Two-dimensional flow-through microcosms - Versatile test systems to study biodegradation processes in porous aquifers

Robert D. Bauer, Massimo Rolle, Petra Kuerzinger, Peter Grathwohl, Rainer U. Meckenstock, Christian Griebler

Research output: Contribution to journalJournal articleResearchpeer-review


A fundamental prerequisite of any remedial activity is a sound knowledge of both the biotic and abiotic processes involved in transport and degradation of contaminants. Investigations of these aspects in situ often seem infeasible due to the complexity of interacting processes. A simplified portrayal of nature can be facilitated in laboratory-based two-dimensional (2D) sediment flow-through microcosms. This paper describes the versatility of such simple aquifer model systems with respect to biodegradation of aromatic hydrocarbons, i.e. toluene and ethylbenzene, under various environmental conditions. Initially constructed to study non-reactive and bioreactive transport of organic contaminants in homogeneous porous media under steady state hydraulic conditions, experimental setups developed towards more realistic heterogeneous sediment packing and transient hydraulic conditions. High-resolution spatial and temporal sampling allowed to obtain new insights on the distribution of bioactivities in contaminant plumes and associated controlling and limiting factors. Major biodegradation activities in saturated porous sediments are located at the fringes of contaminant plumes and are driven by dispersive mixing. These hot-spots of contaminant biotransformation are characterized by steep physical-chemical gradients in the millimeter to centimeter range. Sediment heterogeneity, i.e. high-conductivity zones, was shown to significantly enhance transverse mixing and subsequently biodegradation. On the contrary, transient hydraulic conditions may generate intermediate disturbances to biodegrader populations and thus may interfere with optimized contaminant conversion. However, a bacterial strain aerobically degrading toluene, i.e. Pseudomonas putida F1, was shown to adapt to vertically moving contaminant plumes, in the way that it regained full biodegradation potential two-times faster in areas with a midterm (days to weeks) contamination history than in areas not contaminated before. The 2D flow-through microcosms facilitated to combine a number of physicochemical and microbiological methods, such as high-resolution non-invasive oxygen measurements, conservative tracer tests, compound-specific isotope analysis (CSIA), fluorescence in situ hybridization (FISH), and numerical transport modelling, to name a few. Moreover, due to the defined and well-controlled operating conditions, these bench-scale flow-through systems allow to investigate theoretical concepts and to develop and test predictive models. They represent a valuable tool in helping to bridge the current knowledge gap concerning transport and degradation of contaminants in groundwater from the small-scale (i.e. oversimplified batch systems, disregarding transport processes) to the highly complex field conditions. The promising potential of applications is by far not exhausted. Further possibilities include testing ecological theories such as the resource-ratio theory, island biogeography, area-species richness relationships and relations between community structure, microbial abundance and process rates as well as the importance and effects of bacterial chemotaxis. (C) 2009 Elsevier B.V. All rights reserved.
Original languageEnglish
JournalJournal of Hydrology
Issue number3-4
Pages (from-to)284-295
Number of pages12
Publication statusPublished - 2009
Externally publishedYes


  • Water Science and Technology
  • 2D flow-through system/microcosm
  • Biodegradation
  • Mixing-controlled reactive transport
  • Monoaromatic hydrocarbons
  • Natural attenuation
  • Transverse dispersion
  • Aquifer models
  • Bacterial chemotaxis
  • Bacterial strains
  • Batch systems
  • Biodegradation potentials
  • Biodegradation process
  • Chemical gradients
  • Community structures
  • Complex fields
  • Compound-specific isotope analysis
  • Conservative tracers
  • Contaminant plumes
  • Dispersive mixing
  • Ecological theories
  • Environmental conditions
  • Experimental set-up
  • Flow-through
  • Flow-through systems
  • Fluorescence in situ hybridizations
  • Heterogeneous sediments
  • High resolutions
  • High-conductivity zones
  • Homogeneous porous medias
  • Hot-spots
  • Hydraulic conditions
  • In-situ
  • Interacting process
  • Intermediate disturbances
  • Island biogeographies
  • Knowledge gaps
  • Limiting factors
  • Microbiological methods
  • Non-invasive
  • Numerical transports
  • Operating conditions
  • Organic contaminants
  • Oxygen measurements
  • Porous sediments
  • Predictive models
  • Pseudomonas putida F1
  • Species richness
  • Steady state
  • Temporal samplings
  • Test systems
  • Transport process
  • Transverse mixing
  • Two-dimensional flows
  • Aquifers
  • Aromatic hydrocarbons
  • Bacteriology
  • Biochemistry
  • Contamination
  • Degradation
  • Ethylbenzene
  • Fluorescence microscopy
  • Forestry
  • Fullerenes
  • Groundwater pollution
  • Groundwater resources
  • Hydraulics
  • Hydrogeology
  • Impurities
  • Numerical methods
  • Organic compounds
  • Oxygen
  • Porous materials
  • Sedimentology
  • Toluene
  • Two dimensional
  • aquifer
  • biodegradation
  • microcosm
  • mixing
  • organic pollutant
  • plume
  • remediation
  • sediment transport
  • testing method
  • two-dimensional flow
  • Bacteria (microorganisms)
  • Pseudomonas putida
  • area-species richness relationship
  • bacteria] chernotaxis
  • bioreactive transport
  • groundwater
  • island biogeography
  • microbial abundance
  • resource-ratio theory
  • sediment heterogeneity
  • transient hydraulic condition
  • Gram-Negative Aerobic Rods and Cocci Eubacteria Bacteria Microorganisms (Bacteria, Eubacteria, Microorganisms) - Pseudomonadaceae [06508] Pseudomonas putida species strain-F1, strain-mt-2
  • Microorganisms (Bacteria, Eubacteria, Microorganisms) - Bacteria [05000] Aromatoleum aromaticum species strain-EbN1
  • contaminant pollutant biotransformation
  • ethylbenzene 100-41-4 pollutant aromatic hydrocarbon
  • toluene 108-88-3 pollutant aromatic hydrocarbon
  • 04500, Mathematical biology and statistical methods
  • 10060, Biochemistry studies - General
  • 10515, Biophysics - Biocybernetics
  • 31000, Physiology and biochemistry of bacteria
  • 37015, Public health - Air, water and soil pollution
  • 39008, Food microbiology - General and miscellaneous
  • Computational Biology
  • aquifer model system mathematical and computer techniques
  • biodegradation process applied and field techniques
  • compound-specific isotope analysis CSIA laboratory techniques
  • conservative tracer test laboratory techniques
  • fluorescence in situ hybridization FISH laboratory techniques, genetic techniques
  • high-resolution non-invasive oxygen measurement laboratory techniques
  • numerical transport modelling mathematical and computer techniques
  • physicochernical method laboratory techniques
  • two-dimensional flow-through microcosm mathematical and computer techniques
  • Bioprocess Engineering
  • Models and Simulations
  • Pollution Assessment Control and Management

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