The Free Lab
┃ Microbial Ecology ┃ Environmental Microbiology ┃ Antimicrobial Resistance ┃ Microbiome Research ┃ Biotechnology ┃ Bioremediation ┃ Anaerobic Digestion ┃
The Free Group are a diverse cohort of microbiologists interested in microbial ecology, environmental biotechnology, microbiota, bioremediation and solving contemporary interdisciplinary issues led by Dr Andrew Free at The University of Edinburgh.
Microorganisms constitute the vast majority of the diversity of life on planet Earth, and perform crucial functions ranging from carbon fixation, biogeochemical cycling and degradation of toxic waste to the maintenance of healthy function in the mammalian gut. We are interested in the basic ecological processes which determine the diversity, functionality and variability in natural microbial communities and in model laboratory systems, and in applying this basic knowledge to improving the performance of microbial devices such as anaerobic digestors [Vicky Hu, Karolina Maka and Dr. Leah Herrgen with the UK Biochar Research Centre (Prof. Ondrej Mašek) and Carbogenics Ltd.] as well as in the mammalian intestine. We study such communities using modern genomic, metataxonomic and metagenomic techniques based on next-generation DNA sequencing, proteomics, fingerprinting techniques and subsequent pure-culture isolation, as well as modelling microbial communities in collaboration with Rosalind Allen.
Being able to engineer microbial communities for improved function will depend on the isolation and characterisation of novel microbial species and the partners they interact with in their natural environments. To this end, we are pursuing a project to isolate novel methanogenic Archaea with both neutralphilic and acidophilic lifestyles from freshwater sediments (Michael McDonald). The eventual goal of this work is to enhance the productivity of anaerobic digestor systems using synthetic ecology.
Microorganisms are an integral part of the bodies of mammalian hosts, in particular the gastrointestinal tract, where they contribute to metabolic function, immune system development and resistance to pathogens. We have three current projects which investigate these phenomena. Our work on the interaction between the microbiota and nematode parasites in sheep is conducted in conjunction with Dr. Craig Watkins at the Moredun Research Institute, and involves collaboration with veterinary practices, farmers and the James Hutton Institute. We also characterise the microbiota of the unmanaged and well-studied population of Soay sheep on St. Kilda, in collaboration with Prof. Dan Nussey, Dr. Luke McNally and the St. Kilda Soay Sheep Project. In a recent MRC-funded project Amy Irvine, in collaboration with Dr. Olga Moncayo and NHS Lothian, investigated the role of the intestinal microbiota in resistance to and recurrence of Clostridium difficile-associated dysbiosis, a major form of hospital-acquired infection.
Resistance to antimicrobials is also a topic of major concern in human populations, but at the same time may be crucial to the continued functioning of wastewater treatment plants, the microbial processes of which are exposed to these compounds on a daily basis. In her recently-completed PhD project, Maggie Knight explored these conflicting phenomena and the way in which fundamental microbial ecology influences the abundance of antimicrobial resistance (AMR) genes in these locations and the natural environment. Joana Mends, a Darwin Trust-funded PhD student, is continuing our work on AMR to explore the effect of naturally-occurring levels of antibiotics on aquatic microbial communities and their AMR genes.
Finally, our work on applied microbial ecology is completed by the projects of Hanna Peach, focussing on the bioremediation of organic micropollutants and funded by a Scottish Hydro Nation Scholarship, and Martina Dajak, investigating the optimisation of thraustochytrid protists for omega-3 fatty acid production in collaboration with MiAlgae Ltd.