Bacteriophages affect evolution of bacterial communities in spatially distributed habitats: A simulation study

BMC Microbiology

Volumn 16, Issue 1, 2016, Pages

  Klimenko, Alexandra Igorevna ^a,b   Matushkin, Yury Georgievich ^a   Kolchanov, Nikolay Alexandrovich ^a,b   Lashin, Sergey Alexandrovich ^a,b  

^a INSTITUTE OF CYTOLOGY AND GENETICS   (Russian Federation)

^b NOVOSIBIRSK STATE UNIVERSITY   (Russian Federation)

Author keywords

Archaea; Bacteria; Bacteriophage; Ecological simulation; Evolution; Evolutionary modeling; Microbial community; Phage; Prokaryotes

Indexed keywords

ARTICLE; BACTERIAL CELL; BACTERIAL MUTATION; BACTERIAL VIABILITY; BACTERIOPHAGE; COMPUTER MODEL; COMPUTER SIMULATION; CONTROLLED STUDY; MICROBIAL COMMUNITY; SPECIES DIFFERENTIATION; VIRUS INFECTION; BACTERIUM; BIOLOGICAL MODEL; ECOSYSTEM; EVOLUTION; GENETICS; HOST PATHOGEN INTERACTION; PHYSIOLOGY; VIROLOGY;

BACTERIA; BACTERIOPHAGES; BIOLOGICAL EVOLUTION; ECOSYSTEM; HOST-PATHOGEN INTERACTIONS; MODELS, BIOLOGICAL;

EID: 84955297245     PISSN: None     EISSN: 14712180     Source Type: Journal    
DOI: 10.1186/s12866-015-0620-4     Document Type: Article

References (44)

