Editorial: thematic issue on microbial ecotoxicology of contaminants of emerging concern

Abstract

Ectomycorrhizal fungi disappear after clearcutting, while saprotrophic agaricomycetes initially increase in abundance and decrease again as ectomycorrhizal fungi recolonize – an effect that was more pronounced in previously fertilized stands.

Microorganisms are engineers of the biosphere. Over the course of billions of years, they have adapted to habitats by evolving countless ways to interact with their environment. Yet, the fairly recent substantial anthropogenic impact on our planet comes with daunting challenges for ecosystems and their inhabitants, including prokaryotes and microeukaryotes. These impacts include extensive chemical and biological contamination as a major concern. Microbial ecotoxicology seeks to assess the interactions between microorganisms and contaminants and their consequences for ecoystems and humans from an interdisciplinary perspective. These interactions are investigated per se, in order to understand the toxicokinetics (fate) and toxicodynamics (effects) of contaminants, and to evaluate outcomes in terms of ecosystem health and associated risks. Contaminants of emerging concern (CECs) include synthetic compounds (e.g. pharmaceuticals, personal care products, per- and polyfluoroalkyl substances, phthalates, bisphenols, antibiotics, nanoparticles, microplastics) as well as natural toxins (e.g. cyanotoxins) and biological agents (e.g. antibiotic-resistant microorganisms, antibiotic resistant genes, viruses, or biomolecular contaminants) (Wang et al. 2024). These recently identified environmental contaminants may pose significant threats to humans and ecosystems, hence the urgent need to assess and characterize microbe-CEC interactions and their associated environmental and human health risks.

This thematic issue of FEMS Microbiology Ecology brings together 14 original research papers, two meta-analyses, and one review article that reflect the diversity of research questions, approaches, methods, and challenges in the vast field of microbial ecotoxicology of CECs. Many of these contributions were presented in part at the 4^th International Microbial Ecotoxicology conference in Gothenburg, Sweden, 12–14 November 2024 (https://ecotoxicomic24.sciencesconf.org). This successful meeting brought together expert scientists from various disciplines (microbial ecology, environmental microbiology, environmental chemistry, ecotoxicology, antimicrobial resistance, risk assessment, and big data) as well as many colleagues convinced by the increasing importance of this field for the future of our biosphere.

Taken together, this collection of articles provides a snapshot of today’s efforts in using microbial ecology and state-of-the-art experimental approaches and technologies to best capture the biological effects of exposure to low concentration of bioactive contaminants. The papers address a comprehensive and representative subset of CECs, including plastics, pesticides, nanoparticles, pharmaceuticals, cyanotoxins, and antibiotic resistance agents, while collectively providing a valuable blueprint for the study of many other contaminants (e.g. PFAS) that are currently emerging as major topics for study. These publications also highlight the broad array of techniques available to the field, with high-throughput methods including DNA and RNA sequencing and chemical analytical expertise coming forward as integral elements required for such studies. Also worthy of note, several papers emphasize the importance of microbial functions, rather than taxonomic composition alone, as the most relevant endpoints to evaluate. Indeed, the key priority for microbial ecotoxicology lies in the evaluation of the impact of the staggering diversity of CECs on microbial functions and microbial diversity.

