The Council of the EU will vote tomorrow on a proposed regulation governing the marketing of genetically modified microorganisms

It is urgently necessary to modernize European legislation to bring it in line with current biotechnology. Entirely strategic sectors depend on this, such as food safety and the development of therapies. European legislation, to date, has led to a significant loss of competitiveness in strategic sectors. These directives represent a step forward in addressing this issue regarding genetically modified microorganisms, which play a crucial role in both public health and planetary health challenges.

Under no circumstances should these changes pose greater risks to health or the environment; rather, the opposite is true. Indeed, this legislation should accelerate key technologies for human health, such as microbiome-based therapies; or accelerate solutions for planetary health, such as improved bioremediation solutions [using the metabolic capabilities of living organisms to treat contaminants], reducing dependence on fossil fuels, or producing more sustainable food.

We have a better accounting of the stars in the universe than of the microbes beneath our feet. The past two decades have seen a revolution in our understanding of bacteria aided by new sequencing technologies, but this understanding is limited to detecting the presence of organisms or their genes in the environment, and their characterization is incomplete at best. The vast majority of these organisms have never been directly observed, and how their genes actually function in the environment remains largely a mystery. At the same time, it is increasingly clear that microbes exist in highly interconnected and interdependent communities, that cannot be easily taken apart in a laboratory. Consequently, most available techniques fail at predicting whether microbes will survive, establish, and interact in natural environments. Deregulating the release of GMMs and reducing monitoring against this background of unknowns is dangerous. 

The release of GMMs is an ecological issue. We still don’t understand how microbes disperse in the environment, and research continues to find the surprising mechanisms that microbes employ to move (e.g., bacteria attaching to fungal hyphae to spread). It is therefore not possible to predict how far GMMs will spread from their intended environment. All genetic modifications present risks, but the risks are not equal, and the current proposal overlooks this distinction. Modifications of mobile genetic elements (MGEs) have the potential to ‘jump’ to other microbes, but novel mechanisms for this exchange are continuously being discovered. Even if modifications are made in the microbial chromosomes, which evolve more slowly, microbial evolution can happen within days, drastically affecting the intended function of the genes. For example, ammonia oxidation (involved in nitrification, a target of current GMMs) and methane oxidation (used by methanotrophic bacteria to convert methane into carbon dioxide) share a common evolutionary origin. This means that at some point, randomly in the past, evolution drastically altered the function of these genes, with serious consequences for what those bacteria did in the environment: some fixed nitrogen, and others consumed methane. Given our current knowledge, it is not possible to guarantee that similar transitions won't happen with GMMs, especially as the genes they target have been known to evolve into other functions in the past. Considering these unknowns, the spatial and evolutionary spread of ‘intellectual property’ requires a detailed and empirically-backed regulatory framework that doesn’t yet exist.  

Soils are extremely diverse, and most of the desired genetic capacities are already present in most soils, albeit in low concentrations. This brings into question what the need for GMMs is in the first place. The deregulation of GMMs, especially for agricultural applications, overlooks existing research into microbial inoculants. (The functions of inoculated microbes rapidly plateau because the chemical reactions they are expected to carry out, such as nitrification, are energetically expensive; or because the microbes face competition and predation from local organisms.) From this perspective, the success of GMMs is unlikely. The lack of monitoring requirements in the current legislation may result in the development and sale of products whose efficiency is much lower than expected, reducing consumer protections. Alternatively, in the case that they do succeed, this would probably occur by the massive displacement of the native microbiota. The consequences of such biodiversity loss are hard to predict, especially as ecosystems face increasing compounded pressures from climate change, and here, the reduction of monitoring requirements may mask unintended environmental consequences. 

The European Union's regulatory framework governing the environmental release of genetically modified organisms was established at a time when scientific knowledge of genetics, ecology, and environmental microbiology was far more limited than it is today. In that context, a precautionary approach was both understandable and justified. However, the scientific foundations on which these regulations were built have changed profoundly over the past two decades.

Advances in molecular biology, systems ecology, genomics, and environmental monitoring have greatly improved our ability to understand and predict the behavior of microorganisms in natural ecosystems. At the same time, the emergence of precise gene-editing technologies has blurred the distinction between conventionally bred organisms and those modified in the laboratory. Many modern genetic modifications simply harness natural mechanisms of genetic variation, producing organisms that differ only marginally from variants that could arise through natural evolutionary processes.

Importantly, discussions surrounding genetically modified organisms should distinguish clearly between plants and microorganisms. These are fundamentally different biological systems, developed for different purposes and associated with different patterns of use, risk, and societal benefit. A regulatory framework designed primarily around agricultural crops should not automatically be applied to environmental microorganisms.

