Bacterial evolution in simple microcosms

Microcosms: Ecology, Biological Implications and Environmental Impact

Volumn , Issue , 2013, Pages 107-127

  Spiers, Andrew J ^a  

^a UNIVERSITY OF ABERTAY DUNDEE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84895250127     PISSN: None     EISSN: None     Source Type: Book    
DOI: None     Document Type: Chapter

References (81)

1. Ackert, L.T. (2007). The ''Cycle of Life'' in ecology: Sergei Vinogradskii's soil microbiology, 1885-1940. J. History Biol. 40: 109-145.
2. Bantinaki, B., Kassen, R., Knight, C.G., Robinson, Z., Spiers, A.J. and Rainey, P.B. (2007). Adaptive divergence in experimental populations of Pseudomonas fluorescens. III. Mutational origins of Wrinkly Spreader diversity. Genetics 176: 441-453.
3. Battin, T., Sloan, W.T., Kjelleberg, S., Daims, H., Head, I.M., Curtis, T.P. and Eberl, L. (2007). Microbial landscapes: new paths to biofilm research. Nature Rev. Microbiol. 5: 76-81.
4. Blattner, F.R., Plunkett, G., Bloch, C.A., Perna, N.T., Burland, V., Riley, M., Collado-Vides, J., Glasner, J.D., Rode, C.K., Mayhew, G.F., Gregor, J., Davis, N.W., Kirkpatrick, H.A., Goeden, M.A., Rose, D.J., Mau, B. and Shao, Y. (1997). The complete genome sequence of Escherichia coli K-12. Science 277: 1453-1462.
5. Bren, A. and Eisenbach, M. (2000). How signals are heard during bacterial chemotaxis: protein-protein interactions in sensory signal propagation. J. Bacteriol. 182: 6865-6873.
6. Brockhurst, M.A., Colegrave, N., Hodgson, D.J. and Buckling, A. (2007). Niche occupation limits adaptive radiation in experimental microcosms. PLoS ONE 2: e193.
7. Brockhurst, M.A., Habets, M.G.J.L., Libberton, B., Buckling, A. and Gardner, A. (2010). Ecological drivers of the evolution of public-goods cooperation in bacteria. Ecology 91: 334-340.
8. Brockhurst, M.A., Hochberg, M.E., Bell, T. and Buckling, A. (2006). Character displacement promotes cooperation in bacterial biofilms. Curr. Biol. 16: 1-5.
9. Brockhurst, M.A., Morgan, A.D., Fenton, A. and Buckling, A. (2007). Experimental coevolution with bacteria and phage: The Pseudomonas fluorescens-2 model system. Infect. Genet. Evol. 7: 547-552.
10. Buckling, A., Brockhurst, M.A., Travisano, M. and Rainey, P.B. (2007). Experimental adaptation to high and low quality environments under different scales of temporal variation. J. Evol. Biol. 20: 296-300.
11. Buckling, A., Kassen, R., Bell, G. and Rainey, P.B. (2000). Disturbance and diversity in experimental microcosms. Nature 408: 961-964.
12. Buckling, A., Wills, M.A. and Colegrave, N. (2003). Adaptation limits diversification of experimental bacterial populations. Science 302: 2107-2109.
13. Buckling, A., Maclean, C.R., Brockhurst, M.A. and Colegrave, N. (2009). The Beagle in a bottle. Nature 457: 824-829.
14. Cooper, T.F. (2012). Empirical insights into adaptive landscapes from bacterial experimental evolution. In: The Adaptive Landscape. Svensson, E.I. and Calsbeek, R. (Eds). Oxford University Press, Oxford.
15. Dalziel, A.C., Rogers, S.M. and Schulte, P.M. (2009). Linking genotypes to phenotypes and fitness: how mechanistic biology can inform molecular ecology. Mol. Ecol. 18: 4997-5017.
16. Dworkin, M. (2012). Sergei Winogradsky: a founder of modern microbiology and the first microbial ecologist. FEMS Microbiol. Rev. 36: 364-379.
17. Elena, S.F. and Lenski, R.E. (2003). Evolution experiments with microorganisms: the dynamics and genetic bases of adaptation. Nature Rev. Genet. 4: 457-469.
18. Elias, S. and Banin, E. (2012). Multi-species biofilms: living with friendly neighbors. FEMS Microbiol. Rev. 36: 990-1004.
19. Escobar-Páramo, P., Gougat-Barbera, C. and Hochberg, M.E. (2012). Evolutionary dynamics of separate and combined exposure of Pseudomonas fluorescens SBW25 to antibiotics and bacteriophage. Evol. Applications 5: 583-592.