Among CECs, plastics represent a fast-increasing source of contamination, so plastisphere-related processes including the potential for microbially-mediated degradation is a major and timely research topic. Maday et al (2025) used laboratory plastic leachates to investigate the effect of plastic weathering on marine procaryotic and fungal communities. Metabarcoding and metatranscriptomics analyses showed that leachates alter the composition of marine microbial communities, but not their functional potential for plastic degradation as estimated from expression of biodegradation genes. The paper by Jung et al (2026) addressed whether a shift from conventional (LDPE, PET) to biodegradable (PBAT) microplastics (MPs) in agriculture impacts crop rhizosphere microbiomes (maize and strawberry). Results highlight that biodegradable MPs induce distinct taxonomic shifts compared to conventional MPs. Pesticides are another major type of CECs that impact microbial communities. The study by Müller et al (2026) investigated the effects of three herbicides and of drying–rewetting on soil nitrification activity and nitrification guilds using soil microcosm experiments and qPCR targeting functional genes. Herbicides did not affect nitrification activity or nitrification guild abundance. In contrast, drying–rewetting altered nitrification guilds. Furthermore, differences in nitrate loads between herbicide-exposed and non-exposed soils suggest that a priori herbicide exposure may influence microbial responses to drought. In another nitrification-related study, Kaur-Bhambra et al (2026) focused on investigating the different modes of action and effects of plant-derived biological nitrification inhibitors on two model ammonium-oxidizing bacteria, with implication for their ecological impact and deployment in agroecosystems. Koch et al (2026) propose to use periphyton as a passive sampler to study exposure and response to pesticide bioaccumulation and nutrient pollution in agricultural streams, extending analysis beyond standard surface water monitoring, and allowing correlation of pollutant bioaccumulation with functional markers. Their results show how effects of nutrient availability may interfere and potentially obscure those of pesticide exposure.

CECs most often occur in mixtures, and experimentally investigating cocktail effects on communities is key to disentangling their effects in natural habitats. Lagos et al (2025) experimentally addressed the effects of three microplastic (MP) types, alone or in combination with exposure to the fungicide pyraclostrobin and/or the anthelminthic albendazole, on soil nitrogen cycling in three soils. Observed effects included disruption of soil nitrogen cycling influenced by soil type, with potential consequences for soil fertility. The toxicity of contaminant mixtures to marine microzooplankton, a group rarely taken into account in ecotoxicological assessments despite its ecological relevance, was addressed by Jönander et al (2025). Analysis methods, including a predictive, component-based approach to assessing mixture toxicity and an experimental whole-water approach, were compared and significant effects on the composition and diversity of microzooplankton were observed. The study underlines the importance of developing new assessment methods with ecologically relevant endpoints to improve environmental risk assessment. Oster et al (2025) exposed freshwater biofilms in large scale microcosms to a two-compounds mixture (an antibiotic and an herbicide) and monitored responses using metabarcoding as well as functional proxies (biomass and chlorophyll). This revealed functional stability in communities exposed to the tested chemical mixture despite structural changes, also emphasizing the importance of functional endpoints for a more holistic evaluation of impacts.

Antibiotics are another group of CECs of crucial importance, yet they are still most often only treated from a public health perspective despite their prime relevance to microbial ecology and ecotoxicology. Indeed, the massive use of antibiotics has strong effects on microbial communities associated with the spread of antibiotic resistance in ecosystems. Gómez-Martínez et al (2026) investigate the resistome of high-flow river sediments along the Göta Älv River in Sweden. Characterizing the pollution with antibiotics and the presence of antibiotic resistance genes (ARGs) in sediment through qPCR and shotgun metagenomics revealed higher levels of ARGs and antimicrobial resistance downstream of wastewater treatment plants (WWTPs), demonstrating their role as hotspots for resistance spread and the need for improved wastewater management to mitigate resistance proliferation. The importance of better understanding the effects of antibiotics and other biocides on the microbial compartment becomes evident in the review by Jaen-Luchoro et al (2026), which provides a timely and extensive compilation of available minimum inhibitory concentration (MIC) data for antibacterial biocides, metals, and related compounds from the public literature (289 studies; 1973–2024). The resulting dataset, encompassing over 20 000 MIC values across 164 bacterial species, represents to our knowledge the first centralized database of its kind. Its cross-study comparison also provides a welcome foundation for future analyses of mechanisms of co-selection between susceptibility to metals, biocide tolerance and antibiotic/antimicrobial resistance.

Transformation and degradation of contaminants is another key aspect of microbial CEC research, and chemical transformation mediated by microbial communities has important implications for bioremediation strategies. Two papers address this topic in the case of pesticides. Abbasi et al (2025) evaluated the capacity of individual bacterial strains and of a four-species consortium to degrade atrazine in soils when inoculated with and without zeolite as a carrier. The authors showed that zeolite-based biocomposites containing individual bacterial strains or the consortium both increased the stability and efficiency of atrazine degradation compared with free-cell inoculation, with limited effect on the composition of native soil bacterial communities. This approach has potential as a bioaugmentation technique for bioremediation of atrazine-contaminated agricultural soils. The effect of physical factors in toxicity of CECs is also important. In their study, Artigas et al (2026) show that hydrological disturbance (i.e. frequent or sporadic flow velocity increases) enhances dissipation and bioaccumulation of a pesticide cocktail composed of a herbicide (terbuthylazine), a fungicide (tebuconazole), and an insecticide (imidacloprid) in biofilms.

