Members of Applied Microbiology International (AMI) have urged the European Commission to put microbial communities at the heart of environmental risk assessments for genetically modified microorganisms, as part of its response to the EU Biotech Act consultation.
AMI’s submission addresses proposed amendments to the EU Directive on the deliberate release of genetically modified microorganisms (GMMs) into the environment. Drawing on contributions from several AMI members, the response represents a diverse range of views, but generally highlights opportunities to streamline regulation while emphasising the importance of robust scientific safeguards to protect environmental and public health.
A central message of the submission is that microorganisms should not be considered in isolation. Instead, regulatory assessments must account for their interactions with the wider microbiomes in which they exist, from soil and aquatic ecosystems to the human gut.
Microbial communities underpin essential global processes, including nutrient cycling, ecosystem resilience and climate regulation. AMI argues that these functions, and the potential effects of GMMs on them, must be explicitly reflected in the regulatory framework.
Strengthening environmental risk assessments
AMI members recommend updating environmental risk assessment requirements to reflect advances in environmental microbiology and microbial ecology. Assessments should consider how GMMs could affect the composition and function of existing microbial communities, ecosystem services and long-term ecological resilience.
The submission also calls for greater attention to the persistence and spread of modified microorganisms, their potential to establish themselves in new environments, and the possibility of horizontal gene transfer. This is particularly important where genetic material could contribute to the spread of antimicrobial resistance.
Some AMI members highlight the need for monitoring approaches that are appropriate to microbial applications. Alongside conventional microbiological methods, technologies such as metagenomics, metatranscriptomics and environmental DNA analysis could help researchers detect changes in microbial diversity, gene transfer and ecosystem processes following environmental release.
Balancing innovation with safeguards
The response recognises the potential benefits of a proportionate, risk-based approach to biotechnology regulation. Several of AMI’s members broadly support introducing a simplified authorisation pathway for low-risk GMMs, provided that appropriate safeguards are in place- although differing, much more cautious views were also represented in the submission.
Safeguards should include evidence of genetic stability, consideration of potential harm, and assessment of an organism’s environmental behaviour and interactions with native microbiomes. The submission also stresses that Qualified Presumption of Safety status, which draws on established knowledge of microbial groups, should not be treated as sufficient evidence of environmental safety on its own.
AMI members also raised concerns about proposals for unlimited-duration authorisations, particularly if combined with exemptions from post-market environmental monitoring. The response recommends retaining proportionate mechanisms for periodic review or introducing clear triggers for reassessment when new scientific evidence emerges.
Where genetic modifications cannot be detected using conventional event-specific methods, some AMI members support considering alternative approaches. However, these should be governed by clear, harmonised criteria across EU Member States to maintain effective traceability and risk management.
Bringing microbiological expertise into policy
The submission calls for future technical requirements to be developed with input from across the microbiological sciences, including microbial ecology, molecular microbiology, virology, mycology, antimicrobial resistance and public health. Expertise in synthetic biology, environmental monitoring and analytical chemistry will also be important as biotechnology advances.
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Members further highlight the potential of artificial intelligence and digital environmental surveillance to support predictive ecological modelling, analyse complex datasets and improve the early detection of unexpected environmental effects.
A regulatory framework that supports responsible biotechnology innovation while remaining responsive to scientific advances and environmental risks was also advocated for.
Key recommendations
AMI members’ key recommendations cover eight areas:
1. Definition of microorganisms: The Directive should use clear, scientifically robust and future-proof definitions that reflect modern microbial classification, emerging synthetic biology technologies and complex organisms such as symbiotic partnerships.
2. Environmental risk assessment: Assessments should consider GMMs’ effects on existing microbiomes, ecosystem functions and resilience. Requirements should reflect the diverse applications of microbial biotechnology, including bioremediation and wastewater treatment, rather than focusing primarily on plant-based scenarios.
3. Duration of authorisations: AMI members raised concerns about unlimited-duration consents, particularly where monitoring is also waived. They recommend proportionate periodic reviews or clearly defined review triggers to address emerging scientific evidence and long-term environmental risks.
4. Detection methods: Where identifying a specific genetic modification is technically impossible, alternative detection approaches should be permitted under clear, harmonised EU-wide criteria. Flexibility must not undermine traceability, monitoring or risk management.
5. Low-risk GMMs: AMI members broadly support simplified authorisation for low-risk organisms but recommend additional safeguards covering genetic stability, non-pathogenicity, potential horizontal gene transfer, environmental persistence and interactions with native microbiomes.
6. Post-market environmental monitoring: Monitoring waivers should be exceptional, evidence-based and decided case by case. Qualified Presumption of Safety status alone is insufficient to establish environmental safety. Monitoring should remain proportionate to the risks, particularly for organisms released into the environment.
7. Scientific expertise: Future technical requirements should draw on multidisciplinary expertise, including environmental and molecular microbiology, microbial ecology, antimicrobial resistance, virology, synthetic biology, public health and environmental risk assessment. Independent scientific oversight and periodic review are also recommended.
8. Artificial intelligence: AI-assisted surveillance, predictive ecological modelling and machine learning could strengthen environmental monitoring and help identify unexpected ecological effects.
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