Staff profile

Dr James McDonald

Senior Lecturer in Environnmental Microbiology


Location: Memorial F6

Personal page

Phone: 01248 383077


James McDonald is a microbial ecologist and Senior Lecturer in the School of Biological Sciences at Bangor University. He holds a BSc in Microbiology with industrial experience (University of Manchester) and a PhD in Environmental Microbiology (University of Liverpool). He obtained his PostGraduate Certificate in Higher Education from Bangor University and in 2015 was awarded a Bangor University Teaching Fellowship in recognition of his outstanding contribution to teaching and pastoral care.

Dr McDonald’s research interests include environmental microbiology, molecular microbial ecology and microbiome analysis of natural and managed environments.

Please visit James’ personal webpage for more details.

Research themes:

1. Microbial lignocellulosic biomass conversion

Recent work has focused on the use of molecular biological, (meta)genomics and (meta)transcriptomics techniques to characterise those microbial communities that colonise and degrade cellulose, the most abundant carbon polymer on Earth, in terrestrial and aquatic environments and in managed landfill sites.

Currently, we are using a combined molecular/cultivation-based approach to characterise cellulolytic microorganisms from these environments, with particular focus on members of the Fibrobacteres phylum that appear to have evolved a novel mechanism for cellulose biodegradation. The overarching aim of this work is to provide information on the saccharolytic enzyme systems of these microorganisms in an attempt to understand their role in carbon flow in natural environments, and also to identify enzymes that may be of benefit in biotechnological applications such as the production of second-generation biofuels.

2. Characterising the oak microbiome in Acute Oak Decline

AOD is a complex Decline-disease affecting both native oak species in the UK. Visible stem bleeds that overlie areas of necrotic tissue in the inner bark represent the primary symptom and several novel bacterial species, including Gibbsiella quercinecans and Brenneria goodwinii, have been isolated from necrotic lesions. We are characterising the Oak microbiome through genome analysis of isolated species, in addition to metagenomic, metatranscriptomic, metaproteomic and phenotypic analysis of the microbiota associated with necrotic lesions of Oak tress affected by Acute Oak Decline. Our aim is to elucidate the role of these potential bacterial pathogens in the AOD syndrome. This work is undertaken in collaboration with Dr. Sandra Denman (Forest Research) and others.

3. The ecology and persistence of human microbial pathogens in the freshwater-marine continuum

We are interested in the ecology and persistence of human microbial pathogens (bacterial and viral) in estuarine and coastal environments, their interactions with nutrients, suspended particular material and sediments, and potential impacts on bathing and shellfish water quality.

Microbial Pathogen Ecology Group (MPEG)

Viraqua website

Other projects:

I am also involved in other projects relating to the microbiology of carbon release from wetlands under drought conditions, antibiotic resistance genes in wastewater treatment plants and microbial biodiversity of contrasting Welsh soil types.


  • SBS Teaching Committee
  • SBS Board of Studies
  • SBS Management Committee
  • SBS Student-staff liaison committee
  • CNS Estates Committee

Offices held

Director of Graduate Studies



Denman, S., Barrett, G., Kirk, S.A, McDonald, J.E. and Coetzee, M.P.A (2016) Identification of Armillaria species on declined oak in Britain: implications for oak health. Forestry doi:10.1093/forestry/cpw054[Link]
Ransom-Jones, E. and McDonald, J.E (2016) Draft Genome Sequence of Clostridium sp. strain W14A isolated from a cellulose-degrading biofilm in a landfill leachate microcosm. Genome Announcements 4(5):e00985-16.       doi:10.1128/genomeA.00985-16. [Link]

Winterbourn, J.B., Clements, K., Lowther, J.A., Malham, S.K., McDonald, J.E. and Jones, D.L. (2016) Use of Mytilus edulis biosentinels to investigate spatial patterns of norovirus and faecal indicator organism contamination around coastal sewage discharges. Water Research 105: 241–250. [Link]

Denman, S., Plummer, S., Kirk, S., Peace, A. and McDonald, J.E. (2016) Isolation studies reveal a shift in the cultivable microbiome of oak affected with Acute Oak Decline. Systematic and Applied Microbiology 39(7): 484–490. [Link]

McDonald, J.E., Larsen, N., Pennington, A., Connolly, J., Wallis, C., Rooks, D.J., Hall, N., McCarthy, A.J. and Allison, H.E. (2016) Characterising the canine oral microbiome by direct sequencing of reverse-transcribed rRNA molecules. PLoS ONE 11(6): e0157046. [Link]

Emmett, B.A., Cooper, D., Smart, S., Jackson, B., Thomas, A., Cosby, B., Evans, C., Glanville, H., McDonald, J.E., Malham, S.K., Marshall, M., Jarvis, S., Rajko-Nenow, P., Webb, G.P., Ward, S., Rowe, E., Jones, L., Vanbergen, A.J., Keith, A., Carter, H., Pereira, G.P. et al. (2016) Spatial patterns and environmental constraints on ecosystem services at a catchment scale. Science of The Total Environment.       doi:10.1016/j.scitotenv.2016.04.004

Perkins, T.L., Perrow, K., Rajko-Nenow, P., Jago, C.F., Jones, D.L., Malham, S.K. and McDonald, J.E. (2016) Decay rates of faecal indicator bacteria from sewage and ovine faeces in brackish and freshwater microcosms with contrasting suspended particulate matter concentrations. Science of The Total Environment.

