Quantifying the relative importance of niches and neutrality for coexistence in a model microbial system

Functional Ecology

Volumn 23, Issue 6, 2009, Pages 1139-1147

  Zhang, Quan Guo ^a   Buckling, Angus ^a   Godfray, H Charles J ^a  

^a UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

Biodiversity; Biomass; Equalizing mechanism; Negative frequency dependency; Pseudomonas fluorescens; Stabilizing mechanism

Indexed keywords

BACTERIUM; BIOMASS; COEXISTENCE; EMPIRICAL ANALYSIS; INTRASPECIFIC VARIATION; MICROBIAL COMMUNITY; MICROCOSM; NICHE PARTITIONING; PHENOTYPE; PHENOTYPIC PLASTICITY; POPULATION DENSITY; POPULATION GROWTH; SPECIES DIVERSITY;

BACTERIA (MICROORGANISMS); PSEUDOMONAS FLUORESCENS;

EID: 70449334154     PISSN: 02698463     EISSN: 13652435     Source Type: Journal    
DOI: 10.1111/j.1365-2435.2009.01579.x     Document Type: Article

References (88)

1. Aarssen, L.W. (1997) High productivity in grassland ecosystems: effected by species diversity or productive species? Oikos, 80, 183 184.
2. Adler, P.B., HilleRisLambers, J. Levine, J.M. (2007) A niche for neutrality. Ecology Letters, 10, 95 104.
3. Armstrong, R.A. (1989) Competition, seed predation, and species coexistence. Journal of Theoretical Biology, 141, 191 195.
4. Balvanera, P., Pfisterer, A.B., Buchmann, N., He, J.-S., Nakashizuka, T., Raffaelli, D. Schmid, B. (2006) Quantifying the evidence for biodiversity effects on ecosystem functioning and services. Ecology Letters, 9, 1146 1156.
5. Bantinaki, E., Kassen, R., Knight, C.G., Robinson, Z., Spiers, A.J. Rainey, P.B. (2007) Adaptive divergence in experimental populations of Pseudomonas fluorescens. III. Mutational origins of wrinkly spreader diversity. Genetics, 176, 441 453.
6. Barrett, R.D.H., MacLean, R.C. Bell, G. (2006) Mutations of intermediate effect are responsible for adaptation in evolving Pseudomonas fluorescens populations. Biology Letters, 2, 236 238.
7. Bell, G. (2001) Neutral macroecology. Science, 293, 2413 2418.
8. Bell, G., Lechowicz, M.J. Waterway, M.J. (2006) The comparative evidence relating to functional and neutral interpretations of biological communities. Ecology, 87, 1378 1386.
9. Brockhurst, M.A., Hochberg, M.E., Bell, T. Buckling, A. (2006) Character displacement promotes cooperation in bacterial biofilms. Current Biology, 16, 2030 2034.
10. Brockhurst, M.A., Colegrave, N., Hodgson, D.J. Buckling, A. (2007) Niche occupation limits adaptive radiation in experimental microcosms. PLoS ONE, 2, e193.
11. Buckling, A., Kassen, R., Bell, G. Rainey, P.B. (2000) Disturbance and diversity in experimental microcosms. Nature, 408, 961 964.
12. Cadotte, M.W. (2007) Concurrent niche and neutral processes in the competition-colonization model of species coexistence. Proceedings of the Royal Society B: Biological Sciences, 274, 2739 2744.
13. Cardinale, B.J., Srivastava, D.S., Duffy, J.E., Wright, J.P., Downing, A.L., Sankaran, M. Jouseau, C. (2006) Effects of biodiversity on the functioning of trophic groups and ecosystems. Nature, 443, 989 992.
14. Cardinale, B.J., Wright, J.P., Cadotte, M.W., Carroll, I.T., Hector, A., Srivastava, D.S., Loreau, M. Weis, J.J. (2007) Impacts of plant diversity on biomass production increase through time because of species complementarity. Proceedings of the National Academy of Sciences of the United States of America, 104, 18123 18128.
15. Chase, J.M. (2005) Towards a really unified theory for metacommunities. Functional Ecology, 19, 182 186.
16. Chase, J.M., Abrams, P.A., Grover, J.P., Diehl, S., Chesson, P., Holt, R.D., Richards, S.A., Nisbet, R.M. Case, T.J. (2002) The interaction between predation and competition: a review and synthesis. Ecology Letters, 5, 302 315.
17. Chave, J., Muller-Landau, H.C. Levin, S.A. (2002) Comparing classical community models: theoretical consequences for patterns of diversity. The American Naturalist, 159, 1 23.
18. Chesson, P. (2000) Mechanisms of maintenance of species diversity. Annual Review of Ecology and Systematics, 31, 343 366.
