Professor Andrew Whiteley

Centre for Ecology & Hydrology
Maclean Building
Wallingford
OX10 8BB
T: +44 (0)1491 838800
F: +44 (0)1491 692424
 

Research interests

I am a molecular ecologist with a PhD in marine biology and oceanography, principally interested in the activity and diversity of bacteria in their natural environments. Several research areas underpin my overall work: 1) The in situ detection of microbes in the environment using molecular technologies. 2) The use of stable isotopes to quantify microbial biogeochemical processes in the environment by using microbial molecular biomarkers such as DNA and RNA. 3) The use of naturally occurring microbes as agents of 'green technologies' through recombinant DNA techniques e.g. biosensor design. Habitats in which I work include soils, sediments and aquatic environments - just about any place that microbes exists - which is most! I have organized and taught on several international technology transfer workshops in developing countries and act as a consultant for Cybersense Biosystems, an environmental technology spin out company. I enjoy scuba diving as a hobby, but finding water deep enough around Oxford is a bit of a problem!

Skills

  • Analytical Flow Cytometry
  • DNA / RNA extraction, manipulation and probing from most environments
  • PCR, RT-PCR, cloning, sequencing and DGGE analysis
  • Transposon mutagenesis and chromosomal integration of recombinant DNA
  • cDNA library construction from prokaryotes and eukaryotes
  • mRNA detection in eukaryotes, manipulation and expression in prokaryotes
  • In situ Hybridisation in whole cells
  • Stable Isotopic tracer techniques

Current grants

  • NERC: Microbial Metagenomics
  • EPSRC: The biological basis of enhanced polyphosphate accumulation. In collaboration with Dr John McGrath (Queens University of Belfast)             
  • BBSRC: Optimising wastewater treatment by exploiting bacterial intercellular signalling . In collaboration with Dr Mike Manefield ( University of New South Wales)
  • Macaulay Development Trust. Microbial community function and Rhizodeposition: Insight into the carbon flux paradox of upland soils . In collaboration with Braj Singh.
  • DTI: SenseNET: Networked GM biosensors for protecting bioreactor populations   

Previous grants

  • EU FR-V . BIOGEM. Development and risk assessment of a field based portable biosensor using GM-bioluminescent bacteria
  • NERC CEH Integrated Fund. Resilience of microbial soil ecosystems to ecological perturbations: development of an RNA stable isotope protocol to determine carbon mass balance in the plant rhizosphere
  • NERC-Soil Biodiversity Programme: Influence of Sourhope biodiversity treatments upon carbon flow and functional resilience of key heterotrophic bacterial taxa in the rhizosphere of grassland soils
  • NERC – Non-Thematic, Terrestrial Sciences. Development and application of novel methods that determine the functional phylogeny of microbial communities
  • NERC- Thematic Soil Biodiversity programme. Establishing the link between functional and total bacterial diversity and its response to perturbation

Current and past PhD students

  • Dr Siouxsie Wiles (Napier University, 1997-2001)
  • Dr Rob Griffiths (Newcastle University, 1998-2001)
  • Ms Zoe Keatinge (Newcastle University, 2001-2004)
  • Mr Bruce Thompson (University of Newcastle, 2003-2006)
  • Mrs Ann Gunn (University of Oxford)
  • Ms Lena Ciric (Napier University, 2002-2005)
  • Ms Dominique Chaput (University of Oxford, 2003-2006)

 

 

 

Selected publications

See also the NERC Open Research Archive.

