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A Mechanistic Explanation Linking Adaptive Mutation, Niche Change, and Fitness Advantage for the Wrinkly Spreader

DOI: 10.1155/2014/675432

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Abstract:

Experimental evolution studies have investigated adaptive radiation in static liquid microcosms using the environmental bacterium Pseudomonas fluorescens SBW25. In evolving populations a novel adaptive mutant known as the Wrinkly Spreader arises within days having significant fitness advantage over the ancestral strain. A molecular investigation of the Wrinkly Spreader has provided a mechanistic explanation linking mutation with fitness improvement through the production of a cellulose-based biofilm at the air-liquid interface. Colonisation of this niche provides greater access to oxygen, allowing faster growth than that possible for non-biofilm—forming competitors located in the lower anoxic region of the microcosm. Cellulose is probably normally used for attachment to plant and soil aggregate surfaces and to provide protection in dehydrating conditions. However, the evolutionary innovation of the Wrinkly Spreader in static microcosms is the use of cellulose as the matrix of a robust biofilm, and is achieved through mutations that deregulate multiple diguanylate cyclases leading to the over-production of cyclic-di-GMP and the stimulation of cellulose expression. The mechanistic explanation of the Wrinkly Spreader success is an exemplar of the modern evolutionary synthesis, linking molecular biology with evolutionary ecology, and provides an insight into the phenomenal ability of bacteria to adapt to novel environments. 1. Introduction Competition for limited resources and divergent selection arising from differences in the environment are key drivers of ecological adaptive radiation and ultimately speciation [1]. Although usually illustrated by reference to examples such as Darwin’s finches in the Galapagos or the cichlid fishes in East African Rift Valley lakes [2–4], adaptive radiation has also played an important role in the great phylogenetic and functional diversification of bacteria and can help explain in part bacterial colonisation and niche preferences, as well as bacterial community complexity, interactions, and dynamics (bacterial adaptive radiation differs in some fundamental ways to that seen in sexual populations [4, 5]). Key to adaptive radiation is ecological opportunity which promotes adaptive radiation by changing the selective pressures acting on populations, relaxing stabilising selection and creating conditions that generate diversifying selection [6]. The rate at which bacterial populations become locally adapted depends on both the selective regime as well as the rate at which adaptive mutations arise and are fixed within the

References

[1]  D. Schluter, The Ecology of Adaptive Radiation, Oxford Series in Ecology and Evolution, Oxford University Press, Oxford, UK, 1st edition, 2000.
[2]  D. Lack, Darwin’s Finches, Cambridge University Press, Cambridge, UK, 1947.
[3]  G. Fryer and T. D. Iles, The Cichlid Fishes of the Great Lakes of Africa, Oliver and Boyd, Edinburgh, UK, 1972.
[4]  M. Hau and M. Wikelski, “Darwin's Finches,” in ELS, John Wiley & Sons, Chichester, UK, 2001.
[5]  B. R. Levin and C. T. Bergstrom, “Bacteria are different: observations, interpretations, speculations, and opinions about the mechanisms of adaptive evolution in prokaryotes,” Proceedings of the National Academy of Sciences of the United States of America, vol. 97, no. 13, pp. 6981–6985, 2000.
[6]  J. B. Yoder, E. Clancey, S. Des Roches et al., “Ecological opportunity and the origin of adaptive radiations,” Journal of Evolutionary Biology, vol. 23, no. 8, pp. 1581–1596, 2010.
[7]  R. J. Whitaker, “Allopatric origins of microbial species,” Philosophical Transactions of the Royal Society B, vol. 361, no. 1475, pp. 1975–1984, 2006.
[8]  T. J. Treangen and E. P. C. Rocha, “Horizontal transfer, not duplication, drives the expansion of protein families in prokaryotes,” PLoS Genetics, vol. 7, no. 1, Article ID article e1001284, 2011.
[9]  P. B. Rainey, A. Buckling, R. Kassen, and M. Travisano, “The emergence and maintenance of diversity: insights from experimental bacterial populations,” Trends in Ecology and Evolution, vol. 15, no. 6, pp. 243–247, 2000.
