Recent publications (by subject)

Experimental Evolution; Evolutionary Genetics; Ecological Genetics; Genomics & Informatics; Microbial Genetics; Population Genetics; Biological Theory; Tools; Comment

Experimental Evolution

These papers stem largely from our interest in the causes of ecological diversity and for the most part utilize experimental populations of Pseudomonas fluorescens. The experimental system is described in Rainey & Travisano (1998).

Refardt, D. & Rainey, P. B. (2010). Tuning a genetic switch: experimental evolution and natural variation of prophage induction.  Evolution 64, 1086-1097.

Beaumont, H. J. E., Gallie, J., Kost, K., Ferguson, G. C. & Rainey, P. B. (2009). Experimental evolution of bet hedging. Nature 462, 90-93.

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.

Kirkelund Hansen, S., Rainey, P. B., Haagensen, J. A. J. & Molin, S. (2007). Evolution of species interactions in a biofilm community. Nature 445, 533-536.

Buckling, A., Brockhurst, M. A., Travisano, M. & Rainey, P. B. (2007). Experimental adaptation to high and low quality environments under different scales of temporal variation. Journal of Evolutionary Biology 20, 296-300.

Brockhurst, M. A., Fenton, A., Roulston, B. & Rainey, P. B. (2006). The impact of phages on interspecific competition in experimental populations of bacteria. BMC Ecology 6, 19 doi:10.1186/1472-6785-6-19.

Brockhurst, M. A., Buckling, A. & Rainey, P. B. (2006). Spatial heterogeneity and the stability of host-parastie coexistence. Journal of Evolutionary Biology 19, 374-379.

Rainey, P. B., Brockhurst, M., Buckling, A., Hodgson, D. & Kassen, R. (2005).  The causes and consequences of microbial diversity.  In Biological Diversity and Function in Soils.  (eds Bardgett, R., Hopkins, D & Usher, M.). Cambridge University Press, pp. 83-99.

Rainey, P. B. (2005). Bacteria evolve and function within communities: observations from experimental Pseudomonas populations.  In The Influence of Cooperative Bacteria on Animal Host Biology.  (ed. McFail-Ngai, M., Henderson, B., Ruby, N). Cambridge University Press, pp. 83-102.

Brockhurst, M. A., Buckling, A. & Rainey, P. B. (2005). The effect of a bacteriophage on diversification of the opportunisitic bacterial pathogen Pseudomonas aeruginosa. Proceedings of the Royal Society (London) B 272, 1385-1391.

Kassen, R., Llewellyn, M. & Rainey, P. B. (2004). Ecological constraints in a model adaptive radiation, Nature 431, 984-988.

MacLean, C. Bell, G. & Rainey, P. B. (2004) The evolution of a pleiotropic fitness tradeoff in Pseudomonas fluorescens. Proceedings of the National Academy of Sciences USA 101, 8072-8077.

Kassen, R & Rainey, P. B. (2004). The ecology and genetics of microbial diversity. Annual Review of Microbiology 58, 207-231

Jessup, C. M., Kassen, R., Forde, S. E., Kerr, B., Buckling, A., Rainey, P. B. & Bohannan, B. J. M. (2004) Big questions, small worlds: Microbial model systems in ecology. Trends in Ecology and Evolution 19, 189-197.

Brockhurst, M. A., Rainey, P. B. & Buckling, A. (2004). The effect of spatial heterogeneity and parasites on the evolution of host diversity. Proceedings of the Royal Society (London) B 271, 107-111.

Brockhurst, M. A., Morgan, A. D., Rainey, P. B. & Buckling, A. (2003). Population mixing accelerates coevolution. Ecology Letters 6, 975-979.

Rainey, P. B. & Rainey. K. (2003). Evolution of co-operation and conflict in experimental bacterial populations. Nature 425, 72-74.

Buckling, A. & Rainey, P. B. (2002). The role of parasites on sympatric and allopatric diversification of hosts. Nature 420, 496-499.

Hodgson, D., Rainey, P. B. & Buckling A (2002). Mechanisms linking, productivity and invasibility in experimental bacterial communities. Proceedings of the Royal Society (London) B 269, 2277-2283.

Buckling, A & Rainey, P. B. (2002). Antagonistic coevolution between a bacterium and a bacteriophage. Proceedings of the Royal Society (London) B 269, 931-936.

Buckling, A. Kassen, R. Bell, G. & Rainey, P. B. (2000). Diversity and disturbance in experimental microcosms. Nature 408, 961-964.

