-122;citation_volume=2;citation_year=2013;citation_pmid=23281338;citation_doi=10.1002/mbo3.61"/> <meta name="citation_reference" content="citation_journal_title=FEBS Letters;citation_journal_abbrev=FEBS Letters;citation_author=B. Wu;citation_author=Y. Zhang;citation_author=R. Zheng;citation_author=C. Guo;citation_author=P. G. Wang;citation_title=Bifunctional phosphomannose isomerase/GDP-D-mannose pyrophosphorylase is the point of control for GDP-D-mannose biosynthesis in Helicobacter pylori.;citation_pages=87-92;citation_volume=519;citation_year=2002;citation_issue=1-3;citation_pmid=12023023;citation_doi=10.1016/S0014-5793(02)02717-5"/> <meta name="citation_reference" content="citation_journal_title=Microbiol. Spectr.;citation_author=C. Berne;citation_author=A. Ducret;citation_author=G. G. Hardy;citation_author=Y. V. Brun;citation_title=Adhesins involved in attachment to abiotic surfaces by gram-negative bacteria;citation_volume=3;citation_year=2015;citation_doi=10.1128/microbiolspec.MB-0018-2015"/> <meta name="citation_reference" content="citation_journal_abbrev=PLoS Pathog;citation_author=O. Sulák;citation_title=Burkholderia cenocepacia BC2L-C is a super lectin with dual specificity and proinflammatory activity.;citation_pages=e1002238-e1002238;citation_volume=7;citation_year=2011;citation_issue=9;citation_pmid=21909279;citation_doi=10.1371/journal.ppat.1002238"/> <meta name="citation_reference" content="citation_journal_title=Biochem. J.;citation_author=E. Lameignere;citation_title=Structural basis for mannose recognition by a lectin from opportunistic bacteria Burkholderia cenocepacia;citation_volume=411;citation_year=2008;citation_pmid=18215132;citation_doi=10.1042/BJ20071276"/> <meta name="citation_reference" content="citation_journal_title=J. Evol. Biol.;citation_author=R. Kassen;citation_title=The experimental evolution of specialists, generalists, and the maintenance of diversity;citation_pages=173-190;citation_volume=15;citation_year=2002;citation_doi=10.1046/j.1420-9101.2002.00377.x"/> <meta name="citation_reference" content="citation_journal_title=Appl. Environ. 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Audfray;citation_title=Fucose-binding lectin from opportunistic pathogen Burkholderia ambifaria binds to both plant and human oligosaccharidic epitopes;citation_volume=287;citation_year=2012;citation_pmid=22170069;citation_doi=10.1074/jbc.M111.314831"/> <meta name="citation_reference" content="citation_journal_title=Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases;citation_journal_abbrev=Clin Microbiol Infect;citation_author=P. Drevinek;citation_author=E. Mahenthiralingam;citation_title=Burkholderia cenocepacia in cystic fibrosis: epidemiology and molecular mechanisms of virulence.;citation_pages=821-830;citation_volume=16;citation_year=2010;citation_issue=7;citation_pmid=20880411;citation_doi=10.1111/j.1469-0691.2010.03237.x"/> <meta name="citation_reference" content="citation_journal_title=PLoS Pathog.;citation_author=J. Nunvar;citation_author=V. Capek;citation_author=K. Fiser;citation_author=L. 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Tolker-Nielsen;citation_title=In-frame and unmarked gene deletions in Burkholderia cenocepacia via an allelic exchange system compatible with gateway technology;citation_volume=81;citation_year=2015;citation_pmid=25795676;citation_doi=10.1128/AEM.03909-14"/> <meta name="citation_fulltext_world_readable" content=""/> <meta name="twitter:title" content="One gene, multiple ecological strategies: A biofilm regulator is a capacitor for sustainable diversity"/> <meta name="twitter:card" content="summary_large_image"/> <meta name="twitter:image" content="https://www.pnas.org/content/early/2020/08/18/2008540117/F1.large.jpg"/> <meta name="twitter:description" content="Many organisms, including bacteria, live in fluctuating environments that require attachment and dispersal. These lifestyle decisions require processing of multiple external signals by several genetic pathways, but how they are integrated is largely unknown. We conducted multiple evolution experiments totaling >20,000 generations with Burkholderia cenocepacia populations grown in a model of the biofilm life cycle and identified parallel mutations in one gene, rpfR , that is a conserved central regulator. Because RpfR has multiple sensor and catalytic domains, different mutations can produce different ecological strategies that can coexist and even increase net growth. This study demonstrates that a single gene may coordinate complex life histories in biofilm-dwelling bacteria and that selection in defined environments can reshape niche breadth by single mutations. Many bacteria cycle between sessile and motile forms in which they must sense and respond to internal and external signals to coordinate appropriate