ERC MicroDegrade: Insight from Chemostat Experiments and Simulation (Work package 1)

With compound-specific isotope fractionation analysis (CSIA) of chemical trace contaminants (“micropollutants”) the ERC project MicroDegrade could break ground in revealing bottlenecks of degradation at low, relevant (mg/L) concentrations. As diagnostic tool, this masking of isotope fractionation could detect that cell wall permeation may (Ehrl et al. Environ. Sci. Technol. 2018a) or may not be rate-determining compared to enzyme kinetics depending on whether contaminant concentrations were high (mg/L range) and the membrane was sufficiently permeable (Ehrl et al. Environ. Sci. Technol. 2018b). Specifically, mass transfer of atrazine through the bacterial membrane of Arthrobacter aurescens TC1 became rate-determining for biodegradation below 60 mg/L in chemostat (Ehrl et al. Environ. Sci. Technol., 2019, Gharasoo et al. Environ. Sci. Technol., 2019) with complete rate control at 10 mg/L in retentostat (Kundu et al., ISME J. 2019). Proteomics revealed that this mass transfer limitation served as trigger for physiological adaptation, where catabolic enzymes remained highly expressed, whereas other cellular functions were downregulated. Fluorescent staining experiments with flow cytometric readout further provided evidence of phenotypic diversification (Kundu et al., Environ. Microbiol. 2020).


  • K. Fenner, M. Elsner, T. Lueders, M. McLachlan, L. Wackett, M. Zimmermann, J. Drewes, Methodological advances to study contaminant biotransformation: new prospects for understanding and reducing environmental persistence?, ACS ES+T Water (2021), accepted.
  • F. Sun, A. Mellage, M. Gharasoo, A. Melsbach, X. Cao, R. Zimmermann, C. Griebler, M. Thullner, O. Cirpka, M. Elsner, Mass Transfer-Limited Biodegradation at Low Concentrations – Evidence from Reactive Transport Modeling of Isotope Profiles in a Bench-Scale Aquifer, Environ. Sci. Technol. 55 (2021), pp. 7386–7397;
    DOI: (b)
  • F. Sun, J. Peters, M. Thullner, O. A. Cirpka, M. Elsner, Magnitude of Diffusion- and Transverse Dispersion-Induced Isotope Fractionation of Organic Compounds in Aqueous Systems, Environ. Sci. Technol. 55 (2021), pp. 4772–4782; DOI: 10.1021/acs.est.0c06741 (a)
  • K. Kundu, Nina Weber, Ch. Griebler, M. Elsner, Phenotypic heterogeneity as key factor for growth and survival under oligotrophic conditions, Environmental Microbiology 22 (2020), pp. 3339-3356,DOI: 10.1111/1462-2920.15106
  • S. Marozava, A. Meyer, A. Perez-de-Mora, M. Gharasoo, L. Zhuo, H. Wang, O. Cirpka, R. Meckenstock, and M. Elsner, Mass Transfer Limitation During Slow Anaerobic Biodegradation of 2-Methylnaphthalene, Environ. Sci. Technol. 53 (2019) pp. 9481-9490, DOI:10.1021/acs.est.9b01152
  • K. Kundu, S. Marozava, B. Ehrl, J. Merl-Pham, Ch. Griebler, M. Elsner, Defining lower limits of biodegradation – atrazine degradation regulated by mass transfer and maintenance demand in Arthrobacter aurescens TC1, The ISME Journal 13 (2019) pp. 2236–2251 DOI: 10.1038/s41396-019-0430-z
  • B. Ehrl, K. Kundu, M. Gharasoo, S. Marozava, M. Elsner, Rate-Limiting Mass Transfer in Micropollutant Degradation Revealed by Isotope Fractionation in Chemostat, Environ. Sci. Technol. 53 (2019) pp. 1197–1205, DOI: 10.1021/acs.est.8b05175
  • M. Gholami Gharasoo, B. Ehrl, O. Cirpka, M. Elsner, Modeling of contaminant biodegradation and compound-specific isotope fractionation in chemostats at low dilution rates, Environ. Sci. Technol. 53 (2019) pp. 1186–1196, DOI: 10.1021/acs.est.8b02498
  • B.N. Ehrl, E.O. Mogusu, K. Kim, H. Hofstetter, J.A. Pedersen, M. Elsner, High Permeation Rates in Liposome Systems Explaining Glyphosate Biodegradation Associated with Strong Isotope Fractionation, Environ. Sci. Technol. 52 (2018), pp. 7259-7268, DOI: 10.1021/acs.est.8b01004
  • B.N. Ehrl, M. Gharasoo, M. Elsner, Isotope Fractionation Pinpoints Membrane Permeability as a Barrier to Atrazine Biodegradation in Gram-negative Polaromonas sp. NeaC, Environ. Sci. Technol. 52 (2018), pp. 4137-4144, DOI: 10.1021/acs.est.7b06599
  • M. Elsner, G. Imfeld, Compound-specific Isotope Analysis (CSIA) of Micropollutants in the Environment - Current Developments and Future Challenges; Current Opinion in Biotechnology, 41 (2016) pp 60–72, (invited contribution to the special issue: “Analytical Biotechnology, Stable Isotope Probing”)