Travisano, M. & Rainey, P. B. (2000). Studies of adaptive radiation using model microbial systems. American Naturalist 156, S35-S44.

Kassen, R. Buckling, A. Bell, G. & Rainey, P. B. (2000) Diversity peaks at intermediate productivity in a laboratory microcosm. Nature 406, 508-512.

Rainey, P. B., Buckling, A., Kassen, R. & Travisano, M. (2000). The emergence and maintenance of diversity: Insights from experimental microbial populations. Trends in Ecology and Evolution 15, 243-247.

Rainey, P. B. & Travisano, M. (1998) Adaptive radiation in a heterogeneous environment.  Nature 394, 69-72.

Evolutionary Genetics

These papers describe our efforts to piece together the mechanistic basis of diversity within radiating Pseudomonas fluorescens populations. To date effort has focussed mostly on the wrinkly spreader genotypes. McDonald et al (2009) describes the current state of published knowledge.

McDonald, M. J., Cooper, T. F., Beaumont, H. J. E. & Rainey, P. B. (2011). The distribution of fitness effects of new mutations in Pseudomonas fluorescens. Biology Letters 7, 98-100.

McDonald, M. J., Gehrig, S. M., Meintjes, P. L., Zhang, X.-X. & 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.

Bantinaki, E., Kassen, R., Knight, C. G., Robinson, Z. & Spiers, & Rainey, P. B. (2007). Adaptive divergence in experimental populations of Pseudomonas fluorescens. III. Mutational origins of wrinkly spreader diversity. Genetics 176, 441-453.

Malone, J. G., Williams, R., Christen, M., Jenal, U., Spiers, A. J. & Rainey, P. B. (2007). The structure-function relationship of WspR; a Pseudomonas fluorescens response regulator with a GGDEF output domain. Microbiology 153, 980-994.

Knight, C. G., Zitzmann, N, Prabhakar, S, Antrobus, R, Dwek, R, Hebestreit, H., & Rainey, P. B. (2006). Unravelling adaptive evolution: how a single point mutation affects the protein co-regulation network. Nature Genetics 38, 1015-1022.

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 fluorecens. II. Role of the GGDEF regulator, WspR, in evolution and development of the wrinkly spreader phenotype. Genetics 173, 515-526.

Beaumont, H. J. E., Gehrig, S. M., Kassen, R., Knight, C., Malone, J., Spiers, A. J. & Rainey, P. B. (2006). The genetics of phenotypic innovation.  In Prokaryotic Diversity: Mechanisms and Significance (ed Logan, N.), Cambridge University Press, pp. 91-104.

Spiers, A. J. & Rainey, P. B. (2005). The Pseudomonas fluorescens SBW25 wrinkly spreader A-L biofilm requires attachment factor, cellulose fibre and LPS interactions to maintain strength and integrity. Microbiology 151 2829-2839.

Spiers, A. J., Bohannon, J., Gehrig, S. M. & Rainey, P. B. (2003). Biofilm formation at the air-liquid interface by the Pseudomonas fluorescens SBW25 wrinkly spreader requires an acetylated form of cellulose. Molecular Microbiology 50, 15-27.

Spiers, A. J., Kahn, S. G., Bohannon, J., Travisano, M. & 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.

Massey, R. M., Rainey, P. B., Keane, O., Sheehan, B. & Dorman, C. J. (1999).  Environmentally constrained mutation and adaptive evolution in Salmonella.  Current Biology 9, 1477-1480.

Appleby, B. M., Petty, S. J., Blakey, J. K., Rainey, P. B. & MacDonald, D. W.  Does variation of sex ratio enhance reproductive success of offspring in tawny owls (Strix aluco)? Proceedings of the Royal Society (London) B 264, 1111-1116.

Moxon, E. R., Rainey, P. B., Nowak, M. & Lenski, R. E  (1994). Adaptive evolution of highly mutable loci in pathogenic bacteria.  Current Biology 4, 24-33.

Ecological Genetics

The papers listed here stem largely from our studies of the mechanistic bases of ecological performance in the rhizosophere colonizing bacteria. Mostly the work focuses on P. fluorescens SBW25, which has a vibrant life outside of the bottle.

Zhang, X.-X., Liu, Y.-H. & Rainey P. B. (2010). CbrAB-dependent regulation of pcnB, a poly(A) polymerase gene involved in polyadenylation of RNA in Pseudomonas fluorescens. Environmental Microbiology 12, 1674-1683.

