{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,12]],"date-time":"2025-11-12T13:58:55Z","timestamp":1762955935474,"version":"3.37.3"},"reference-count":79,"publisher":"Springer Science and Business Media LLC","issue":"4","license":[{"start":{"date-parts":[[2018,8,28]],"date-time":"2018-08-28T00:00:00Z","timestamp":1535414400000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Nat Comput"],"published-print":{"date-parts":[[2018,12]]},"DOI":"10.1007\/s11047-018-9708-8","type":"journal-article","created":{"date-parts":[[2018,8,28]],"date-time":"2018-08-28T12:08:18Z","timestamp":1535458098000},"page":"811-822","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":5,"title":["Ecological effects of cellular computing in microbial populations"],"prefix":"10.1007","volume":"17","author":[{"given":"Maia","family":"Baskerville","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Arielle","family":"Biro","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mike","family":"Blazanin","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chang-Yu","family":"Chang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Amelia","family":"Hallworth","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nicole","family":"Sonnert","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jean C. C.","family":"Vila","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2292-5608","authenticated-orcid":false,"given":"Alvaro","family":"Sanchez","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2018,8,28]]},"reference":[{"key":"9708_CR1","doi-asserted-by":"publisher","first-page":"471","DOI":"10.1038\/ng.110","volume":"40","author":"M Acar","year":"2008","unstructured":"Acar M, Mettetal JT, van Oudenaarden A (2008) Stochastic switching as a survival strategy in fluctuating environments. Nat Genet 40:471\u2013475","journal-title":"Nat Genet"},{"key":"9708_CR2","doi-asserted-by":"publisher","first-page":"101","DOI":"10.3389\/fmicb.2011.00101","volume":"2","author":"BMM Ahmer","year":"2011","unstructured":"Ahmer BMM, Gunn JS (2011) Interaction of Salmonella spp. with the Intestinal Microbiota. Front Microbiol 2:101","journal-title":"Front Microbiol"},{"key":"9708_CR3","doi-asserted-by":"publisher","first-page":"133","DOI":"10.1186\/s12918-014-0133-z","volume":"8","author":"G Aidelberg","year":"2014","unstructured":"Aidelberg G, Towbin BD, Rothschild D et al (2014) Hierarchy of non-glucose sugars in Escherichia coli. BMC Syst Biol 8:133","journal-title":"BMC Syst Biol"},{"key":"9708_CR4","doi-asserted-by":"publisher","first-page":"e1001928","DOI":"10.1371\/journal.pbio.1001928","volume":"12","author":"M Arnoldini","year":"2014","unstructured":"Arnoldini M, Vizcarra IA, Pe\u00f1a-Miller R et al (2014) Bistable expression of virulence genes in salmonella leads to the formation of an antibiotic-tolerant subpopulation. PLoS Biol 12:e1001928","journal-title":"PLoS Biol"},{"key":"9708_CR5","doi-asserted-by":"publisher","first-page":"e07935","DOI":"10.7554\/eLife.07935","volume":"4","author":"K Axelrod","year":"2015","unstructured":"Axelrod K, Sanchez A, Gore J (2015) Phenotypic states become increasingly sensitive to perturbations near a bifurcation in a synthetic gene network. Elife 4:e07935. https:\/\/doi.org\/10.7554\/eLife.07935","journal-title":"Elife"},{"key":"9708_CR6","doi-asserted-by":"publisher","first-page":"827","DOI":"10.1038\/nrg3564","volume":"14","author":"JE Barrick","year":"2013","unstructured":"Barrick JE, Lenski RE (2013) Genome dynamics during experimental evolution. Nat Rev Genet 14:827\u2013839","journal-title":"Nat Rev Genet"},{"key":"9708_CR7","doi-asserted-by":"publisher","first-page":"259","DOI":"10.1038\/nature18301","volume":"534","author":"A Bashan","year":"2016","unstructured":"Bashan A, Gibson TE, Friedman J et al (2016) Universality