MIBIREM: letting microbes do the heavy lifting on Europe’s toxic past

Working towards providing a practical toolbox for bioremediation, the project is now conducting field trials as the scientific coordinator Thomas Reichenauer from the AIT – Austrian Institute of Technology, explains.

Thomas Reichenauer from the AIT – Austrian Institute of Technology, is the scientific coordinator of the MIBIREM project, an EU-funded research effort with 12 partners developing microbiome-based solutions for cleaning up contaminated soils and groundwater.

The overall coordination lies with the Austrian EU funding consultancy RTDS Association, yet in reality, this partnership extends far beyond the 12-strong consortium as it also includes countless billions of microbes and bacteria that inhabit our planet, and with whom MIBIREM is working to repair our damaged environments. For decades now, we have contaminated land, soils and groundwater with industrial chemicals, making places uninhabitable, endangering health and degrading ecosystems essential to biodiversity. “It’s a worldwide problem,” says Reichenauer. “And we are still contaminating today, so it is an ongoing problem as well.”

Microbiome-based remediation, or bioremediation for short, uses living microbes to degrade organic pollutants in soil and water. “In our case we are working with bacteria to break down organic contaminants and we mainly focus on groundwater and soil.” explains Reichenauer. “In Austria, for instance, 100 per cent of drinking water comes from springs or groundwater, so it’s very important.”

The approach can replace or complement energy-intensive methods such as chemical oxidation/reduction or thermal treatments. “Bioremediation is comparatively cheap because you don’t need much energy input,” continues Reichenauer. The trade-off is time: clean-ups typically take two to five years, whereas chemical methods can act within months, but at higher costs and with greater ecological disruption.

Within bioremediation itself, MIBIREM distinguishes two modes: biostimulation (tuning site conditions so native degraders thrive) and bioaugmentation (cultivating degraders in the lab and re-introducing them to the site). MIBIREM concentrates on the latter, but isn’t just cultivating one bacterial degrader, but whole groups of them, moving beyond single “hero strains” of bacteria and working with microbial consortia. “We aim to enrich whole microbiomes, networks of bacteria that are more robust and have a broader set of enzymes,” Reichenauer continues. “That robustness matters when organisms are introduced into complex, variable real-world conditions.”

The contaminants in the project’s sights are very common in Europe: petroleum hydrocarbons, cyanides, and hexachlorocyclohexane (HCH), including the pesticide lindane’s persistent isomers. “During lindane production, for example, large amounts of unusable isomers were disposed of on site. They still contaminate more than 100 sites across Europe.”

The project aligns squarely with EU ambitions on sustainability and the bioeconomy: restoring soils and aquifers, reducing the footprint of remediation itself, and building safer, biology-based industrial practices. Sustainability is the key word and by being more sustainable, bioremediation could be applied more often than it currently is.

At the heart of MIBIREM’s objectives is the creation of a practical TOOLBOX that translates the cutting-edge microbiome science being done in the lab and in the field into usable solutions for industry and regulators. Rather than a single product, the toolbox is a suite of complementary resources, ranging from conserved microbial consortia and standardised lab tests to monitoring assays and predictive models.

Together, these tools provide a step-by-step pathway for assessing whether bioremediation is feasible at a site, selecting the right microbial approach and tracking its effectiveness in the field. The MIBIREM TOOLBOX includes:

• Cryo-conserved microbial consortia ready for testing and potential deployment.
• qPCR assays (and next-generation sequencing workflows) to monitor the fate of introduced microbes and track key degraders.
• A predictive model to assess whether bioremediation is feasible at a given site and to plan interventions.
• Standardised microcosm degradation tests for petroleum hydrocarbons, cyanides and HCH to check if, and how fast, degradation proceeds before field work.

“These elements can be put together and applied for the remediation of a site,” says Reichenauer. “In practice, this means that a site manager could begin with the predictive model to see if bioremediation is suitable, then run microcosm tests to check whether degradation occurs under lab conditions, before moving on to field applications of enriched microbiomes supported by monitoring through qPCR or sequencing tools.”  The aim is not to offer a single solution but to provide companies and authorities with a flexible set of instruments that can be combined to design, implement and track biological remediation strategies.

MIBIREM has a long way to go before the toolbox is fully functional. But even at this halfway point in the project, the signs are good that it is on the right path “So far we’ve enriched our microbiomes and selected the best-degrading ones,” Reichenauer explains. “We’ve isolated individual strains and are characterising them.

“The consortia are conserved and available to the community, and pilots at three European sites are scheduled to begin at the end of this year or early next. The predictive tool is a ‘work in progress’, while assay development is well underway.”

The step from lab to field remains the biggest hurdle. “Coming from the lab back to the field is always a big step,” Reichenauer continues. “Monitoring is another. It’s easy to monitor something in the lab, but in the field it’s much more difficult,” he notes, pointing to primer development for qPCR and complementary sequencing approaches.

Regulation and acceptance matter, too. In countries such as Austria and Germany, groundwater is classified as highly sensitive. “We need to negotiate with local authorities to be allowed to put something into the groundwater,” he says. Encouragingly, however, many authorities now apply a ‘repair principle’ for contaminated sites rather than a strict precautionary stance, easing in-situ methods. But worker safety is non-negotiable. “We screen our bacteria for pathogenicity and risky genes because people handling enriched cultures may be exposed to higher concentrations.” Public perception is another important factor the project must consider – and the reaction is often mixed.

“On one hand, biological remediation is regarded as a soft, nice method,” says Reichenauer. “On the other hand, when you say you put bacteria into the environment, some people react negatively.”

Part of MIBIREM’s mission, therefore, is education through publications, outreach and a clear explanation of methods and safeguards. If MIBIREM succeeds, the benefits extend from those for industry and remediation companies to local authorities, regulators and communities. Cheaper, lower-energy clean-ups mean more sites can be treated faster, reducing risks to public health, safeguarding drinking-water sources and returning land to productive use. “Ideally, at least one of our microbiomes will be applied to remediate contaminated sites – more would be even better,” Reichenauer says. “And our tools should be usable for other contaminants, too.”

Reichenauer hopes that MIBIREM’s lasting legacy will be a trusted biological pathway that sits confidently alongside chemical and physical methods for cleaning up our contaminated land and groundwater. “Bioremediation is one possibility, but it could be applied more often than it currently is,” he says.

With conserved consortia, open tools and pilot studies completed, the project aims to make that possibility a reality and to get the project’s microbe partners to quietly undo decades of damage, one site at a time.