Sympatric metabolic diversification of experimentally evolved Escherichia coli in a complex environment

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• 作者：Pilar Eliana Puentes-Téllez (1)
  Jan Dirk van Elsas (1)
  
• 关键词：Experimental evolution ; Adaptive diversification ; Metabolism ; Escherichia coli
• 刊名：Antonie van Leeuwenhoek
• 出版年：2014
• 出版时间：September 2014
• 年：2014
• 卷：106
• 期：3
• 页码：565-576
• 全文大小：816 KB
• 参考文献：1. Adams J, Puskas-Rozsa S, Simlar J, Wilke CM (1992) Adaptation and major chromosomal changes in populations of / Saccharomyces cerevisiae. Curr Genet 22:13-9 CrossRef
  2. Baev MV, Baev D, Janeso A, Campbell JW (2006) Growth of / Escherichia coli MG1655 on LB medium: monitoring utilization of sugars, alcohols and organic acids with transcriptional microarrays. Appl Microbiol Biotechnol 71:310-16 CrossRef
  3. Chan TT, Newman EB (1981) Threonine as a carbon source for / Escherichia coli. J Bacteriol 145(3):1150-153
  4. Chen LM, Maloy S (1991) Regulation of proline utilization in enteric bacteria: cloning and characterization of the Klebsiella put control region. J Bacteriol 173(2):783-90
  5. Claassen PAM, Kortstee GJJ, Oosterveld-van Vliet WM, van Neerven ARW (1986) Colonial heterogeneity of / Thiobacillus versutus. J Bacteriol 168:791-94
  6. Clarke K, Gorley R (2006) PRIMER v6. User manual/tutorial PRIMER-E, Plymouth
  7. Dettman JR, Rodrigue N, Melnyk H, Wong A, Bailey SF, Kassen R (2012) Evolutionary insight from whole-genome sequencing of experimentally evolved microbes. Mol Ecol 21:2058-077 CrossRef
  8. Dittrich CR, Vadali RV, Bennett GN, San K (2005) Redistribution of metabolic fluxes in the central aerobic metabolic pathway of / E. coli mutant strains with deletion of the / ackA- / pta and / poxB pathways for the synthesis of isoamyl acetate. Biotechnol Prog 21:627-31 CrossRef
  9. Dover S, Halpern YS (1972) Utilization of aminobutyric acid as the sole carbon and nitrogen source by / Escherichia coli k-12 mutants. J Bacteriol 109(2):835-43
  10. 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(2):245-60 CrossRef
  11. Hall AR, Colegrave N (2007) How does resource supply affect evolutionary diversification? Proc R Soc B 274:73-8 CrossRef
  12. Halpern YS, Umbarger HE (1961) Utilization of L-glutarnic and 2-oxoglutaric acid as sole sources of carbon by / Escherichia coli. J Gen Microbiol 26:175-83 CrossRef
  13. Han, L (2002) Physiology of / Escherichia coli in Batch and Fed-batch Cultures with Special Emphasis on Amino Acid and Glucose Metabolism Bioteknologi, Stockholm ISBN 91-7283-276-2
  14. Han K, Lim HC, Hong J (1992) Acetic acid formation in Escherichia coli fermentation. Biotechnol Bioeng 39:663-71 CrossRef
  15. Hanko VP, Rohrer J (2000) Determination of carbohydrates, sugar alcohols, and glycols in cell cultures and fermentation broths using high-performance anion-exchange chromatography with pulsed amperometric detection. Anal Biochem 283(2):192-99 CrossRef
  16. Hanko VP, Rohrer J (2004) Determination of amino acids in cell culture and fermentation broth media using anion-exchange chromatography with integrated pulsed amperometric detection. Anal Biochem 324:29-8 CrossRef
  17. Hardin G (1960) The competitive exclusion principle. Science 131(3409):1292-297 CrossRef
  18. Helling RB, Vargas CN, Adams J (1987) Evolution of / Escherichia coli during growth in a constant environment. Genetics 116:349-58
  19. Herron MD, Doebeli M (2013) Parallel evolutionary dynamics of adaptive diversification in / Escherichia coli. Plos Biol 11(2):e1001490. doi:10.1371/journalpbio1001490 CrossRef
  20. Jiménez DJ, Korenblum E, van Elsas JD (2013) Novel multispecies microbial consortia involved in lignocellulose and 5-hydroxymethylfurfural bioconversion. Appl Microbiol Biotechnol. doi:10.1007/s00253-013-5253-7
  21. Kassen R (2002) The experimental evolution of specialists, generalists, and the maintenance of diversity. Science 15:173-90
  22. Kassen R, Rainey PB (2004) The ecology and genetics of microbial diversity. Annu Rev Microbiol 58:207-31 CrossRef
  23. Kinnersley MA, Holben WE, Rosenzweig F (2009) / E Unibus Plurum: genomic analysis of an experimentally evolved polymorphism in / Escherichia coli. Plos Genet 5(11):e1000713. doi:10.1371/journalpgen1000713 CrossRef
  24. Kleman GL, Strohl WR (1994) Acetate metabolism by / Escherichia coli in high-cell-density fermentation. Appl Environ Microbiol 60(11):3952
  25. Korona R (1996) Adaptation to structurally different environments. P Roy Soc Lond B Bio 263(1377):1665-669 CrossRef
  26. Kotrba P, Inui M, Yukawa H (2001) Bacterial phosphotransferase system (PTS) in carbohydrate uptake and control of carbon metabolism. J Biosci Bioeng 92(6):502-17 CrossRef
  27. Kurlandzka A, Rosenzweig RF, Adams J (1991) Identification of adaptive changes in an evolving population of / Escherichia coli: the role of changes with regulatory and highly pleiotropic effects. Mol Biol Evol 8:261-81
  28. Le Gac M, Brazas MD, Bertrand M, Tyerman JG, Spencer CC, Hancock RE, Doebeli M (2008) Metabolic changes associated with adaptive diversification in / Escherichia coli. Genetics 178:1049-060 CrossRef
  29. Lin H, Castro N, Bennett G, San KY (2006) Acetyl-CoA synthetase overexpression in / Escherichia coli demonstrates more efficient acetate assimilation and lower acetate accumulation: a potential tool in metabolic engineering Appl Microbiol. Biotech 71(6):870-74
  30. MacLean RC, Dickson A, Bell G (2005) Resource competition and adaptive radiation in a microbial microcosm. Ecol Lett 8:38-6 CrossRef
  31. Maharjan RP, Seeto S, Ferenci T (2007) Divergence and redundancy of transport and metabolic rate-yield strategies in a single / Escherichia coli population. J Bacteriol 189:2350-358 CrossRef
  32. Marcus M, Halpern YS (1969) Genetic analysis of the glutamate permease in / Escherichia coli K-12. J Bacteriol 97:1118-128
  33. Martínez-Gómez K, Flores N, Casta?eda HM, Martínez-Batallar G, Hernández-Chávez G, Ramírez OT, Gosset G, Encarnación S, Bolivar F (2012) New insights into / Escherichia coli metabolism: carbon scavenging, acetate metabolism and carbon recycling responses during growth on glycerol. Microb Cell Fact 11:46 CrossRef
  34. Notley L, Ferenci T (1996) Induction of RpoS-dependent functions in glucose-limited continuous culture: what level of nutrient limitation induces the stationary phase of / Escherichia coli? J Bacteriol 178:1465-468
  35. Ponciano JM, La HJ, Joyce P, Forney LJ (2009) Evolution of diversity in spatially structured / Escherichia coli populations. Appl Environ Microb 75(19):6047-054 CrossRef
  36. Puentes-Téllez PE, Hansen MA, S?rensen SJ, van Elsas JD (2013) Adaptation and heterogeneity of / Escherichia coli MC1000 growing in complex environments. Appl Environ Microbiol 79:1008-017 CrossRef
  37. Puentes-Téllez PE, Kovacs AT, Kuipers OP, van Elsas JD (2014) Comparative genomics and transcriptomics analysis of experimentally evolved / Escherichia coli MC1000 in complex environments. Environ Microbiol 16(3):856-70 CrossRef
  38. Rainey P, Travisano M (1998) Adaptive radiation in a heterogeneous environment. Nature 394:69-2 CrossRef
  39. Reboud X, Bell G (1997) Experimental evolution in Chlamydomonas III Evolution of specialist and generalist types in environments that vary in space and time. Heredity 78:507-14 CrossRef
  40. Rosenzweig RF, Sharp RR, Treves DS, Adams J (1994) Microbial evolution in a simple unstructured environment: genetic differentiation in / Escherichia coli. Genetics 137:903-17
  41. Sezonov G, Joseleau-Petit D, D’Ari R (2007) / Escherichia coli physiology in Luria Bertani broth. J Bacteriol 189(23):8746-749 CrossRef
  42. Tyerman J, Havard N, Saxer G, Travisano M, Doebeli M (2005) Unparallel diversification in bacterial microcosms. Proc Biol Sci 272(1570):1393-398 CrossRef
  43. Vasi F, Travisano M, Lenski RE (1994) Long term experimental evolution in / Escherichia coli II changes in life-history traits during adaptation to a seasonal environment. Am Nat 144(3):422-56 CrossRef
  44. Versalovic J, Koeuth T, Lupski JR (1991) Distribution of repetitive DNA sequences in eubacteria and application to fingerprinting of bacterial genomes. Nucleic Acids Res 19:6823-831 CrossRef
  