Knight, C. G., Zhang, X.-X., Gunn, A., Brenner, T., Jackson, R. W., Giddens, S. R., Sripardi, P., Zitzmann, N. & Rainey, P. B. (2010). Testing temperature induced proteomic changes in the plant associated bacterium Pseudomonas fluorescens SBW25. Environmental Microbiology Reports 2, 396-402.

Zhang X.-X. & Rainey, P. B. (2008). Regulation of copper homeostasis in Pseudomonas fluorescens SBW25. Environmental Microbiology 10, 3284-3294.

Zhang X.-X. & Rainey, P. B. (2008). Dual involvement of CbrAB and NtrBC in the regulation of histidine utilization in Pseudomonas fluorescens SBW25. Genetics 178, 185-195.

Zhang X.-X., Scott, K. Meffin, R. & Rainey, P. B. (2007). Genetic characterization of psp encoding the DING protein in Pseudomonas fluorescens SBW25. BMC Microbiology 7, 114.

Giddens, S. R., Jackson, R. W., Moon, C. D., Jacobs, M. A., Zhang, X.-X., Gehrig, S. M. & Rainey, P. B. (2007). Mutational activation of niche-specific genes provides insight into regulatory networks and bacterial function in a complex enviroment. Proceedings of the National Academy of Sciences, USA 104, 18247-18252.

Moon, C. D., Zhang, X.-X., Matthijs, S. Schäfer, M, Budzikiewicz, H. & Rainey, P. B. (2008). Pyoverdine-mediated iron acquisition in the plant growth-promoting bacterium, Pseudomonas fluorescens SBW25. BMC Microbiology 8, 7.

Zhang X.-X. & Rainey, P. B. (2007). Genetic analysis of the histidine utilization (hut) genes in Pseudomonas fluorescens SBW25. Genetics 176, 2165-2176.

Zhang, X.-X. & Rainey, P. B. (2007). Biological and ecological significance of a plant-inducible copper-transporting P1-type ATPase from Pseudomonas fluorescens SBW25. Molecular Plant-Microbe Interactions 20, 581-588.

Zhang, X.-X., George, A., Bailey, M. J. & Rainey, P. B. (2006). The histidine uptake and degradation operon (hut) of Pseudomonas fluorescens SBW25 is active on plant surfaces, but is not required for colonisation of sugar beet seedlings. Microbiology 152, 1867-1875.

Jackson, R. J., Preston G. M. & Rainey, P. B. (2005) Genetic characterisation of Pseudomonas fluorescens SBW25 rsp gene expression in the phytosphere and in vitro. Journal of Bacteriology 187, 8477-8488.

Rediers, H., Rainey, P. B., Vanderleyden, J. & De Mot, R. (2005). Unravelling the secret lives of bacteria: IVET and DFI promoter traps as tools for exploring niche-specific gene expression. Microbiology and Molecular Biology Reviews 69, 217-261.

Zhang, X.-X., Lilley, A. K., Bailey, M. J. & Rainey, P. B. (2004). The indigenous Pseudomonas plasmid pQBR103 encodes plant-inducible genes including three putative helicases. FEMS Microbiology Ecology 51, 9-17.

Zhang, X.-X., Lilley, A. K., Bailey, M. J. & Rainey, P. B. (2004). Functional and phylogenetic analysis of a plant-inducible oligoribonuclease (orn) gene from an indigenous Pseudomonas plasmid. Microbiology 150, 2889-2898.

Rediers, H., Bonnecarrere, V., Rainey, P. B., Hamonts, K., Vanderleyden, J. & De Mot, R. (2003). Development and application of a dapB-based IVET system to study colonization of rice by the endophytic nitrogen-fixing bacterium Pseudomonas stutzeri A15. Applied and Environmental Microbiology 69, 6864-6874.

Gal, M., Preston, G. M., Massey, R. M., Spiers, A. J. & Rainey, P. B. (2003). Genes encoding a cellulosic polymer contribute toward the ecological success of Pseudomonas fluorescens SBW25 on plant surfaces. Molecular Ecology, 12, 3109-3121.

Preston, G. M. Bertrand, N. & Rainey, P. B. (2001). Type III (Hrp) secretion in plant growth-promoting Pseudomonas fluorescens SBW25. Molecular Microbiology 41, 999-1014.