Robins, P.E., Skov, M.W., Lewis, M.J., Giménez, L., Davies, A.G., Malham, S.K., Neill, S.P., McDonald, J.E., Whitton, T.A., Jackson, S., Jago, C.F., (2016) Impact of climate change on UK estuaries: A review of past trends and potential projections. Estuarine, Coastal and Shelf Science 169: 119-135. [Link]


Rhymes, J., Jones, L., Lapworth, D.J., White, D., Fenner, N., McDonald, J.E. and Perkins, T.L. (2015) Using chemical, microbial and fluorescence techniques to understand contaminant sources and pathways to wetlands in a conservation site. Science of The Total Environment 511: 703-710. [Link]

Doonan, J., Denman, S., Gertler, C., Pachebat, J.A., Golyshin, P.N., and McDonald, J.E. (2015) The intergenic transcribed spacer region 1 as a molecular marker for identification and discrimination of Enterobacteriaceae associated with acute oak decline. Journal of Applied Microbiology 118(1): 193-201. [Link]


Perkins, T.L., Clements, K., Baas, J.H., Jago, C.F., Jones, D.L., Malham, S.K. and McDonald, J.E. (2014) Sediment Composition Influences Spatial Variation in the Abundance of Human Pathogen Indicator Bacteria within an Estuarine Environment. PLoS ONE 9(11): e112951. [Link]

Malham, S.K., Rajko-Nenow, P., Howlett, E., Tuson, K.E., Perkins, T.L., Pallett, D.W., Wang, H., Jago, C.F., Jones, D.L. and McDonald, J.E. (2014) The interaction of human microbial pathogens, particulate material and nutrients in estuarine environments and their impacts on recreational and shellfish waters. Environmental Science: Processes and Impacts 16: 2145-2155. [Link]

Ransom-Jones, E., Edwards, A., Jones, D.L. and McDonald, J.E. (2014) Environmental Distribution and Diversity of Members of the Cellulolytic Bacterial Phylum Fibrobacteres. Systematic and Applied Microbiology 37(7): 502-509. [Link]

McDonald, J.E. and Robinson, R.L. (2014) Enhancing First Year Undergraduate Student Engagement via the School of Biological Sciences Tutorials Module. Bioscience Education 22(1): 54-69. [Link]

Robinson, R.L. and McDonald, J.E. (2014) Developing skills in second year biological science undergraduates. Bioscience Education 22(1): 42-53. [Link]


Gwyther, C.L., Jones, D.L., Golyshin, P.N., Edwards-Jones, G., McKillen, J., McNair, I., McDonald, J.E., Williams, A.P. (2013) Bioreduction of sheep carcasses effectively contains and reduces pathogen levels under operational and simulated breakdown conditions. Environmental Science & Technology 47, 5627-5275.


McDonald, J.E., Rooks, D.J. and McCarthy A.J. (2012) Methods for the isolation of cellulose degrading microorganisms. Methods in Enzymology. 510: 375-394.

Rooks, D.J., McDonald, J.E. and McCarthy A.J. (2012) Metagenomic approaches to the discovery of cellulases. Methods in Enzymology. 510: 349-374.

de Menezes, A.B., McDonald, J.E., Allison, H.E. and McCarthy, A.J. (2012) The importance of Micromonospora spp. as colonisers of cellulose in a freshwater lake demonstrated by RT-qPCR of 16S rRNA. Applied and Environmental Microbiology. 78(9): 3495-3499.

McDonald, J.E., Houghton, J., Rooks, D.J., Allison, H.E., and McCarthy, A.J. (2012) The Molecular Ecology of Cellulose-Degrading Microbial Communities in Municipal Waste Landfill Site: Evidence for a role of Fibrobacters. Environmental Microbiology. 14(4): 1077-1087.

Ransom-Jones, E., Jones, D.L., McCarthy, A.J. and McDonald J.E. (2012) The Fibrobacteres: an important Phylum of cellulose-degrading bacteria. Microbial Ecology 63(2): 271-281.


Rooks, D.J., Smith, D.L., McDonald, J.E., Woodward, M.J., McCarthy, A.J., and Allison, H.E. (2010) 454-Pyrosequencing: A Molecular Battiscope for Freshwater Viral Ecology. Genes 1(3): 210-226.

Edwards, J.L., Smith, D.L., Connolly, J., McDonald, J.E., Cox, M.J., Joint, I., Edwards, C. and McCarthy, A.J. (2010) Identification of carbohydrate metabolism genes in the metagenome of a marine biofilm community shown to be dominated by Gammaproteobacteria and Bacteroidetes. Genes 1(3): 371-384.

Rooks, D.J., Yan, Y., McDonald, J.E., Woodward, M.J., McCarthy, A.J. and Allison, H.E. (2010) Development and validation of a qPCR-based method for quantifying Shiga toxin-encoding and other lambdoid bacteriophages. Environmental Microbiology 12: 1194-1204.

McDonald, J.E., Smith, D.L., Fogg, P.C.M., McCarthy, A.J., and Allison, H.E. (2010) Method for Rapid Induction of Prophages from Lysogens and Its Application in the Study of Shiga Toxin-Encoding Escherichia coli Strains. Applied and Environmental Microbiology, 76: 2360-2365.

McDonald, J.E., Allison, H.E., and McCarthy, A.J. (2010) Composition of the Landfill Microbial Community as Determined by Application of Domain- and Group-Specific 16S and 18S rRNA- Targeted Oligonucleotide Probes. Applied and Environmental Microbiology, 76: 1301-1306.


McDonald, J.E., de Menezes, A.B., Allison, H.E. and McCarthy, A.J. (2009) Molecular biological detection and quantification of novel Fibrobacter populations in freshwater lakes. Applied and Environmental Microbiology 75: 5148-5152.


McDonald, J.E., Lockhart, R.J., Cox, M.J., Allison, H.E., and McCarthy, A.J. (2008) Detection of novel Fibrobacter populations in landfill sites and determination of their relative abundance via quantitative PCR. Environmental Microbiology 10: 1310-1319.