Extinction, coexistence, and localized patterns of a bacterial population with contact-dependent inhibition

BMC Systems Biology

Volumn 8, Issue 1, 2014, Pages

  Blanchard, Andrew E ^a   Celik, Venhar ^a   Lu, Ting ^a,b  

^a University of Illinois at Urbana Champaign   (United States)

^b UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

Author keywords

Bacterial population; Competition; Contact dependent inhibition; Extinction and coexistence; Spatial aggregation

Indexed keywords

BACTERIA (MICROORGANISMS);

ARTICLE; BACTERIUM; BIOLOGICAL MODEL; CONTACT INHIBITION; CYTOLOGY; SPECIES EXTINCTION;

BACTERIA; CONTACT INHIBITION; EXTINCTION, BIOLOGICAL; MODELS, BIOLOGICAL;

EID: 84897654866     PISSN: None     EISSN: 17520509     Source Type: Journal    
DOI: 10.1186/1752-0509-8-23     Document Type: Article

References (55)

1. Faust K, Raes J. Microbial interactions: from networks to models. Nat Rev Microbiol 2012, 10(8):538-550. 10.1038/nrmicro2832, 22796884.
2. West SA, Digle SP, Buckling A, Gardner A, Griffin AS. The social lives of microbes. Annu Rev Ecol Evol Systematics 2007, 38:53-57.
3. Foster KR. The sociobiology of molecular systems. Nat Rev Genet 2011, 12:193-203. 10.1038/nrg2903, 21301472.
4. Mitri S, Foster KR. The genotypic view of social interactions in microbial communities. Annu Rev Genet 2013, 4:265-291.
5. Foster KR, Bell T. Competition, not cooperation, dominates interactions among culturable microbial species. Curr Biol 2012, 22:1845-1850. 10.1016/j.cub.2012.08.005, 22959348.
6. Cornforth DM, Foster KR. Competition sensing: the social side of bacterial stress responses. Nat Rev Microbiol 2013, 22:285-293.
7. Little AE, Robinson CJ, Peterson SB, Raffa KF, Handelsman J. Rules of engagement: interspecies interactions that regulate microbial communities. Annu Rev Microbiol 2008, 62:375-401. 10.1146/annurev.micro.030608.101423, 18544040.
8. Hibbing ME, Fuqua C, Parsek MR, Peterson SB. Bacterial competition: surviving and thriving in the microbial jungle. Nat Rev Microbiol 2010, 8(1):15-25. 10.1038/nrmicro2259, 2879262, 19946288.
9. Nadell CD, Xavier JB, Levin SA, Foster KR. The evolution of quorum sensing in bacterial biofilms. PLoS Biol 2008, 6(1):14-01710179.
10. Keller L, Surette MG. Communication in bacteria: an ecological and evolutionary perpective. Nat Rev Microbiol 2006, 4:249-257. 10.1038/nrmicro1383, 16501584.
11. Diggle S, Griffin A, Campbell G, West S. Cooperation and conflict in quorum-sensing bacterial populations. Nature 2007, 450:411-414. 10.1038/nature06279, 18004383.
12. Chatterjee C, Paul M, Xie L, van der Donk WA. Biosynthesis and mode of action of Lantibiotics. Chem Rev 2005, 105:633-683. 10.1021/cr030105v, 15700960.
13. Russell AB, Hod RD, Bui NK, LeRoux M, Vollmer W, Mougous JD. Type VI secretion delivers bacteriolytic effectors to target cells. Nature 2011, 475:343-347. 10.1038/nature10244, 3146020, 21776080.
14. Aoki SK, Pamma R, Hernday AD, Bickham JE, Braaten BA, Low DA. Contact-dependent inhibition of growth in Escherichia coli. Science 2005, 309(5738):1245-8. 10.1126/science.1115109, 16109881.
15. Hayes CS, Aoki SK, Low DA. Bacterial contact-dependent delivery systems. Annu Rev Genet 2010, 44:71-90. 10.1146/annurev.genet.42.110807.091449, 21047256.