Engineered microorganisms are increasingly being developed to address some of society's most pressing challenges. They can reduce dependence on chemical fertilizers by enhancing biological nitrogen fixation, improve crop productivity through beneficial interactions with plant roots, decrease the use of chemical pesticides, and contribute to the remediation of polluted soils, waters, and industrial sites. They have also been proposed as tools for restoring environments damaged by military conflicts and industrial accidents. In these applications, the objective is not private gain alone, but the delivery of measurable public benefits in agriculture, environmental protection, and sustainability.

Yet despite these opportunities, the current European regulatory framework remains a major obstacle to the practical deployment of such technologies. Bringing an engineered microorganism from laboratory development to environmental application often requires seven to ten years of regulatory procedures, imposing costs and uncertainties that discourage investment and significantly slow innovation. As a result, many promising technologies never progress beyond proof-of-concept studies, despite having been developed through substantial public investment.

The ongoing discussions surrounding the European Biotechnology Act II provide a unique opportunity to modernize this framework. Regulation should remain rigorous and science-based, but it should also be proportionate to actual risk and adapted to contemporary scientific knowledge. In particular, procedures for testing and deploying beneficial microorganisms in environmental applications should be streamlined, accelerated, and made more predictable, while maintaining appropriate safeguards and monitoring mechanisms.

Failure to do so would carry significant consequences. Europe risks forfeiting leadership in a strategically important technological field while other regions, notably the United States and China, move rapidly toward implementation. More importantly, it would prevent European citizens from benefiting from innovations that they have already helped finance through national and European research programs.

A modernized regulatory framework is therefore not simply a matter of supporting innovation. It is a matter of ensuring that publicly funded scientific knowledge can be translated into tangible environmental, agricultural, and societal benefits. European taxpayers deserve a system that converts scientific excellence into real-world solutions rather than allowing promising technologies to remain indefinitely confined to the laboratory for others’ benefit.

A major problem with the proposed relaxation of Directive 2001/18/EC for the release of genetically modified microorganisms (GMM) is, that it has been inspired by little scientific evidence, and with no consultation of ecology researchers. Considering that ecologists are the experts in the study of the interactions of organisms with the environment, this oversight compromises the scientific credibility of the proposal. Namely, many statements in the proposal about both benefits and risks of GMM release are based on belief instead of sound scientific evidence.

Additionally, postulated benefits for e.g., agriculture, are not weighed against the backdrop of myriads of studies suggesting highly effective solutions to adverse environmental effects of intensive agriculture, such as diversification. Instead, from a scientific point of view, the proposal may yield many potential environmental risks.

Due to the manifold biological interactions in natural systems, the release of novel organisms is, as shown in myriads of ecological studies, a gamble with a completely uncertain outcome. Even the behaviour of novel plants, which can be better monitored, and for which most species have been described, is largely impossible to predict. Vice-versa, less than 1% of the microbial diversity is currently known, and their ecological role is speculative. GMM taxa span across the entire tree of life, such as fungi, bacteria, archaea, protists, or microalgae, whose lumping into a common category contradicts the most basic scientific knowledge.

The European Commission has recently repeated that deregulation of e.g. New Genomic Techniques should not apply to microorganisms and animals, due to our insufficient knowledge about them. It appears almost cynical that even before a deregulation for NGT plants is confirmed, the Commission proposes a ‘low risk’ category of GMM, for which risk assessment and monitoring would be waived. Moreover, the proposed criteria for such GMMs are vague, partly circular, and at odds with scientific evidence. For example, there is no such thing as a gene of ‘low concern’, given that we do not even know what GMMs will do in the environment. We also know that biotic interactions, such as competition, predation, or facilitation, with the unknown microbial diversity in the wild cannot be derived from lab studies, explaining both observed failures of ‘desired’ GMM effects, as well as potential risks. Furthermore, microorganisms can transfer genetic material across species, and while highly detrimental consequences of this are well-known (e.g. spread of antibiotic resistances), such horizontal gene transfer is an active area of research.

Where the existing directive takes full account of the dearly needed precautionary principle, the proposed changes may create major environmental risks. These include the alterations of the microbiome of other organisms, including humans, changes of complex biotic interaction networks of the rhizosphere, displacement of native microbes, endangerment of local microbial diversity before it is even described, reduced resistance and resilience to future environmental change, and cascading effects to higher trophic levels.

GMMs will evolve fast, interact with a multitude of other organisms, will be difficult to trace, and cannot be called back. With billions of microbes in soils and microbiomes of ‘higher’ taxa, GMM release also affects plants, animals, humans, and non-target microbes which, under the proposed changes, may not even be monitored. This makes GMMs a moving target for environmental assessments, suggesting much more strict regulation of GMM release than for all other organisms.

Overall, GMM should not be released into the environment without scientifically sound, case-by-case risk assessment. They must be traceable, release should be strictly time-limited, and effects re-evaluated regularly. Ecologists must be involved in both developing, as well as conducting scientifically sound and reliable approaches for GMM risk and benefit assessments.