Ecological effects of cellular computing in microbial populations

Acar M, Mettetal JT, van Oudenaarden A (2008) Stochastic switching as a survival strategy in fluctuating environments. Nat Genet 40:471–475 Ahmer BMM, Gunn JS (2011) Interaction of Salmonella spp. with the Intestinal Microbiota. Front Microbiol 2:101 Aidelberg G, Towbin BD, Rothschild D et al (2014) Hierarchy of non-glucose sugars in Escherichia coli. BMC Syst Biol 8:133 Arnoldini M, Vizcarra IA, Peña-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 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 Barrick JE, Lenski RE (2013) Genome dynamics during experimental evolution. Nat Rev Genet 14:827–839 Bashan A, Gibson TE, Friedman J et al (2016) Universality of human microbial dynamics. Nature 534:259–262 Beardmore RE, Gudelj I, Lipson DA, Hurst LD (2011) Metabolic trade-offs and the maintenance of the fittest and the flattest. Nature 472:342–346 Beisel CL, Afroz T (2015) Rethinking the hierarchy of sugar utilization in bacteria. J Bacteriol 198:374–376 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 105:7899–7906 Blount ZD, Barrick JE, Davidson CJ, Lenski RE (2012) Genomic analysis of a key innovation in an experimental Escherichia coli population. Nature 489:513–518 Bohannan BJM, Kerr B, Jessup CM et al (2002) Trade-offs and coexistence in microbial microcosms. Antonie Van Leeuwenhoek 81:107–115 Cavaliere M, Sanchez A (2016) The evolutionary resilience of distributed cellular computing. In: Membrane computing. Springer, Cham, pp 3–15 Chen A, Sanchez A, Dai L, Gore J (2014) Dynamics of a producer-freeloader ecosystem on the brink of collapse. Nat Commun 5:3713 Chesson P (1990) MacArthur’s consumer-resource model. Theor Popul Biol 37:26–38 Desai TA, Rao CV (2010) Regulation of arabinose and xylose metabolism in Escherichia coli. Appl Environ Microbiol 76:1524–1532 Diard M, Garcia V, Maier L et al (2013) Stabilization of cooperative virulence by the expression of an avirulent phenotype. Nature 494:353–356 Diard M, Sellin ME, Dolowschiak T et al (2014) Antibiotic treatment selects for cooperative virulence of Salmonella typhimurium. Curr Biol 24:2000–2005 Dickens B, Fisher CK, Mehta P (2016) Analytically tractable model for community ecology with many species. Phys Rev E 94:022423 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 112:1636–1641 Friesen ML, Saxer G, Travisano M, Doebeli M (2004) Experimental evidence for sympatric ecological diversification due to frequency-dependent competition in Escherichia coli. Evolution 58:245–260 Goldford JE, Lu N, Bajic D et al (2018) Emergent simplicity in microbial community assembly. Science 361:469–474 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 Gutiérrez M, Gregorio-Godoy P, Pérez Del Pulgar G et al (2017) A new improved and extended version of the multicell bacterial simulator gro. ACS Synth Biol 6:1496–1508 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 24:898–908 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 Harrington KI, Sanchez A (2014) Eco-evolutionary dynamics of complex social strategies in microbial communities. Commun Integr Biol 7:e28230 Herron MD, Doebeli M (2013) Parallel evolutionary dynamics of adaptive diversification in Escherichia coli. PLoS Biol 11:e1001490 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 91:1118–1133 Høyland-Kroghsbo NM, Maerkedahl RB, Svenningsen SL (2013) A quorum-sensing-induced bacteriophage defense mechanism. MBio 4:e00362–12 Jang SS, Oishi KT, Egbert RG, Klavins E (2012) Specification and simulation of synthetic multicelled behaviors. ACS Synth Biol 1:365–374 Koirala S, Wang X, Rao CV (2015) Reciprocal regulation of l-arabinose and d-xylose metabolism in Escherichia coli. J Bacteriol 198:386–393 Kotte O, Volkmer B, Radzikowski JL, Heinemann M (2014) Phenotypic bistability in Escherichia coli’s central carbon metabolism. Mol Syst Biol 10:736 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 76:403–416 Le Gac M, Brazas MD, Bertrand M et al (2008) Metabolic changes associated with adaptive diversification in Escherichia coli. Genetics 178:1049–1060 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 Levine JM, Bascompte J, Adler PB, Allesina S (2017) Beyond pairwise mechanisms of species coexistence in complex communities. Nature 546:56–64 Li G, Kesler BK, Thiemicke A et al (2017) Linearly changing stress environment causes cellular