Geomicrobiology is the area of science where biology meets geology and is a growing Earth Science discipline. At BGS the Geomicrobiology Laboratory examines the processes and effects of microbes on contaminant breakdown, transport and containment in a range of geological settings. The Laboratory is part of the Centre of Excellence in Physical Properties providing fundamental support to many science programmes through measurement and understanding of biological properties of geological materials. The Geomicrobiology Laboratory also forms part of the Centre of Excellence in Environmental Tracers and Geochemistry and is developing bioassay and bio-indicator techniques to understand and quantify the impacts of environmental changes on ecosystems in the zone of human interaction.


The Geomicrobiology Laboratory has Containment Level 2 facilities and is capable of isolating microbial groups from geological materials (core materials and groundwaters).

The facilities include:

  • biological flow apparatus (BFA), which carries out bespoke flow-through experiments under in-situ conditions to quantitatively evaluate the impacts of microbial activity on transport properties in a variety of geological settings
  • microaerophilic/anaerobic chamber — a variable atmosphere workstation for the study of oxygen sensitive microbes
  • Microtox analyser — the Microtox system provides a quick and reliable biological test system for the measurement of toxicity in aquatic and solid phase samples
  • Deltatox analyser — provides portable rapid screening of potentially contaminated waters. It can also be used for total viable biomass quantification using ATP analysis
  • refrigerated and programmable incubators for the cultivation and isolation of bacteria
  • refrigerated centrifuge for the isolation of temperature sensitive organisms
  • laminar airflow cabinet with protection barrier to prevent contamination of samples
  • epifluorescence microscopy for the assessment of microbial numbers
  • ecological field equipment for use to evaluate the impacts of contaminants on near-surface and surface ecosystems

Additionally, the facilities and expertise in the all Fluid Processes Research Laboratories are available for geomicrobiology studies.

Examples of Applications

  • the influences of microbes and biofilms on mass transport properties through geological media using the BFA
  • biological controls on the formation of redox fronts in natural analogues in both shallow and deep environments
  • microbial effects on mineral dissolution and precipitation
  • environmental issues such as the geological storage of carbon dioxide — extensive research has been undertaken in the UK and overseas into the effects of CO2 leakage on ecosystems
  • groundwater quality — transport and viability of microbes in groundwater systems
  • development of an in-house code to determine controls on subsurface microbial growth — the code has been already been used in projects to evaluate the potential for microbial activity in different geological settings and to scope experimental work.

Selected recent publications

West, J M, McKinley, I G, Palumbo-Roe, B and Rochelle, C A. Potential impact of CO2 storage on subsurface microbial ecosystems and implications for groundwater quality. Submitted to Energy Procedia.

McKinley, I G, West, J M, Alexander, W R, Yoshida, H and Kawamura, H. Microbial catalysis of redox reactions in deep geological environments. Submitted to Chemical Geology.

West, J M, Shaw, R P and Pearce, J M. Environmental Issues in the Geological Disposal of Carbon Dioxide and Radioactive Waste. Book chapter commissioned by the IAEA (in press).

Coombs, P, Wagner, D, Bateman, K, Harrison, H, Milodowski, A E, Noy, D and West, J M. 2010. The role of biofilms in subsurface transport processes. Quarterly Journal of Engineering Geology 43, 131—139.

West, J M, Pearce, J M, Coombs, P, Ford, J R, Scheib, C, Colls, J J, Smith, K L and Steven, M. 2009. The impact of controlled injection of CO2 on the soil ecosystem and chemistry of an English lowland pasture. Energy Procedia 1, pp 1863—1870.

Maul, P, Beaubien, S, Bond, A, Limer, L, Lombardi, S, Pearce, J, Thorne, M and West, J M. 2009. Modelling the fate of carbon dioxide in the near-surface environment at the Latera natural analogue site. Energy Procedia 1, pp 1879—1885.

Krüger, M, West, J M, Oppermann, B, Dictor, M-C, Frerichs, J, Joulian, C, Jones, D, Coombs, P, Green, K, Pearce, J, May, F and Möller, I. 2009. Ecosystem effects of elevated CO2 concentrations on microbial populations at a terrestrial CO2 vent at Laacher See, Germany. Energy Procedia 1, pp 1933—1939.

Maul, P, Beaubien, S, Bond, A, Limer, L, Lombardi, S, Pearce, J, Thorne, M and West, J M. 2009. Modelling the fate of carbon dioxide in the near-surface environment at the Latera natural analogue site. Energy Procedia 1, pp 1879-—885.

Coombs, P, West, J M, Wagner, D, Turner, G, Noy, D J, Milodowski, A E, Lacinska, A, Harrison, H and Bateman, K. 2008. Influence of biofilms on transport of fluids in subsurface granitic environments – Some mineralogical and petrographical observations of materials from column experiments. Mineralogical Magazine 72(1) pp 393-—97.

Beaubien, S E, Ciotoli, G, Coombs, P, Dictor, M C, Krueger, M, Lombardi, S, Pearce, J M and West, J M. 2008. The impact of a naturally occurring CO2 gas vent on the shallow ecosystem and soil chemistry of a Mediterranean pasture (Latera, Italy). International Journal of Greenhouse Gas Control 2 pp 373—387.

West, J M, McKinley, I G, Neall, F B, Rochelle, C A and Bateman, K. 2006. Microbiological effects on the cavern extended storage (CES) repository for radioactive waste. Journal of Geochemical Exploration 90 (1—2) pp 114—122.

Tuck, V M, Edyvean, R G J, West, J M, Bateman, K, Coombs, P, Milodowski, A E and McKervey, J A. 2006. Biologically induced clay formation in subsurface granitic environments. Journal of Geochemical Exploration 90 (1—2) pp 123—133.

Pedley, S, Yates, M, Schijven, J F, West, J M, Howard, G and Barrett, M. 2006. Pathogens: Health relevance, transport and attenuation. In: Protecting Groundwater for health: Managing the quality of Drinking Water Sources. World Health Organisation Drinking Water Quality Series pp 49—80. Schmoll, O, Howard, G, Chilton, J and Chorus, I (editors). (IWA Publishing, London, UK.)

West, J M, Pearce, J, Bentham, M and Maul, P. 2005. Environmental issues and the geological storage of CO2. Environment Europe, 15 pp 250—259.

West, J M and McKinley, I G. 2002. The geomicrobiology of radioactive waste disposal. In: The Encyclopedia of Environmental Microbiology pp 2661—2674. Bitton, G (editor). John Wiley & Sons Inc. (publisher).

Hama, K, Bateman, K, Coombs, P, Hards, V L, Milodowski, A E, West, J M, Wetton, P D, Yoshida, H and Aoki, K. 2001. Influence of bacteria on rock-water interaction, and clay mineral formation in subsurface granitic environments. Clay Minerals. 36 pp 599—613.