[10]  J. Adams, “Microbial evolution in laboratory environments,” Research in Microbiology, vol. 155, no. 5, pp. 311–318, 2004.
[11]  R. C. MacLean, “Adaptive radiation in microbial microcosms,” Journal of Evolutionary Biology, vol. 18, no. 6, pp. 1376–1386, 2005.
[12]  A. Buckling, R. C. MacLean, M. A. Brockhurst, and N. Colegrave, “The beagle in a bottle,” Nature, vol. 457, no. 7231, pp. 824–829, 2009.
[13]  A. J. Spiers, “Bacterial evolution in simple microcosms,” in Microcosms: Ecology, Biological Implications and Environmental Impact, C. H. Harris, Ed., Microbiology Research Advances Series, Nova Publishers, Hauppauge, NY, USA, 2013.
[14]  J. N. Thompson, Relentless Evolution, The University of Chicago Press, Chicago, Ill, USA, 2013.
[15]  R. E. Lenski, M. R. Rose, S. C. Simpson, and S. C. Tadler, “Long-term experimental evolution in Escherichia coli. I. adaptation and divergence during 2000 generations,” The American Naturalist, vol. 138, no. 6, pp. 1315–1341, 1991.
[16]  H. A. Orr, “Fitness and its role in evolutionary genetics,” Nature Reviews Genetics, vol. 10, no. 8, pp. 531–539, 2009.
[17]  L.-M. Chevin, “On measuring selection in experimental evolution,” Biology Letters, vol. 7, no. 2, pp. 210–213, 2011.
[18]  A. C. Dalziel, S. M. Rogers, and P. M. Schulte, “Linking genotypes to phenotypes and fitness: how mechanistic biology can inform molecular ecology,” Molecular Ecology, vol. 18, no. 24, pp. 4997–5017, 2009.
[19]  P. B. Rainey and M. Travisano, “Adaptive radiation in a heterogeneous environment,” Nature, vol. 394, no. 6688, pp. 69–72, 1998.
[20]  R. Hengge, “Principles of c-di-GMP signalling in bacteria,” Nature Reviews Microbiology, vol. 7, no. 4, pp. 263–273, 2009.
[21]  T. L. Povolotsky and R. Hengge, “‘Life-style ’ control networks in Escherichia coli: signaling by the second messenger c-di-GMP,” Journal of Biotechnology, vol. 160, no. 1-2, pp. 10–16, 2012.
[22]  D. Srivastava and C. M. Waters, “A tangled web: regulatory connections between quorum sensing and cyclic di-GMP,” Journal of Bacteriology, vol. 194, no. 17, pp. 4485–4493, 2012.
[23]  H. Sondermann, N. J. Shikuma, and F. H. Yildiz, “You've come a long way: c-di-GMP signaling,” Current Opinion in Microbiology, vol. 15, no. 2, pp. 140–146, 2012.
[24]  U. R?mling, M. Y. Galperin, and M. Gomelsky, “Cyclic di-GMP: the first 25 years of a universal bacterial second messenger,” Microbiology and Molecular Biology Reviews, vol. 77, no. 1, pp. 1–52, 2013.
[25]  L. Wang, F. F. Wang, and W. Qian, “Evolutionary rewiring and reprogramming of bacterial transcription regulation,” Journal of Genetics and Genomics, vol. 38, no. 7, pp. 279–288, 2011.
[26]  P. B. Rainey and M. J. Bailey, “Physical and genetic map of the Pseudomonas fluorescens SBW25 chromosome,” Molecular Microbiology, vol. 19, no. 3, pp. 521–533, 1996.
[27]  G. M. Preston, N. Bertrand, and P. B. Rainey, “Type III secretion in plant growth-promoting Pseudomonas fluorescens SBW25,” Molecular Microbiology, vol. 41, no. 5, pp. 999–1014, 2001.
[28]  I. de Bruijn, M. J. D. de Kock, M. Yang, P. de Waard, T. A. Van Beek, and J. M. Raaijmakers, “Genome-based discovery, structure prediction and functional analysis of cyclic lipopeptide antibiotics in Pseudomonas species,” Molecular Microbiology, vol. 63, no. 2, pp. 417–428, 2007.
