Adaptive evolution of synthetic cooperating communities improves growth performance

PLoS ONE

Volumn 9, Issue 10, 2014, Pages

  Zhang, Xiaolin ^a   Reed, Jennifer L ^b  

^a UNIVERSITY OF WISCONSIN MADISON   (United States)

^b University of Wisconsin Madison   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

LEUCINE; LYSINE; CULTURE MEDIUM; GLUCOSE;

AMINO ACID TRANSPORT; ARTICLE; AUXOTROPHY; BACTERIUM MUTANT; COCULTURE; COMMUNITY STRUCTURE; CONTROLLED STUDY; ESCHERICHIA COLI; EVOLUTIONARY ADAPTATION; GENOME SCALE METABOLIC MODEL; GROWTH RATE; MATHEMATICAL MODEL; MICROBIAL COMMUNITY; NONHUMAN; PHENOTYPE; POPULATION DYNAMICS; STARVATION; SURVIVAL; BIOLOGICAL MODEL; CULTURE MEDIUM; EVOLUTION; GROWTH, DEVELOPMENT AND AGING; METABOLISM; ORGANISMAL INTERACTION; PHYSIOLOGICAL PROCESS; PHYSIOLOGY; PROCEDURES;

BIOLOGICAL EVOLUTION; COCULTURE TECHNIQUES; CULTURE MEDIA; ESCHERICHIA COLI; GLUCOSE; LEUCINE; MICROBIAL INTERACTIONS; MODELS, BIOLOGICAL; PHYSIOLOGICAL PROCESSES;

EID: 84907741816     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0108297     Document Type: Article

References (46)

