Dr Andrew Spiers
Reader
Environmental & Molecular Microbiology
General Information
Current
My research interests are focussed on the adaptation of bacteria and plasmids to the soil and plant environments. This particular research area is interesting because the microbial community in soils and in intimate contact with plant root surfaces (the rhizosphere) are key factors influencing soil and plant health, disease resistance and productivity. My approach to this research is to combine aspects of molecular microbiology, microbial ecology and evolution with the use of artificial microcosms ranging in complexity from the very simple (liquid media in glass tubes) to the more complex (soil cores).
An understanding of the molecular biology of model bacteria such as Pseudomonas fluorescens SBW25 and P. putida KT2440 allow us to identify functions which may play an important role in the colonization ability, activity and fitness in soils and the rhizosphere. Using standard molecular biology techniques, it is possible to make defined mutations in these functions (e.g. gene knock-outs) which enable comparisons of behaviour with the fully-functional wild-type in simple to complex microcosms.
Previously, I have been involved in projects seeking to understand the fit between genomic potential (biochemistry, physiology, behaviour) and environment for both SBW25 (Spiers et al., 2001; Gal et al., 2003; Huang et al., 2007a; Silby et al., 2009) and the environmental plasmid, pQBR103 (Ude et al., 2007; Tett et al., 2007). I have also been investigating the molecular biology underlying biofilm formation and cellulose expression amongst Pseudomonas (Spiers et al., 2002; 2003; Spiers & Rainey, 2005; Goymer et al., 2006; Ude et al., 2006; Bantinaki et al., 2007; malone et al., 2007; Koza et al., 2009). My work has increasingly adopted an evolutionary perspective in which the fitness benefits of cellulose production and biofilm formation have been examined (Spiers, 2007; Koza et al., 2009), and includes recent collaboration with others to investigate bacterial-phage co-evolution (Patterson et al., 2010). Many of these papers are available as PDFs; please contact me by e-mail if you would like one of them sent to you.
Since joining the SIMBIOS Centre in 2007 I have supported a number of Undergraduate and MSc-level research projects in the Microbial Ecology Laboratory run jointly with Dr Wilfred Otten. I currently have one full-time PhD student, Anna Koza, and one part-time student, Patsy Dello-Sterpaio who began her degree with Prof. Iain Young. I am also a co-supervisor of a joint SIMBIOS-SCRI student, Helen Downie.
Background
I completed my Bachelor of Science (with a double major in Cell Biology and Zoology), Master of Science with First Class Honours (with a specialisation in Cell Biology) and Doctor of Philosophy (in Cellular and Molecular Biology) at the University of Auckland, New Zealand. Both MSc and PhD research theses were on the molecular characterization of the RepFIB replicon of the P307 plasmid, originally recovered from a porcine Salmonella spp. isolate. I completed two postdoctoral research appointments at the University of Oxford, focussing on the Xer site-specific recombination system of Escherichia coli (1994-1998) and the molecular biology of Pseudomonas fluorescens SBW25 (1998-2002). In 2002 I became a University Research Lecturer in the Department of Plant Sciences, University of Oxford, and during 2006 I was a senior CEH-Oxford Research Fellow at the Centre for Ecology and Hydrology in Oxford. In 2007 I joined the SIMBIOS Centre at the University of Abertay Dundee as a Reader in Environmental and Molecular Microbiology
Published Papers
2010:
1 S. Paterson, T. Vogwill, A. Buckling, R. Benmayor, A.J. Spiers, N.R. Thomson, M. Quail, F. Smith, D. Walker, B. Libberton, A. Fenton, N. Hall & M.A. Brockhurst (2010). Antagonistic coevolution accelerates molecular evolution. Nature 464:275-278.
2009:
1 A. Koza, P.D. Hallett, C.D. Moon & A.J. Spiers (2009). Characterisation of a novel air–liquid interface biofilm of Pseudomonas fluorescens SBW25. Microbiology 155:1397-1406.