16. Aoki SK, Malinverni JC, Jacoby K, Thomas B, Pamma R, Trinh BN, Remers S, Webb J, Braaten BA, Silhavy TJ, Low DA. Contact-dependent growth inhibition requires the essential outer membrane protein BamA (YaeT) as the receptor and the inner membrane transport protein AcrB. Mol Microbiol 2008, 70(2):323-40. 10.1111/j.1365-2958.2008.06404.x, 2579741, 18761695.
17. Aoki SK, Diner EJ, de Roodenbeke CT, Burgess BR, Poole SJ, Braaten BA, Jones AM, Webb JS, Hayes CS, Cotter PA, Low DA. A widespread family of polymorphic contact-dependent toxin delivery systems in bacteria. Nature 2010, 468:439-42. 10.1038/nature09490, 3058911, 21085179.
18. Holberger LE, Sanchez FG, Lamoureux J, Low DA. A novel family of toxin/antitoxin proteins in Bacillus species. Fed Eur Biochem Societies Lett 2008, 586:132-136.
19. Braun V, Patzer SI. Intercellular communication by related bacterial protein toxins: colicin, contact-dependent inhibitors, and proteins exported by the type VI secretion system. Fed Eur Microbiol Societies Microbiol Lett 2013, 345:13-21.
20. Zhang D, Iyer LM, Aravind LA. A novel immunity system for bacterial nucleic acid degrading toxins and its recruitment in various eukaryotic and DNA viral systems. Nucleic Acids Res 2011, 39(11):4532-4552. 10.1093/nar/gkr036, 3113570, 21306995.
21. Zhang D, de Souza RF, Anantharaman V, Iyer LM, Aravind L. Polymorphic toxin systems: comprehensive characterization of trafficking modes, processing, mechanisms of action, immunity and ecology using comparative genomics. Biol Direct 2012, 7(18):1-76. 3284417, 22221860.
22. Ashida H, Ogawa M, Kim M, Mimuro H, Sasakawa C. Bacteria and host interactions in the gut epithelial barrier. Nat Chem Biol 2012, 8:36-44.
23. Basler M, Ho BT, Mekalanos JJ. Tit-for-Tat: Type VI secretion system counterattack during bacterial cell-cell interactions. Cell 2013, 152:884-894. 10.1016/j.cell.2013.01.042, 3616380, 23415234.
24. Ruhe ZC, Low DA, Hayes CS. Bacterial contact-dependent growth inhibition. Trends Microbiol 2013, 21(5):230-7. 10.1016/j.tim.2013.02.003, 23473845.
25. Lemonnier M, Levin BR, Romeo T, Garner K, Baquero MR, Mercante J, Lemichez E, Baquero F, Blazquez J. The evolution of contact-dependent inhibition in non-growing populations of Escherichia coli. Proc R Soc B: Biol Sci 2008, 275:3-10.
26. Aoki SK, Webb JS, Braaten BA, Low DA. Contact-dependent growth inhibition causes reversible metabolic downregulation in Escherichia coli. J Bacteriol 2009, 191(6):1777-1786. 10.1128/JB.01437-08, 2648372, 19124575.
27. Lotka AJ. Elements of Physical Biology 1925, Baltimore: Williams & Wilkins.
28. Volterra V. Variazioni e fluttuazioni del numero d'individui in specie animali conviventi. Mem R Accad Lincei Ser 1926, 2:31-113.
29. Levin S. Dispersion and population interactions. Am Nat 1974, 108(960):207-228.
30. Takeuchi Y. Diffusion-mediated persistence in two-species competition Lotka-Volterra model. Math Biosci 1989, 95:65-83. 10.1016/0025-5564(89)90052-7, 2520178.
31. López-Gómez J, Gil RS. Coexistence regions in lotka-volterra models with diffusion. Nonlinear Anal: Theory Methods Appl 1992, 19(1):11-28.
32. Kishimoto K. Instability of non-constant equilibrium solutions of a system of competition-diffusion equations. J Math Biol 1981, 13:105-114.
