Figure 1. Pyrite coated with microbial structures in a biofilm

BGS has been working with the Japan Atomic Energy Agency (JAEA) on sedimentary rock environments in northern Japan. We have been investigating changes in transport properties resulting from microbial activity in short experiments (39 days maximum) using the BGS developed Biological Flow Apparatus.

Experiments have shown for the first time that the denitrifying bacterium Pseudomonas denitrificans can survive and thrive when injected into flow-through column experiments containing fractured diatomaceous mudstone and synthetic groundwater under pressurised conditions (Figure 1).


The BioTran study investigates the significance of the impacts of microbial activity on the transport properties of rocks and subsequent movement of contaminants.

Our recent work has focused on geological environments, which are relevant to the disposal of radioactive waste.

Recent BioTran results

Monitoring during column experiments in the Japan study revealed few significant changes in fluid chemistry but changes in the permeability of the biotic column were observed. These can be explained by biofilm formation. Such changes have the potential to inhibit the transport of radionuclides.

Additionally, the microbes etched and dissolved some of the minerals (Figure 2).

Figure 2. Biofilament etching and dissolution of pyrite and silicate structures
Figure 2. Biofilament etching and dissolution of pyrite and silicate structures

Wider implications

The methodologies used in these experiments could be adapted to obtain information from cores originating from a variety of geological environments including oil reservoirs, aquifers and toxic waste disposal sites. Such investigations provide an improved understanding of the impact of microbial activity on the transport of a range of solutes, such as groundwater contaminants and gases (e.g. injected carbon dioxide).

The methodologies can also be applied to investigate the role that microbes play in the mobilisation of potentially harmful elements in soil, particularly in the context of contaminated land.

Recent publications

Microbiology and mudstone environments

Harrison, H, West, J M, Milodowski, A E, Bateman, K, Coombs, P, Harrington, J, Holyoake, S, Lacinska, A, Turner, G and Wagner, D. 2010. Microbial influences on fracture surfaces of intact Horonobe mudstone. BioTran Progress Report Sept 2009 – January 2010. British Geological Survey Report OR/10/067. Available from

Microbiology and granitic environments<

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) 393—397. Available from

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, 599—613. (Abstract).

Tuck, V A, 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, 123—133. DOI: 10.1016/j.gexplo.2005.09.007.

Biofilms and transport properties

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 and Hydrogeology 43, 131—139. Available from

Microbiology and redox reactions in deep geological environments

West, J M, McKinley, I G and Stroes-Gascoyne, S. 2009. Implications of microbial redox catalysis in analogue systems for repository safety cases. Proceedings 12th International Conference on Environmental Remediation and Radioactive Waste ICEM 2009. ASME. (Available on CD-ROM). ICEM2009-16336. ISBN 978-0-7918-3865-X.

Microbiology and Radioactive Waste Disposal

Humphreys, P N, West, J M and Metcalfe, R. 2009. Microbial effects on repository performance. Technical Report QRS-1378Q-1. Livelink reference number: 12208035. UK Nuclear Decommissioning Agency. Available from NDA bibliography

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. Available from

West, J M and McKinley, I G. 2002. The geomicrobiology of radioactive waste disposal. In: The Encyclopaedia of Environmental Microbiology Biutton, G (editor). (John Wiley, New York, 2661—2674.) ISBN: 978-0-471-35450-5. Available through,descCd-description.html).

West, J M, McKinley, I G and Stroes-Gascoyne, S. 2002. Microbial effects on waste repository materials. In: Microbiology and Radioactivity Keith-Loach, M and Livens, F (editors). (Elsevier.) pp 255—278 ISBN 978-0080437088 DOI: 10.1016/S1569-4860(02)80038-9.

Microbiology and Carbon Capture and Storage

West, J M, McKinley, I G, Palumbo-Roe, B and Rochelle, C A. Potential impact of CO2 storage on subsurface microbial ecosystems and implication for groundwater quality. Energy Procedia (in press).

Jones, D G, Lister, T R, Smith, D J, West, J M Coombs, P, Gadalia, A, Brach. M, Annunziatellis, A and Lombardi, S. In Salah Gas CO2 Storage JIP: Surface gas and biological monitoring. Energy Procedia (in press).

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. Available from

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. DOI:10.1016/j.egypro.2009.01.252.

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. DOI: 10.1016/j.egypro.2009.01.245

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


Contact Dr Julia West for further information