[29]  A. J. Spiers, A. Buckling, and P. B. Rainey, “The causes of Pseudomonas diversity,” Microbiology, vol. 146, no. 10, pp. 2345–2350, 2000.
[30]  M. W. Silby, A. M. Cerde?o-Tárraga, G. S. Vernikos et al., “Genomic and genetic analyses of diversity and plant interactions of Pseudomonas fluorescens,” Genome Biology, vol. 10, no. 5, article R51, 2009.
[31]  M. W. Silby, C. Winstanley, S. A. C. Godfrey, S. B. Levy, and R. W. Jackson, “Pseudomonas genomes: diverse and adaptable,” FEMS Microbiology Reviews, vol. 35, no. 4, pp. 652–680, 2011.
[32]  A. J. Spiers, D. Field, M. Bailey, and P. B. Rainey, “Notes on designing a partial genomic database: the PfSBW25 encyclopaedia, a sequence database for Pseudomonas fluorescens SBW25,” Microbiology, vol. 147, no. 2, pp. 247–249, 2001.
[33]  M. Gal, G. M. Preston, R. C. Massey, A. J. Spiers, and P. B. Rainey, “Genes encoding a cellulosic polymer contribute toward the ecological success of Pseudomonas fluorescens SBW25 on plant surfaces,” Molecular Ecology, vol. 12, no. 11, pp. 3109–3121, 2003.
[34]  S. R. Giddens, R. W. Jackson, C. D. Moon et al., “Mutational activation of niche-specific genes provides insight into regulatory networks and bacterial function in a complex environment,” Proceedings of the National Academy of Sciences of the United States of America, vol. 104, no. 46, pp. 18247–18252, 2007.
[35]  A. J. Spiers, S. G. Kahn, J. Bohannon, M. Travisano, and P. B. Rainey, “Adaptive divergence in experimental populations of Pseudomonas fluorescens. I. Genetic and phenotypic bases of wrinkly spreader fitness,” Genetics, vol. 161, no. 1, pp. 33–46, 2002.
[36]  S. Ude, D. L. Arnold, C. D. Moon, T. Timms-Wilson, and A. J. Spiers, “Biofilm formation and cellulose expression among diverse environmental Pseudomonas isolates,” Environmental Microbiology, vol. 8, no. 11, pp. 1997–2011, 2006.
[37]  A. Koza, P. D. Hallett, C. D. Moon, and A. J. Spiers, “Characterization of a novel air-liquid interface biofilm of Pseudomonas fluorescens SBW25,” Microbiology, vol. 155, no. 5, pp. 1397–1406, 2009.
[38]  M. Robertson, S. M. Hapca, O. Moshynets, and A. J. Spiers, “Air-liquid interface biofilm formation by psychrotrophic pseudomonads recovered from spoilt meat,” Antonie Van Leeuwenhoek, vol. 103, no. 1, pp. 251–259, 2013.
[39]  A. J. Spiers, Y. Y. Deeni, A. O. Folorunso, A. Koza, O. Moshynets, and K. Zawadzki, “Cellulose expression in Pseudomonas fluorescens SBW25 and other environmental pseudomonads,” in Cellulose, T. G. M. Van De Ven and L. Godbout, Eds., InTech, Rijeka, Croatia, 2013.
[40]  E. O. King, M. K. Ward, and D. E. Raney, “Two simple media for the demonstration of pyocyanin and fluorescin,” The Journal of Laboratory and Clinical Medicine, vol. 44, no. 2, pp. 301–307, 1954.
[41]  R. Kassen, A. Buckling, G. Bell, and P. B. Ralney, “Diversity peaks at intermediate productivity in a laboratory microcosm,” Nature, vol. 406, no. 6795, pp. 508–512, 2000.
[42]  A. Buckling, M. A. Wills, and N. Colegrave, “Adaptation limits diversification of experimental bacterial populations,” Science, vol. 302, no. 5653, pp. 2107–2109, 2003.