of human microbial dynamics. Nature 534:259\u2013262","journal-title":"Nature"},{"key":"9708_CR8","doi-asserted-by":"publisher","first-page":"342","DOI":"10.1038\/nature09905","volume":"472","author":"RE Beardmore","year":"2011","unstructured":"Beardmore RE, Gudelj I, Lipson DA, Hurst LD (2011) Metabolic trade-offs and the maintenance of the fittest and the flattest. Nature 472:342\u2013346","journal-title":"Nature"},{"key":"9708_CR9","doi-asserted-by":"publisher","first-page":"374","DOI":"10.1128\/JB.00890-15","volume":"198","author":"CL Beisel","year":"2015","unstructured":"Beisel CL, Afroz T (2015) Rethinking the hierarchy of sugar utilization in bacteria. J Bacteriol 198:374\u2013376","journal-title":"J Bacteriol"},{"key":"9708_CR10","doi-asserted-by":"publisher","first-page":"7899","DOI":"10.1073\/pnas.0803151105","volume":"105","author":"ZD Blount","year":"2008","unstructured":"Blount ZD, Borland CZ, Lenski RE (2008) Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli. Proc Natl Acad Sci U S A 105:7899\u20137906","journal-title":"Proc Natl Acad Sci U S A"},{"key":"9708_CR11","doi-asserted-by":"publisher","first-page":"513","DOI":"10.1038\/nature11514","volume":"489","author":"ZD Blount","year":"2012","unstructured":"Blount ZD, Barrick JE, Davidson CJ, Lenski RE (2012) Genomic analysis of a key innovation in an experimental Escherichia coli population. Nature 489:513\u2013518","journal-title":"Nature"},{"key":"9708_CR12","doi-asserted-by":"publisher","first-page":"107","DOI":"10.1023\/A:1020585711378","volume":"81","author":"BJM Bohannan","year":"2002","unstructured":"Bohannan BJM, Kerr B, Jessup CM et al (2002) Trade-offs and coexistence in microbial microcosms. Antonie Van Leeuwenhoek 81:107\u2013115","journal-title":"Antonie Van Leeuwenhoek"},{"key":"9708_CR13","doi-asserted-by":"publisher","first-page":"3","DOI":"10.1007\/978-3-319-54072-6_1","volume-title":"Membrane Computing","author":"Matteo Cavaliere","year":"2017","unstructured":"Cavaliere M, Sanchez A (2016) The evolutionary resilience of distributed cellular computing. In: Membrane computing. Springer, Cham, pp 3\u201315"},{"key":"9708_CR14","doi-asserted-by":"publisher","first-page":"3713","DOI":"10.1038\/ncomms4713","volume":"5","author":"A Chen","year":"2014","unstructured":"Chen A, Sanchez A, Dai L, Gore J (2014) Dynamics of a producer-freeloader ecosystem on the brink of collapse. Nat Commun 5:3713","journal-title":"Nat Commun"},{"key":"9708_CR15","doi-asserted-by":"publisher","first-page":"26","DOI":"10.1016\/0040-5809(90)90025-Q","volume":"37","author":"P Chesson","year":"1990","unstructured":"Chesson P (1990) MacArthur\u2019s consumer-resource model. Theor Popul Biol 37:26\u201338","journal-title":"Theor Popul Biol"},{"key":"9708_CR16","doi-asserted-by":"publisher","first-page":"1524","DOI":"10.1128\/AEM.01970-09","volume":"76","author":"TA Desai","year":"2010","unstructured":"Desai TA, Rao CV (2010) Regulation of arabinose and xylose metabolism in Escherichia coli. Appl Environ Microbiol 76:1524\u20131532","journal-title":"Appl Environ Microbiol"},{"key":"9708_CR17","doi-asserted-by":"publisher","first-page":"353","DOI":"10.1038\/nature11913","volume":"494","author":"M Diard","year":"2013","unstructured":"Diard M, Garcia V, Maier L et al (2013) Stabilization of cooperative virulence by the expression of an avirulent phenotype. Nature 494:353\u2013356","journal-title":"Nature"},{"key":"9708_CR18","doi-asserted-by":"publisher","first-page":"2000","DOI":"10.1016\/j.cub.2014.07.028","volume":"24","author":"M Diard","year":"2014","unstructured":"Diard M, Sellin ME, Dolowschiak T et al (2014) Antibiotic treatment selects for cooperative virulence of Salmonella typhimurium. Curr Biol 24:2000\u20132005","journal-title":"Curr