Elucidating the impact of micro-scale heterogeneous bacterial distribution on biodegradation

Research output: Contribution to journalArticlepeer-review


Colleges, School and Institutes

External organisations

  • Department of Biotechnology, Faculty of Applied Sciences, Delft University of Technology
  • Department of Environmental Microbiology, UFZ – Helmholtz Centre for Environmental Research


Groundwater microorganisms hardly ever cover the solid matrix uniformly–instead they form micro-scale colonies. To which extent such colony formation limits the bioavailability and biodegradation of a substrate is poorly understood. We used a high-resolution numerical model of a single pore channel inhabited by bacterial colonies to simulate the transport and biodegradation of organic substrates. These high-resolution 2D simulation results were compared to 1D simulations that were based on effective rate laws for bioavailability-limited biodegradation. We i) quantified the observed bioavailability limitations and ii) evaluated the applicability of previously established effective rate concepts if microorganisms are heterogeneously distributed. Effective bioavailability reductions of up to more than one order of magnitude were observed, showing that the micro-scale aggregation of bacterial cells into colonies can severely restrict the bioavailability of a substrate and reduce in situ degradation rates. Effective rate laws proved applicable for upscaling when using the introduced effective colony sizes.


Original languageEnglish
JournalAdvances in Water Resources
Early online date31 Jan 2018
Publication statusE-pub ahead of print - 31 Jan 2018


  • Bioavailability, Effective rate laws, Pore-scale microbial degradation, Upscaling