[43]  L. Van Valen, “A new evolutionary law,” Evolutionary Theory, vol. 1, pp. 1–30, 1973.
[44]  L. H. Liow, L. Van Valen, and N. C. Stenseth, “Red queen: from populations to taxa and communities,” Trends in Ecology and Evolution, vol. 26, no. 7, pp. 349–358, 2011.
[45]  M. A. Brockhurst, M. E. Hochberg, T. Bell, and A. Buckling, “Character displacement promotes cooperation in bacterial biofilms,” Current Biology, vol. 16, no. 20, pp. 2030–2034, 2006.
[46]  E. Bantinaki, R. Kassen, C. G. Knight, Z. Robinson, A. J. Spiers, and P. B. Rainey, “Adaptive divergence in experimental populations of Pseudomonas fluorescens. III. Mutational origins of wrinkly spreader diversity,” Genetics, vol. 176, no. 1, pp. 441–453, 2007.
[47]  D. J. P. Engelmoer and D. E. Rozen, “Fitness trade-offs modify community composition under contrasting disturbance regimes in pseudomonas fluorescens microcosms,” Evolution, vol. 63, no. 11, pp. 3031–3037, 2009.
[48]  J. R. Meyer, S. E. Schoustra, J. Lachapelle, and R. Kassen, “Overshooting dynamics in a model adaptive radiation,” Proceedings of the Royal Society B, vol. 278, no. 1704, pp. 392–398, 2011.
[49]  J. H. Green, A. Koza, O. Moshynets, R. Pajor, M. R. Ritchie, and A. J. Spiers, “Evolution in a test tube: rise of the wrinkly spreaders,” Journal of Biological Education, vol. 45, no. 1, pp. 54–59, 2011.
[50]  A. Koza, O. Moshynets, W. Otten, and A. J. Spiers, “Environmental modification and niche construction: developing O2 gradients drive the evolution of the wrinkly spreader,” International Society of Microbial Ecology Journal, vol. 5, no. 4, pp. 665–673, 2011.
[51]  A. J. Spiers, J. Bohannon, S. M. Gehrig, and P. B. Rainey, “Biofilm formation at the air-liquid interface by the Pseudomonas fluorescens SBW25 wrinkly spreader requires an acetylated form of cellulose,” Molecular Microbiology, vol. 50, no. 1, pp. 15–27, 2003.
[52]  S. S. Branda, ?. Vik, L. Friedman, and R. Kolter, “Biofilms: the matrix revisited,” Trends in Microbiology, vol. 13, no. 1, pp. 20–26, 2005.
[53]  W. E. Huang, S. Ude, and A. J. Spiers, “Pseudomonas fluorescens SBW25 biofilm and planktonic cells have differentiable Raman spectral profiles,” Microbial Ecology, vol. 53, no. 3, pp. 471–474, 2007.
[54]  A. J. Spiers and P. B. Rainey, “The Pdeudomonas fluorescens SBW25 wrinkly spreader biofilm requires attachment factor, cellulose fibre and LPS interactions to maintain strength and integrity,” Microbiology, vol. 151, no. 9, pp. 2829–2839, 2005.
[55]  F. Pelletier, D. Garant, and A. P. Hendry, “Eco-evolutionary dynamics,” Philosophical Transactions of the Royal Society B, vol. 364, no. 1523, pp. 1483–1489, 2009.
[56]  D. M. Post and E. P. Palkovacs, “Eco-evolutionary feedbacks in community and ecosystem ecology: interactions between the ecological theatre and the evolutionary play,” Philosophical Transactions of the Royal Society B, vol. 364, no. 1523, pp. 1629–1640, 2009.
[57]  O. V. Moshynets, A. Koza, P. Dello Sterpaio, V. A. Kordium, and A. J. Spiers, “Up-dating the Cholodny method using PET films to sample microbial communities in soil,” Biopolymers and Cell, vol. 27, no. 3, pp. 199–205, 2011.
[58]  S. A. West, A. S. Griffin, A. Gardner, and S. P. Diggle, “Social evolution theory for microorganisms,” Nature Reviews Microbiology, vol. 4, no. 8, pp. 597–607, 2006.
