Genetically Modified Microorganisms
Microorganisms: small, diverse, essential
Definition
Microorganisms are microscopically small organisms that cannot be seen with the naked eye. The term ‘microorganism’ is a collective term for organisms smaller than 0.1 mm. They occur in all three domains of life: Archaea (formerly archaebacteria), Bacteria, and Eukarya. Microbial eukaryotes include single-celled fungi, slime moulds, single-celled algae (microalgae) and single-celled animals (so called protists such as amoebae and paramecia). Legally speaking, viruses and viroids are also considered microorganisms.
Importance
Microorganisms are essential not only for humans but also for all plants, animals and the functioning of ecosystems. Almost all fundamental biological processes on this planet are based on microorganisms or are closely linked to them. For example, they perform central tasks in building up and breaking down organic substances, such as in compost. During these processes, microorganisms release nutrients and contribute significantly to material cycles such as the carbon and nitrogen cycles. In this way, they influence not only soil fertility but entire food webs.
Interaction
In addition, microorganisms interact with other organisms in many different ways. Examples include nitrogen-fixing bacteria in the roots of legumes and the microbiome in the gut of humans and animals, which is essential for digestion and supports the immune system. At the same time, microorganisms can also have negative effects, for instance as pathogens or invasive species affecting health, agriculture and ecosystems.
State of research
Taken as a whole, and with a few important exceptions, microorganisms are among the least studied organisms. This is due partly to their immense diversity and partly to the limited ability to cultivate them in the laboratory. It is currently estimated that less than 1% of bacteria and other microbial groups are culturable, meaning they can be grown in the laboratory. In addition, microorganisms in the environment can differ greatly from culturable microorganisms in terms of size, dispersal ability, rate of development and ecology. Although the diversity of microorganisms can be measured using modern molecular methods, distinguishing between species is more difficult than for plants or animals.
Fields of application of genetically modified microorganisms
Automation, digitalisation and new genetic engineering methods such as CRISPR/Cas, together with the use of artificial intelligence, are currently driving a dynamic development in the field of biotechnology and enabling a wide range of new applications with new, sometimes complex properties. This is also broadening the range of possible GMM applications. GMMs are no longer developed only for closed systems such as fermenters; increasingly, they are also intended to be released into the environment. The fields being explored are diverse. They include agricultural applications designed to achieve various effects: controlling insects, promoting disease resistance in crops, and nitrogen fixation or nutrient release in soil. In animal husbandry, GMMs are intended to be used, for example, as vaccines against diseases or as dietary supplements that adjust the gut environment to change feed conversion. GMMs are also being developed for bioremediation (biological cleanup) of contaminated soils and water bodies, as well as for immunising wild animals against diseases.
BfN research on environmental risk assessment and monitoring
The BfN is involved at both national and European level in the authorisation procedure for genetically modified organisms (GMOs) and, in particular, assesses risks to nature and the environment.
The biological characteristics of microorganisms pose major challenges for the authorisation of GMMs for release into the environment. Microorganisms differ in key aspects, such as size, ecology and functions, from plants and animals that risk assessment has so far been focused on. This raises the question of how potential short-and long-term effects on the environment can be reliably assessed. Unlike with GM crops, there is a lack of experience and of established assessment concepts, and it is not possible to retrieve GMMs from the environment once they have been released.
To address these regulatory issues, the BfN addresses environmental risk assessment and the monitoring of GMMs in various research and development projects. A particular difficulty is that the biology of the organisms grouped under the term microorganisms varies widely. Despite their fundamental importance for all life, knowledge about microorganisms and their diversity in the environment remains very limited. Possible long-term environmental consequences of GMM releases are therefore difficult to predict.
Key areas
To support the legally required environmental risk assessment and monitoring of GMMs in the authorisation procedure, BfN research focuses on three key areas in this regard:
Given the rapid pace of technological development, continuous analysis of the current state of the art is needed to track which fields of application are being researched and which developments may become relevant for risk assessment in the future, for example the use of artificial intelligence to ‘design’ novel metabolic pathways or proteins for subsequent production in GMMs.
Another part of the research addresses the question of which methods are available to examine the effects of GMMs before they are released into the environment. New methods are also needed for monitoring GMMs after approval. Methods also include modelling effects, for example to transfer results from the laboratory to the field. Additionally, in order for test results to be comparable across different applications and uses, agreement on the precise methods is required, meaning that methods must be standardised for risk assessment.
The BfN develops and researches assessment concepts. These not only structure the data requirements for an environmental risk assessment but are also necessary to determine at what point a change in the environment should be classified as harm. Assessment concepts are needed both for risk assessment and for interpreting monitoring data.
EU legislative procedure on genetically modified microorganisms
Amendment to the Directive
The deliberate release of GMOs, and therefore also of GMMs, into the environment is regulated by EU Directive 2001/18/EC. On 16 December 2025, the European Commission presented a proposal for a directive “amending Directives 2001/18/EC and 2010/53/EU as regards the placing on the market of genetically modified microorganisms and the processing of organs.” The aim is to facilitate the authorisation requirements for placing GMMs on the market.
In the view of the BfN, there are considerable doubts as to whether this proposal to amend the Directive complies with the EU’s precautionary principle and the requirement for a high level of environmental protection, particularly because long-term environmental impacts are not sufficiently taken into account.
European Biotech Act I and its scope
The proposed amendment to the Directive is intended to legally complement European Biotech Act I (EBA I), which was proposed at the same time. EBA I is a proposed regulation aimed at strengthening the biotechnology and bioproduction sectors in the EU, and its scope covers biotechnological products and services that are frequently based on genetic modifications, particularly of microorganisms. Although EBA I focuses on so-called ‘health biotechnology’, this is understood very broadly, covering areas such as human medicine, veterinary medicine, pharmaceuticals and plant protection. As a result, EBA I also affects, for example, agricultural applications of GMMs such as pesticides (for instance RNAi-based pesticides), plant strengthening agents, and fertilisers. Among other things, this affects the risk assessment of GMOs and thus also the scope of the Release Directive 2001/18/EC.
The regulatory initiative is to be completed by a second part, EBA II, which will focus on industrial biotechnology and bioproduction and will therefore address, among other things, GMOs used as food and feed.
To support the legislative process, the BfN has issued an expert opinion on the individual provisions of the proposed directive (English version coming soon).