  1. Whiteley, A. S., Barer, M. R. and O'Donnell, A. G. (2000). Density gradient separation of active and non-active cells from natural environments. Antonie van Leeuwenhoek 77. 173-177.
  2. Whiteley, A.S. & Bailey, M.J. (2000). Bacterial community structure and physiological state within an industrial phenol bioremediation system. Appl. Env. Microbiol. 66:2400-2407.
  3. Griffiths, R., Whiteley, A.S., O'Donnell, A.G. & Bailey, M.J. (2000). Rapid method for coextraction of DNA and RNA from natural environments for analysis of ribosomal DNA and RNA-based microbial community. Appl. Env. Microbiol. 66, 5488 –5491.
  4. Whiteley, A.S., Wiles, S, Lilley, A.K., Philp, J & Bailey, M.J. (2001). Ecological and physiological analyses of Pseudomonad species within a phenol remediation system. J. Microbiolological Methods 44. 79-88.
  5. Wiles, S., Whiteley , A.S., Philp, J. and Bailey, M.J. (2001). Biomate: development of custom-designed bioluminescent sensors for toxicity testing. In Proceedings of the 11th International symposium on bioluminescence and chemiluminescence. Monterey, September 2000.
  6. Manefield, M. Whiteley, A.S., Ostle, N. Ineson, P. and Bailey, M.J. (2002). Technical considerations for RNA based stable isotope probing: an approach to associating microbial diversity with microbial community function. Rapid Communications in Mass Spectrometry 16, 2179-2183.
  7. Manefield, M., Whiteley, A. S., Griffiths, R. I. And Bailey, M. J. (2002). RNA stable isotope probing: A novel means of linking microbial community function to phylogeny. Appl. Env. Microbiol. 68, 5367-5373.
  8. Griffiths, R, Whiteley, A.S., O'Donnell, A.G. and Bailey, M.J. (2003) Influence of depth, sampling time and rhizodeposition on bacterial community structure in an upland grassland soil. FEMS Microbial. Ecol. 43:35-43.
  9. Johnson, D, Booth, R.E., Whiteley, A. S., Bailey, M. J., Read, D. J., Grime, J. P. and J.R.Leake. (2003) Plant community composition affects the biomass, activity and diversity of soil microorganisms in reconstituted calcareous grassland. Eur. J. Soil Sci. 54: 671-677.
  10. Ostle, N., Whiteley, A. S., Bailey, M.J., Sleep, D., Ineson,. P. and Manefield, M. J. (2003). Microbial Turnover in a grassland soil using a 13 C02 ‘spike'. Soil Biol. Biochem. 35:877-885.
  11. Philp, J. C. Balmand, S., Hajto, E., Bailey, M. J., Wiles, S., Whiteley, A.S., Hajto, J., and Dunbar, S. (2003). Whole cell immobilised biosensors for toxicity assessment of a wastewater treatment plant treating phenolics containing waste. Analytica Chimica Acta. 2003 487:61-74.
  12. Van der Gast, C. J., Whiteley, A. S., Lilley, A. K., Knowles, C. J., Thompson, I. P. (2003). Bacterial community structure and function in a metal-working fluid. Environmental Microbiology. 5:453-461.
  13. Van der Gast, C. J., Whiteley, A. S., Starkey, M., Knowles, C. J., Thompson, I.P. (2003). Bioauagmentation strategies for remediating mixed chemical effluents. Biotechnology Progress. 19: 1156-1161.
  14. Whiteley, A. S. Griffiths, R.I. and Bailey, M.J. (2003). Analysis of the microbial functional diversity within water stressed soil communities by flow cytometric analysis and CTC+ cell sorting. Journal of Microbiological Methods. 54:257-267.
  15. Griffiths , R. I., Whiteley, A.S O'Donnell, A.G. and Bailey, M.J., (2003). Physiological and community response of established grassland bacterial populations to water stress. Appl. Env Microbiol. 69. 6961-6968.
  16. Wiles, S., Whiteley, A.S., Philip, J. and Bailey, M.J. (2003). Development of Bespoke Bioluminescent Reporters with the Potential for In-situ Deployment within a Phenolic-Remediating Wastewater Treatment System. Journal of Microbiological Methods. 55:667-677.
  17. Ciric,L., Whiteley, A. S., Manefield, M., Griffiths , R., Bailey, M.J., Philp, J. (2003). Approaches for analysing the diversity of diesel degrading microbial communities. Proceedings of the International Biodegradation and Biodeteriorotion Society, Greece , 2003.
  18. Valle, A Bailey, M.J., Whiteley, A.S., and Manefield, M.J (2004). Bacterial Intercellular signalling effects microbial community composition and function. Environmental Microbiology. 6: 424-433.
  19. Van der Gast, C.J., Whiteley, A.S. and Thompson, I.P. (2004). Temporal dynamics and degradation activity of a bacterial inoculum for treating waste metal-working fluid. Environmental Microbiology. 6: 254-263.
  20. Whiteley, A.S. (2004). So what do Microbes have to do with paper clips? NERC Planet Earth. Summer Edition
  21. Philp, J.C., French, C., Bell , J.M.L, Wiles, S., Whiteley, A.S. & Bailey, M.J. (2004). Wastewater toxicity assessment by whole cell biosensor. Chapter 12. In: Handbook of Environmental Chemistry, Volume 5: Water Pollution; Emerging Organic Pollutants in Wastewaters and Sludge (2004). O. Hutzinger, O & Barceló, D (eds.). Springer.
  22. Manefield, M., Griffiths , R.I. , Whiteley, A.S. and Bailey, M. J. (In Press). Stable Isotope Probing: A critique of its role in linking phylogeny and function. In Nucleic acids and Proteins in Soil. Ed. Smalla, K. Springer - Verlag.
  23. Griffiths , R.I. , Manefield, M. J., Whiteley, A. S. and Bailey, M. J. (In Press). DNA and RNA extraction from soils. In Handbook of Molecular Ecology. Eds Kowalchuk et al ., 3rd Edition.
  24. Singh, B., Millard, P Whiteley, A.S., Murrell, C.,. (In Press). Unravelling Plant-Microbial interactions using molecular and genomic techniques. Trends in Microbiology.
  25. Manefield, M., Whiteley, A.S. and Bailey, M.J. (In Press). What can stable isotope probing do for bioremediation. In. Proceedings of the International Biodegradation and Biodeterioration Society, Prague , 2002 .
  26. Griffiths, R.I. , et al. 13 CO 2 Pulse Labelling in Tandem with Stable Isotope Probing: Methodological Considerations for Examining Rhizospheric Microbial Function. Journal of Microbiological Methods. 58:119-129.
    Huang,W., Griffiths , R. I., Thompson, I.P., Bailey, M.J., Whiteley, A. S. (2004). Raman Microscopic Analysis of Single Microbial Cells. Analytical Chemistry. 76:4452-4458.
  27. Whiteley, A. S., Manefield, M. J., Turner, S. L., Bailey, M. J. (In Press). Lessons from the genomes: Microbial Ecology and Genomics. BIOS Series.
  28. Whiteley, A.S., Manefield, M. J., Bailey, M. J., Philp, J., Wiles, S., Fisher and Whitby , P. (In Press). The Microbiology of an ‘undisclosed Vitox system in the north of England'. The Coke Oven Managers Association Yearbook, 2004.
  29. Wiles, S., Whiteley, A.S. , Lilley, A.K., Philp, J. and Bailey, M. J. (In Press) Calibration and deployment of Custom Designed Biosensors for Protecting Biological Remediation Consortia. Environmental Microbiology.
  30. Ciric, L., Philp, J. and Whiteley, A.S. (In Press). Molecular biology tools for monitoring biodiversity in wastewater treatment plants. ASM Handbook on Molecular Ecology. Eds Atlas, R and Philp, J.
  31. Manefield, M., Griffiths, R. I., Leigh, M. B., Fisher, R., and Whiteley, A.S. (In Press). Functional and Compositional comparison of two activated sludge communities remediating coking effluent. Environmental Microbiology.