20. Gal, M., Preston, G.M., Massey, R.C., Spiers, A.J. and Rainey, P.B. (2003). Genes encoding a cellulosic polymer contribute toward the ecological success of Pseudomonas fluorescens SBW25 on plant surfaces. Mol. Ecol. 12: 3109-3121.
21. Gehrig, S.M. (2005). Adaptation of Pseudomonas fluorescens SBW25 to the air-liquid interface: a study in evolutionary genetics. DPhil thesis. University of Oxford, Oxford.
22. Giddens, S.R., Jackson, R.W., Moon, C.D., Jacobs, M.A., Zhang, X-X., Gehrig, S.M. and Rainey, P.B. (2007). Mutational activation of niche-specific genes provides insight into regulatory networks and bacterial function in a complex environment. Proc. Natl. Acad. Sci. (USA) 104: 18247-18252.
23. Goymer, P., Kahn, S.G., Malone, J.G., Gehrig, S.M., Spiers, A.J. and Rainey, P.B. (2006). Adaptive divergence in experimental populations of Pseudomonas fluorescens. II. Role of the GGDEF regulator WspR in evolution and development of the Wrinkly Spreader phenotype. Genetics 173: 515-526.
24. Green, J.H., Koza, A., Moshynets, O., Pajor, R., Ritchie, M.R. and Spiers, A.J. (2011). Evolution in a test tube: rise of the Wrinkly Spreaders. J. Biol. Educ. 45: 54-59.
25. Hall-Stoodley, L., Costerton, J.W. and Stoodley, P. (2004). Bacterial biofilms: from the natural environment to infectious diseases. Nature Rev. Microbiol. 2: 95-108.
26. Huang, W.E., Bailey, M.J., Thompson, I.P., Whiteley, A.S. and Spiers, A.J. (2007). Single-cell Raman spectral profiles of Pseudomonas fluorescens SBW25 reflects in vitro and in planta metabolic history. Microb. Ecol. 53: 414-425.
27. Huang, W.E. and Spiers, A.J. (2006). Consideration of future requirements for Raman microbiology as an examplar for the ab initio development of informatics frameworks for emergent OMIC technologies. OMICS: J. Integ. Biol. 10: 238-241.
28. Huang, W.E., Ude, S. and Spiers, A.J. (2007). Pseudomonas fluorescens SBW25 biofilm and planktonic cells have differentiable Raman spectral profiles. Microb. Ecol. 53: 471-474.
29. Hoshino, E., Wada, Y. and Nishizawa, K. (1999). Improvements in the hygroscopic properties of cotton cellulose by treatment with an endo-type cellulase from Streptomyces sp. KSM-26. J. Biosci. Bioeng. 88: 519-525.
30. Jackson, R.W. and Giddens, S.R. (2006). Development and application of in vivo expression technology (IVET) for analysing microbial gene expression in complex environments. Infect. Disord. Drug Targets 6: 207-240.
31. Jenal, U. and Malone, J. (2006). Mechanisms of cyclic-di-GMP signaling in bacteria. Annu. Rev. Genet. 40: 385-407.
32. King, E.O., Ward, M.K. and Raney, D.C. (1954). Two simple media for the demonstration of pyocyanin and fluorescin. J. Lab. Clin. Med. 44: 301-307.
33. Knope, M.L., Forde, S.E. and Fukami, T. (2012). Evolutionary history, immigration history, and the extent of diversification in community assembly. Frontiers Microbiol. 2: 273.
34. Koza, A., Hallett, P.D., Moon, C.D. and Spiers, A.J. (2009). Characterization of a novel air-liquid interface biofilm of Pseudomonas fluorescens SBW25. Microbiology 155: 1397-1406.
35. Koza, A., Moshynets, O., Otten, W. and Spiers, A.J. (2011). Environmental modification and niche construction: Developing O2 gradients drive the evolution of the Wrinkly Spreader. ISME J. 5: 665-673.
36. Kreft, J-U. and Bonhoeffer, S. (2005). The evolution of groups of cooperating bacteria and the growth rate versus yield trade-off. Microbiology 151: 637-641.
37. Lenski, R.E., Rose, M.R., Simpson, S.C. and Tadler, S.C. (1991). Long-term experimental evolution in Escherichia coli. I. Adaptation and divergence during 2,000 generations. Amer. Nat. 138: 1315-1341.
38. Le Quéré, B. and Ghigo, J.M. (2009). BcsQ is an essential component of the Escherichia coli cellulose biosynthesis apparatus that localizes at the bacterial cell pole. Mol. Microbiol. 72: 724-740.
39. MacLean, R.C. (2005). Adaptive radiation in microbial microcosms. J. Evol. Biol. 18: 1376-1386.
40. MacLean, R.C. (2008). The tragedy of the commons in microbial populations: insights from theoretical, comparative and experimental studies. Heredity 100: 471-477.
