Long-term diversity and genome adaptation of Acinetobacter baylyi in a minimal-medium chemostat

Genome Biology and Evolution

Volumn 5, Issue 1, 2013, Pages 87-97

  Jezequel, Nadia ^a,b   Lagomarsino, Marco Cosentino ^a,c,d   Heslot, Francois ^a,b   Thomen, Philippe ^a,b  

^a SORBONNE UNIVERSITÉ   (France)

^b UNIVERSITÉ PARIS DESCARTES   (France)

^c UMR 7238   (France)

^d UNIVERSITY OF TURIN   (Italy)

Author keywords

Acinetobacter; Chemostat; Experimental evolution; Large population; Nitrogen limitation; Resequencing

Indexed keywords

ACINETOBACTER; ACINETOBACTER BAYLYI; BACTERIA (MICROORGANISMS);

EID: 84876525850     PISSN: None     EISSN: 17596653     Source Type: Journal    
DOI: 10.1093/gbe/evs120     Document Type: Article

References (40)

1. Barbe V, et al. 2004. Unique features revealed by the genome sequence of Acinetobacter sp. ADP1, a versatile and naturally transformation competent bacterium. Nucleic Acids Res. 32:5766-5779.
2. Bachmann H, Starrenburg MJ, Molenaar D, Kleerebezem M, van Hylckama Vlieg JE. 2012. Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution. Genome Res. 22:115-124.
3. Barrick JE, Lenski RE. 2009. Genome-wide mutational diversity in an evolving population of Escherichia coli. Cold Spring Harb Symp Quant Biol. 74:119-129.
4. Barrick JE, et al. 2009. Genome evolution and adaptation in a long-term experiment with Escherichia coli. Nature 461:1243-1247.
5. 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.
6. Brunet E, Rouzine IM, Wilke CO. 2008. The stochastic edge in adaptive evolution. Genetics 179:603-620.
7. Buckling A, Maclean RC, Brockhurst MA, Colegrave N. 2009. The Beagle in a bottle. Nature 457:824-829.
8. Chou HH, Chiu HC, Delaney NF, Segra D, Marx CJ. 2011. Diminishing returns epistasis among beneficial mutations decelerates adaptation. Science 332:1190-1192.
9. Conrad TM, Lewis NE, Palsson BO. 2011. Microbial laboratory evolution in the era of genome-scale science. Mol Syst Biol. 7:509.
10. Conrad TM, et al. 2009. Whole-genome resequencing of Escherichia coli K-12 MG1655 undergoing short-term laboratory evolution in lactate minimal media reveals flexible selection of adaptive mutations. Genome Biol. 10:R118.
11. de Cré cy-Lagard VA, Bellalou J, Mutzel R, Marlière P. 2001. Long term adaptation of a microbial population to a permanent metabolic constraint: overcoming thymineless death by experimental evolution of Escherichia coli. BMC Biotechnol. 1:10-16.
12. Desai MM, Fisher DS. 2007. Beneficial mutation-selection balance and the effect of linkage on positive selection. Genetics 176:1759-1798.
13. Desai MM, Fisher DS, Murray AW. 2007. The speed of evolution and maintenance of variation in asexual populations. Curr Biol. 17: 385-394.
14. Doebeli M, Ispolatov I. 2010. Complexity and diversity. Science 328: 494-497.
15. FriesenML, SaxerG, Travisano M, DoebeliM. 2004. Experimental evidence for sympatric ecological diversification due to frequency-dependent competition in Escherichia coli. Evolution 58:245-260.
16. Gause GF. 1934. The struggle for existence. Baltimore (MD): Williams and Wilkins.
17. Gerrish PJ, Lenski RE. 1998. The fate of competing beneficial mutations in an asexual population. Genetica 102(103):127-144.
18. Good BH, Rouzine IM, Balick DJ, Hallatschek O, Desai MM. 2012. Distribution of fixed beneficial mutations and the rate of adaptation in asexual populations. Proc Natl Acad Sci U S A. 109:4950-4955.
19. Gresham D, et al. 2008. The repertoire and dynamics of evolutionary adaptations to controlled nutrient-limited environments in yeast. PLoS Genet. 4:e1000303.
20. Hardin G. 1960. The competitive exclusion principle. Science 131: 1292-1297.
21. Herring CD, et al. 2006. Comparative genome sequencing of Escherichia coli allows observation of bacterial evolution on a laboratory timescale. Nat Genet. 38:1406-1412.
22. Hervas AB, Canosa I, Santero E. 2008. Transcriptome analysis of Pseudomonas putida in response to nitrogen availability. J Bacteriol. 190:416-420.
23. Hindré T, Knibbe C, Beslon G, Schneider D. 2012. New insights into bacterial adaptation through in vivo and in silico experimental evolution. Nat Rev Microbiol. 10:352-365.
24. Hughes JM, et al. 2012. The role of clonal interference in the evolutionary dynamics of plasmid-host adaptation. MBio 3(4):e00077-12.
25. Jackson RW, Johnson LJ, Clarke SR, Arnold DL. 2011. Bacterial pathogen evolution; breaking news. Trends Genet. 27:32-40.
26. Khan AI, Dinh DM, Schneider D, Lenski RE, Cooper TF. 2011. Negative epistasis between beneficialmutations in an evolving bacterial population. Science 332:1193-1196.
27. Langmead B, Trapnell C, Pop M, Salzberg SL. 2009. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10:R25.
28. Levin BR. 1988. Frequency-dependent selection in bacterial populations (and discussion). Philos Trans R Soc Lond B Biol Sci. 319: 459-472.
29. Li H, et al. 2009. The sequence alignment/map format and SAM tools. Bioinformatics 25:2078-2079.
30. Maharjan R, Seeto S, Notley-McRobb L, Ferenci T. 2006. Clonal adaptive radiation in a constant environment. Science 313:514-517.
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. 189:2350-2358.
32. Maharjan RP, et al. 2012. The multiplicity of divergence mechanisms in a single evolving population. Genome Biol. 13:R41.
33. Milne I, et al. 2010. Tablet-next generation sequence assembly visualization. Bioinformatics 26:401-402.
34. Park SC, Krug J. 2007. Clonal interference in large populations. Proc Natl Acad Sci U S A. 104:18135-18140.
35. Rosenzweig RF, Sharp RR, Treves DS, Adams J. 1994. Microbial evolution in a simple unstructured environment: genetic differentiation in Escherichia coli. Genetics 137:903-917.
36. Tenaillon O, et al. 2012. The molecular diversity of adaptive convergence. Science 335:457-461.
37. Toft C, Andersson SG. 2010. Evolutionary microbial genomics; insights into bacterial host adaptation. Nature Rev Genet. 11: 465-475.
38. Wang L, et al. 2010. Divergence involving global regulatory gene mutations in an Escherichia coli population evolving under phosphate limitation. Genome Biol Evol. 2:478-487.
39. Woods RJ, et al. 2011. Second-order selection for evolvability in a large Escherichia coli population. Science 331(6023): 1433-1436.
40. Zerbino DR, Birney E. 2008. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 18:821-829.