People

Dr Andrew Free

Location: Roger Land 1.56

Telephone: 650 5338

Email: Andrew.Free@ed.ac.uk

Website: No details available

Group members: Michael McDonald: BBSRC EASTBIO Ph.D. student; Amy Irvine & Maggie Knight: MRC Precision Medicine Ph.D. students; Martina Dajak: Research Assistant; Salvatore Galgano: SRUC Ph.D. student; Vicky Hu: Geosciences Ph.D. student

C.V.

Research groupings

No details available

Teaching

• M.Sc. Biotechnology
• M.Sc. Synthetic Biology & Biotechnology
• M.Sc. Industrial Biotechnology (University of Strathclyde)
• Biotechnology Honours
• Biotechnology 3
• The Microbial World 2

Research interests

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 and Martina Dajak with the UK Biochar Research Centre (Dr. 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 Dr. Rosalind Allen (School of Physics & Astronomy).

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 developing a project to isolate novel methanogenic Archaea with both neutralphilic and acidophilic lifestyles from freshwater sediments (Michael McDonald in collaboration with Dr. James Chong [University of York]). 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 an MRC-funded project Amy Irvine, in collaboration with Dr. Olga Moncayo and NHS Lothian, is investigating 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 a new Ph.D. project, Maggie Knight will be exploring 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. This work is in collaboration with Rosalind Allen and Dr. Eulyn Pagaling at the James Hutton Institute.

Microbial communities in model and bioreactor systems: mixed community of sulphate reducers, cellulose degraders, methanogens and assorted phototrophs in a laboratory sediment-water microcosm (left panel); biofilm of exoelectrogenic Arcobacter butzleri ED-1 growing on the anode of a microbial fuel cell (right panel).

Representative publications

Free, A., M.A. McDonald and E. Pagaling (2018). Diversity-function relationships in natural, applied and engineered microbial ecosystems. Adv Appl Microbiol 105: 131-189.

Bird, C., Darling, K.F., Russell, A.D.,  Fehrenbacher, J.S., Davis, C.V., Free, A., and Ngwenya, B.T. (2018) 16S rRNA gene metabarcoding and TEM reveals different ecological strategies within the genus Neogloboquadrina (planktonic foraminifer). PLoS ONE 13: e0191653.

Pagaling, E., Vassileva, K., Mills, C.G., Bush, T., Blythe, R.A., Schwarz-Linek, J., Strathdee, F., Allen, R.J. and Free, A. (2017) Assembly of microbial communities in replicate nutrient-cycling model ecosystems follows divergent trajectories, leading to alternate stable states. Env Microbiol 19: 3374–3386.

Bird, C., Darling, K.F., Russell, A.D., Davis, C.V., Fehrenbacher, J., Free, A., Wyman, M. and Ngwenya, B.T. (2017) Cyanobacterial endobionts within a major marine, planktonic, calcifier (Globigerina bulloides, Foraminifera) revealed by 16S rRNA metabarcoding. Biogeosciences, 14: 901-920.

Robinson, G., Caldwell, G.S., Wade, M.J., Free, A., Jones, C.L.W. and Stead, S.M. (2016) Profiling bacterial communities associated with sediment-based aquaculture bioremediation systems under contrasting redox regimes. Scientific Rep, 6: 38850. doi: 10.1038/srep38850

Widder, S., Allen, R., Pfeiffer, T., Curtis, T., Wiuf, C., Sloan, W., Cordero, O., Brown, S., Momeni, B., Shou, W., Kettle, H., Flint, H., Haas, A., Kreft, J., Laroche, B., Rainey, P., Milferstedt, K., Grosskopf, T., Jin, Q., Freilich, S., Schuster, S., Huisman, J., Free, A., Quince, C., Labarthe, S., Wang, H., Smeths, B., Klapper, I., Picioreanu, C., Isaac Newton Institute Fellows and Soyer, O. (2016) Challenges in microbial ecology: building predictive understanding of community behaviour. ISME J, 10: 2557-2568.

Bush, T., Butler, I.B., Free, A. and Allen, R.J. (2015) Redox regime shifts in microbially mediated biogeochemical cycles. Biogeosciences, 12: 3713-3724.

Glendinning, L., Nausch, N., Free, A., Taylor, D.W. and Mutapi, F. (2014) The microbiota and helminths: Sharing the same niche in the human host. Parasitology, 141: 1255-1271.

Glendinning, L. and Free, A. (2014) Supra-organismal interactions in the human intestine. Front Cell Infect Microbiol, 4: 47. doi: 10.3389/fcimb.2014.00047

Pagaling, E., Strathdee, F., Spears, B.M., Cates, M.E., Allen, R.J. and Free, A. (2014) Community history affects the predictability of microbial ecosystem development. ISME J, 8: 19-30.

Strathdee, F. and Free, A. (2013). Denaturing gradient gel electrophoresis. In DNA Electrophoresis: Methods and Protocols. Ed: S. Makovets. Methods in Molecular Biology series, Humana Press, USA, pp. 145-157.

Pereira-Medrano, A., Knighton, M., Fowler, G.J.S., Ler, Z.Y., Pham, T.K., Ow, S.W., Free, A., Ward, F.B. and Wright, P.C. (2013). Quantitative proteomic analysis of the exoelectrogenic bacterium Arcobacter butzleri ED-1 reveals increased abundance of a flagellin protein under anaerobic growth on an insoluble electrode. J Proteomics, 78: 197-210.

Khatri, B.S., Free, A. and Allen, R.J. (2012). Oscillating microbial dynamics driven by small populations, limited nutrient supply and high death rates. J Theor Biol, 314: 120-129.

Toh, H., Sharma, V.K., Oshima, K., Kondo, S., Hattori, M., Ward, F.B., Free, A. and Taylor, T.D. (2011) Complete genome sequences of Arcobacter butzleri ED-1 and Arcobacter sp.-L, isolated from a microbial fuel cell. J Bacteriol 193: 6411-6412.

Tota-Maharaj, K., Scholz, M., Ahmed, T., French, C. and Pagaling, E. (2010) The synergy of permeable pavements and geothermal heat pumps for stormwater treatment and reuse. Env Technol 31: 1517-1531.

Fedorovich, V., Knighton, M.C., Pagaling, E., Ward, F.B., Free, A. and Goryanin, I. (2009) A novel electrochemically active bacterium phylogenetically related to Arcobacter butzleri isolated from a microbial fuel cell. Appl Env Microbiol 75: 7326-7334.

Stoebel, D.M., Free, A. and Dorman, C.J. (2008) Anti-silencing: overcoming H-NS-mediated repression of transcription in Gram-negative enteric bacteria. Microbiology 154: 2533-2545.

Free, A. and Barton, N.H. (2007) Do evolution and ecology need the Gaia hypothesis? Trends Ecol Evol 22: 611-619.