Biol"},{"key":"9708_CR19","doi-asserted-by":"publisher","first-page":"022423","DOI":"10.1103\/PhysRevE.94.022423","volume":"94","author":"B Dickens","year":"2016","unstructured":"Dickens B, Fisher CK, Mehta P (2016) Analytically tractable model for community ecology with many species. Phys Rev E 94:022423","journal-title":"Phys Rev E"},{"key":"9708_CR20","doi-asserted-by":"publisher","first-page":"1636","DOI":"10.1073\/pnas.1418058112","volume":"112","author":"R Escalante-Chong","year":"2015","unstructured":"Escalante-Chong R, Savir Y, Carroll SM et al (2015) Galactose metabolic genes in yeast respond to a ratio of galactose and glucose. Proc Natl Acad Sci U S A 112:1636\u20131641","journal-title":"Proc Natl Acad Sci U S A"},{"key":"9708_CR21","doi-asserted-by":"publisher","first-page":"245","DOI":"10.1111\/j.0014-3820.2004.tb01642.x","volume":"58","author":"ML Friesen","year":"2004","unstructured":"Friesen ML, Saxer G, Travisano M, Doebeli M (2004) Experimental evidence for sympatric ecological diversification due to frequency-dependent competition in Escherichia coli. Evolution 58:245\u2013260","journal-title":"Evolution"},{"key":"9708_CR22","doi-asserted-by":"publisher","first-page":"469","DOI":"10.1126\/science.aat1168","volume":"361","author":"JE Goldford","year":"2018","unstructured":"Goldford JE, Lu N, Bajic D et al (2018) Emergent simplicity in microbial community assembly. Science 361:469\u2013474","journal-title":"Science"},{"key":"9708_CR23","doi-asserted-by":"publisher","first-page":"e21415","DOI":"10.7554\/eLife.21415","volume":"6","author":"AA Granados","year":"2017","unstructured":"Granados AA, Crane MM, Montano-Gutierrez LF et al (2017) Distributing tasks via multiple input pathways increases cellular survival in stress. Elife 6:e21415. https:\/\/doi.org\/10.7554\/eLife.21415","journal-title":"Elife"},{"key":"9708_CR24","doi-asserted-by":"publisher","first-page":"1496","DOI":"10.1021\/acssynbio.7b00003","volume":"6","author":"M Guti\u00e9rrez","year":"2017","unstructured":"Guti\u00e9rrez M, Gregorio-Godoy P, P\u00e9rez Del Pulgar G et al (2017) A new improved and extended version of the multicell bacterial simulator gro. ACS Synth Biol 6:1496\u20131508","journal-title":"ACS Synth Biol"},{"key":"9708_CR25","doi-asserted-by":"publisher","first-page":"898","DOI":"10.1111\/j.1365-2435.2010.01707.x","volume":"24","author":"EK Hall","year":"2010","unstructured":"Hall EK, Singer GA, Kainz MJ, Lennon JT (2010) Evidence for a temperature acclimation mechanism in bacteria: an empirical test of a membrane-mediated trade-off. Funct Ecol 24:898\u2013908","journal-title":"Funct Ecol"},{"key":"9708_CR26","doi-asserted-by":"publisher","first-page":"e1003091","DOI":"10.1371\/journal.pcbi.1003091","volume":"9","author":"WR Harcombe","year":"2013","unstructured":"Harcombe WR, Delaney NF, Leiby N et al (2013) The ability of flux balance analysis to predict evolution of central metabolism scales with the initial distance to the optimum. PLoS Comput Biol 9:e1003091","journal-title":"PLoS Comput Biol"},{"key":"9708_CR27","doi-asserted-by":"publisher","first-page":"e28230","DOI":"10.4161\/cib.28230","volume":"7","author":"KI Harrington","year":"2014","unstructured":"Harrington KI, Sanchez A (2014) Eco-evolutionary dynamics of complex social strategies in microbial communities. Commun Integr Biol 7:e28230","journal-title":"Commun Integr Biol"},{"key":"9708_CR28","doi-asserted-by":"publisher","first-page":"e1001490","DOI":"10.1371\/journal.pbio.1001490","volume":"11","author":"MD Herron","year":"2013","unstructured":"Herron MD, Doebeli M (2013) Parallel evolutionary dynamics of adaptive diversification in Escherichia coli. PLoS Biol 11:e1001490","journal-title":"PLoS Biol"},{"key":"9708_CR29","doi-asserted-by":"publisher","first-page":"1118","DOI":"10.1111\/brv.12215","volume":"91","author":"M