19. Chesson, P. Warner, R.R. (1981) Environmental variability promotes coexistence in Lottery competitive systems. The American Naturalist, 117, 923 943.
20. Cooper, T.F. (2007) Recombination speeds adaptation by reducing competition between beneficial mutations in populations of Escherichia coli. Plos Biology, 5, e225.
21. Day, T. Young, K.A. (2004) Competitive and facilitative evolutionary diversification. Bioscience, 54, 101 109.
22. Diaz, S., Symstad, A.J., Chapin, F.S., III., Wardle, D.A. Huenneke, L.F. (2003) Functional diversity revealed by removal experiments. Trends in Ecology & Evolution, 18, 140 146.
23. Fox, J.W. (2003) The long-term relationship between plant diversity and total plant biomass depends on the mechanism maintaining diversity. Oikos, 102, 630 640.
24. Fox, J.W. (2005) Interpreting the 'selection effect' of biodiversity on ecosystem function. Ecology Letters, 8, 846 856.
25. Fox, J.W. (2006) Using the Price Equation to partition the effects of biodiversity loss on ecosystem function. Ecology, 87, 2687 2696.
26. Fukami, T., Beaumont, H.J.E., Zhang, X.-X. Rainey, P.B. (2007) Immigration history controls diversification in experimental adaptive radiation. Nature, 446, 436 439.
27. Gerrish, P. Lenski, R. (1998) The fate of competing beneficial mutations in an asexual population. Genetica, 102-103, 127 144.
28. Gilbert, B., Srivastava, D.S. Kirby, K.R. (2008) Niche partitioning at multiple scales facilitates coexistence among mosquito larvae. Oikos, 117, 944 950.
29. Goymer, P., Kahn, S.G., Malone, J.G., Gehrig, S.M., Spiers, A.J. 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.
30. Gravel, D., Canham, C.D., Beaudet, M. Messier, C. (2006) Reconciling niche and neutrality: the continuum hypothesis. Ecology Letters, 9, 399 409.
31. Grime, J.P. (1998) Benefits of plant diversity to ecosystems: immediate, filter and founder effects. Journal of Ecology, 86, 902 910.
32. Grubb, P. (1977) The maintenance of species richness in plant communities: the importance of the regeneration niche. Biological Reviews, 52, 107 145.
33. Harper, J.L. (1977) Population Biology of Plants. Academic Press, London.
34. Harpole, W.S. Tilman, D. (2007) Grassland species loss resulting from reduced niche dimension. Nature, 446, 791 793.
35. Hector, A. (1998) The effect of diversity on productivity: detecting the role of species complementarity. Oikos, 82, 597 599.
36. Hodgson, D.J., Rainey, P.B. Buckling, A. (2002) Mechanisms linking diversity, productivity and invasibility in experimental bacterial community. Proceedings of the Royal Society B: Biological Sciences, 269, 2277 2283.
37. Holt, R.D. (2006) Emergent neutrality. Trends in Ecology & Evolution, 21, 531 533.
38. Hooper, D.U. (1998) The role of complementarity and competition in ecosystem responses to variation in plant diversity. Ecology, 79, 704 719.
39. Hooper, D.U., Chapin, F.S., Ewel, J.J., Hector, A., Inchausti, P., Lavorel, S., Lawton, J.H., Lodge, D.M., Loreau, M., Naeem, S., Schmid, B., Setala, H., Symstad, A.J., Vandermeer, J. Wardle, D.A. (2005) Effect of biodiversity on ecosystem functioning: a consensus of current knowledge. Ecological Monographs, 75, 3 35.
40. Hubbell, S.P. (2001) The Unified Neutral Theory of Biodiversity and Biogeography. Princeton University Press, Princeton.
41. Huston, M.A. (1997) Hidden treatments in ecological experiments: re-evaluating the ecosystem function of biodiversity. Oecologia, 110, 449 460.
42. Hutchinson, G.E. (1961) The paradox of the plankton. The American Naturalist, 95, 137 145.
43. Janzen, D.H. (1970) Herbivores and the number of tree species in tropical forests. The American Naturalist, 104, 501 528.
44. Kassen, R., Buckling, A., Bell, G. Rainey, P.B. (2000) Diversity peaks at intermediate productivity in a laboratory microcosm. Nature, 406, 508 512.
45. Kinzig, A. Pacala, S. (2001) Successional biodiversity and ecosystem functioning. The Functional Consequences of Biodiversity: Empirical Progress and Theoretical Extensions (eds A. Kinzig, S. Pacala D. Tilman pp. 175 212, Princeton University Press, Princeton.