[59]  Q. G. Zhang, A. Buckling, R. J. Ellis, and H. C. J. Godfray, “Coevolution between cooperators and cheats in a microbial system,” Evolution, vol. 63, no. 9, pp. 2248–2256, 2009.
[60]  J. B. Xavier and K. R. Foster, “Cooperation and conflict in microbial biofilms,” Proceedings of the National Academy of Sciences of the United States of America, vol. 104, no. 3, pp. 876–881, 2007.
[61]  F. Baquero and M. Lemonnier, “Generational coexistence and ancestor's inhibition in bacterial populations,” FEMS Microbiology Reviews, vol. 33, no. 5, pp. 958–967, 2009.
[62]  A. J. Spiers, “Wrinkly-spreader fitness in the two-dimensional agar plate microcosm: maladaptation, compensation and ecological success,” PLoS One, vol. 2, no. 1, article e740, 2007.
[63]  P. Goymer, S. G. Kahn, J. G. Malone, S. M. Gehrig, A. J. Spiers, and P. B. Rainey, “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, vol. 173, no. 2, pp. 515–526, 2006.
[64]  J. G. Malone, R. Williams, M. Christen, U. Jenal, A. J. Spiers, and P. B. Rainey, “The structure-function relationship of WspR, a Pseudomonas fluorescens response regulator with a GGDEF output domain,” Microbiology, vol. 153, no. 4, pp. 980–994, 2007.
[65]  A. Bren and M. Eisenbach, “How signals are heard during bacterial chemotaxis: protein-protein interactions in sensory signal propagation,” Journal of Bacteriology, vol. 182, no. 24, pp. 6865–6873, 2000.
[66]  J. W. Hickman, D. F. Tifrea, and C. S. Harwood, “A chemosensory system that regulates biofilm formation through modulation of cyclic diguanylate levels,” Proceedings of the National Academy of Sciences of the United States of America, vol. 102, no. 40, pp. 14422–14427, 2005.
[67]  Z. T. Güvener and C. S. Harwood, “Subcellular location characteristics of the Pseudomonas aeruginosa GGDEF protein, WspR, indicate that it produces cyclic-di-GMP in response to growth on surfaces,” Molecular Microbiology, vol. 66, no. 6, pp. 1459–1473, 2007.
[68]  G. L. Winsor, D. K. W. Lam, L. Fleming et al., “Pseudomonas genome database: improved comparative analysis and population genomics capability for Pseudomonas genomes,” Nucleic Acids Research, vol. 39, no. 1, pp. D596–D600, 2011.
[69]  M. J. McDonald, S. M. Gehrig, P. L. Meintjes, X. X. Zhang, and P. B. Rainey, “Adaptive divergence in experimental populations of Pseudomonas fluorescens. IV. Genetic constraints guide evolutionary trajectories in a parallel adaptive radiation,” Genetics, vol. 183, no. 3, pp. 1041–1053, 2009.
[70]  S. M. Gehrig, Adaptation of Pseudomonas fluorescens SBW25 to the air-liquid interface: a study in evolutionary genetics [Ph.D. thesis], University of Oxford, Oxford, UK, 2005.
[71]  M. J. McDonald, T. F. Cooper, H. J. E. Beaumont, and P. B. Rainey, “The distribution of fitness effects of new beneficial mutations in Pseudomonas fluorescens,” Biology Letters, vol. 7, no. 1, pp. 98–100, 2011.
[72]  P. D. Newell, S. Yoshioka, K. L. Hvorecny, R. D. Monds, and G. A. O'Toole, “Systematic analysis of diguanylate cyclases that promote biofilm formation by Pseudomonas fluorescens Pf0-1,” Journal of Bacteriology, vol. 193, no. 18, pp. 4685–4698, 2011.
[73]  I. M. Saxena, K. Kudlicka, K. Okuda, and R. M. Brown Jr., “Characterization of genes in the cellulose-synthesizing operon (acs operon) of Acetobacter xylinum: implications for cellulose crystallization,” Journal of Bacteriology, vol. 176, no. 18, pp. 5735–5752, 1994.