• 作者单位：Pilar Eliana Puentes-Téllez (1)
  Jan Dirk van Elsas (1)
  
  1. Department of Microbial Ecology, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
  
• ISSN：1572-9699

文摘

Sympatric diversification in bacteria has been found to contravene initial evolutionary theories affirming the selection of the fittest type by competition for the same resource. Studies in unstructured (well-mixed) environments have discovered divergence of an ancestor strain into genomically and phenotypically divergent types growing both on single and mixed energy sources. This study addresses the metabolic diversification in an Escherichia coli population that evolved over ~1,000 generations under aerobic conditions in the nutritional complexity offered by Luria–Bertani (LB) broth. The medium lacked glucose but contained a variety of other resources. Two distinct metabolically-diverged types, coinciding with colony morphologies, were found to dominate the populations. One type was an avid carbohydrate consumer, which could quickly utilize the available (alternative) substrates feeding into glycolysis. The second type was a slow grower, which was able to specifically consume acetate. The capacity to utilize acetate might be providing an advantage to this second type, suggesting an increased capability to deal with adverse conditions that occur in the later stages of growth. The diverged metabolic preferences of the two forms suggested differential and interactive ecological roles within the population. We postulate that these types used different alternative metabolic strategies occupying different niches in a sympatric manner as an outcome of adaptation to the complex environment.