46. Leibold, M.A. McPeek, M.A. (2006) Coexistence of the niche and neutral perspectives in community ecology. Ecology, 87, 1399 1410.
47. Lenski, R.E., Rose, M.R., Simpson, S.C. Tadler, S.C. (1991) Long-term experimental evolution in Escherichia coli. I. Adaptation and divergence during 2,000 generations. The American Naturalist, 138, 1315 1341.
48. Leps, J., Brown, V.K., Diaz Len, T.A., Gormsen, D., Hedlund, K., Kailova, J., Korthals, G.W., Mortimer, S.R., Rodriguez-Barrueco, C., Roy, J., Santa Regina, I., van Dijk, C. van der Putten, W.H. (2001) Separating the chance effect from other diversity effects in the functioning of plant communities. Oikos, 92, 123 134.
49. Loreau, M. (2000) Biodiversity and ecosystem functioning: recent theoretical advances. Oikos, 91, 3 17.
50. Loreau, M. (2004) Does functional redundancy exist? Oikos, 104, 606 611.
51. Loreau, M. Hector, A. (2001) Partitioning selection and complementarity in biodiversity experiments. Nature, 412, 72 76.
52. Loreau, M., Naeem, S., Inchausti, P., Bengtsson, J., Grime, J.P., Hector, A., Hooper, D.U., Huston, M.A., Raffaelli, D., Schmid, B., Tilman, D. Wardle, D.A. (2001) Biodiversity and ecosystem functioning: current knowledge and future challenges. Science, 294, 804 808.
53. MacLean, R. (2005) Adaptive radiation in microbial microcosms. Journal of Evolutionary Biology, 18, 1376 1386.
54. MacLean, R.C., Bell, G. Rainey, P.B. (2004) The evolution of a pleiotropic fitness tradeoff in Pseudomonas fluorescens. Proceedings of the National Academy of Sciences of the United States of America, 101, 8072 8077.
55. MacLean, R.C., Dickson, A. Bell, G. (2005) Resource competition and adaptive radiation in a microbial microcosm. Ecology Letters, 8, 38 46.
56. Maharjan, R., Seeto, S., Notley-McRobb, L. Ferenci, T. (2006) Clonal adaptive radiation in a constant environment. Science, 313, 514 517.
57. McGill, B.J. (2003) A test of the unified neutral theory of biodiversity. Nature, 422, 881 885.
58. Mokany, K., Ash, J. Roxburgh, S. (2008) Functional identity is more important than diversity in influencing ecosystem processes in a temperate native grassland. Journal of Ecology, 96, 884 893.
59. Mouquet, N., Moore, J.L. Loreau, M. (2002) Plant species richness and community productivity: why mechanism that promotes coexistence matters. Ecology Letters, 5, 56 65.
60. Perfeito, L., Fernandes, L., Mota, C. Gordo, I. (2007) Adaptive mutations in bacteria: high rate and small effects. Science, 317, 813 815.
61. Pueyo, S., He, F. Zillio, T. (2007) The maximum entropy formalism and the idiosyncratic theory of biodiversity. Ecology Letters, 10, 1017 1028.
62. Purves, D.W. Pacala, S.W. (2005) Ecological drift in niche-structured communities: neutral pattern does not imply neutral processes. Biotic Interaction in the Tropics: Their Role in the Maintenance of Species Diversity (eds D. Burslem, M. A. Pinard S. E. Hartley pp. 107 140, Cambridge University Press, Cambridge.
63. Rainey, P.B. (2005) Bacteria evolve and function within communities: observations from experimental Pseudomonas populations. The Influence of Cooperative Bacteria on Animal Host Biology (eds M. McFail-Ngai, B. Henderson N. Ruby pp. 83 102, Cambridge University Press, Cambridge.
64. Rainey, P.B. Bailey, M.J. (1996) Physical and genetic map of the Pseudomonas fluorescens SBW25 chromosome. Molecular Microbiology, 19, 521 533.
65. Rainey, P.B. Travisano, M. (1998) Adaptive radiation in a heterogeneous environment. Nature, 394, 69 72.
66. Rainey, P.B., Buckling, A., Kassen, R. Travisano, M. (2000) The emergence and maintenance of diversity: insights from experimental bacterial populations. Trends in Ecology & Evolution, 15, 243 247.
67. Rozen, D.E., de Visser, J. Gerrish, P.J. (2002) Fitness effects of fixed beneficial mutations in microbial populations. Current Biology, 12, 1040 1045.