[74]  F. R. Blattner, G. Plunkett III, C. A. Bloch et al., “The complete genome sequence of Escherichia coli K-12,” Science, vol. 277, no. 5331, pp. 1453–1462, 1997.
[75]  B. Le Quéré and J. M. Ghigo, “BcsQ is an essential component of the Escherichia coli cellulose biosynthesis apparatus that localizes at the bacterial cell pole,” Molecular Microbiology, vol. 72, no. 3, pp. 724–740, 2009.
[76]  M. J. Franklin and D. E. Ohman, “Identification of algI and algI in the Pseudomonas aeruginosa alginate biosynthetic gene cluster which are required for alginate O acetylation,” Journal of Bacteriology, vol. 178, no. 8, pp. 2186–2195, 1996.
[77]  R. D. Monds, P. D. Newell, R. H. Gross, and G. A. O'Toole, “Phosphate-dependent modulation of c-di-GMP levels regulates Pseudomonas fluorescens Pf0-1 biofilm formation by controlling secretion of the adhesin LapA,” Molecular Microbiology, vol. 63, no. 3, pp. 656–679, 2007.
[78]  D. López, H. Vlamakis, and R. Kolter, “Biofilms,” Cold Spring Harbor Perspectives in Biology, vol. 2, no. 7, article a000398, 2010.
[79]  A. J. Spiers, D. L. Arnold, C. D. Moon, and T. M. Timms-Wilson, “A survey of A-L biofilm formation and cellulose expression amongst soil and plant-associated Pseudomonas isolates,” in Microbial Ecology of Aerial Plant Surfaces, M. J. Bailey, A. K. Lilley, T. M. Timms-Wilson, and P. T. N. Spencer-Phillips, Eds., pp. 121–132, CABI, Wallingford, UK, 2006.
[80]  L. Hall-Stoodley, J. W. Costerton, and P. Stoodley, “Bacterial biofilms: from the natural environment to infectious diseases,” Nature Reviews Microbiology, vol. 2, no. 2, pp. 95–108, 2004.
[81]  T. J. Battin, W. T. Sloan, S. Kjelleberg et al., “Microbial landscapes: new paths to biofilm research,” Nature Reviews Microbiology, vol. 5, no. 1, pp. 76–81, 2007.
[82]  H. C. Flemming and J. Wingender, “The biofilm matrix,” Nature Reviews Microbiology, vol. 8, no. 9, pp. 623–633, 2010.
[83]  S. Elias and E. Banin, “Multi-species biofilms: living with friendly neighbors,” FEMS Microbiology Reviews, vol. 36, no. 5, pp. 990–1004, 2012.
[84]  O. Rendueles and J. M. Ghigo, “Multi-species biofilms: how to avoid unfriendly neighbors,” FEMS Microbiology Reviews, vol. 36, no. 5, pp. 972–989, 2012.
[85]  G. O'Toole, H. B. Kaplan, and R. Kolter, “Biofilm formation as microbial development,” Annual Review of Microbiology, vol. 54, pp. 49–79, 2000.
[86]  J.-U. Kreft and S. Bonhoeffer, “The evolution of groups of cooperating bacteria and the growth rate versus yield trade-off,” Microbiology, vol. 151, no. 3, pp. 637–641, 2005.
[87]  J. J. Morris, R. E. Lenski, and E. R. Zinser, “The black queen hypothesis: evolution of dependencies through adaptive gene loss,” MBio, vol. 3, no. 2, article e00036-12, 2012.
[88]  J. L. Sachs and A. C. Hollowell, “The origins of cooperative bacterial communities,” MBio, vol. 3, no. 3, article e00099-12, 2012.
[89]  E. Hoshino, Y. Wada, and K. Nishizawa, “Improvements in the hygroscopic properties of cotton cellulose by treatment with an endo-type cellulase from Streptomyces sp. KSM-26,” Journal of Bioscience and Bioengineering, vol. 88, no. 5, pp. 519–525, 1999.

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