DeepThought: Evaluating nitrate transformation in aquifers using microbiological, molecular and isotopic tools

Nitrates are a major pollutant threatening groundwater quality worldwide. However, their impact can be mitigated by in situ denitrification. Co-ordinated by BRGM and funded under the 2023 Water4All call for proposals, the DeepThought project, which began in April 2025, focuses on assessing nitrate transformation in aquifers to improve the management of key groundwater ecosystem services.

24 September 2026

The DeepThought project focuses on assessing nitrate transformation in aquifers using microbiological, molecular and isotopic tools, with a view to improving the management of key groundwater ecosystem services.

Coordinated by BRGM and funded under the 2023 Water4All call for proposals on aquatic ecosystem services, the project began in April 2025 and will run for three years. The main objective is to understand the mechanisms that optimise denitrification in aquifers and to assess the impacts of human activities and climate change on this ecosystem service provided by the microbial communities found in the water.

Challenges

Aquifers are the main source of drinking water for people worldwide. This use of groundwater relies on ecosystem services provided by aquifers. Among these, natural water purification is a fundamental ecosystem service, which, in particular, mitigates the increase in pollutants released into groundwater as a result of human activities. To date, this service has been given insufficient consideration in aquifer management and regulatory policies, as illustrated by the case of nitrates. Nitrates are a major pollutant threatening groundwater quality on a worldwide scale. However, their impact can be mitigated by in situ denitrification.

Although denitrification under (micro)aerobic conditions has been described, the process occurs mainly in the anoxic environments of soils and aquifers. The groundwater denitrifying community, which breaks down nitrates, thus plays an active role in water purification and constitutes a relevant Nature-based Solution (NbS). Research in this field has highlighted key issues, which the DeepThought project will help to address and which will enhance our understanding of how to detect, protect, improve and, consequently, manage in situ denitrification in order to improve the health of underground ecosystems, thereby contributing to the provision of groundwater ecosystem services.

Concepts from the DeepThought project.

Objectives

DeepThought aims to understand the mechanisms underlying denitrification in groundwater and to assess the impacts of stress factors (both anthropogenic and climate change-related) on denitrification rates. This will provide a set of holistic tools for improved aquifer management. The shared objective will be achieved through the use of microbiological, hydrogeological, geochemical and isotopic approaches, combined with laboratory experiments, in situ sampling at three study sites representing different contexts, and engagement with key stakeholders through workshops in each country.

DeepThought’s five specific objectives are as follows:

Identify the microbial communities responsible for denitrification and quantify their potential and activity in situ;
Link denitrification processes to hydrogeological and biogeochemical conditions and variations;
Examine and compare the diversity of denitrifying bacteria and their activities at oxic-anoxic interfaces;
Identify the stress factors (anthropogenic and climate change-related) and their impacts on denitrification, drawing on data from four test sites representing different land uses and pressures;
Provide and integrate new indicators combining biogeochemical and isotopic measurements in order to improve the management of aquifers with regard to nitrate contamination.

Contexts of the study sites within the DeepThought project.

Research programme

The project consists of four tasks. The first task focuses on coordination, project management, and communication; two tasks are dedicated to technical work, one addressing the microbiological and isotopic tools used in the project, and the other addressing in situ and laboratory assessments of the impacts of environmental pressures on denitrification. Finally, the last task is dedicated to interactions with stakeholders and the prospects for integrating the studied tools into water monitoring policies.

All of the work is based on three study sites, one in each partner country, each addressing different issues.

BRGM’s role

BRGM is the project coordinator and is responsible for integrating the protocols into the monitoring of groundwater quality. The Groundwater Quality and near-surface aquifer teams from the Water Directorate, as well as the microbiologists from our P2M team (innovative processes for mineral materials) and the microbiology unit, are involved in the project. The study site in France is the Beauce aquifer, located to the south and east of Pithiviers, at the interfaces between different geological formations in the subsurface (both confined and unconfined aquifers) and between the forest of Orléans and areas of intensive agriculture. Teams there are studying microbial diversity and activity in relation to the nitrogen cycle over time and in different contexts. As part of this project, a PhD programme began in October 2025 and a two-year post-doctoral contract began in April 2026.