growth phenotype. bioRxiv 155267 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 10:1170–1181 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 Mayfield MM, Stouffer DB (2017) Higher-order interactions capture unexplained complexity in diverse communities. Nat Ecol Evol 1:62 Mehta P, Schwab DJ (2012) Energetic costs of cellular computation. Proc Natl Acad Sci U S A 109:17978–17982 Mitchell A, Pilpel Y (2011) A mathematical model for adaptive prediction of environmental changes by microorganisms. Proc Natl Acad Sci U S A 108:7271–7276 Mitchell A, Romano GH, Groisman B et al (2009) Adaptive prediction of environmental changes by microorganisms. Nature 460:220–224 Mitchell A, Wei P, Lim WA (2015) Oscillatory stress stimulation uncovers an Achilles’ heel of the yeast MAPK signaling network. Science 350:1379–1383 Monod J (1949) The growth of bacterial cultures. Annu Rev Microbiol 3:371–394 Monod J (1966) From enzymatic adaptation to allosteric transitions. Science 154:475–483 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 Perkins TJ, Swain PS (2009) Strategies for cellular decision-making. Mol Syst Biol 5:326 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 180:4160–4165 Posfai A, Taillefumier T, Wingreen NS (2017) Metabolic trade-offs promote diversity in a model ecosystem. Phys Rev Lett 118:028103 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 57:162–170 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 Ranea JAG, Grant A, Thornton JM, Orengo CA (2005) Microeconomic principles explain an optimal genome size in bacteria. Trends Genet 21:21–25 Regot S, Macia J, Conde N et al (2011) Distributed biological computation with multicellular engineered networks. Nature 469:207–211 Rillig MC, Rolff J, Tietjen B et al (2015) Community priming—effects of sequential stressors on microbial assemblages. FEMS Microbiol Ecol. https://doi.org/10.1093/femsec/fiv040 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 Rojo F (2010) Carbon catabolite repression in Pseudomonas: optimizing metabolic versatility and interactions with the environment. FEMS Microbiol Rev 34:658–684 Sanchez A, Gore J (2013) Feedback between population and evolutionary dynamics determines the fate of social microbial populations. PLoS Biol 11:e1001547 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 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:E1236–43 Singh KD, Schmalisch MH, Stülke J, Görke B (2008) Carbon catabolite repression in Bacillus subtilis: quantitative analysis of repression exerted by different carbon sources. J Bacteriol 190:7275–7284 Skerker JM, Perchuk BS, Siryaporn A et al (2008) Rewiring the specificity of two-component signal transduction systems. Cell 133:1043–1054 Spencer CC, Bertrand M, Travisano M, Doebeli M (2007) Adaptive diversification in genes that regulate resource use in Escherichia coli. PLoS Genet 3:e15 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 Tagkopoulos I, Liu Y-C, Tavazoie S (2008) Predictive behavior within microbial genetic networks. Science 320:1313–1317 Tan D, Dahl A, Middelboe M (2015) Vibriophages differentially influence biofilm formation by Vibrio anguillarum strains. Appl Environ Microbiol 81:4489–4497 Taylor TB, Mulley G, Dills AH et al (2015) Evolution. evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system. Science 347:1014–1017 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 108:17480–17485 Toll-Riera M, San Millan A, Wagner A, MacLean RC (2016) The genomic basis of evolutionary innovation in Pseudomonas aeruginosa. PLoS Genet 12:e1006005 Turkarslan S, Reiss DJ, Gibbins G et al (2011) Niche adaptation by expansion and reprogramming of general transcription factors. Mol Syst Biol 7:554 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 van Nimwegen E (2003) Scaling laws in the functional content of genomes. Trends Genet 19:479–484 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 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 Xie L, Wu X-L (2014) Bacterial motility patterns reveal importance of exploitation over exploration in marine microhabitats. Part I: theory. Biophys J 107:1712–1720 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 111:5622–5627 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 Young JW, Locke JCW, Elowitz MB (2013) Rate of environmental change determines stress response specificity. Proc Natl Acad Sci U S A 110:4140–4145