41. MacLean, R.C. and Bell, G. (2003). Divergent evolution during an experimental adaptive radiation. Proc. R. Soc. Lond. B 270: 1645-1650.
42. MacLean, R.C., Bell, G. and Rainey, P.B. (2004). The evolution of a pleiotropic fitness tradeoff in Pseudomonas fluorescens. Proc. Natl. Acad. Sci. USA 101: 8072-8077.
43. MacLean, R.C., Dickson, A. and Bell, G. (2005). Resource competition and adaptive radiation in a microbial microcosm. Ecol. Lett. 8: 38-46.
44. Magee, J. (1993). Whole-organism fingerprinting. In: Handbook of New Bacterial Systematics. Goodfellow, M. and O'Donnell, A.G. (Eds.). Harcourt Brace, New York.
45. Malone, J.G., Williams, R., Christen, M., Jenal, U., Spiers, A.J. and Rainey, P.B. (2007). The structure-function relationship of WspR, a Pseudomonas fluorescens response regulator with a GGDEF output domain. Microbiology 153: 980-994.
46. McDonald, M.J., Cooper, T.F., Beaumont, H.J.E. and Rainey, P.B. (2011). The distribution of fitness effects of new beneficial mutations in Pseudomonas fluorescens. Biol. Lett. 7: 98-100.
47. McDonald, M.J., Gehrig, S.M., Meintjes, P.L., Zhang, X. and Rainey, P.B. (2009). Adaptive divergence in experimental populations of Pseudomonas fluorescens. IV. Genetic constraints guide evolutionary trajectories in a parallel adaptive radiation. Genetics 183: 1041-1053.
48. McDougald, D., Rice, S.A., Barraud, N., Steinberg, P.D. and Kjelleberg, S. (2011). Should we stay or should we go: mechanisms and ecological consequences for biofilm dispersal. Nature Rev. Microbiol. 10: 39-50.
49. Meyer, R. and Kassen, R. (2007). The effects of competition and predation on diversification in a model adaptive radiation. Nature 446: 432-435.
50. Meyer, J.R., Schoustra, S.E., Lachapelle, J. and Kassen, R. (2011). Overshooting dynamics in a model adaptive radiation. Proc. R. Soc. B 278: 392-398.
51. Morris, J.J., Lenski, R.E. and Zinser, E.R. (2012). The Black Queen Hypothesis: evolution of dependencies through adaptive gene loss. mBio 3: e00036-12.
52. O'Toole, G., Kaplan, H.B. and Kolter, R. (2000). Biofilm formation as microbial development. Annu. Rev. Microbiol. 54: 49-79.
53. Rainey, P.B. and Bailey, M.J. (1996). Physical map of the Pseudomonas fluorescens SBW25 chromosome. Mol. Microbiol. 19: 521-533.
54. Rainey, P.B., Buckling, A., Kassen, R. and Travisano, M. (2000). The emergence and maintenance of diversity: insights from experimental bacterial populations. Trends Ecol. Evol. 15: 243-247.
55. Rainey, P.B. and Travisano, M. (1998). Adaptive radiation in a heterogeneous environment. Nature 394: 69-72.
56. Rendueles, O. and Ghigo, J.M. (2012). Multi-species biofilms: how to avoid unfriendly neighbors. FEMS Microbiol. Rev. 36: 972-989.
57. Robertson, M., Hapca, S.M, Moshynets, O. and Spiers, A.J (2013). Air-liquid interface biofilm formation by psychrotrophic pseudomonads recovered from spoilt meat. Antonie van Leeuwenhoek 103: 251-259.
58. Römling, U. (2005). Characterization of the rdar morphotype, a multicellular behaviour in Enterobacteriaceae. Cell. Mol. Life Sci. 62: 1234-1246.
59. Sachs, J.L. and Hollowell, A.C. (2012). The origins of cooperative bacterial communities. mBio 3: e00099-12.
60. Saxena, I.M., Kudlicka, K., Okuda, K. and Brown, R.M. (1994). Characterization of genes in the cellulose-synthesizing operon (acs operon) of Acetobacter xylinum: implications for cellulose crystallization. J. Bacteriol. 176: 5735-5752.
61. Schirmer, T. and Jenal, U. (2009). Structural and mechanistic determinants of c-di-GMP signaling. Nature Rev. Microbiol. 7: 724-735.
62. Schrecker, S.T. and Gostomski, P.A. (2005). Determining the water holding capacity of microbial cellulose. Biotechnol. Lett. 27: 1435-1438.