Rainey, P. B. (1999). Adaptation of Pseudomonas fluorescens to the plant rhizosphere. Environmental Microbiology 1, 243-258.

Preston, G. M., Haubold, B. & Rainey, P. B. (1998) Bacterial genomics and adaptation to life on plants: Implications for the evolution of pathogenicity and symbiosis.  Current Opinion in Microbiology 1, 589-597.

Genomics & Informatics

Bertels, F. and Rainey, P. B. (2011). Within genome evolution of REPINs: A new family of miniature mobile DNA in bacteria. Under review.

Silby, M. W., Cerdeno-Tarranga, A. M., Vernikos, G., Giddens, S. R., Jackson, R. W., Preston, G. M., Zhang, X.-X., Moon, C. D., Gehrig, S. M., Godfrey, S. A. C., Knight, C. G., Malone, J. G., Robinson, Z., Spiers, A. J., Harris, S., Challis, G. L., Yaxley, A. M., Harris, D., Seeger, K., Murphy, L., Rutter, S., Squares, R., Quail, M. A., Saunders, E., Anderson, I., Mavromat, K., Brettin, T. S., Bentley, S., Hothersall, J., Stephens, E., Thomas, C. M., Parkhill, J., Levy, S. B., Rainey, P. B. & Thomson, N. R. (2009). Genomic and genetic analyses of diversity and plant interactions of Pseudomonas fluorescens. Genome Biology 10, R51.

Tett, A., Spiers, A. J., Crossman, L. C., Aagar, D., Ciric, L., Dow, M., Fry, J., Harris, D., Lilley, A. K., Parkhill, J., Quail, M. A., Seeger, K., Squares, R., Snyder, L., Saunders, N., Rainey, P. B., Thomas, C., Turner, S. L., Zhang, X.-X., Field, D. & Bailey, M. J. (2007). Sequence-based analysis of pQBR103, a representative of a unique, transfer proficient mega plasmid resident in the microbial community of sugar beet. The ISME Journal 1, 331-340.

Knight, C. G., Kassen, R, Hebestreit, H. & Rainey, P. B. (2004) Global analysis of predicted proteomes: functional adaptation and physical properties. Proceedings of the National Academy of Sciences USA 101, 8390-8395.

Microbial Genetics

Arcus, V. L., Rainey, P. B. & Turner, S. J. (2005). The PIN-domain toxin-antitoxin array in mycobacteria. Trends in Microbiology 13, 360-365.

Aldrige, P., Paul, R., Goymer, P. J., Rainey, P. B. & Jenal, U. (2003). Role of the GGDEF regulator PleD in polar development of Caulobacter crescentus. Molecular Microbiology 47, 1695-1708.

D’Argenio, D. A., Calfee, M. W., Rainey, P. B. & Pesci, E. C. (2002) Autolysis and autoaggregation in Pseudomonas aeruginosa colony morphology mutants. Journal of Bacteriology 184, 6481-6489.

Spiers, A. J., Buckling, A. & Rainey, P. B. (2000). The causes of Pseudomonas diversity. Microbiology 146, 2345-2350.

Ebert, D., Rainey, P. B., Embley, M. & Scholz, D. (1996). Development, life cycle, ultrastructure and phylogenetic position of Pasteuria ramosa Metchnikoff 1888:rediscovery of an obligate endoparasite of Daphnia magna Straus. Philosophical Transactions of the Royal Society (London) B 351, 1689-1701.

Rainey, P. B. & Bailey, M. J. (1996).  Physical and genetic map of the Pseudomonas fluorescens SBW25 chromosome. Molecular Microbiology 19, 521-533.

Rainey, P. B., Brodey, C. L. & Johnstone, K.  (1993). Identification of a gene cluster encoding three high molecular weight proteins which is required for synthesis of tolaasin by the mushroom pathogen Pseudomonas tolaasii.  Molecular Microbiology 8, 643-652.

Population Genetics

Kidd, T. J., Ramsay, K. A., Grimwood, K., Rainey, P. B. & Bell, S. C. (2011). Comparison of pulsed-field gel electrophoresis and multi-locus sequence typing of Pseudomonas aeruginosa isolates in cystic fibrosis sputum. Journal of Clinical Microbiology, in press.

Best, N, Fraser, J. D., Rainey, P. B., Roberts, S. A., Thomas, M. G. & Ritchie, S. R. (2011). Nasal carriage of Staphylococcus aureus in healthy Aucklanders. New Zealand Medical Journal, in press.

