Soil Sampling for Degrading Microbiomes Complete

The initial phase of the MIBIREM project has recently concluded, following the completion of a sampling campaign at contaminated sites across Europe. This phase involved the search for microbiomes capable of degrading organic contaminants. The MIBIREM consortium gathered samples from soil, groundwater, and bac-traps at 13 different contaminated sites in 7 European countries.

The focus was on sites contaminated with cyanides (primarily from former gasworks), petroleum hydrocarbons (PHCs), and lindane (also known as HCH or γ-hexachlorocyclohexane) and its isomers. The samples were analyzed for physical-chemical properties and community composition based on 16S rDNA.

Soil sampling in Rinteln, Germany 2023 by (C) Sensatec

Three different contaminants

Petroleum Hydrocarbons (PHCs) are among the most common contaminants in soil and groundwater in Europe and worldwide. Finding effective microbiomes and gaining a better understanding of the environmental conditions for microbial degradation can help address environmental contamination in many locations.

Although lindane is no longer produced in Europe, localized contamination remains at production and storage sites, requiring remediation due to its high toxicity. Cyanides, previously overlooked in favor of seemingly more critical contaminants, have become a significant problem at many former gasworks across Europe.

Initial microcosm tests with samples from these sites yielded promising results, suggesting that microbiomes with high potential for degrading these contaminants are present.


Author: Thomas Reichenauer,

Scientific Co-ordinator, AIT

Nature-based: new opportunities in soil remediation

Development of and experience with nature-based solutions – Nature-based: new opportunities in soil remediation

A summary of the original article in the Dutch paper ‘Bodem’ (nr. 1, February 2024).

Nature-based solutions (NBS) are a crucial element in making soil and groundwater remediation more sustainable. Considering the approximately 300,000 seriously contaminated sites yet to be remediated in Europe, the use of NBS will be indispensable and will have a positive impact. Some of these techniques have already proven their value over several decades. In recent years, significant investments have been made in new techniques, variations of existing NBS and combinations of NBS with conventional techniques.

In a general sense, NBS offer several advantages over conventional high-tech techniques, such as cost-effectiveness (limited maintenance, lower energy costs, cheaper materials, less waste), reduced environmental impact, opportunities for integration with other themes (climate mitigation, biodiversity, carbon storage), and resilience in remote locations.

(c)TauwNL: Artist impression Natural CatchTAUW (Interreg RESANAT)

Certainly, there are also some focus areas and limitations of NBS, such as larger spatial requirements, longer duration, adaptation to local climates, and fluctuation of efficiency over time. Nevertheless, the exploration of possibilities and deployment of NBS for contaminated soils and surface waters are increasing due to the growing global awareness of the need for sustainability in all our activities (UN SDGs and EU Green Deal). This is evidenced by initiatives such as the EU Soil Strategy 2030 and the international standard ISO 18504 for sustainable remediation.

NBS research and development are financially supported by the EU through programs such as Horizon Europe, Interreg, and LIFE. Examples of these projects involving TAUW include GREENER (2019-2023), RESANAT (2019-2022), POPWAT (2020-2023), and MIBIREM (2022-2027). Additionally, organizations like NICOLE (Network for Industrially Coordinated Sustainable Land Management in Europe), major private stakeholders, and some government agencies (including OVAM in Flanders) are encouraging the adoption of NBS.

(c)TauwNL: Situation constructed wetland as Wetland+TM in Hájek. (Source: LIFE POPWAT, Layman’s report)

NBS aim to utilize and support natural processes, materials, and energy to facilitate the degradation, immobilization, or capture of contaminants. The mechanisms for dealing with contaminants primarily include adsorption, precipitation, biological, chemical, and photochemical degradation, as well as geohydrological isolation. Also NBS consider:

  • Utilizing the natural flow of (ground) water as a driving force for permeable reactive barriers and dispersion of admixtures.
  • Using solar energy in the form of UV radiation for photochemical degradation, heat for increasing biodegradation, and electricity for driving control units/pumps or electrochemical processes.
  • Harnessing wind for creating negative pressure for bioventing or using compressed air for biosparging.
  • Incorporating inert organic materials such as biochar, plant fibers, or peat for adsorption.
  • Employing bacteria and fungi for degradation or immobilization.
  • Utilizing trees, reeds, and other plants for phytoextraction, phytostabilization, or geohydrological control.
  • Leveraging atmospheric oxygen for chemical oxidation or aerobic biodegradation.
  • Using alkaline materials for neutralizing acidic environments, metal precipitation, and biostimulation.