2. M.W. Silby, A.M. Cerdeño-Tárraga, G. Vernikos, S.R. Giddens, R. Jackson, G. Preston, X-X. Zhang, S. Godfrey, A.J. Spiers, S. Harris, G.L. Challis, A. Morningstar, D. Harris, K. Seeger, L. Murphy, S. Rutter, R. Squares, M.A. Quail, E. Saunders, I. Anderson, K. Mavromat, T.S. Brettin, S. Bentley, C.M. Thomas, J. Parkhill, S.B. Levy, P.B. Rainey & N.R. Thomson (2009). Genomic and functional analyses of diversity and plant interactions of Pseudomonas fluorescens. Genome Biology 10:R51.
2008:
1 D. Field, G. Garrity, J. Selengut, P. Sterk, T. Tatusova, N. Thomson, M. Ashburner, J. Boore, G. Cochrane, J. Cole, C. De Pamphilus, R. Edwards, N. Faruque, R. Feldman, T. Gray, S. Gurr, D. Haft, D. Hancock, C. Hertz-Fowler, J. Hughes, I. Joint, M. Kane, J. Kennedy, E. Kolker, N. Kyripides, J. Leebens-Mack, S. Lewis, N. Maltsev, V. Markowitz, B. Methe, N. Morrison, K. Nelson, J. Parkhill, S.-A. Sansone, A. Spiers, R. Stevens, P. Swift, C. Taylor, Y. Tateno, A. Tett, S. Turner, D. Ussery, B. Vaughan, T. Whetzel, G. Wilson & A. Wipat (2008). Towards richer descriptions of our collection of genomes and metagenomes. Nature Biotechnology 26:541-547
2. W.E. Huang, Y. Li, A.C. Singer, A.J. Spiers, G. M. Preston & A.S. Whiteley (2008). Characterising the regulation of the Pu promoter in Acinetobacter baylyi ADP1. Environmental Microbiology 10:1668-1680.
3. I.M. Young, J.W. Crawford, N. Nunan, W. Otten & A. Spiers (2008). Microbial distribution in soils: physics and scaling. Advances in Agronomy 100:81-121.
2007:
1 J.G. Malone, R. Williams, A.J. Spiers and P.B. Rainey* (2007). The structure-function relationship of WspR: a Pseudomonas fluorescens response-regulator with a GGDEF output domain. Microbiology 153: 980-994.
2. S. Ude, M.J. Bailey, W.E. Huang, and A.J. Spiers*. The environmental plasmid pQBR103 alters the single-cell Raman spectral profile of Pseudomonas fluorescens SBW25. Microbial Ecology 53: 494–497.
3. E. Bantinaki, R. Kassen, C. Knight, Z. Robinson, A.J. Spiers and P.B. Rainey* (2007). Adaptive divergence in experimental populations of Pseudomonas fluorescens. III. Mutational origins of wrinkly spreader diversity. Genetics 176: 441–453.
4. W.E. Huang, S. Ude and A.J. Spiers* (2007). Pseudomonas fluorescens SBW25 biofilm and planktonic cells have differentiable Raman spectral profiles. Microbial Ecology 53: 471–474.
5. W.E. Huang, M.J. Bailey, I.P. Thompson, A.S. Whiteley, and A.J. Spiers* (2007). Single-cell Raman spectral profiles of Pseudomonas fluorescens SBW25 reflects in vitro and in planta metabolic history. Microbial Ecology 53: 414–425.
6. A. Tett., A.J. Spiers, L.C. Crossman, D. Ager, L. Ciric, J.M. Dow, J. Fry, D. Harris, A. Lilley, J. Parkhill, M.A. Quail, P.B. Rainey, N.J. Saunders, K. Seeger, L.A.S. Snyder, R. Squares, C. Thomas, S.L. Turner, X-X. Zhang, D. Field and M.J. Bailey*. 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.
7. A.J. Spiers* (2007). Wrinkly-Spreader Fitness in the Two-dimensional Agar Plate Microcosm: Maladaptation, Compensation and Ecological Success. PLoS ONE 2(8): e740.
2006:
1. A.J. Spiers*, D.L. Arnold, C.D. Moon and T.M. Timms-Wilson (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., and Timms-Wilson, T.M. (Eds). CABI. 2006.
2. S. Ude, D.L. Arnold, C.D. Moon, T. Timms-Wilson, and A.J. Spiers* (2006). Biofilm formation and cellulose expression among diverse environmental Pseudomonas isolates. Environmental Microbiology 8: 1997-2011.
