I am a molecular biologist working with DNA and RNA; developing techniques and applying them to answer ecological questions. Most recently my work has been geared around next generation sequencing (NGS). I have knowledge of amplicon (gene specific), whole genome, metagenome (all DNA), transcriptome (all RNA) and methylation sequencing on both Illumina MiSeq and Ion Torrent platforms. I also use techniques such as qPCR to accurately quantify specific environmental genes within an environment.
Most of my experience has been gained investigating environmental microorganisms (predominantly bacteria and fungi) which are integral to all biogeochemical processes. I have studied the microbial biodiversity -composition of microbial communities- of many environments (including: soil; water; sediments; plants; invertebrates), their relationship with one another and their environment. Further, how those microbes are governed, change or adapt to both biotic (e.g. disease; pests; plant cover) and abiotic factors (e.g. climate change; water and nutrient availability; pesticides; pollutants).
More recently I have been optimizing and using these molecular techniques to study non-microbial communities: fish, invertebrates and plants.
Current Research Interests Include:
National Honey Monitoring Scheme
Aim: To collect honey samples from across the UK every year for the analysis of their pollen content (using molecular techniques) and pesticide residues. This will provide an early warning of any changes in bee diet and new threats from exposure to pesticides.
NERC Innovation Fund: Developing bee health monitoring services
Aim: To explore whether sub-clinical levels of disease causing organisms can be detected in honey, and whether this could be delivered as a fee-paying service for bee keepers. Traces of disease causing organisms and their DNA are likely to be present in honey and may represent a powerful tool to assess bee colony health before the disease outbreak occurs. This proof-of-concept project will test established molecular assays based on quantitative PCR (qPCR) for detecting both species of foulbrood bacteria, as well as the fungi causing Nosema diseases. When fully optimised this approach will allow sensitive, high-throughput and rapid sample turnaround at detection levels which would inform the farmer about colony health prior to observable clinical symptoms.
PuRpOsE: PRotecting Oak Ecosystems
Aim: To understand how acute oak decline (AOD) manifests in oak trees. Also, are there any possible mitigation strategies? The project involves analysis of the soil characteristics and microbiome; the tree microbiome; and tree traits.
NanoFASE: The effect of Nano silver upon rhizosphere microbial interactions
Aim: To investigate the fate of silver nanoparticles and the effect they have upon wheat rhizosphere microbial communities. Bacterial (16S) and fungal (ITS) NGS will be undertaken on different soil fractions associated with the roots of wheat plants grown in the presence of 3 different silver substrates. Controls will include non- plant soil and plants grown in the absence of any silver substrates.
Roots of decline? Assembly and function of the rhizosphere microbiome in relation to yield decline
Aim: To determine the microbial community structure of the oil seed rape rhizosphere and differentiate it into core (local, abundant) and satellite (infrequent, rare) species. Further, to investigate the role of soil management, environmental variables and distance as drivers of community assembly in relation to yield decline.
Education: October 1996 - January 2000
Division of Parasitology, National Institute for Medical Research. Degree awarded from University College London.
Project: A functional study of bacterial orthologues of the malarial plastid gene, ycf 24 (MRC studentship)
Employment: September 2000 - May 2002
Post-doctoral Research Fellow
Department of Engineering, University of Oxford.
Project: Isolate, characterise and optimise novel, thermo-stable DNA polymerases with regards to their application in PCR (LINK project between OCEB (Oxford Centre for Environmental Biotechnology), CEH Oxford (Oxford Centre for Ecology and Hydrology), University of Oxford, ABgene and the Department of Trade and Industry).
June 2002 - Present day
NERC Centre for Ecology and Hydrology, Wallingford
Senior Molecular Biologist, Laboratory Manager and acting Biological Safety Officer