The microbial compartment is also being increasingly considered as a potential tool for environmental risk assessment of CECs. Changes in community composition following CEC exposure were exploited by Smith et al (2025), using the power of high-throughput approaches to monitor the effects of contamination by 168 chemicals on 28 lab-grown strains as well as 6 environmental communities in microplate format, followed by Nanopore sequencing. Phylogenetic clustering of community composition in response to pollutant exposure in laboratory experiments is proposed as a simple biomarker for environmental monitoring. The meta-analysis by Swaine et al (2025) assessed the effects of pesticides on soil health parameters, with the aim of identifying key biological indicators for potential use in environmental risk assessment. The abundance of ammonia-oxidizing archaeal and bacterial amoA (ammonia monooxygenase) genes emerges as a consistent indicator of pesticide exposure, with inhibition primarily driven by herbicides and fungicides, highlighting the potential of ammonia-oxidizing micro-organisms as sensitive bioindicators of pesticide toxicity to soil microbiota.

The microbiome of higher organisms, as a dynamic interface between hosts and their environment, is also of interest in the context of such studies. Ouwehand et al (2025) address bacterium-mediated resistance as a mechanism underlying the ability of holobionts to cope with metallic nanoparticle toxicity. The authors show that the presence of silver ion-resistant bacteria, which are core members of the microbiome, enhance the resistance of Daphnia magna neonates to silver ions released during the dissolution of silver nanoparticles, and propose that this is due to active bacterial uptake of silver ions. The review by Le Meur et al (2026) summarizes current knowledge regarding the role of animal gut microbiota in modulating cyanobacterial toxicity in the context of increasingly frequent and intense blooms worldwide associated with global change. The paper addresses microbiota and holobionts responses to cyanobacterial and cyanotoxin exposure and explores several known and candidate mechanisms underlying cyanobacteria-host-microbiota interactions.

To conclude, this set of 17 articles offers a timely overview of ongoing research in microbial ecotoxicology of CECs. Modelling and predictive approaches were still limited, reflecting their overall rarity in the current literature, and emphasizing the need for more solid data to feed appropriate models. More satisfyingly, what the papers of this thematic issue show is that investigations are increasingly shifting from the description of correlations, as observed in complex environments, to forays into direct causality. At present, this can essentially only be tested on simple, controlled artificial communities from microcosms or cultures. Due to the challenges of maintaining environmental micro-organisms in the lab, experimental approaches are not yet as standardized as in human toxicology. However, this first in lab step is required to adequately explore the mechanisms underlying interactions between micro-organisms and CECs. Scaling up from microcosms to mesocosms and to real world ecosystems, possibly also with support of AI, will be key to address the transferability of lab-based findings to whole ecosystems and mitigation strategies in the future. Despite these challenges, this clearly comes with promising perspectives for applications in terms of bioindication, bioremediation and bioaugmentation, as well as for the development of probiotics. We expect the upcoming fifth EcotoxicoMic Network International Conference in Thessaloniki, Greece, from 12 to 14 October 2026 (https://ecotoxicomic26.sciencesconf.org) to showcase new advances in this dynamic and rapidly growing field along the lines mapped out in the series of papers in this thematic issue.

Author contributions

Sébastien Duperron (Conceptualization, Writing—original draft, Writing—review & editing), Stéphane Vuilleumier (Conceptualization, Writing—original draft, Writing—review & editing), Kristian K. Brandt (Conceptualization, Writing—original draft, Writing—review & editing), Mechthild Schmitt-Jansen (Conceptualization, Writing—original draft, Writing—review & editing), and Natàlia Corcoll (Conceptualization, Writing—original draft, Writing—review & editing)

Conflicts of interest

None declared.