PhD position on non-destructive 3D characterization and 4D monitoring of microbial-induced pore-scale processes inside stone (4 yrs) (1.0 FTE)

PhD position on non-destructive 3D characterization and 4D monitoring of microbial-induced pore-scale processes inside stone (4 yrs) (1.0 FTE)

Published Deadline Location
15 Oct 15 Nov Utrecht

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Does studying the impact of microbial treatment on the weathering behaviour of rocks sound interesting to you? Read more and apply!

Job description

The Department of Earth Sciences is now looking for highly-motivated, high-potential applicant to fill a PhD position on the impact of microbial treatment on the weathering behaviour of rocks. Physical, chemical and biological weathering has a profound impact on the Earth’s landscape and on its building infrastructure. Rock and masonry are constantly damaged and disaggregated by chemical reactions, water infiltration and temperature changes. Strengthening efforts to protect and safeguard the world’s cultural and natural heritage is one of the United Nations’ Targets for Sustainable Cities and Communities in the 2030 Agenda for Sustainable Development. Fluids are a major driver of rock weathering: they trigger, among others, dissolution, precipitation, frost and salt weathering. The key to manipulating weathering lies in understanding and controlling fluid flow within the internal pore structure of rocks and thereby influencing the related pore-scale processes. While microbial organisms are generally known to alter rock surfaces, some actually display physiological capabilities that have beneficial effects on rock properties due to their production of bio-cement, gas and acids. Before we can harness these beneficial effects, we must first study how these organisms impact fluid flow at the pore scale.
The Dutch Research Council VICI project, led by Prof. Veerle Cnudde, 'Towards protecting and improving building stones through microbial manipulation of pore structure' (short: BugControl), will focus on the understanding of bio-manipulated pore-scale processes inside rocks. The 4-year PhD project aims at understanding fluid-rock interaction in the presence of microbial organisms using advanced 4D imaging techniques. The outcomes of this PhD project will be incorporated into a team-effort to predict the impact of microbial organisms on rock properties and develop smart bio-conservation strategies. The PhD project will develop a protocol for biofilm visualization inside rock by applying X-ray tomography. Via advanced imaging techniques, correlative microscopy strategies with next-generation automated electron microscopy and 4D micro-CT a better understanding into the bacteria-induced pore scale processes will be obtained. Therefore, pathfinder materials will be fully characterized using advanced imaging techniques and lab measurements. After application of specific bacteria on these pathfinder stones in the lab, the induced bio-activity will be characterized.

The PhD candidate will engage in a trans-disciplinary research environment by closely collaborating with two postdoctoral fellows and one other PhD student, who are all part of the BugControl project and numerous PhD students and Postdoctoral fellows working in the field of advanced imaging techniques and pore scale processes. Fieldwork campaigns are planned to take place in The Netherlands and Belgium. Advanced imaging is planned in Belgium and at the synchrotron facilities in Switzerland (SLS-PSI) and France (ESRF). As such, the PhD candidate will be co-supervised by a professor from the Centre for X-ray imaging (UGCT), Belgium, and a minimum research visit of a total of 6 months at Ghent University is anticipated. A personalised training programme will be set up, which will reflect the candidate's training needs and career objectives. As part of this training, up to 10% of the candidate's time will be dedicated to assisting in Bachelor's and Master's teaching programmes.


Utrecht University


We are seeking a PhD candidate with a Master's degree (obtained by the time the position starts) in geology, sciences, engineering or bioengineering with a strong interest in advanced image processing techniques and/or image processing and analysis. Experience in earth sciences with a demonstrable affinity for natural stones, microstructural analysis, and geochemistry is a plus. The applicant must have good practical lab skills and is ideally familiar with advanced imaging techniques. Moreover, the applicant should have excellent written and spoken English skills and be highly motivated to work in an international multidisciplinary team.

Conditions of employment

You will be offered a temporary PhD position (1.0 FTE), initially for one year with an extension to a total of four years upon a successful assessment in the first year, and with the specific intent that it results in a doctorate within this period. The gross salary ranges between €2,434 in the first year and €3,111 in the fourth year of employment (scale P according to the Collective Labour Agreement Dutch Universities) per month for a full-time employment. Salaries are supplemented with a holiday bonus of 8% and a year-end bonus of 8.3% per year. In addition, Utrecht University offers excellent secondary conditions, including an attractive retirement scheme, (partly paid) parental leave and flexible employment conditions (multiple choice model). More information about working at Utrecht University can be found here.


A better future for everyone. This ambition motivates our scientists in executing their leading research and inspiring teaching. At Utrecht University, the various disciplines collaborate intensively towards major societal themes. Our focus is on Dynamics of Youth, Institutions for Open Societies, Life Sciences and Sustainability.
Utrecht University's Faculty of Geosciences studies the Earth: from the Earth's core to its surface, including man's spatial and material utilisation of the Earth - always with a focus on sustainability and innovation. With 3,400 students (BSc and MSc) and 720 staff, the Faculty is a strong and challenging organisation. The Faculty of Geosciences is organised in four Departments: Earth Sciences, Human Geography & Spatial Planning, Physical Geography, and Sustainable Development.

The Department of Earth Sciences conducts teaching and research across the full range of the solid Earth and environmental Earth sciences, with activities in almost all areas of geology, geochemistry, geophysics, biogeology and hydrogeology. The department hosts a highly international tenured staff of over 45 scientists and more than 110 PhD students and postdoctoral researchers. Our research programme spans four intertwined themes: Climate & Life, Earth interior, Earth materials, and Environmental Earth Sciences. We house or have access to a wide variety of world-class laboratories.

The PhD project is based within the Environmental Hydrogeology Group. The Environmental Hydrogeology Group performs fundamental and applied research on the transport of fluids, colloids, and reactive chemical components in the shallow and deep subsurface. We apply a combination of theoretical, statistical, computational, and experimental methods to upscale processes from micro (pore) scale to column, and up to the field scale. Our work is related to environment and subsurface remediation, geo‑resources, and CO2 storage. The generated knowledge on upscaling in porous materials is highly cross disciplinary fostering collaborations with many scientific groups from (Earth) Science, applied research, as well as industrial partners.


  • PhD
  • Natural sciences
  • 36—40 hours per week
  • max. €2434 per month
  • University graduate
  • 1173752



Domplein 29, 3512 JE, Utrecht

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