Hilker","year":"2016","unstructured":"Hilker M, Schwachtje J, Baier M et al (2016) Priming and memory of stress responses in organisms lacking a nervous system. Biol Rev Camb Philos Soc 91:1118\u20131133","journal-title":"Biol Rev Camb Philos Soc"},{"key":"9708_CR30","doi-asserted-by":"publisher","first-page":"e00362\u201312","DOI":"10.1128\/mBio.00362-12","volume":"4","author":"NM H\u00f8yland-Kroghsbo","year":"2013","unstructured":"H\u00f8yland-Kroghsbo NM, Maerkedahl RB, Svenningsen SL (2013) A quorum-sensing-induced bacteriophage defense mechanism. MBio 4:e00362\u201312","journal-title":"MBio"},{"key":"9708_CR31","doi-asserted-by":"publisher","first-page":"365","DOI":"10.1021\/sb300034m","volume":"1","author":"SS Jang","year":"2012","unstructured":"Jang SS, Oishi KT, Egbert RG, Klavins E (2012) Specification and simulation of synthetic multicelled behaviors. ACS Synth Biol 1:365\u2013374","journal-title":"ACS Synth Biol"},{"key":"9708_CR32","doi-asserted-by":"publisher","first-page":"386","DOI":"10.1128\/JB.00709-15","volume":"198","author":"S Koirala","year":"2015","unstructured":"Koirala S, Wang X, Rao CV (2015) Reciprocal regulation of l-arabinose and d-xylose metabolism in Escherichia coli. J Bacteriol 198:386\u2013393","journal-title":"J Bacteriol"},{"key":"9708_CR33","doi-asserted-by":"publisher","first-page":"736","DOI":"10.15252\/msb.20135022","volume":"10","author":"O Kotte","year":"2014","unstructured":"Kotte O, Volkmer B, Radzikowski JL, Heinemann M (2014) Phenotypic bistability in Escherichia coli\u2019s central carbon metabolism. Mol Syst Biol 10:736","journal-title":"Mol Syst Biol"},{"key":"9708_CR34","doi-asserted-by":"publisher","first-page":"403","DOI":"10.1128\/IAI.01189-07","volume":"76","author":"TD Lawley","year":"2008","unstructured":"Lawley TD, Bouley DM, Hoy YE et al (2008) Host transmission of Salmonella enterica serovar Typhimurium is controlled by virulence factors and indigenous intestinal microbiota. Infect Immun 76:403\u2013416","journal-title":"Infect Immun"},{"key":"9708_CR35","doi-asserted-by":"publisher","first-page":"1049","DOI":"10.1534\/genetics.107.082040","volume":"178","author":"M Gac Le","year":"2008","unstructured":"Le Gac M, Brazas MD, Bertrand M et al (2008) Metabolic changes associated with adaptive diversification in Escherichia coli. Genetics 178:1049\u20131060","journal-title":"Genetics"},{"key":"9708_CR36","doi-asserted-by":"publisher","first-page":"e1001789","DOI":"10.1371\/journal.pbio.1001789","volume":"12","author":"N Leiby","year":"2014","unstructured":"Leiby N, Marx CJ (2014) Metabolic erosion primarily through mutation accumulation, and not tradeoffs, drives limited evolution of substrate specificity in Escherichia coli. PLoS Biol 12:e1001789","journal-title":"PLoS Biol"},{"key":"9708_CR37","doi-asserted-by":"publisher","first-page":"56","DOI":"10.1038\/nature22898","volume":"546","author":"JM Levine","year":"2017","unstructured":"Levine JM, Bascompte J, Adler PB, Allesina S (2017) Beyond pairwise mechanisms of species coexistence in complex communities. Nature 546:56\u201364","journal-title":"Nature"},{"key":"9708_CR38","doi-asserted-by":"crossref","unstructured":"Li G, Kesler BK, Thiemicke A et al (2017) Linearly changing stress environment causes cellular growth phenotype. bioRxiv 155267","DOI":"10.1101\/155267"},{"key":"9708_CR39","doi-asserted-by":"publisher","first-page":"1170","DOI":"10.1111\/j.1461-0248.2007.01117.x","volume":"10","author":"E Litchman","year":"2007","unstructured":"Litchman E, Klausmeier CA, Schofield OM, Falkowski PG (2007) The role of functional traits and trade-offs in structuring phytoplankton communities: scaling from cellular to ecosystem level. Ecol Lett 10:1170\u20131181","journal-title":"Ecol