3. W.E. Huang and A.J. Spiers* (2006). Consideration of future requirements for Raman microbiology as an examplar for the ab initio development of informatics frameworks for emergent OMIC technologies. OMICS: A Journal of Integrative Biology 10: 238-241.
4. H.J.E. Beaumont, S.M. Gehrig, R. Kassen, C. Knight, J. Malone, A.J. Spiers and P.B. Rainey* (2006). The genetics of phenotypic innovation. In ‘SGM symposium 66: Prokaryotic diversity – mechanisms and significance’. Logan, N.A., Lappin-Scott H.M., and Oyston, P.C.F. (Eds). Cambridge University Press. 2006.
5. P. Goymer, S.G. Kahn, J.G. Malone, S.M. Gehrig, A.J. Spiers and P.B. Rainey* (2006). Adaptive divergence in experimental populations of Pseudomonas fluorescens. II. Role of WspR in evolution and the development of the wrinkly spreader phenotype. Genetics 173: 515-526.
2005:
1. A.J. Spiers* and P.B. Rainey (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.
2003:
1. A.J. Spiers*, J. Bohannon, S. Gehrig and P.B. Rainey (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.
2. M. Gal, G.M. Preston, R.C. Massey, A.J. Spiers and P.B. Rainey* (2003). Genes encoding a cellulosic polymer contribute toward the ecological success of Pseudomonas fluorescens SBW25 on plant surfaces. Molecular Ecology 12: 3109-3121.
3. G.M. Preston*, A. Spiers, A., X.-X. Zhang, R. Jackson, R., M. Gal, C. Knight, S. Gehrig, J. Malone, C. Moon, S. Godfrey, Z. Robinson, N. Bertrand, D. Field, and P.B. Rainey (2003). Pseudomonas in the underworld: the secret life of Pseudomonas fluorescens SBW25. In ‘Pseudomonas syringae and related pathogens’. Lacobellis, N. (Ed). Kluwer Academic Publishers. 2003.
2002:
1. A.J. Spiers, S.G. Kahn, M. Travisano, J. Bohannon and P.B. Rainey* (2002). Adaptive divergence in Pseudomonas fluorescens. 1. Determinants of Wrinkly Spreader fitness and the cause of an evolutionary transition. Genetics 161: 33-46.
2001:
1. A.J. Spiers*, D. Field, M. Bailey and P. Rainey (2001). Notes on Designing a Partial Genomic Database: The PfSBW25 Encyclopaedia, a sequence database for Pseudomonas fluorescens SBW25. Microbiology 147: 247-249.
2000:
1. A.J. Spiers, A. Buckling and P. Rainey* (2000). The causes of Pseudomonas diversity. Microbiology 146: 2345-2350.
Pre 2000:
1. A.J. Spiers and D.J. Sherratt* (1998). C-terminal interactions between the XerC and XerD site-specific recombinases. Molecular Microbiology 32: 1031-1042.
2. A.J. Spiers and D.J. Sherratt* (1997). Relating primary structure to function in the Escherichia coli XerD site-specific recombinase. Molecular Microbiology 24: 1071-1082.
3. A.J. Spiers, N. Bhana and P.L. Bergquist* (1993). Regulatory interactions between RepA, an essential replication protein, and the DNA repeats of RepFIB from the plasmid P307. J. Bacteriology 175: 4016-4024.
4. M.D. Gibbs, A.J. Spiers and P.L. Bergquist* (1993). RepFIB: A basic replicon of large plasmids. Plasmid 29: 165-179.
5. A.J. Spiers and P.L. Bergquist* (1992). Expression and regulation of the RepA protein of the RepFIB replicon from plasmid P307. J. Bacteriology 174: 7533-7541.
6. D. Saul, A.J. Spiers, J. McAnulty, M.D. Gibbs, P.L. Bergquist* and D.F. Hill (1989). Nucleotide sequence and replication characteristics of RepFIB, a basic replicon of incF plasmids. J. Bacteriology 171: 2697-2707.
7. S.W. Serjeantson*, A. Spiers, P. Ranford and B.R. Hawkins (1986). The distribution of non-HLA blood genetic markers in Hong Kong and Singapore. In ‘Human Leucocyte Antigens in Chinese’. Hawkins, B.R. (Ed). Hong Kong University Press. 1986.
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