Modeling mICRObial LIFE in Polluted AQuiferS

Project Information

MICROLIFEPAQS

Grant agreement ID: 101064993

DOI

10.3030/101064993

Project closed

EC signature date 17 August 2022

Start date 1 October 2022

End date 31 October 2024

Funded under

• Marie Skłodowska-Curie Actions (MSCA)

Total cost

No data

EU contribution

€ 187 624,32

Coordinated by

TECHNISCHE UNIVERSITEIT DELFT
Netherlands

Periodic Reporting for period 1 - MICROLIFEPAQS (Modeling mICRObial LIFE in Polluted AQuiferS)

Reporting period: 2022-10-01 to 2024-10-31

Summary of the context and overall objectives of the project

The MICROLIFEPAQS project (Modelling mICRObial LIFE in Polluted AQuiferS) addressed one of the pressing environmental challenges of our time: groundwater pollution. Groundwater contamination by industrial pollutants, such as chlorinated ethenes, poses risks to human health and ecosystems. Natural biological processes, driven by microorganisms capable of breaking down these pollutants (e.g. Dehalococcoides), offer a promising solution. However, understanding and predicting the behaviour of these microorganisms in complex groundwater systems is challenging.
The MICROLIFEPAQS project aimed at developing a new modeling approach to assess and optimize chlorinated ethene biodegradation in groundwater. By integrating advanced molecular biological data into numerical Reactive Transport Models (RTMs), the project sought to link chlorinated ethene biodegradation to functional gene expression and reductive dehalogenase enzyme production in Dehalococcoides, which were considered both mobile and immobile in saturated porous media. This innovative method allows for more accurate simulations of how degrading bacteria interact with chlorinated ethenes in groundwater, enabling better design and monitoring of remediation strategies.
Scientific specific objectives were defined to meet the overall aim of the project:

1) To compile and homogenize existing data into a comprehensive database and define a detailed conceptual model of the evolution of chlorinated ethene contamination in the selected case study.

2) To collect and analyze groundwater samples and perform molecular biological analyses to quantify target biomarkers.

3) To develop and integrate a kinetic model into RTMs to simulate chlorinated ethene biodegradation.

The following non-scientific specific objectives were additionally considered to ensure successful MICROLIFEPAQS project implementation and maximise its impact at different levels:

4) To disseminate findings effectively to maximize scientific and societal impact.

5) To manage and coordinate activities for successful project implementation.

The MICROLIFEPAQS project aligns with the European Union’s “Zero Pollution for Air, Water and Soil” Action Plan and the United Nations’ Sustainable Development Goals, striving to contribute to pollution elimination by 2050 and 2030, respectively.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

Over the course of the project, significant progress was made in all scientific and non-scientific specific objectives, through the activities carried out in the different work packages (WPs).

1. Data Integration and Conceptual Modelling (WP1). Existing datasets were reviewed, merged, and homogenised into a comprehensive database. This included hydrogeological, chemical, and molecular biological data from the Grindsted plume, the selected case study. Based on the created dataset, it was possible to develop a detailed conceptual model of the chlorinated ethene contamination evolution in the Grindsted plume (i.e. the selected case study), which was essential for the Grindsted plume's RTM implementation.

2. Chemical and Molecular Biological Analysis of Groundwater Samples (WP2). Groundwater samples were collected and analysed to assess microbial activity and chemical changes within the aquifer. Advanced molecular techniques, such as quantitative polymerase chain reaction (qPCR) and reverse transcription qPCR (RT-qPCR), were used to quantify DNA and RNA of targeted bacteria and functional genes involved in chlorinated ethene degradation. These analyses identified key biomarkers linked to the biotic reductive dechlorination of chlorinated ethenes, providing critical input for model development. These newly collected molecular biological and chemical data were used to calibrate the RTM simulating the Grindsted plume.

3. Modelling Approach Implementation (WP3). The project introduced a novel kinetic model, Enzyme-Based Kinetics (EBK), which links reductive dechlorination of chlorinated ethenes to functional gene expression. This modelling approach was incorporated into RTMs to simulate groundwater contamination under field conditions. Moreover, it was also was successfully applied to the Grindsted plume, demonstrating how environmental factors influence pollutant breakdown.

4. Dissemination and Communication (WP4). Research findings were widely shared through high-impact scientific papers, oral and poster presentations at international conferences, communication papers, and social media.

5. Project Management (WP5). The project was implemented successfully, with regular meetings, efficient coordination among international collaborators, and careful oversight of financial and administrative aspects.

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

Within the MICROLIFEPAQS project, new Enzyme-Based Kinetics linking RDase functional expression in Dehalococcoides to chlorinated ethene biodegradation were developed. The model introduces key features that were never incorporated in previous attempts, making it more flexible: (i) the presence of homologous functional genes expressed by different Dehalococcoides strains at a community level, (ii) nonunique transcription regulation mechanisms in chlorinated ethene-respiring bacteria, and (iii) degrading explicitly growing on multiple chlorinated ethenes. Furthermore, these kinetics were successfully integrated for the first time into full-aquifer-scale 1D RTMs simulating chlorinated ethene plumes, additionally considering the partitioning of Dehalococcoides the solid and aqueous phase, as experimentally observed in the literature. To test this novel modelling approach, molecular biological analyses were performed on newly collected groundwater samples from the test site (i.e. the Grindsted plume). These data were used to implement and calibrate the 1D RTM of the Grindsted plume, which was used to interpret for the first time the observed chemical and biomarker patterns and allowed providing insights into the effect of local field condition on Dehaloccoccoides ecological strategy, metabolic regulation dynamics, and biotic reductive dechlorination efficiency.
Key scientific innovations include:

1) The development of EBK, a flexible model linking chlorinated ethene biodegradation to specific metabolic functions (i.e. functional gene expression and enzyme production) in Dehalococcoides.

2) Successful integration in RTMs simulating chlorinated ethene plumes' evolution

3) Successful application of this modeling approach to a real case study, such as the Grindsted plume.

4) Insights into how environmental conditions, such as nutrient availability, chemical gradients, and aquifer hydrodynamics, influence microbial activity and biotic chlorinated ethene breakdown.

These advancements have implications for both science and society. For researchers, the models provide a powerful tool to study and predict biotic degradation processes in contaminated sites, especially reductive dechlorination. For specialists, they offer a robust modeling framework to design and optimize remediation strategies. On a broader scale, the project aligns with the European Union and United Nations’ objectives to eliminate environmental pollution in the next future. By enhancing our ability to manage and remediate polluted groundwater, MICROLIFEPAQS contributes to safer water resources, healthier ecosystems, and improved quality of life. Through its interdisciplinary approach and innovative outcomes, MICROLIFEPAQS sets a new benchmark for environmental research, paving the way for future advancements in hydrobiogeochemical reactive transport modelling.