physiology. Maintaining fitness requires genetic networks that have been honed in variable environments to integrate these signals. The identity of the major regulators and how their control mechanisms evolved remain largely unknown in most organisms. During four different evolution experiments with the opportunist betaproteobacterium Burkholderia cenocepacia in a biofilm model, mutations were most frequently selected in the conserved gene rpfR . RpfR uniquely integrates two major signaling systems—quorum sensing and the motile–sessile switch mediated by cyclic-di-GMP—by two domains that sense, respond to, and control the synthesis of the autoinducer cis-2-dodecenoic acid (BDSF). The BDSF response in turn regulates the activity of diguanylate cyclase and phosphodiesterase domains acting on cyclic-di-GMP. Parallel adaptive substitutions evolved in each of these domains to produce unique life history strategies by regulating cyclic-di-GMP levels, global transcriptional responses, biofilm production, and polysaccharide composition. These phenotypes translated into distinct ecology and biofilm structures that enabled mutants to coexist and produce more biomass than expected from their constituents grown alone. This study shows that when bacterial populations are selected in environments challenging the limits of their plasticity, the evolved mutations not only alter genes at the nexus of signaling networks but also reveal the scope of their regulatory functions. RNA sequencing data have been deposited in the National Center for Biotechnology Information (NCBI) BioProject database under accession no. [PRJNA607303][1]. [1]: https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA607303"/> <meta name="og-title" property="og:title" content="One gene, multiple ecological strategies: A biofilm regulator is a capacitor for sustainable diversity"/> <meta name="og-url" property="og:url" content="https://www.pnas.org/content/early/2020/08/18/2008540117"/> <meta name="og-site-name" property="og:site_name" content="PNAS"/> <meta name="og-description" property="og:description" content="Many organisms, including bacteria, live in fluctuating environments that require attachment and dispersal. These lifestyle decisions require processing of multiple external signals by several genetic pathways, but how they are integrated is largely unknown. We conducted multiple evolution experiments totaling >20,000 generations with Burkholderia cenocepacia populations grown in a model of the biofilm life cycle and identified parallel mutations in one gene, rpfR , that is a conserved central regulator. Because RpfR has multiple sensor and catalytic domains, different mutations can produce different ecological strategies that can coexist and even increase net growth. This study demonstrates that a single gene may coordinate complex life histories in biofilm-dwelling bacteria and that selection in defined environments can reshape niche breadth by single mutations. Many bacteria cycle between sessile and motile forms in which they must sense and respond to internal and external signals to coordinate appropriate physiology. Maintaining fitness requires genetic networks that have been honed in variable environments to integrate these signals. The identity of the major regulators and how their control mechanisms evolved remain largely unknown in most organisms. During four different evolution experiments with the opportunist betaproteobacterium Burkholderia cenocepacia in a biofilm model, mutations were most frequently selected in the conserved gene rpfR . RpfR uniquely integrates two major signaling systems—quorum sensing and the motile–sessile switch mediated by cyclic-di-GMP—by two domains that sense, respond to, and control the synthesis of the autoinducer cis-2-dodecenoic acid (BDSF). The BDSF response in turn regulates the activity of diguanylate cyclase and phosphodiesterase domains acting on cyclic-di-GMP. Parallel adaptive substitutions evolved in each of these domains to produce unique life history strategies by regulating cyclic-di-GMP levels, global transcriptional responses, biofilm production, and polysaccharide composition. These phenotypes translated into distinct ecology and biofilm structures that enabled mutants to coexist and produce more biomass than expected from their constituents grown alone. This study shows that when bacterial populations are selected in environments challenging the limits of their plasticity, the evolved mutations not only alter genes at the nexus of signaling networks but also reveal the scope of their regulatory functions. RNA sequencing data have been deposited in the National Center for Biotechnology Information (NCBI) BioProject database under accession no. [PRJNA607303][1]. 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