Final Report Summary - MICRODEGRADE (Identifying and Overcoming Bottlenecks of Micropollutant Degradation at Low Concentrations)
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 (ug/L) concentrations. When enzyme-associated isotope effects were observable, this provided evidence that molecules could diffuse freely into and out of bacterial cells demonstrating that mass transfer was not limiting. In contrast, if isotope fractionation was pronounced at high concentrations, but isotope effects were masked at trace levels, this provided evidence that mass transfer into and out of the cell became limiting for biodegradation specifically at low concentrations (Ehrl et al., Environ. Sci. Technol. 2019, Marozava et al. Environ. Sci. Technol. 2019).
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 ug/L in chemostat (Ehrl et al. Environ. Sci. Technol., 2019, Gharasoo et al. Environ. Sci. Technol., 2019) with complete rate control at 10 ug/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).
CSIA also demonstrated the existence of mass transfer limitations in a quasi-two dimensional sediment tank system mimicking realistic conditions in a natural aquifer. High, unmasked isotope fractionation in the center of the plume indicated that 2,6-dichlorobenzamide degradation by Aminobacter sp. MSH1 was unlimited with respect to substrate, but limited by supply of oxygen. In contrast, reactive transport modelling of masked isotope fractionation pinpointed mass transfer limitations during cellular uptake as rate-determining step in degradation of 2,6-dichlorobenzamide towards the lower end of the concentration profile. (Sun et al., in communication) In parallel, dedicated diffusion and dispersion experiments could exclude the possibility of artefacts from isotope effects of aqueous diffusion and dispersion. This suggests that the potential influence of aqueous diffusion on isotope profiles in contaminant hydrology has been exaggerated in recent years (Sun et al., in communication).
For bioremediation approaches of low-level concentrations, the direct observation of limitations offers an enabling tool to identify the relevant bottlenecks. Pillaring on this, we found that fluctuations in concentrations are generally faster than build-up and decay of degrader biomass, yet can profoundly influence bacterial adaptation and diversification (Kundu et al., Environ. Microbiol. 2020). Hence, variations in substrate concentrations and flow conditions may be a promising remediation approach.
With the ability to directly observe mass transfer limitation, and to characterize associated physiological adaptation MicroDegrade has introduced a novel analytical approach to the investigation of microbial activity at low concentrations. It also brings forward a mechanistic explanation for the “persistence by dilution” hypothesis: that low-level water constituents such as NOM may not persistent because of inherent recalcitrance, but because of low concentrations. For Isotope Biogeochemistry the project’s findings have pronounced implications for the interpretation of isotope profiles at low concentrations: they imply that, based on isotopic evidence, turnover of substances at low concentrations may have been underestimated so far.
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 ug/L in chemostat (Ehrl et al. Environ. Sci. Technol., 2019, Gharasoo et al. Environ. Sci. Technol., 2019) with complete rate control at 10 ug/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).
CSIA also demonstrated the existence of mass transfer limitations in a quasi-two dimensional sediment tank system mimicking realistic conditions in a natural aquifer. High, unmasked isotope fractionation in the center of the plume indicated that 2,6-dichlorobenzamide degradation by Aminobacter sp. MSH1 was unlimited with respect to substrate, but limited by supply of oxygen. In contrast, reactive transport modelling of masked isotope fractionation pinpointed mass transfer limitations during cellular uptake as rate-determining step in degradation of 2,6-dichlorobenzamide towards the lower end of the concentration profile. (Sun et al., in communication) In parallel, dedicated diffusion and dispersion experiments could exclude the possibility of artefacts from isotope effects of aqueous diffusion and dispersion. This suggests that the potential influence of aqueous diffusion on isotope profiles in contaminant hydrology has been exaggerated in recent years (Sun et al., in communication).
For bioremediation approaches of low-level concentrations, the direct observation of limitations offers an enabling tool to identify the relevant bottlenecks. Pillaring on this, we found that fluctuations in concentrations are generally faster than build-up and decay of degrader biomass, yet can profoundly influence bacterial adaptation and diversification (Kundu et al., Environ. Microbiol. 2020). Hence, variations in substrate concentrations and flow conditions may be a promising remediation approach.
With the ability to directly observe mass transfer limitation, and to characterize associated physiological adaptation MicroDegrade has introduced a novel analytical approach to the investigation of microbial activity at low concentrations. It also brings forward a mechanistic explanation for the “persistence by dilution” hypothesis: that low-level water constituents such as NOM may not persistent because of inherent recalcitrance, but because of low concentrations. For Isotope Biogeochemistry the project’s findings have pronounced implications for the interpretation of isotope profiles at low concentrations: they imply that, based on isotopic evidence, turnover of substances at low concentrations may have been underestimated so far.