63. Silby, M.W., Cerdeño-Tárraga, A.M., Vernikos, G., Giddens, S.R., Jackson, R., Preston, G., Zhang, X-X., Godfrey, S., Spiers, A.J., Harris, S., Challis, G.L., Morningstar, A., Harris, D., Seeger, K., Murphy, L., Rutter, S., Squares, R., Quail, M.A., Saunders, E., Anderson, I., Mavromat, K., Brettin, T.S., Bentley, S., Thomas, C.M., Parkhill, J., Levy, S.B., Rainey, P.B. and Thomson, N.R. (2009). Genomic and functional analyses of diversity and plant interactions of Pseudomonas fluorescens. Genome Biol. 10: R51.
64. Solomon, E.B., Niemira, B.A., Sapers, G.M. and Annous, B.A. (2005). Biofilm formation, cellulose production, and curli biosynthesis by Salmonella originating from produce, animal, and clinical sources. J. Food Prot. 68: 906-912.
65. Spiers, A.J. (2007). Wrinkly-Spreader fitness in the two-dimensional agar plate microcosm: maladaptation, compensation and ecological success. PLoS ONE 2: e740.
66. Spiers, A.J., Arnold, D.L., Moon, C.D. and Timms-Wilson, T.M. (2006). A survey of A-L biofilm formation and cellulose expression amongst soil and plant-associated Pseudomonas isolates. In: Microbial Ecology of Aerial Plant Surfaces. Bailey, M.J., Lilley, A.K., Timms-Wilson, T.M. and Spencer-Phillips, P.T.N. (Eds.). CABI, Wallingford.
67. Spiers, A.J., Bohannon, J., Gehrig, S.M. and Rainey, P.B. (2003). Biofilm formation at the air-liquid interface by the Pseudomonas fluorescens SBW25 Wrinkly Spreader requires an acetylated form of cellulose. Mol. Microbiol. 50: 15-27.
68. Spiers, A.J., Deeni, Y.Y., Folorunso, A.O., Koza, A., Moshynets, O. and Zawadzki, K. (2013). Cellulose expression in Pseudomonas fluorescens SBW25 and other environmental pseudomonads. In: Cellulose. Van De Ven, T.G.M. and Trdine, J. (Eds.). InTech, Rijeka.
69. Spiers, A.J., Kahn, S.G., Bohannon, J., Travisano, M. and Rainey, P.B. (2002). Adaptive divergence in experimental populations of Pseudomonas fluorescens. I. Genetic and phenotypic bases of Wrinkly Spreader fitness. Genetics 161: 33-46.
70. Spiers, A.J. and Rainey, P.B. (2005). The Pseudomonas fluorescens SBW25 Wrinkly Spreader biofilm requires attachment factor, cellulose fibre and LPS interactions to maintain strength and integrity. Microbiology 151: 2829-2839.
71. Sullivan, S.M. and Maddock, J.R. (2000). Bacterial division: finding the dividing line. Curr. Biol. 10: R249-252.
72. Travisano, M. (2001). Evolution: Towards a genetical theory of adaptation. Curr. Biol. 11: R440-R442.
73. Travisano, M. and Rainey, P.B. (2000). Studies of Adaptive Radiation Using Model Microbial Systems. Amer. Nat. 156: S35-S44.
74. Ude, S., Arnold, D.L., Moon, C.D., Timms-Wilson, T. and Spiers, A.J. (2006). Biofilm formation and cellulose expression among diverse environmental Pseudomonas isolates. Environ. Microbiol. 8: 1997-2011.
75. Ude, S., Bailey, M.J., Huang, W.E. and Spiers, A.J. (2007). The environmental plasmid pQBR103 alters the single-cell Raman spectral profile of Pseudomonas fluorescens SBW25. Microb. Ecol. 53: 494-497.
76. Van Valen, L. (1973). A New Evolutionary Law. Evol. Theory 1: 1-30.
77. Verschuren, P.G., Cardona, T.D., Nout, M.H.R., De Gooijer, K.D. and Van Den Heuvel, J.C. (2000). Location and limitation of cellulose production by Acetobacter xylinum established from oxygen profiles. J. Biosc. Bioeng. 89: 414-419.
78. Webb, J.S., Givskovy, M. and Kjelleberg, S. (2003). Bacterial biofilms: prokaryotic adventures in multicellularity. Curr. Opin. Microbiol. 6: 578-585.
79. West, S.A., Griffin, A.S., Gardner, A. and Diggle, S.P. (2006). Social evolution theory for microorganisms. Nature Rev. Microbiol. 4: 597-607.
80. Winogradsky, S. (1887). Ueber Schwefelbacterien. Bot. Zeit. 45: 489-610.
81. Zogaj, X., Bokranz, W., Nimtz, M. and Römling, U. (2003). Production of cellulose and curli fimbriae by members of the family Enterobacteriaceae isolated from the human gastrointestinal tract. Infect. Immun. 71: 4151-4158.