33. Eilbeck J, Furter J, Lopezgomez J. Coexistence in the competition model with diffusion. J Differential Equations 1994, 107:96-139.
34. Ito M. Global aspect of steady-states for competitive-diffusive systems with homogeneous Dirichlet conditions. Physica D: Nonlinear Phenomena 1984, 14:1-28.
35. Murray JD. Mathematical Biology 2002, New York: Springer.
36. Tang Y, Yuan R, Ma Y. Dynamical behaviors determined by the Lyapunov function in competitive Lotka-Voltera systems. Phys Rev E 2013, 87:012708.
37. Britton NF. Aggregation and the competitive exclusion principle. J Theor Biol 1989, 136:57-66. 10.1016/S0022-5193(89)80189-4, 2779260.
38. Cook JN, Oono Y. Competitive localization. Physica A: Stat Mech Appl 2010, 389:1849-1860.
39. Sasaki A. Clumped distribution by neighborhood competition. J Theor Biol 1997, 186:415-430.
40. Segal BL, Volpert VA, Bayliss A. Pattern formation in a model of competing populations with nonlocal interactions. Physica D: Nonlinear Phenomena 2013, 253:12-22.
41. da Cunha JAR, Penna ALA, Oliveira FA. Pattern formation and coexistence domains for a nonlocal population dynamics. Phys Rev E 2011, 83:015201.
42. Fuentes M, Kuperman M, Kenkre V. Nonlocal interaction effects on pattern formation in population dynamics. Phys Rev Lett 2003, 91(15):158104.
43. Fernandez-Oto C, Clerc MG, Escaff D, Tlidi M. Strong nonlocal coupling stabilizes localized structures: an analysis based on front dynamics. Phys Rev Lett 2013, 110:174101.
44. Clerc MG, Escaff D, Kenkre VM. Analytical studies of fronts, colonies, and patterns: combination of the Allee effect and nonlocal competition interactions. Phys Rev E 2010, 82:036210.
45. Shnerb N. Pattern formation and nonlocal logistic growth. Phys Rev E 2004, 69:061917.
46. Maruvka Y, Shnerb N. Nonlocal competition and logistic growth: patterns, defects, and fronts. Physical Review E 2006, 73:011903.
47. Pigolotti S, López C, Hernández-García E. Species clustering in competitive Lotka-Volterra models. Phys Rev Lett 2007, 98:258101.
48. Gourley S, Britton N. A predator-prey reaction-diffusion system with nonlocal effects. J Math Biol 1996, 34:297-333.
49. Chao L, Levin BR. Structured habitats and the evolution of anticompetitor toxins in bacteria. Proc Nat Acad Sci 1981, 78(10):6324-6328. 10.1073/pnas.78.10.6324, 349031, 7031647.
50. Turing AM. The chemical basis of morphogenesis. Philos Trans R Soc London. Series B, Biol Sci 1952, 237(641):37-72.
51. Lu T, Shen T, Bennett MR, Wolynes PG, Hasty J. Phenotypic variability of growing cellular populations. Proc Nat Acad Sci 2007, 104(48):18982-18987. 10.1073/pnas.0706115104, 2141894, 18025471.
52. Murat D, Goncalves L, Dassa E. Deletion of the Escherichia coli uup gene encoding a protein of the ATPbinding cassette superfamily affects bacterial competitiveness. Res Microbiol 2008, 159:671-677. 10.1016/j.resmic.2008.09.004, 18848624.
53. Press WH, Teukolsky SA, Vetterling WT, Flannery BP. Numerical Recipes in C 1992, New York: Cambridge University Press.
54. Cash J, Karp A. A variable order Runge-Kutta method for initial value problems with rapidly varying right-hand sides. Assoc Comput Machinery Trans Math Softw 2005, 16(3):201-222.
55. Holmes MH. Introduction to Perturbation Methods 2013, New York: Springer.