EU projects such as RESANAT, GREENER, and POPWAT, along with other initiatives, have yielded initial results. Promising new NBS approaches are expected to be implemented in practice within 3-5 years, given their positive impact on the dimensions of People, Planet, and Prosperity. It’s time to take them into consideration and give them the space they deserve!


Author: Tobias Praamstra,

Consultant Soil, Groundwater & Sustainability, TAUW


Advancements in lab work thanks to new robot for soil DNA analysis

Healthy ecosystems are vital for biomass, food supply, diverse nature, water management, and human well-being. The EU and Flanders target healthy soils and water bodies, while the Air Policy Plan 2030 aims to cut air pollution’s health impact by 2030. Despite agricultural climate efforts, more research is needed, and rules are enforced for environmental impact reduction.

In this respect, our project partner Sofie Thijs, co-developed the NGSxpress DNA platform together with Interscience, Illumina, Oxford Nanopore, and Filterservice.

(c)CMK- Hasselt University lab and the NGSxpress DNA Platform, Sofie Thijs on the right

The DNA robot

What is this flexible, innovative NGSxpress platform, and what is its purpose?

● It is an automated robot and a long-read sequencer to further develop and expand various new and existing DNA analyses and applications;

● It addresses existing technical bottlenecks in DNA analyses: increasing efficiency, high throughput, accuracy, quality control, and customization;

● It allows for expanding services to Flemish (and international) companies and improving knowledge dissemination. It is a critical success factor for enabling a circular economy and mitigating the effects of climate change.

● With this purchase and installation, VLAIO/EFRO strengthens Flemish DNA expertise with applications in sectors such as healthcare, agriculture, soil biodiversity, and soil remediation.

(c) CMK- Hasselt University: DNA robot

This project is made possible thanks to the support from Europe (EFRO), VLAIO, University of Hasselt-the Centre for Environmental Sciences (CMK), Witteveen+Bos Belgium NV, and Vereecken Farms. Read more here.

Microbiome analysis, cultivation and evolution in the MIBIREM project

Sofie Thijs is a postdoc at Hasselt University, specializing in bioremediation, identification of bioactive compounds, and biotechnological applications. In the MIBIREM project, the Centre for Environmental Sciences (CMK) at Hasselt University is responsible for the microbiome analyses, cultivation, and evolution. In particular, it will use next-generation sequencing to identify bacteria with pollutant-degrading properties, trap and identify active pollutant-degrading bacteria, apply new approaches in cultivation, and improve selected microbial consortia by natural evolution. Lastly, CMK will monitor the microbiomes, bioaugmented strains, and consortia during field pilot tests.


Author: Sofie Thijs

Postdoc at Hasselt University

European Culture Collections’ Organisation ECCO- platform for bioremediation

Culture collections play a vital role in the conservation and sustainable use of microbial resources. They offer a range of services including the supply of quality-controlled biological material for research, teaching and valorisation in the form of reference strains. ECCO, the European Culture Collections’ organisation, organizes annual meetings since the 1980’s. These annual meetings have become a unique European platform for over 80 culture collections to convene and exchange information of scientific, managerial and practical importance.

(c) ECCO XLI in Brussels, September 2023

The objectives of the ECCO conference are to provide a platform to initiate collaborations, to exchange new scientific insights, to discuss legal developments related to culture collections, to provide examples of how culture collections can contribute to society and to discuss developments in management, and policy of microbial cultures. The themes vary widely and address aspects of micro-organisms in disease and health, food and agriculture, ecological applications, new taxonomic tools, and data management, infrastructures, career skills.

(c) Ghent University: MIBIREM at the ECCO XLI in Brussels, in September 2023

ECCO XLI was held in Brussels in September 2023. Peter Vandamme joined ECCO XLI and moderated a session on new techniques and approaches. In the frame of MIBIREM, his team aims to develop quality standards for the preservation and distribution of bioremediation consortia that are able to degrade petroleum hydrocarbons, cyanides and lindane which are all important chemical pollutants. Whilst ECCO XLI came too early to present MIBIREM results, forthcoming ECCO meetings will be a key platform to present and disseminate their findings.


