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Opening the black box: Imaging microbial behaviour inside rock


The ubiquity and diversity of microbes make them natural, cost effective and sustainable agents for driving a wide range of subsurface engineering and remediation technologies, such as CO2 sequestration, oil recovery, sealing rock for CO2 and nuclear waste storage, and erosion control. Yet, their implementation is limited because we know too little about i) how to inject the microbes to the precise location where they are needed, and once there, ii) how they behave. The subsurface is a black box. MIRO will open this box, using X-ray and electron nanotomography, to provide 3D movies of microbe - rock – fluid interactions. Nanoscale understanding is needed for predicting how to inject microbes for decontaminating aquifers and for enhancing oil recovery from reservoirs nearing the end of their productive lifetime. Researchers have already used X-ray tomography to visualize internal structures in single cells and the nanostructure of rocks. During MIRO, I will transfer this approach to biogeochemistry and add new length and time scales to the study of microbial processes in situ, inside rock pores. Strong industry links, provided by my host, and collaboration with scientists and engineers, who will test my developments at field scale, will ensure implementation. MIRO is a multidisciplinary project that builds on my background in biogeochemistry and will diversify my competencies in tomography, computational methods and additional nanoscale techniques. Being able to pioneer a whole new approach, and contribute to advancing Europe’s technology assets for solving imminent environmental, energy and engineering challenges, will open new collaborations and projects with leading scientists in academia and industry. The training, mentoring and support offered by my host, Prof. Susan Stipp and the Nano-Science Center in Copenhagen, will sharpen my competencies and further build the skills I need to become an independent scientist, ready for a permanent academic position.

Field of science

  • /humanities/arts/modern and contemporary art/film
  • /natural sciences/earth and related environmental sciences/geochemistry/biogeochemistry

Call for proposal

See other projects for this call

Funding Scheme

MC-IEF - Intra-European Fellowships (IEF)


Norregade 10
1165 Kobenhavn
Activity type
Higher or Secondary Education Establishments
EU contribution
€ 221 154,60
Administrative Contact
Bjarne Friis Ploumark (Mr.)