Lett"},{"key":"9708_CR40","doi-asserted-by":"publisher","first-page":"254","DOI":"10.3389\/fmicb.2015.00254","volume":"6","author":"E Litchman","year":"2015","unstructured":"Litchman E, Edwards KF, Klausmeier CA (2015) Microbial resource utilization traits and trade-offs: implications for community structure, functioning, and biogeochemical impacts at present and in the future. Front Microbiol 6:254","journal-title":"Front Microbiol"},{"key":"9708_CR41","doi-asserted-by":"publisher","first-page":"62","DOI":"10.1038\/s41559-016-0062","volume":"1","author":"MM Mayfield","year":"2017","unstructured":"Mayfield MM, Stouffer DB (2017) Higher-order interactions capture unexplained complexity in diverse communities. Nat Ecol Evol 1:62","journal-title":"Nat Ecol Evol"},{"key":"9708_CR42","doi-asserted-by":"publisher","first-page":"17978","DOI":"10.1073\/pnas.1207814109","volume":"109","author":"P Mehta","year":"2012","unstructured":"Mehta P, Schwab DJ (2012) Energetic costs of cellular computation. Proc Natl Acad Sci U S A 109:17978\u201317982","journal-title":"Proc Natl Acad Sci U S A"},{"key":"9708_CR43","doi-asserted-by":"publisher","first-page":"7271","DOI":"10.1073\/pnas.1019754108","volume":"108","author":"A Mitchell","year":"2011","unstructured":"Mitchell A, Pilpel Y (2011) A mathematical model for adaptive prediction of environmental changes by microorganisms. Proc Natl Acad Sci U S A 108:7271\u20137276","journal-title":"Proc Natl Acad Sci U S A"},{"key":"9708_CR44","doi-asserted-by":"publisher","first-page":"220","DOI":"10.1038\/nature08112","volume":"460","author":"A Mitchell","year":"2009","unstructured":"Mitchell A, Romano GH, Groisman B et al (2009) Adaptive prediction of environmental changes by microorganisms. Nature 460:220\u2013224","journal-title":"Nature"},{"key":"9708_CR45","doi-asserted-by":"publisher","first-page":"1379","DOI":"10.1126\/science.aab0892","volume":"350","author":"A Mitchell","year":"2015","unstructured":"Mitchell A, Wei P, Lim WA (2015) Oscillatory stress stimulation uncovers an Achilles\u2019 heel of the yeast MAPK signaling network. Science 350:1379\u20131383","journal-title":"Science"},{"key":"9708_CR46","doi-asserted-by":"publisher","first-page":"371","DOI":"10.1146\/annurev.mi.03.100149.002103","volume":"3","author":"J Monod","year":"1949","unstructured":"Monod J (1949) The growth of bacterial cultures. Annu Rev Microbiol 3:371\u2013394","journal-title":"Annu Rev Microbiol"},{"key":"9708_CR47","doi-asserted-by":"publisher","first-page":"475","DOI":"10.1126\/science.154.3748.475","volume":"154","author":"J Monod","year":"1966","unstructured":"Monod J (1966) From enzymatic adaptation to allosteric transitions. Science 154:475\u2013483","journal-title":"Science"},{"key":"9708_CR48","doi-asserted-by":"publisher","first-page":"e1001764","DOI":"10.1371\/journal.pbio.1001764","volume":"12","author":"AM New","year":"2014","unstructured":"New AM, Cerulus B, Govers SK et al (2014) Different levels of catabolite repression optimize growth in stable and variable environments. PLoS Biol 12:e1001764","journal-title":"PLoS Biol"},{"key":"9708_CR49","doi-asserted-by":"publisher","first-page":"326","DOI":"10.1038\/msb.2009.83","volume":"5","author":"TJ Perkins","year":"2009","unstructured":"Perkins TJ, Swain PS (2009) Strategies for cellular decision-making. Mol Syst Biol 5:326","journal-title":"Mol Syst Biol"},{"key":"9708_CR50","doi-asserted-by":"crossref","first-page":"4160","DOI":"10.1128\/JB.180.16.4160-4165.1998","volume":"180","author":"KM Pos","year":"1998","unstructured":"Pos KM, Dimroth P, Bott M (1998) The Escherichia coli citrate carrier CitT: a member of a novel eubacterial transporter family related to the 2-oxoglutarate\/malate translocator from spinach chloroplasts. J Bacteriol 180:4160\u20134165","journal-title":"J