Author: Peter Vandamme

Professor in microbiology

Faculty of Sciences, Ghent University

Soil Mission Week: Connecting People to Soil Health

The European Mission Soil Week Conference, organized by the European Commission’s Directorate-General for Agriculture and Rural Development (DG AGRI), under the Horizon Europe Mission ‘A Soil Deal for Europe’ (Mission Soil), unfolded from November 21 to 23, 2023. Hosted by the Spanish National Research Council (CSIC-INIA) in Madrid during the Spanish Presidency of the EU Council, the event saw the participation of the MIBIREM project, represented by RTDS. MIBIREM focuses on developing biotechnology for soil decontamination using bacteria and was among several soil health projects present at the conference.

The idea behind European Mission Soil Week is to raise awareness about the critical importance of soil health and translate this awareness into actionable measures for soil protection and restoration. The event served as a valuable platform to communicate innovative solutions based on the latest research findings for the promotion of healthy soils. A significant number of participants, both on-site in Madrid and online, represented various stakeholders, including the research community (most numerous), policy makers, farmers, landowners, and industry, with local communities and projects outside the scope of the Soil Health Mission initiative also in attendance.

(c)RTDS: Mission Soil Week Opening, Madrid 21 November 2023

Caring for soil is caring for life

“Caring for soil is caring for life” was a resonating theme throughout the conference. Soil health is a top priority on the EU political agenda – and for good reason. Soil is crucial in supporting human health, providing the basis for food, and sustaining vital ecosystems. Furthermore, healthy soils play a pivotal role in carbon capture, contributing to climate stability and neutrality. Astonishingly enough, approximately 60% of European soil is considered unhealthy, with 2.8 million sites potentially contaminated.

To address these challenges, various European projects, including PrepSoil, InBestSoil, Loess, ISLANDR, Solo, Edaphos, Biosysmo and MIBIREM were brought together to mobilize communities working on diverse aspects related to soil health. Additionally, numerous projects were showcased, sharing experiences, lessons learned and the knowledge gained from research in tackling soil-related issues.

The conference underscored the inseparable connection between healthy soils, food security, and climate. The significance of soil carbon to soil health was highlighted, leading to the inauguration of the international research consortium on soil carbon (IRC).

(c)RTDS: Project community coming together: MIBIREM, Biosysmo, Edaphos and InBestSoil

Speaking simple is a key starting point

Beyond scientific challenges, the conference identified common issues faced by many projects and communities engaged in soil health. Both simplifying language to make it accessible to all stakeholders and bridging the gap between scientific and policy language were emphasized.

Involving local communities more actively and communicating with a wide range of stakeholders were deemed similarly crucial. A bottom-to-top communication approach and a holistic view of the subject were identified as necessary. The importance of engaging citizens in the subject of soil health and involving a broad spectrum of stakeholders was also emphasized as vital for effectively utilizing scientific knowledge.

Knowledge and data sharing on spot

The knowledge gained from research and data sharing were highlighted as essential aspects that need to be properly facilitated. An example of this was the InBestSoil platform initiative, where over 50 participants spontaneously gathered at the venue outskirts to discuss future steps in regular meetings and engagement on data and knowledge-sharing regarding soil health. Stakeholder mapping and engagement, creating synergies in terms of information sharing and joint events were some of the topics discussed.

(c) Graphic visualisation Session Assessing Soil Health: Mission Soil Week in Madrid, 23 November 2023

Another relevant topic highlighted for MIBIREM at the conference was soil assessment and mapping. In the MIBIREM project, soil sampling is conducted within the framework of microbiome-based bioremediation. The conference emphasized the interconnected nature of soil systems, with the suggestion that a simple set of indicators should serve as a starting point. This idea was communicated by the Benchmark project, which focuses on co-creating a Soil Health Monitoring Framework. Moreover, the EU Soil Observatory (EUSO) was thoroughly presented as one of the instruments providing a comprehensive approach to European soil assessment and mapping. The conference also emphasized the need for increased data sharing and harmonization in the context of soil assessment.

