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.

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

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.

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.

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

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.

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).

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.

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

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.

Located in Brittany, western France, the Ploufragan site housed a soap factory in the 20^th 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).