Phage-bacteria infection networks

Trends in Microbiology

Volumn 21, Issue 2, 2013, Pages 82-91

  Weitz, Joshua S ^a   Poisot, Timothée ^b,c   Meyer, Justin R ^d   Flores, Cesar O ^a   Valverde, Sergi ^e   Sullivan, Matthew B ^f   Hochberg, Michael E ^g,h  

^a GEORGIA INSTITUTE OF TECHNOLOGY   (United States)

^b UNIVERSITÉ DU QUÉBEC À RIMOUSKI   (Canada)

^c QC Centre for Biodiversity Science   (Canada)

^d MICHIGAN STATE UNIVERSITY   (United States)

^e CSIC   (Spain)

^f The University of Arizona   (United States)

^g INSTITUT DES SCIENCES DE L EVOLUTION   (France)

^h SANTA FE INSTITUTE   (United States)

Author keywords

Biodiversity; Complex networks; Ecosystem; Functional diversity; Microbial ecology; Theory

Indexed keywords

BACTERIAL GROWTH; BACTERIOPHAGE; BIODIVERSITY; BIOGEOCHEMISTRY; BIOGEOGRAPHY; ECOSYSTEM; ENVIRONMENTAL TEMPERATURE; FLAVOBACTERIUM; GENOTYPE; INFORMATION PROCESSING; MICROBIAL COMMUNITY; MICROBIOME; MOLECULAR BIOLOGY; NONHUMAN; PHAGE BACTERIA INFECTION NETWORK; POPULATION DISPERSAL; PRIORITY JOURNAL; PROCHLOROCOCCUS; QUANTITATIVE ANALYSIS; REVIEW; SPECIES DIVERSITY; SYNECHOCOCCUS; TAXONOMY;

BACTERIA; BACTERIOPHAGES; BIOLOGICAL EVOLUTION; ENVIRONMENT; RESEARCH; VIRAL TROPISM;

BACTERIA (MICROORGANISMS);

EID: 84873174809     PISSN: 0966842X     EISSN: 18784380     Source Type: Journal    
DOI: 10.1016/j.tim.2012.11.003     Document Type: Review

References (80)