Bacteriol"},{"key":"9708_CR51","doi-asserted-by":"publisher","first-page":"028103","DOI":"10.1103\/PhysRevLett.118.028103","volume":"118","author":"A Posfai","year":"2017","unstructured":"Posfai A, Taillefumier T, Wingreen NS (2017) Metabolic trade-offs promote diversity in a model ecosystem. Phys Rev Lett 118:028103","journal-title":"Phys Rev Lett"},{"key":"9708_CR52","doi-asserted-by":"publisher","first-page":"162","DOI":"10.1002\/jobm.201600510","volume":"57","author":"X Qin","year":"2017","unstructured":"Qin X, Sun Q, Yang B et al (2017) Quorum sensing influences phage infection efficiency via affecting cell population and physiological state. J Basic Microbiol 57:162\u2013170","journal-title":"J Basic Microbiol"},{"key":"9708_CR53","doi-asserted-by":"publisher","first-page":"e09696","DOI":"10.7554\/eLife.09696","volume":"4","author":"EM Quandt","year":"2015","unstructured":"Quandt EM, Gollihar J, Blount ZD et al (2015) Fine-tuning citrate synthase flux potentiates and refines metabolic innovation in the Lenski evolution experiment. Elife 4:e09696. https:\/\/doi.org\/10.7554\/eLife.09696","journal-title":"Elife"},{"key":"9708_CR54","doi-asserted-by":"publisher","first-page":"21","DOI":"10.1016\/j.tig.2004.11.014","volume":"21","author":"JAG Ranea","year":"2005","unstructured":"Ranea JAG, Grant A, Thornton JM, Orengo CA (2005) Microeconomic principles explain an optimal genome size in bacteria. Trends Genet 21:21\u201325","journal-title":"Trends Genet"},{"key":"9708_CR55","doi-asserted-by":"publisher","first-page":"207","DOI":"10.1038\/nature09679","volume":"469","author":"S Regot","year":"2011","unstructured":"Regot S, Macia J, Conde N et al (2011) Distributed biological computation with multicellular engineered networks. Nature 469:207\u2013211","journal-title":"Nature"},{"key":"9708_CR56","doi-asserted-by":"publisher","DOI":"10.1093\/femsec\/fiv040","author":"MC Rillig","year":"2015","unstructured":"Rillig MC, Rolff J, Tietjen B et al (2015) Community priming\u2014effects of sequential stressors on microbial assemblages. FEMS Microbiol Ecol. https:\/\/doi.org\/10.1093\/femsec\/fiv040","journal-title":"FEMS Microbiol Ecol"},{"key":"9708_CR57","doi-asserted-by":"publisher","first-page":"357","DOI":"10.1038\/msb.2010.12","volume":"6","author":"L Robert","year":"2010","unstructured":"Robert L, Paul G, Chen Y et al (2010) Pre-dispositions and epigenetic inheritance in the Escherichia coli lactose operon bistable switch. Mol Syst Biol 6:357","journal-title":"Mol Syst Biol"},{"key":"9708_CR58","doi-asserted-by":"publisher","first-page":"658","DOI":"10.1111\/j.1574-6976.2010.00218.x","volume":"34","author":"F Rojo","year":"2010","unstructured":"Rojo F (2010) Carbon catabolite repression in Pseudomonas: optimizing metabolic versatility and interactions with the environment. FEMS Microbiol Rev 34:658\u2013684","journal-title":"FEMS Microbiol Rev"},{"key":"9708_CR59","doi-asserted-by":"publisher","first-page":"e1001547","DOI":"10.1371\/journal.pbio.1001547","volume":"11","author":"A Sanchez","year":"2013","unstructured":"Sanchez A, Gore J (2013) Feedback between population and evolutionary dynamics determines the fate of social microbial populations. PLoS Biol 11:e1001547","journal-title":"PLoS Biol"},{"key":"9708_CR60","doi-asserted-by":"publisher","first-page":"R59","DOI":"10.1186\/gb-2013-14-6-r59","volume":"14","author":"E Sani","year":"2013","unstructured":"Sani E, Herzyk P, Perrella G et al (2013) Hyperosmotic priming of Arabidopsis seedlings establishes a long-term somatic memory accompanied by specific changes of the epigenome. Genome Biol 14:R59","journal-title":"Genome Biol"},{"key":"9708_CR61","doi-asserted-by":"publisher","first-page":"E1236\u201343","DOI":"10.1073\/pnas.1103630108","volume":"108","author":"EA Shank","year":"2011","unstructured":"Shank EA, Klepac-Ceraj V, Collado-Torres