68. Scheffer, M. van Nes, E.H. (2006) Self-organized similarity, the evolutionary emergence of groups of similar species. Proceedings of the National Academy of Sciences of the United States of America, 103, 6230 6235.
69. Schoener, T.W. (1974) Resource partitioning in ecological communities. Science, 185, 27 39.
70. Spehn, E.M., Hector, A., Joshi, J., Scherer-Lorenzen, M., Schmid, B., Bazeley-White, E., Beierkuhnlein, C., Caldeira, M.C., Diemer, M., Dimitrakopoulos, P.G., Finn, J.A., Freitas, H., Giller, P.S., Good, J., Harris, R., Hogberg, P., Huss-Danell, K., Jumpponen, A., Koricheva, J., Leadley, P.W., Loreau, M., Minns, A., Mulder, C.P.H., O'Donovan, G., Otway, S.J., Palmborg, C., Pereira, J.S., Pfisterer, A.B., Prinz, A., Read, D.J., Schulze, E.-D., Siamantziouras, A.-S.D., Terry, A.C., Troumbis, A.Y., Woodward, F.I., Yachi, S. Lawton, J.H. (2005) Ecosystem effects of biodiversity manipulations in European grasslands. Ecological Monographs, 75, 37 63. (Pubitemid 40295187)
71. Spiers, A.J. Rainey, P.B. (2005) The Pseudomonas fluorescens SBW25 wrinkly spreader biofilm requires attachment factor, cellulose fibre and LIPS interactions to maintain strength and integrity. Microbiology-Sgm, 151, 2829 2839.
72. Sugihara, G., Bersier, L.-F., Southwood, T.R.E., Pimm, S.L. May, R.M. (2003) Predicted correspondence between species abundances and dendrograms of niche similarities. Proceedings of the National Academy of Sciences of the United States of America, 100, 5246 5251.
73. Tilman, D. (1982) Resource Competition and Community Structure. Princeton University Press, Princeton.
74. Tilman, D. (1999) The ecological consequences of changes in biodiversity: a search for general principles. Ecology, 80, 1455 1474.
75. Tilman, D. (2004) Niche tradeoffs, neutrality, and community structure: a stochastic theory of resource competition, invasion, and community assembly. Proceedings of the National Academy of Sciences of the United States of America, 101, 10854 10861.
76. Tilman, D. Pacala, S. (1993) The maintenance of species richness in plant communities. Species Diversity in Ecological Communities (eds R. E. Ricklefs D. Schluter pp. 13 25, University of Chicago Press, Chicago.
77. Travisano, M. Rainey, K. (2000) Studies of adaptive radiation using model microbial systems. The American Naturalist, 156, S35 S44.
78. Trenbath, B.R. (1974) Biomass productivity of mixtures. Advances in Agronomy, 26, 177 210.
79. Vandermeer, J. (1989) The Ecology of Intercropping. Cambridge University Press, Cambridge.
80. Venail, P.A., MacLean, R.C., Bouvier, T., Brockhurst, M.A., Hochberg, M.E. Mouquet, N. (2008) Diversity and productivity peak at intermediate dispersal rate in evolving metacommunities. Nature, 452, 210 214.
81. de Visser, J., Zeyl, C.W., Gerrish, P.J., Blanchard, J.L. Lenski, R.E. (1999) Diminishing returns from mutation supply rate in asexual populations. Science, 283, 404 406.
82. Wardle, D.A. (1999) Is "sampling effect" a problem for experiments investigating biodiversity-ecosystem function relationships? Oikos, 87, 403 407.
83. Wardle, D.A. (2001) No observational evidence for diversity enhancing productivity in Mediterranean shrublands. Oecologia, 129, 620 621.
84. Wardle, D.A., Zackrisson, O., Hornberg, G. Gallet, C. (1997) The influence of island area on ecosystem properties. Science, 277, 1296 1299.
85. Weeks, A.R. Hoffmann, A.A. (2008) Frequency-dependent selection maintains clonal diversity in an asexual organism. Proceedings of the National Academy of Sciences of the United States of America, 105, 17872 17877.
86. Wills, C., Condit, R., Foster, R.B. Hubbell, S.P. (1997) Strong density- and diversity-related effects help to maintain tree species diversity in a neotropical forest. Proceedings of the National Academy of Sciences of the United States of America, 94, 1252 1257.
87. Zhang, Q.-G. Zhang, D.-Y. (2007) Colonization sequence influences selection and complementarity effects on biomass production in experimental algal microcosms. Oikos, 116, 1748 1758.
88. Zhou, S.-R. Zhang, D.-Y. (2008) A nearly neutral model of biodiversity. Ecology, 89, 248 258.