What is soil to me

The eventful three days of Soil Mission Week concluded with a ceremony in the grand Spanish royal-style conference hall, featuring a photo competition award. Individuals working on soil-related subjects showcased what soil means to them by visually capturing the beauty of nature, or indeed its vulnerability to factors such as drought, degradation or contamination. This moving conclusion brought the science, funding and policies to a human and personal level, reflecting the intrinsic connection that starts off the entire journey.


Author: Ana Babic

RTDS Group

MIBIREM Communication Manager

Testimonial from the Bioremediation Symposium Battelle in the US

The 2023 Bioremediation Symposium, organized by Battelle and held in Austin on May 8-11th, was an outstanding event for bioremediators!

The technical details of the presentations were exceptional, as was the level of expertise of the people present. Within this framework, presenting the MIBIREM project was an honor and I have to say that we certainly were not out of place amongst the many international experts! This demonstrates that Europe is capable of achieving high levels of competence, though to keep up we will need to work hard since, on the other side of the Atlantic, a lot of funding is available for R&D activities.

(c)DND Biotech: Cosimo Masini at the 6th Int. Symposium on Bioremetiation – Battelle

During my presentation, titled ‘A Molecular Approach to Lindane Biodegradation’, the problem of this pesticide was discussed, describing some previous results obtained from a study funded by DND Biotech on samples from a contaminated site in Italy. Lindane was produced and used as a broad-spectrum insecticide and treatment against ectoparasites between 1945 and 2000. Production was inefficient because each ton of lindane resulted in the production of 8 to 12 tons of waste isomers. These waste isomers were dumped at production facilities and often led to huge landfills. More than 4.8 million tons of HCH-waste were and, for the most part, still are present worldwide. Lindane and the other HCH isomers barely degrade in the environment, bio-accumulate through the food chain, and present a risk to human health and the environment. They were banned in the EU in 2000 and placed under the Stockholm Convention on POPs in 2009.

(C)DND Biotech: Presentation of MIBIREM at Battelle on May 8, 2023

The Italian model site I described is polluted as a consequence of lindane production from the mid ‘40s to late ‘70s and two nearby disused waste disposal areas have reported high concentrations of HCH isomers (𝛼, 𝛽, 𝛾). In 2005, high concentrations of the beta isomer were detected in cow milk and dairy products from farms in the area. A state of environmental crisis was declared by the Italian government for the area and epidemiological surveillance was implemented. The two disposal areas were studied and characterized; containment plans were put in place to permanently separate the contaminated soil. However, the sediments of the river, as well as agricultural soil, have absorbed the contaminant, releasing it during flooding events. Soil and groundwater samples have been taken, characterized and used as baseline to create microbial enrichment cultures. Several fungal and bacterial strains have been isolated as able to grow on HCH as sole carbon source.

Within this framework, I introduced the Horizon Europe project MIBIREM, as a multidisciplinary venture involving experts in molecular biology, microbiology, environmental engineering, analytical chemistry, from various European research institutes, universities and SMEs. I explained the final goal of the project: the exploitation of microbiomes to implement a sustainable and cost-effective approach for widespread diffused contamination, particularly petroleum hydrocarbons, cyanides and HCH isomers. I highlighted the envisioned output of the MIBIREM project: the creation of a toolbox to identify, analyze, cultivate and upscale the microbiomes for bioremediation applications, while ensuring safety and policy alignment.

(C)DND Biotech: Cosimo Masini, MIBIREM Partner at the Battelle Symposium

(c)DND BioTech: Stand at the Bioremediation Symposium with MIBIREM flyers

Within the MIBIREM project, DND Biotech aims to be a provider of know-how in on-site, in-field bioremediation and will be responsible for the optimization and pilot implementation of the use of selected microorganisms for the removal of various contaminants (cyanides, lindane/HCH and petroleum hydrocarbons) from polluted soils. For this scope, our piloting system RoboNova will be used, providing useful data to bridge lab scale findings and field works.

Cosimo Masini

CEO of DND Biotech, MIBIREM partner


Second MIBIREM project meeting marks successful end to the first project year

MIBIREM project partners met from 27 to 29 September 2023 for the occasion of the second consortium meeting in Utrecht, Netherlands. The meeting was hosted by the Faculty of Geosciences at Utrecht University, and marked a successful end to the project’s first year.