1. Sachs JL, Skophammer RG, Regus JU (2011) Evolutionary transitions in bacterial symbiosis. Proceedings of the National Academy of Sciences of the United States of America 108: 10800-10807.
2. Sachs JL, Mueller UG, Wilcox TP, Bull JJ (2004) The evolution of cooperation. Quarterly Review of Biology 79: 135-160.
3. Morris JJ, Lenski RE, Zinser ER (2012) The black queen hypothesis: evolution of dependencies through adaptive gene loss. Mbio 3(2): e00036-12.
4. Axelrod R, Hamilton WD (1981) The evolution of cooperation. Science 211: 1390-1396.
5. Nowak MA (2006) Five rules for the evolution of cooperation. Science 314: 1560-1563.
6. Kaeberlein T, Lewis K, Epstein SS (2002) Isolating "uncultivable" microorganisms in pure culture in a simulated natural environment. Science 296: 1127-1129.
7. Stoodley P, Cargo R, Rupp CJ, Wilson S, Klapper I (2002) Biofilm material properties as related to shear-induced deformation and detachment phenomena. Journal of Industrial Microbiology & Biotechnology 29: 361-367.
8. Shin CS, Kim HJ, Kim MJ, Ju JY (1998) Morphological change and enhanced pigment production of monascus when cocultured with Saccharomyces cerevisiae or Aspergillus oryzae. Biotechnology and Bioengineering 59: 576-581.
9. Kerner A, Park J, Williams A, Lin XN (2012) A programmable Escherichia coli consortium via tunable symbiosis. PLoS One 7: e34032.
10. Wintermute EH, Silver PA (2010) Emergent cooperation in microbial metabolism. Molecular Systems Biology 6: 407.
11. Hosoda K, Suzuki S, Yamauchi Y, Shiroguchi Y, Kashiwagi A, et al. (2011) Cooperative adaptation to establishment of a synthetic bacterial mutualism. PLoS One 6: e17105.
12. Pande S, Merker H, Bohl K, Reichelt M, Schuster S, et al. (2013) Fitness and stability of obligate cross-feeding interactions that emerge upon gene loss in bacteria. ISME J 8: 953-962.
13. Harcombe W (2010) Novel cooperation experimentally evolved between species. Evolution 64: 2166-2172.
14. Hillesland KL, Stahl DA (2010) Rapid evolution of stability and productivity at the origin of a microbial mutualism. Proceedings of the National Academy of Sciences of the United States of America 107: 2124-2129.
15. Shou WY, Ram S, Vilar JMG (2007) Synthetic cooperation in engineered yeast populations. Proceedings of the National Academy of Sciences of the United States of America 104: 1877-1882.
16. Bull JJ, Harcombe WR (2009) Population dynamics constrain the cooperative evolution of cross-feeding. PLoS One 4: e4115.
17. Stolyar S, Van Dien S, Hillesland KL, Pinel N, Lie TJ, et al. (2007) Metabolic modeling of a mutualistic microbial community. Molecular Systems Biology 3: 92.
18. Nagarajan H, Embree M, Rotaru AE, Shrestha PM, Feist AM, et al. (2013) Characterization and modelling of interspecies electron transfer mechanisms and microbial community dynamics of a syntrophic association. Nature Communications 4: 2809.
19. Zomorrodi AR, Maranas CD (2012) OptCom: a multi-level optimization framework for the metabolic modeling and analysis of microbial communities. PloS Computational Biology 8: e1002363.
20. Brenner K, You LC, Arnold FH (2008) Engineering microbial consortia: a new frontier in synthetic biology. Trends in Biotechnology 26: 483-489.
21. Purnick PEM, Weiss R (2009) The second wave of synthetic biology: from modules to systems. Nature Reviews Molecular Cell Biology 10: 410-422.
22. Rawlings DE, Johnson DB (2007) The microbiology of biomining: development and optimization of mineral-oxidizing microbial consortia. Microbiology-Sgm 153: 315-324.
23. Waks Z, Silver PA (2009) Engineering a synthetic dual-organism system for hydrogen production. Applied and Environmental Microbiology 75: 1867-1875.
24. Charusanti P, Fong NL, Nagarajan H, Pereira AR, Li HJ, et al. (2012) Exploiting adaptive laboratory evolution of Streptomyces clavuligerus for antibiotic discovery and overproduction. PLoS One 7: e33727.
25. Minty JJ, Singer ME, Scholz SA, Bae CH, Ahn JH, et al. (2013) Design and characterization of synthetic fungal-bacterial consortia for direct production of isobutanol from cellulosic biomass. Proceedings of the National Academy of Sciences of the United States of America 110: 14592-14597.
26. Mee MT, Collins JJ, Church GM, Wang HH (2014) Syntrophic exchange in synthetic microbial communities. Proceedings of the National Academy of Sciences of the United States of America 111: E2149-E2156.
27. Kim HJ, Boedicker JQ, Choi JW, Ismagilov RF (2008) Defined spatial structure stabilizes a synthetic multispecies bacterial community. Proceedings of the National Academy of Sciences of the United States of America 105: 18188-18193.
28. You LC, Cox RS, Weiss R, Arnold FH (2004) Programmed population control by cell-cell communication and regulated killing. Nature 428: 868-871.
29. Wintermute EH, Silver PA (2010) Dynamics in the mixed microbial concourse. Genes & Development 24: 2603-2614.
30. Datsenko KA, Wanner BL (2000) One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proceedings of the National Academy of Sciences of the United States of America 97: 6640-6645.
31. Sternberg N, Hoess R (1983) The molecular-genetics of bacteriophage-P1. Annual Review of Genetics 17: 123-154.
32. Christensen JE, Steele JL (2003) Impaired growth rates in milk of Lactobacillus helveticus peptidase mutants can be overcome by use of amino acid supplements. Journal of Bacteriology 185: 3297-3306.
33. Baumler DJ, Peplinski RG, Reed JL, Glasner JD, Perna NT (2011) The evolution of metabolic networks of E. coli. Bmc Systems Biology 5: 182.
34. Higgins BT, VanderGheynst JS (2014) Effects of Escherichia coli on mixotrophic growth of Chlorella minutissima and production of biofuel precursors. PLoS One 9: e96807.
35. Salimi F, Mahadevan R (2013) Characterizing metabolic interactions in a clostridial co-culture for consolidated bioprocessing. BMC Biotechnol 13: 95.
36. Harris DC (2003) Calibration methods. In: Harris DC. Quantitative chemical analysis. 6th edition. New York: W.H. Freeman and Company. pp. 80-98.
37. Feist AM, Henry CS, Reed JL, Krummenacker M, Joyce AR, et al. (2007) A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information. Molecular Systems Biology 3: 121.
38. Varma A, Palsson BO (1994) Stoichiometric flux balance models quantitatively predict growth and metabolic by-product secretion in wild-type Escherichia coli W3110. Applied and Environmental Microbiology 60: 3724-3731.
39. Neidhardt FC, Umbarger EH (1996) Chemical composition of Escherichia coli. In: Neidhardt FC, editor. Escherichia coli and Salmonella: Cellular and molecular biology. 2nd ed. Washington DC: ASM Press. pp. 13-16.
40. Fong SS, Joyce AR, Palsson BO (2005) Parallel adaptive evolution cultures of Escherichia coli lead to convergent growth phenotypes with different gene expression states. Genome Research 15: 1365-1372.
41. Fong SS, Palsson BO (2004) Metabolic gene-deletion strains of Escherichia coli evolve to computationally predicted growth phenotypes. Nature Genetics 36: 1056-1058.
42. Davis BD (1952) Biosynthetic interrelations of lysine, diaminopimelic acid, and threonine in mutants of Escherichia coli. Nature 169: 534-536.
43. Casida L (1956) Preparation of diaminopimelic acid and lysine. U.S. Patent 2771396A.
44. Connor RC (1995) The benefits of mutualism: a conceptual framework. Biological Reviews of the Cambridge Philosophical Society 70: 427-457.
45. Cooper VS, Schneider D, Blot M, Lenski RE (2001) Mechanisms causing rapid and parallel losses of ribose catabolism in evolving populations of Escherichia coli B. Journal of Bacteriology 183: 2834-2841.
46. Mongold JA, Bennett AF, Lenski RE (1996) Evolutionary adaptation to temperature. IV. Adaptation of Escherichia coli at a niche boundary. Evolution 50: 35-43.