Haubold, B., Travisano, M., Rainey, P. B. & Hudson, R. R. (1998). Testing linkage equilibrium in bacterial populations. Genetics 150, 1342-1348.

Haubold, B. & Rainey, P. B. (1996). Genetic and ecotypic structure of a fluorescent Pseudomonas population. Molecular Ecology 5, 747-761.

Thompson, I. P., Bailey, M. J., Ellis, R. J., Lilley, A. K., McCormack, P. J., Purdy, K. J., & Rainey, P. B. (1995). Short-term community dynamics in the phyllosphere microbiology of field-grown sugar beet. FEMS Microbiology Ecology 16, 205-212.

Rainey, P. B., Bailey, M. J. & Thompson, I. P. (1994).  Phenotypic and genotypic diversity of fluorescent pseudomonads isolated from the phyllosphere of sugar beet. Microbiology 140, 2315-2331.

Rainey, P. B., Thompson, I. P. & Palleroni, N. J. (1994). Genome and fatty acid analysis of Pseudomonas stutzeri.  International Journal of Systematic Bacteriology 44, 54-61.

Biological Theory

Libby, E. and Rainey, P. B. (2011). Exclusion rules, population bottlenecks, and the evolution of stochastic switching. Under review.

Rainey, P. B. & Kerr, B. (2011). Conflicts among levels of selection as fuel for the evolution of individuality. In The Major Transitions Revisited: The Evolution of Individuality. (eds Calcott, B. & Sterelny K.). The Vienna Series in Theoretical Biology, MIT Press, in press.

Rainey, P. B. and Kerr, B. (2010). Cheats as first propagules: A new hypothesis for the evolution of individuality during the transition from single cells to multicellularity. BioEssays 32, 872-880.

Rainey, P. B. (2007). Unity from conflict. Nature 446, 616.

Rainey, P. B. & Cooper, T. F (2004). Evolution of bacterial diversity and the origins of modularity. Research in Microbiology 155, 370-375. [A special issue on genome plasticity dedicated to the memory of our friend and colleague Michel Blot]

Tools

Zhang X.-X. & Rainey, P. B. (2007). Construction and validation of a neutrally marked strain of Pseudomonas fluorescens SBW25. Journal of Microbiological Methods 71, 78-81.

Rainey, P. B. & Preston, G. M. (2000). IVET strategies: valuable tools for biotechnology. Current Opinion in Biotechnology 11, 440-444.

Rainey, P. B., Heithoff, D. & Mahan, M. (1997). Single-step conjugative cloning of gene fusions involved in microbial-host interactions. Molecular and General Genetics 256, 84-87.

Comment

Rainey, P. B. (2011). Advances in evolution by convergence. New Zealand Science Teacher 126, 12-13.

Zhang, X.-X. & Rainey, P. B. (2010). Bet hedging in the underworld. Genome Biology 11, 137.

Rainey, P. B. (2009). Arrhythmia of tempo and mode. Nature 461, 1219-1221.

Cooper, T. F., Beaumont, H. J. E. & Rainey, P. B. (2005). Biofilm diversity as a test of the insurance hypothesis. Microbiology 151, 2815-2816.

Rainey, P. B. (2004). Bacteria adapt – genetically, by natural selection – even in the lab!  Microbiology Today 31, 160-162.

Silby, M. W. Rainey, P. B. & Levy, S. B. (2004). IVET experiments in Pseudomonas fluorescens reveal cryptic promoters at loci associated with recognizable overlapping genes. Microbiology 150, 518-520.

Rainey, P. B. (2003).  Big questions in evolution.  New Scientist.  14th June 2003 issue

Spiers, A. J., Field, D., Bailey, M. J. & Rainey, P. B. (2001). Notes on designing a partial genomic database: The PfSBW25 Encyclopaedia, a sequence database for Pseudomonas fluorescens SBW25. Microbiology 147, 247-249.

Rainey, P. B. & Moxon, E. R. (2000). When being hyper keeps you fit. Science 288, 1186-1187.

Rainey, P. B. (1999). Economics of mutation. Current Biology 9, R371-R373.

Moxon, E. R, Lenski, R. E. & Rainey, P. B. (1998). Perspectives in Biology and Medicine 42, 154-155.

Rainey, P. B. & Moxon, E. R. (1993).  Unusual mutational mechanisms and evolution.  Science 260, 1958.

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