Geomicrobial Reactive Transport Systems:
Model Development and Environmental Applications
(GReaT MoDE)

Research Group Geomicrobial Reactive Transport Systems
Stephan Richter, Ali Mongol, Shuang Jin, Sara König, Florian Centler, Martin Thullner, Falk Heße, Alexandros Stefanakis (from left to right)

Research Topics

Reactive transport models have emerged as an essential diagnostic tool for the quantitative analysis of the biogeochemical functioning of complex subsurface environments. In particular, these models are crucial for the assessment of the fate biodegradable compounds and the interpretation of the distribution of reactive chemical species in e.g., groundwater aquifers, soils or aquatic sediments.

Besides their function as a diagnostic tool, reactive transport models also provide a platform for testing hypotheses derived from experimental observations or from the theoretical knowledge of biological, chemical or physical processes. Therefore, these models bridge the gap between fundamental, process-oriented research and applied research, along with the gap between results from laboratory experiments and observations in the field.

Nonetheless, existing reactive transport modeling concepts would benefit from several novel lines of approach including the development of realistic model representations of microbial reaction kinetics and microbially-driven reaction networks, the description of scale dependent mixing processes and appropriate considerations of chemical, biological plus physical heterogeneities at various length scales.

It is the aim of this research group to address these challenges by developing advanced modeling concepts and tools for the simulation of reactive transport processes in porous media systems. The emphasis is on microbially driven processes (e.g., biodegradation organic compounds) and the link between microbial activity and chemical transformation rates.

Own model developments

GeoSysBRNS A highly flexible simulation tool for modeling reactive transport processes in subsurface environments

PNBRNS A pore network model for the simulation of reactive transport processes in heterogeneous pore structures


DFG funded CRC (Phase 2: 2017-

  • Exploratory Modeling of Water and Biogeochemical Dynamics in the Earth’s Critical Zone

Controlling Chemicals' Fate
UFZ funded (2012-

  • Modeling microbial degradation in soils
  • Functional resilience of contaminant degradation under the influence of environmental stress

Phenols in Wetlands
BP funded (2012-2013)

  • Wetland systems for wastewater treatment

Higrade fellowship
UFZ funded (2010-2013)

  • Determining the influence of metabolic pathway interactions on the contaminant degradation performance of microbial multi-species consortia

Junior Research Group 'GReaT MoDE'
HGF funded (2007-2013)

  • Development a three-dimensional geomicrobial reaction network model
  • More realistic microbial reaction networks including e.g., diversity, physiological state and ecological interactions of microorganisms
  • Model approaches for the simulation of stable isotope signals in complex environmental systems

UFZ funded (2007-2013)

  • Numerical modeling and experimental investigation of the biodegradation of volatilized groundwater contaminants
  • Modeling the interaction between physical, chemical and microbial processes in constructed wetlands

KAUST-GRP funded (2008-2011)

  • Reactive transport modeling of biodegradation processes in coastal aquifers
  • Pore scale simulation of microbial processes and their upscaling to the continuum scale

Selected Publications

König, S., Worrich, A., Centler, F., Wick, L.Y., Miltner, A., Kästner, M., Thullner, M., Frank, K., Banitz, T., (2017): Modelling functional resilience of microbial ecosystems: analysis of governing processes
 Environ. Modell. Softw. 89 , 31 - 39

Alvarez-Zaldívar, P., Centler, F., Maier, U., Thullner, M., Imfeld, G. (2016): Biogeochemical modelling of in situ biodegradation and stable isotope fractionation of intermediate chloroethenes in a horizontal subsurface flow wetland Ecol. Eng. 90 , 170 - 179

Khan, A.M., Wick, L.Y., Harms, H., Thullner, M. (2016): Biodegradation of vapor-phase toluene in unsaturated porous media: Column experiments Environ. Pollut. 211 , 325 - 331

Stefanakis, A.I., Seeger, E., Dorer, C., Sinke, A., Thullner, M. (2016): Performance of pilot-scale horizontal subsurface flow constructed wetlands treating groundwater contaminated with phenols and petroleum derivatives Ecol. Eng. 95 , 514 - 526

Stolpovsky, K., Fetzer, I., van Cappellen, P., Thullner, M. (2016): Influence of dormancy on microbial competition under intermittent substrate supply: insights from model simulations FEMS Microbiol. Ecol. 92 (6), fiw071

Centler, F., Thullner, M. (2015): Chemotactic preferences govern competition and pattern formation in simulated two-strain microbial communities Frontiers in Microbiology 6 , art. 40

Gharasoo, M., Centler, F., van Cappellen, P., Wick, L.Y., Thullner, M. (2015): Kinetics of substrate biodegradation under the cumulative effects of bioavailability and self-inhibition Environ. Sci. Technol. 49 (9), 5529 - 5537

Heße, F., Prykhodko, V., Attinger, S., Thullner, M. (2014): Assessment of the impact of pore-scale mass-transfer restrictions on microbially-induced stable-isotope fractionation Adv. Water Resour. 74 , 79 - 90

De Biase, C., Carminati, A., Oswald, S.E., Thullner, M. (2013): Numerical modeling analysis of VOC removal processes in different aerobic vertical flow systems for groundwater remediation J. Contam. Hydrol. 154 , 53 - 69

Centler, F., Heße, F., Thullner, M. (2013): Estimating pathway-specific contributions to biodegradation in aquifers based on dual isotope analysis: theoretical analysis and reactive transport simulations J. Contam. Hydrol. 152 , 97 - 116

Thullner, M., Fischer, A., Richnow, H.-H., Wick, L.Y. (2013): Influence of mass transfer on stable isotope fractionation Appl. Microbiol. Biotechnol. 97 (2), 441 - 452

Gharasoo, M., Centler, F., Regnier, P., Harms, H., Thullner, M. (2012): A reactive transport modeling approach to simulate biogeochemical processes in pore structures with pore-scale heterogeneities Environ. Modell. Softw. 30 (1), 102 - 114

Thullner, M., Centler, F., Richnow, H.-H., Fischer, A. (2012): Quantification of organic pollutant degradation in contaminated aquifers using compound specific stable isotope analysis – Review of recent developments Org. Geochem. 42 (12), 1440 - 1460

Stolpovsky, K., Martínez-Lavanchy, P.M., Heipieper, H.-J., van Cappellen, P., Thullner, M. (2011): Incorporating dormancy in dynamic microbial community models Ecol.Model. 222 (17), 3092 - 3102

Centler F., H. Shao, C. De Biase, C.-H. Park, P. Regnier, O. Kolditz and M. Thullner (2010): GeoSysBRNS - A flexible multidimensional reactive transport model for simulating subsurface processes Computers & Geosciences 36 (3), 397-405

Thullner, M. (2010): Comparison of bioclogging effects in saturated porous media within one- and two-dimensional flow systems Ecol.Eng. 36 (2), 176-196

Hesse, F., Harms, H., Attinger, S., Thullner, M. (2010): Linear exchange model for the description of mass transfer limited bioavailability at the pore scale Environ.Sci.Technol. 44 (6), 2064-2071

Thullner M., P. Regnier and P. Van Cappellen (2007): Modeling microbially induced carbon degradation in redox stratified subsurface environments: concepts and open questions Geomicrobiology Journal 24 (3-4), 139-155.