EASTBIO funded PhD student. Hello! I’m Michael, a final year EASTBIO funded PhD student in the Free Lab.My research focuses on microbial communities which can survive in extreme conditions, and I have a particular interest in acid mine drainage (AMD); the waste stream resulting from previous mining activities which contaminates freshwater and soil with heavy metals. How the microbial communities present in these contaminated systems contribute to wider ecosystem functioning is poorly understood, despite AMD being hazardous to human and environmental health. Routes to environmental recovery driven by microbial metabolic potential also remain underexplored, as does the fate of carbon in low pH systems. The completion of the carbon cycle results in the production of methane, making these systems overlooked potential sources of greenhouse gases. My work aims to explore the microbial community native to AMD sites and understand how these taxa persist, drive biogeochemical cycling and how we can potentially derive specific functional members of the microbial consortia in applied microbial ecosystems. I utilise a polyphasic approach to my work, including metabolic and chemical profiling, cultivation strategies and more recently, applying long-read DNA sequencing technology (metagenomics) to reconstruct chromosomes of key microbial species to assess their genomic organisation and metabolic potential.I have a BSc (Hons) [First Class] in Biological Sciences and a MSc (Distinction) in Biotechnology and Environmental Sustainability, both from Edinburgh Napier University (ENU) where I first became interested in the incredible diversity of microorganisms, and the evolution of their metabolic capabilities which underpin life on our planet. Prior to my PhD, I continued at ENU as a research assistant where I explored the ability members of the Actinobacteria isolated from soil and activated sludge to produce bioactive secondary metabolites, such as antimicrobials and biosurfactants. This involved co-culturing techniques using members of the ESKAPE pathogens, batch-scale growth studies and microscopy.Additionally, I am interested in promoting effective pedagogy within molecular microbiology. During 2018 and 2019 I acted as the lab-group manager for Edinburgh’s postgraduate iGEM teams, with both teams awarded prizes following completion of their projects. In 2019 I was awarded an Edinburgh Teaching Award for Contribution to the Postgraduate Student Experience. I also contribute to demonstrating on several postgraduate classes and enjoy supervising undergraduate students in our lab on a diverse range of microbe-related projects. This has included exploring host-associated microbiomes which I also have an interest in, particularly the role of Archaea within the mammalian GI tract. I have also taken science out of the lab to schools to share how microbes can help us have a greener future!When I’m not in the lab or writing my thesis, you can find me outside with my dog, playing violin, or trying to improve my Gaelic.You can email me at: m.a.mcdonald@sms.ed.ac.ukPublicationsPublications on Google ScholarFree, A., McDonald, M. A. and Pagaling, E. (2018). Diversity-function relationships in natural, host-associated and applied microbial ecosystems. In: Advances in Applied Microbiology. 105. 131-189. This article was published on 2025-12-15