1. Cairns J., et al. Phage and the Origins of Molecular Biology 2000, Cold Spring Harbor Laboratory Press.
2. Rohwer F., Thurber R.V. Viruses manipulate the marine environment. Nature 2009, 459:207-212.
3. Suttle C.A. Marine viruses - major players in the global ecosystem. Nat. Rev. Microbiol. 2007, 5:801-812.
4. Weinbauer M.G. Ecology of prokaryotic viruses. FEMS Microbiol. Rev. 2004, 28:127-181.
5. Fuhrman J.A. Marine viruses and their biogeochemical and ecological effects. Nature 1999, 399:541-548.
6. Wilhelm S.W., Suttle C.A. Viruses and nutrient cycles in the sea. Bioscience 1999, 49:781-788.
7. Sano E., et al. Movement of viruses between biomes. Appl. Environ. Microbiol. 2004, 70:5842-5846.
8. Nelson E.J., et al. Cholera transmission: the host, pathogen and bacteriophage dynamic. Nat. Rev. Micro 2009, 7:693-702.
9. Reyes A., et al. Viruses in the faecal microbiota of monozygotic twins and their mothers. Nature 2010, 466:334-338.
10. Rho M., et al. Diverse CRISPRs evolving in human microbiomes. PLoS Genet. 2012, 8:e1002441.
11. Sullivan M.B., et al. Cyanophages infecting the oceanic cyanobacterium Prochlorococcus. Nature 2003, 424:1047-1051.
12. Flores C.O., et al. Statistical structure of host-phage interactions. Proc. Natl. Acad. Sci. U.S.A. 2011, 108:E288-E297.
13. Poisot T., et al. Resource availability affects the structure of a natural bacteria-bacteriophage community. Biol. Lett. 2011, 7:201-204.
14. Pascual M., Dunne J.A. Ecological Networks: Linking Structure to Dynamics in Food Webs 2006, Oxford University Press.
15. Bascompte J., et al. The nested assembly of plant-animal mutualistic networks. Proc. Natl. Acad. Sci. U.S.A. 2003, 100:9383-9387.
16. Bascompte J. Disentangling the web of life. Science 2009, 325:416-419.
17. Newman M. Networks: An Introduction 2010, Oxford University Press.
18. Fortuna M.A., et al. Nestedness versus modularity in ecological networks: two sides of the same coin?. J. Anim. Ecol. 2010, 79:811-817.
19. Lenski R.E., Levin B.R. Constraints on the coevolution of bacteria and virulent phage: a model, some experiments, and predictions for natural communities. Am. Nat. 1985, 125:585-602.
20. Agrawal A.F., Lively C.M. Modelling infection as a two-step process combining gene-for-gene and matching-allele genetics. Proc. R. Soc. Lond. B: Biol. Sci. 2003, 270:323-334.
21. Stern A., Sorek R. The phage-host arms race: shaping the evolution of microbes. Bioessays 2011, 33:43-51.
22. Duffy S., et al. Pleiotropic costs of niche expansion in the RNA bacteriophage Φ6. Genetics 2006, 172:751-757.
23. Inouye B., Stinchcombe J.R. Relationships between ecological interaction modifications and diffuse coevolution: similarities, differences, and causal links. Oikos 2001, 95:353-360.
24. Forde S.E., et al. Understanding the limits to generalizability of experimental evolutionary models. Nature 2008, 455:220-223.
25. Leibold M.A., et al. The metacommunity concept: a framework for multi-scale community ecology. Ecol. Lett. 2004, 7:601-613.
26. Wichels A., et al. Bacteriophage diversity in the North Sea. Appl. Environ. Microbiol. 1998, 64:4128-4133.
27. Holmfeldt K., et al. Large variabilities in host strain susceptibility and phage host range govern interactions between lytic marine phages and their Flavobacterium hosts. Appl. Environ. Microbiol. 2007, 73:6730-6739.
28. Koskella B., et al. Local biotic environment shapes the spatial scale of bacteriophage adaptation to bacteria. Am. Nat. 2011, 177:440-451.
29. Vos M., et al. Local adaptation of bacteriophages to their bacterial hosts in soil. Science 2009, 325:833.
30. Hanson C.A., et al. Beyond biogeographic patterns: processes shaping the microbial landscape. Nat. Rev. Microbiol. 2012, 10:497-506.
31. Waterbury J., Valois F. Resistance to co-occurring phages enables marine Synechococcus communities to coexist with cyanophages abundant in seawater. Appl. Environ. Microb. 1993, 59:3393-3399.
32. Hall A.R., et al. Host-parasite coevolutionary arms races give way to fluctuating selection. Ecol. Lett. 2011, 14:635-642.
33. Wilson W.H., et al. The effect of phosphate status on the kinetics of cyanophage infection in the oceanic cyanobacterium Synechococcus sp WH7803. J. Phycol. 1996, 32:506-516.
34. Comeau A.M., et al. Genetic richness of vibriophages isolated in a coastal environment. Environ. Microbiol. 2006, 8:1164-1176.
35. Thompson J.N. The Geographic Mosaic of Coevolution 2005, University of Chicago Press.
36. Jessup C.M., et al. Big questions, small worlds: microbial model systems in ecology. Trends Ecol. Evol. 2004, 19:189-197.
37. Buckling A., et al. The Beagle in a bottle. Nature 2009, 457:824-829.
38. Buckling A., Rainey P.B. Antagonistic coevolution between a bacterium and a bacteriophage. Proc. R. Soc. Lond. B: Biol. Sci. 2002, 269:931-936.
39. Gómez P., Buckling A. Bacteria-phage antagonistic coevolution in soil. Science 2011, 332:106-109.
40. Paterson S., et al. Antagonistic coevolution accelerates molecular evolution. Nature 2010, 464:275-278.
41. Poullain V., et al. The evolution of specificity in evolving and coevolving antagonistic interactions between a bacteria and its phage. Evolution 2008, 62:1-11.
42. Meyer J.R., et al. Repeatability and contingency in the evolution of a key innovation in phage lambda. Science 2012, 335:428-432.