Bioremediation best practice sharing at the first cluster workshop

The first EU Bioremediation Projects Cluster Workshop was successfully convened on 28 June 2023 as a satellite event of the BioRemid2023 Conference. This workshop was organized by 7 ongoing and recently completed EU-funded projects working on bioremediation with the aim of sharing knowledge and experiences about innovative bioremediation techniques for cleaning up the environment in Europe, as well as creating the synergies needed for future work.

Bioremediation EU Projects Cluster at the BioRemid23 Workshop- (c) AXIA Innovation

First bioremediation cluster workshop at BioRemid23

More than 100 participants were present both online and in person at the FHNW Campus in Muttenz, Switzerland, to listen to the project coordinators from 7 projects: SYMBIOREM, MIBIREM, BIOSYSMO, Nymphe, ELECTRA, EiCLaR and GREENER. Thomas Reichenauer of the Austrian Institute of Technology (AIT), as the scientific project Coordinator of MIBIREM, opened the workshop and introduced the MIBIREM project partners and the idea behind the innovative toolbox for microbiome-based bioremediation. The workshop was also addressed by a representative of the European Commission, Directorate General for Research and Innovation in the context of the bioremediation policy.

The main questions and topics of the workshop included effective bioremediation technologies for different pollutants and the need for further testing and improvements. As suggested in the BIOSYSMO, NYMPHE, and MIBIREM projects, the employment of microbiomes in bioremediation processes offer good nature-based alternatives to conventional bioremediation techniques that are often too costly and time-consuming and not environmentally friendly. Finally, it was brought to the attention of the participants that a combination of bio-remediation technologies may be needed in specific cases. The use of optimisation tools, like artificial intelligence, to select them was therefore also introduced.

MIBIREM presentation by the SCO Thomas Reichenauer of the AIT

Call for more synergies and better data sharing

After the individual project presentations were completed, a lively debate was chaired by the BioRemid23 organiser, prof. Philippe Corivini, Lecturer of Environmental Biotechnology at the School of Life Sciences FHNW Institute for Ecopreneurship. The technical roundtable with coordinators stressed that a large amount of important bioremediation-related data has been produced over the past few years but there is no centralized platform. A common database would be very useful; however, the issue of data management is a complex one that requires additional funding and effort related to data collection, sharing, and alignment.

The presenters also discussed the need for harmonization of policies within the European Union (EU) to ensure consistency and facilitate cross-border activities. There was a common understanding that achieving full harmonization across policy areas is time-consuming and challenging, but that progress is being made through ongoing discussions, negotiations, and the adoption of common frameworks. Last but not least, participants mentioned the need for an initiative to carefully assess the results of the different EU projects over the last 10 years, in order to foster cooperation and knowledge transfer, and to ensure the work is not duplicated.

The workshop debate chaired by prof. Philippe Corvini

The EU Bioremediation Projects Cluster Workshop was successfully concluded by announcing the next workshop will take place as a side event of the 7th International Symposium on Biosorption and Biodegradation/Bioremediation – BioBio2024 taking place in Prague, from 16-20 June 2024.

The recording of the workshop is available here on Youtube.

First hydrocarbon soil and water sampling in Brittany, France: the story behind

Located in Brittany, western France, the Ploufragan site housed a soap factory in the 20th century. A soap, le Brochin, that made the hands of workers and mechanics white was invented there in 1919. In 1948, the Renaud-Lucienne bought the factory and was authorised to produce the soap from 1951. This meant the site was used for caustic and paint manufacturing activity and also used motor oil regeneration activity. However, gradually, the activity declined and the company closed in 1994.

For nearly thirty years, the buildings of the former soap factory were derelict and the site was recognized as abandoned by the Ministry of the Environment in 1996. Due to the pollution on the site, the French government has charged the ADEME (Agency for the Environment and Energy Management) with ensuring its decontamination. The buildings of the factory were demolished in 2017 and the site was fully examined for contamination in autumn 2021. The findings were alarming as the pollution levels of the soil and groundwater reached very high values of hydrocarbon contamination.