1. Hendrix RW. Bacteriophage Evolution and the Role of Phages in Host Evolution. In: Waldor MK, et al. Phages: their role in bacterial pathogenesis and biotechnology. American Society of Microbiology; 2005:55-65.
2. Koskella B, Brockhurst MA. Bacteria-phage coevolution as a driver of ecological and evolutionary processes in microbial communities. FEMS Microbiol Rev. 2014;38:916-31.
3. Pride D, Wassenaar T, Ghose C, Blaser M. Evidence of host-virus co-evolution in tetranucleotide usage patterns of bacteriophages and eukaryotic viruses. BMC Genomics. 2006;7:8.
4. Fuhrman JA. Marine viruses and their biogeochemical and ecological effects. Nature. 1999;399:541-8.
5. Ochman H, Lawrence JG, Groisman EA. Lateral gene transfer and the nature of bacterial innovation. Nature. 2000;405:299-304.
6. Canchaya C, Fournous G, Chibani-Chennoufi S, Dillmann M-L, Brüssow H. Phage as agents of lateral gene transfer. Curr Opin Microbiol. 2003;6:417-24.
7. Skippington E, Ragan MA. Lateral genetic transfer and the construction of genetic exchange communities. FEMS Microbiol Rev. 2011;35:707-35.
8. Bohannan BJM, Lenski RE. Linking genetic change to community evolution: insights from studies of bacteria and bacteriophage. Ecol Lett. 2000;3:362-77.
9. Desiere F, McShan WM, van Sinderen D, Ferretti JJ, Brüssow H. Comparative genomics reveals close genetic relationships between phages from dairy bacteria and pathogenic streptococci: evolutionary implications for prophage-host interactions. Virology. 2001;288:325-41.
10. Williams HT. Phage-induced diversification improves host evolvability. BMC Evol Biol. 2013;13:17.
11. Berngruber TW, Froissart R, Choisy M, Gandon S. Evolution of virulence in emerging epidemics. PLoS Pathog. 2013;9, e1003209.
12. Roberts PD, Portfors CV. Design principles of sensory processing in cerebellum-like structures. Early stage processing of electrosensory and auditory objects. Biol Cybern. 2008;98:491-507.
13. Gomez P, Ashby B, Buckling A. Population mixing promotes arms race host-parasite coevolution. Proc R Soc B Biol Sci. 2014;282:20142297-7.
14. Heilmann S, Sneppen K, Krishna S. Sustainability of virulence in a phage-bacterial ecosystem. J Virol. 2010;84:3016-22.
15. Levin BR, Moineau S, Bushman M, Barrangou R. The population and evolutionary dynamics of phage and bacteria with CRISPR-mediated immunity. PLoS Genet. 2013;9, e1003312.
16. Perfeito L, Pereira MI, Campos PRA, Gordo I. The effect of spatial structure on adaptation in Escherichia coli. Biol Lett. 2008;4:57-9.
17. Mitri S, Xavier JB, Foster KR. Social evolution in multispecies biofilms. Proc Natl Acad Sci U S A. 2011;108(Suppl):10839-46.
18. Lion S, Gandon S. Evolution of spatially structured host-parasite interactions. J Evol Biol. 2015;28:10-28.
19. Roychoudhury P, Shrestha N, Wiss VR, Krone SM. Fitness benefits of low infectivity in a spatially structured population of bacteriophages. Proc R Soc B Biol Sci. 2013;281:20132563-3.
20. Koskella B, Parr N. The evolution of bacterial resistance against bacteriophages in the horse chestnut phyllosphere is general across both space and time. Philos Trans R Soc B Biol Sci. 2015;370:20140297.
21. Lopez Pascua L, Hall AR, Best A, Morgan AD, Boots M, Buckling A. Higher resources decrease fluctuating selection during host-parasite coevolution. Ecol Lett. 2014;17:1380-8.
22. Scanlan PD, Hall AR, Blackshields G, Friman V-P, Davis MR, Goldberg JB, et al. Coevolution with bacteriophages drives genome-wide host evolution and constrains the acquisition of abiotic-beneficial mutations. Mol Biol Evol. 2015;32:1425-35.
23. Heilmann S, Sneppen K, Krishna S. Coexistence of phage and bacteria on the boundary of self-organized refuges. Proc Natl Acad Sci. 2012;109:12828-33.
24. Childs LM, Held NL, Young MJ, Whitaker RJ, Weitz JS. Multiscale model of crispr-induced coevolutionary dynamics: diversification at the interface of lamarck and darwin. Evolution (N Y). 2012;66:2015-29.
25. Ashby B, Gupta S, Buckling A. Spatial structure mitigates fitness costs in host-parasite coevolution. Am Nat. 2014;183:E64-74.
26. Lashin SA, Matushkin YG, Suslov VV, Kolchanov NA. Evolutionary trends in the prokaryotic community and prokaryotic community-phage systems. Russ J Genet. 2011;47:1487-95.
27. Lenski RE, Levin BR. Constraints on the coevolution of bacteria and virulent phage: a model, some experiments, and predictions for natural communities. Am Nat. 1985;125:582-602.
28. Wang I-N, Dykhuizen DE, Slobodkin LB. The evolution of phage lysis timing. Evol Ecol. 1996;10:545-58.
29. Nowak MA, May RM. Superinfection and the evolution of parasite virulence. Proc R Soc B Biol Sci. 1994;255:81-9.
30. Abedon ST, Culler RR. Bacteriophage evolution given spatial constraint. J Theor Biol. 2007;248:111-9.
31. Bull JJ, Crandall C, Rodriguez A, Krone SM. Models for the directed evolution of bacterial allelopathy: bacteriophage lysins. PeerJ. 2015;3, e879.
32. Weitz JS, Hartman H, Levin SA. Coevolutionary arms races between bacteria and bacteriophage. Proc Natl Acad Sci U S A. 2005;102:9535-40.
33. Iranzo J, Lobkovsky AE, Wolf YI, Koonin EV. Immunity, suicide or both? Ecological determinants for the combined evolution of anti-pathogen defense systems. BMC Evol Biol. 2015;15:43.
34. Lashin SA, Matushkin YG. Haploid evolutionary constructor: new features and further challenges. In Silico Biol. 2012;11:125-35.
35. Lashin SA, Klimenko AI, Mustafin ZS, Kolchanov NA, Matushkin YG. HEC 2.0: improved simulation of the evolution of prokaryotic communities. Math Biol Bioinform. 2014;9:585-96.
36. Scheffer M, Baveco JM, DeAngelis DL, Rose KA, van Nes EH. Super-individuals a simple solution for modelling large populations on an individual basis. Ecol Modell. 1995;80:161-70.
37. Hellweger FL, Bucci V. A bunch of tiny individuals - Individual-based modeling for microbes. Ecol Modell. 2009;220:8-22.
38. Klimenko AI, Matushkin YG, Kolchanov NA, Lashin SA. Modeling evolution of spatially distributed bacterial communities: a simulation with the haploid evolutionary constructor. BMC Evol Biol. 2015;15:S3.
39. Ptashne M. A genetic switch: Gene control and phage. lambda. Elsevier B.V., 1986.
40. Lashin SA, Matushkin YG, Suslov VV, Kolchanov NA. Computer modeling of genome complexity variation trends in prokaryotic communities under varying habitat conditions. Ecol Modell. 2012;224:124-9.
41. Steward GF, Smith DC, Azam F. Abundance and production of bacteria and viruses in the Bering and Chukchi Seas. Mar Ecol Prog Ser. 1996;131:287-300.
42. France SC, Hessler RR, Vrijenhoek RC. Genetic differentiation between spatially-disjunct populations of the deep-sea, hydrothermal vent-endemic amphipod Ventiella sulfuris. Mar Biol. 1992;114:551-9.
43. Gavrilets S, Li H, Vose MD. Patterns of parapatric speciation. Evolution (N Y). 2000;54:1126-34.
44. Won Y, Young CR, Lutz RA, Vrijenhoek RC. Dispersal barriers and isolation among deep-sea mussel populations (Mytilidae: Bathymodiolus) from eastern Pacific hydrothermal vents. Mol Ecol. 2002;12:169-84.