L et al (2011) Interspecies interactions that result in Bacillus subtilis forming biofilms are mediated mainly by members of its own genus. Proc Natl Acad Sci U S A 108:E1236\u201343","journal-title":"Proc Natl Acad Sci U S A"},{"key":"9708_CR62","doi-asserted-by":"publisher","first-page":"7275","DOI":"10.1128\/JB.00848-08","volume":"190","author":"KD Singh","year":"2008","unstructured":"Singh KD, Schmalisch MH, St\u00fclke J, G\u00f6rke B (2008) Carbon catabolite repression in Bacillus subtilis: quantitative analysis of repression exerted by different carbon sources. J Bacteriol 190:7275\u20137284","journal-title":"J Bacteriol"},{"key":"9708_CR63","doi-asserted-by":"publisher","first-page":"1043","DOI":"10.1016\/j.cell.2008.04.040","volume":"133","author":"JM Skerker","year":"2008","unstructured":"Skerker JM, Perchuk BS, Siryaporn A et al (2008) Rewiring the specificity of two-component signal transduction systems. Cell 133:1043\u20131054","journal-title":"Cell"},{"key":"9708_CR64","doi-asserted-by":"publisher","first-page":"e15","DOI":"10.1371\/journal.pgen.0030015","volume":"3","author":"CC Spencer","year":"2007","unstructured":"Spencer CC, Bertrand M, Travisano M, Doebeli M (2007) Adaptive diversification in genes that regulate resource use in Escherichia coli. PLoS Genet 3:e15","journal-title":"PLoS Genet"},{"key":"9708_CR65","doi-asserted-by":"publisher","first-page":"e1003388","DOI":"10.1371\/journal.pcbi.1003388","volume":"9","author":"RR Stein","year":"2013","unstructured":"Stein RR, Bucci V, Toussaint NC et al (2013) Ecological modeling from time-series inference: insight into dynamics and stability of intestinal microbiota. PLoS Comput Biol 9:e1003388","journal-title":"PLoS Comput Biol"},{"key":"9708_CR66","doi-asserted-by":"publisher","first-page":"1313","DOI":"10.1126\/science.1154456","volume":"320","author":"I Tagkopoulos","year":"2008","unstructured":"Tagkopoulos I, Liu Y-C, Tavazoie S (2008) Predictive behavior within microbial genetic networks. Science 320:1313\u20131317","journal-title":"Science"},{"key":"9708_CR67","doi-asserted-by":"publisher","first-page":"4489","DOI":"10.1128\/AEM.00518-15","volume":"81","author":"D Tan","year":"2015","unstructured":"Tan D, Dahl A, Middelboe M (2015) Vibriophages differentially influence biofilm formation by Vibrio anguillarum strains. Appl Environ Microbiol 81:4489\u20134497","journal-title":"Appl Environ Microbiol"},{"key":"9708_CR68","doi-asserted-by":"publisher","first-page":"1014","DOI":"10.1126\/science.1259145","volume":"347","author":"TB Taylor","year":"2015","unstructured":"Taylor TB, Mulley G, Dills AH et al (2015) Evolution. evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system. Science 347:1014\u20131017","journal-title":"Science"},{"key":"9708_CR69","doi-asserted-by":"publisher","first-page":"17480","DOI":"10.1073\/pnas.1107857108","volume":"108","author":"P Thiennimitr","year":"2011","unstructured":"Thiennimitr P, Winter SE, Winter MG et al (2011) Intestinal inflammation allows Salmonella to use ethanolamine to compete with the microbiota. Proc Natl Acad Sci U S A 108:17480\u201317485","journal-title":"Proc Natl Acad Sci U S A"},{"key":"9708_CR70","doi-asserted-by":"publisher","first-page":"e1006005","DOI":"10.1371\/journal.pgen.1006005","volume":"12","author":"M Toll-Riera","year":"2016","unstructured":"Toll-Riera M, San Millan A, Wagner A, MacLean RC (2016) The genomic basis of evolutionary innovation in Pseudomonas aeruginosa. PLoS Genet 12:e1006005","journal-title":"PLoS Genet"},{"key":"9708_CR71","doi-asserted-by":"publisher","first-page":"554","DOI":"10.1038\/msb.2011.87","volume":"7","author":"S Turkarslan","year":"2011","unstructured":"Turkarslan S, Reiss DJ, Gibbins G et al (2011) Niche adaptation by expansion and reprogramming of general transcription