Interest of the society and MIBIREM research

Through ADEME, the partners of the Laboratoire Interdisciplinaire des Environnements Continentaux (LIEC) in Nancy, France, which is part of the CNRS (Centre National de la Recherche Scientifique) became aware of this site. The site is also of interest of the research to the MIBIREM project. “We are looking for sites contaminated with hydrocarbons to carry out our research, which is aimed at developing a bioremediation process by identifying microorganisms capable of breaking down the hydrocarbons”- says Dr. Aurélie Cébron, research director at the CNRS.

Experience on site Ploufragan

LIEC researchers went to take soil and groundwater samples in early April 2023. Led by Dr. Aurélie Cébron, alongside Christophe Gauthier and Audrey Vauloup – both assistant engineers at the CNRS, the researchers spent two days in the field sampling the water from piezometers (wells installed in the ground to access the water table) and the soil from five sub-sites about ten meters apart. Water sampling was facilitated by Erwan Goulian of DND Biotech – a partner in the MIBIREM consortium. For the soil samples, a mechanical drill was used to sample at depths of 0 to 2m and then 2 to 4m.

Dr. Aurélie Cébron further explains: “the pollution was there, no doubt about it, on the surface of the water in the piezometers we observed a layer of almost 40cm of floating (pure hydrocarbons), like a pool of oil floating on the surface of the water table. The soil cores were literally dripping with a black viscous liquid: hydrocarbons. The smell of hydrocarbons also accompanied us during these two days: we had the impression of being in a service station.”

What happens next?

The samples were collected to measure the contaminants present and assess their chemical characteristics. The microbial diversity (mainly bacteria) present in these samples will be determined using molecular tools: after extracting the DNA and sequencing it, the researchers will be able to see whether certain microorganisms are found in greater numbers in the most polluted areas. The researchers will also evaluate the biodegradation of hydrocarbons by setting up microcosms in the laboratory; furthermore, they will try to isolate bacterial consortia capable of efficiently degrading hydrocarbons for the rest of the project.

This site is only one of fifteen in total that will be sampled as part of the MIBIREM project, and hydrocarbons are only one type of contaminant studied among the three considered in the project, the others being cyanides and hexachlorocyclohexane (HCH).


BioRemid2023 – EU Bioremediation Projects Cluster Workshop

MIBIREM is among the co-organisers of the EU Bioremediation Projects Cluster Workshop that will take place alongside the GREENER Project H2020 conference as a satellite event of the BioRemid2023 on 28 June in FHNW Campus Muttenz, in Switzerland. This workshop is organized by 7 ongoing and recently ended projects working on bioremediation: SYMBIOREM, MIBIREM, BIOSYSMO, Nymphe, ELECTRA, EiCLaR and GREENER. The aim of the workshop is to share knowledge about innovative bioremediation techniques for cleaning up the environment in Europe.

Register here: 28th of June 2023 14:00 – 17:30 CET – hybrid event


Bioremediation as a nature-based solution for the environment

Bioremediation helps to create healthier soils, clean up groundwater and improve air quality. Unlike conventional remediation technologies, bioremediation offers an environmentally friendly approach to remove contaminants from the environment. It draws on natural processes and uses microorganisms (e.g. bacteria, fungi, algae) to remediate the environment without damaging delicate ecosystems. As a clean, cost-efficient, and green strategy, bioremediation plays a key role in meeting Europe’s zero pollution ambitions.

Benefits of attending the Workshop

In this first workshop of the EU bioremediation project cluster, Horizon Europe and Horizon 2020 bioremediation projects come together to present their innovative bioremediation solutions to clean up Europe’s environment. By relying on a broad range of cutting-edge, cross-cutting biotechnologies, they seek to address the highly complex and varied pollutant mixtures present in the soil and (ground)water of contaminated sites.

The workshop will kick-off with short presentations of the projects by the coordinators. The recently started Horizon Europe projects will give an outline on their planned bioremediation innovations, while the Horizon 2020 projects will share key outcomes of their projects. This will be followed by a technical discussion on the role of bioremediation in restoring Europe’s environment and helping it to meet its zero-pollution ambitions.

AGENDA BioRemid23 EU Projects Cluster Workshop