43. Weitz J.S., et al. Coevolutionary arms races between bacteria and bacteriophage. Proc. Natl. Acad. Sci. U.S.A. 2005, 102:9535-9540.
44. Childs L.M., et al. Multi-scale model of CRISPR-induced coevolutionary dynamics: diversification at the interface of Lamarck and Darwin. Evolution 2012, 66:2015-2029.
45. Weinberger A.D., et al. Persisting viral sequences shape microbial CRISPR-based immunity. PLoS Comput. Biol. 2012, 8:e1002475.
46. Appleyard R., et al. Mutation to extended host range and the occurrence of phenotypic mixing in the temperate coliphage lambda. Virology 1956, 2:565-574.
47. Luria S.E. Mutations of bacterial viruses affecting their host range. Genetics 1945, 30:84-99.
48. Hershey A.D. Spontaneous mutations in bacterial viruses. Cold Spring Harb. Symp. Quant. Biol. 1946, 11:67-77.
49. Bowen L., Vuren D.V. Insular endemic plants lack defenses against herbivores. Conserv. Biol. 1997, 11:1249-1254.
50. Brodie E.D. Evolutionary response of predators to dangerous prey: reduction of toxicity of newts and resistance of garter snakes in island populations. Evolution 1991, 45:221-224.
51. Mizoguchi K., et al. Coevolution of bacteriophage PP01 and Escherichia coli O157:H7 in continuous culture. Appl. Environ. Microbiol. 2003, 69:170-176.
52. Crill W.D., et al. Evolutionary reversals during viral adaptation to alternating hosts. Genetics 2000, 154:27-37.
53. Ferris M.T., et al. High frequency of mutations that expand the host range of an RNA virus. Genetics 2007, 176:1013-1022.
54. Duplessis M., Moineau S. Identification of a genetic determinant responsible for host specificity in Streptococcus thermophilus bacteriophages. Mol. Microbiol. 2001, 41:325-336.
55. Quiberoni A., et al. Comparative analysis of Streptococcus thermophilus bacteriophages isolated from a yogurt industrial plant. Food Microbiol. 2003, 20:461-469.
56. Zinno P., et al. Characterization of Streptococcus thermophilus lytic bacteriophages from mozzarella cheese plants. Int. J. Food Microbiol. 2010, 138:137-144.
57. Deveau H., et al. CRISPR/Cas system and its role in phage-bacteria interactions. Annu. Rev. Microbiol. 2010, 64:475-493.
58. Marraffini L.A., Sontheimer E.J. CRISPR interference: RNA-directed adaptive immunity in bacteria and archaea. Nat. Rev. Genet. 2010, 11:181-190.
59. Horvath P., Barrangou R. CRISPR/Cas, the immune system of bacteria and archaea. Science 2010, 327:167-170.
60. Andersson A.F., Banfield J.F. Virus population dynamics and acquired virus resistance in natural microbial communities. Science 2008, 320:1047-1050.
61. Heidelberg J.F., et al. Germ warfare in a microbial mat community: CRISPRs provide insights into the co-evolution of host and viral genomes. PLoS ONE 2009, 4:e4169.
62. Held N.L., Whitaker R.J. Viral biogeography revealed by signatures in Sulfolobus islandicus genomes. Environ. Microbiol. 2009, 11:457-466.
63. Guimerá R., Amaral L.A.N. Functional cartography of complex metabolic networks. Nature 2005, 433:895-900.
64. Labrie S.J., et al. Bacteriophage resistance mechanisms. Nat. Rev. Microbiol. 2010, 8:317-327.
65. Refardt D. Within-host competition determines reproductive success of temperate bacteriophages. ISME J. 2011, 5:1451-1460.
66. Oliver K.M., et al. Bacteriophages encode factors required for protection in a symbiotic mutualism. Science 2009, 325:992-994.
67. Sturino J.M., Klaenhammer T.R. Engineered bacteriophage-defence systems in bioprocessing. Nat. Rev. Microbiol. 2006, 4:395-404.
68. Bohannan B.J.M., Lenski R.E. Effect of prey heterogeneity on the response of a model food chain to resource enrichment. Am. Nat. 1999, 153:73-82.
69. Lennon J.T., Martiny J.B.H. Rapid evolution buffers ecosystem impacts of viruses in a microbial food web. Ecol. Lett. 2008, 11:1178-1188.
70. Avrani S., et al. Genomic island variability facilitates Prochlorococcus-virus coexistence. Nature 2011, 474:604-608.
71. Allen L.Z., et al. Single virus genomics: a new tool for virus discovery. PLoS ONE 2011, 6:e17722.
72. Tadmor A.D., et al. Probing individual environmental bacteria for viruses by using microfluidic digital PCR. Science 2011, 333:58-62.
73. Deng L., et al. Contrasting life strategies of viruses that infect photo- and heterotrophic bacteria, as revealed by viral-tagging. MBio 2012, 3:e00373-12.
74. Atmar W., Patterson B.D. The measure of order and disorder in the distribution of species in fragmented habitat. Oecologia 1993, 96:373-382.
75. Almeida-Neto M., et al. A consistent metric for nestedness analysis in ecological systems: reconciling concept and measurement. Oikos 2008, 117:1-13.
76. Barber M. Modularity and community detection in bipartite networks. Phys. Rev. E 2007, 76:066102.
77. Guimerà R., et al. Module identification in bipartite and directed networks. Phys. Rev. E 2007, 76:036102.
78. Stenholm A.R., et al. Isolation and characterization of bacteriophages infecting the fish pathogen Flavobacterium psychrophilum. Appl. Environ. Microbiol. 2008, 74:4070-4078.
79. Miklič A., Rogelj I. Characterization of lactococcal bacteriophages isolated from Slovenian dairies. Int. J. Food Sci. Technol. 2003, 38:305-311.
80. Capparelli R., et al. Bacteriophage therapy of Salmonella enterica: a fresh appraisal of bacteriophage therapy. J. Infect. Dis. 2010, 201:52-61.