factors. Mol Syst Biol 7:554","journal-title":"Mol Syst Biol"},{"key":"9708_CR72","unstructured":"Turner CB, Blount ZD, Mitchell DH, Lenski RE (2015) Evolution and coexistence in response to a key innovation in a long-term evolution experiment with Escherichia coli. bioRxiv 020958"},{"key":"9708_CR73","doi-asserted-by":"publisher","first-page":"479","DOI":"10.1016\/S0168-9525(03)00203-8","volume":"19","author":"E Nimwegen van","year":"2003","unstructured":"van Nimwegen E (2003) Scaling laws in the functional content of genomes. Trends Genet 19:479\u2013484","journal-title":"Trends Genet"},{"key":"9708_CR74","doi-asserted-by":"publisher","first-page":"e1002042","DOI":"10.1371\/journal.pbio.1002042","volume":"13","author":"OS Venturelli","year":"2015","unstructured":"Venturelli OS, Zuleta I, Murray RM, El-Samad H (2015) Population diversification in a yeast metabolic program promotes anticipation of environmental shifts. PLoS Biol 13:e1002042","journal-title":"PLoS Biol"},{"key":"9708_CR75","doi-asserted-by":"publisher","first-page":"e1002041","DOI":"10.1371\/journal.pbio.1002041","volume":"13","author":"J Wang","year":"2015","unstructured":"Wang J, Atolia E, Hua B et al (2015) Natural variation in preparation for nutrient depletion reveals a cost-benefit tradeoff. PLoS Biol 13:e1002041","journal-title":"PLoS Biol"},{"key":"9708_CR76","doi-asserted-by":"publisher","first-page":"1712","DOI":"10.1016\/j.bpj.2014.07.058","volume":"107","author":"L Xie","year":"2014","unstructured":"Xie L, Wu X-L (2014) Bacterial motility patterns reveal importance of exploitation over exploration in marine microhabitats. Part I: theory. Biophys J 107:1712\u20131720","journal-title":"Biophys J"},{"key":"9708_CR77","doi-asserted-by":"publisher","first-page":"5622","DOI":"10.1073\/pnas.1318943111","volume":"111","author":"Y Yawata","year":"2014","unstructured":"Yawata Y, Cordero OX, Menolascina F et al (2014) Competition-dispersal tradeoff ecologically differentiates recently speciated marine bacterioplankton populations. Proc Natl Acad Sci U S A 111:5622\u20135627","journal-title":"Proc Natl Acad Sci U S A"},{"key":"9708_CR78","doi-asserted-by":"publisher","first-page":"e19307","DOI":"10.7554\/eLife.19307","volume":"5","author":"X Yi","year":"2016","unstructured":"Yi X, Dean AM (2016) Phenotypic plasticity as an adaptation to a functional trade-off. Elife 5:e19307. https:\/\/doi.org\/10.7554\/eLife.19307","journal-title":"Elife"},{"key":"9708_CR79","doi-asserted-by":"publisher","first-page":"4140","DOI":"10.1073\/pnas.1213060110","volume":"110","author":"JW Young","year":"2013","unstructured":"Young JW, Locke JCW, Elowitz MB (2013) Rate of environmental change determines stress response specificity. Proc Natl Acad Sci U S A 110:4140\u20134145","journal-title":"Proc Natl Acad Sci U S A"}],"container-title":["Natural Computing"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/article\/10.1007\/s11047-018-9708-8\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/s11047-018-9708-8.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/s11047-018-9708-8.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,11,8]],"date-time":"2020-11-08T10:55:00Z","timestamp":1604832900000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/s11047-018-9708-8"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2018,8,28]]},"references-count":79,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2018,12]]}},"alternative-id":["9708"],"URL":"https:\/\/doi.org\/10.1007\/s11047-018-9708-8","relation":{},"ISSN":["1567-7818","1572-9796"],"issn-type":[{"type":"print","value":"1567-7818"},{"type":"electronic","value":"1572-9796"}],"subject":[],"published":{"date-parts":[[2018,8,28]]},"assertion":[{"value":"28 August 2018","order":1,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}]}}