Today, thousands of chemical substances are released into the environment because of human activities. It is thus crucial to identify all relevant chemicals that contribute to toxic effects on living organisms, also potentially disturbing the community functioning and the ecosystem services that flow from them. Once identified, chemical substances need to be associated with ecotoxicity factors. Nevertheless, getting such factors usually requires time-, resources- and animal-costly experiments that it should be possible to avoid. In this perspective, modelling approaches may be particularly helpful if they rely on easy-to-obtain information to be used as predictive variables.

Within this context, the paper of Servien et al. (2022) illustrates the use of machine learning algorithms to predict toxicity and ecotoxicity factors that were missing for a collection of compounds. Their modelling approach involve a collection of molecular descriptors as input variables. A total of 40 molecular descriptors were extracted from the TyPol database (Servien et al., 2014) as those describing the best how organic compounds behave within the environment. These molecular descriptors also have the advantage to be easily quantifiable for new chemical substances under evaluation. The performances of the proposed models were systematically checked and compared to the classical linear partial least square method, based on the calculation of the absolute error (namely, the difference between prediction and true value). This finally led to different best models (that is associated to the lowest median absolute error) according to the classification of the 526 compounds comprised in the TyPol database in five clusters. These five clusters of different sizes gather chemical substances with different but specific molecular characteristics, also corresponding to different estimates of the characterization factors both in their median and within-variability.

In a final step, predictions of characterization factors were performed for 102 missing values in the USEtox® database (Rosenbaum et al., 2008) but also referenced in TyPol. This paper highlights that the molecular descriptors that explain the most the toxicity of the chemical substances in each cluster strongly differ. Nevertheless, these predictions, whatever the cluster, appear precise enough to be considered as relevant despite everything.

As a conclusion, this paper is a promising proof-of-concept in using machine learning modelling to go beyond some constraints around the toxicity evaluation of chemical substances, especially handling non-linearities and data-demanding calculations, in in an ever-changing world that is gradually depleting its resources without sufficient concern for the short-term risks to the environment and human health.

References

Rosenbaum RK, Bachmann TM, Gold LS, Huijbregts MAJ, Jolliet O, Juraske R, Koehler A, Larsen HF, MacLeod M, Margni M, McKone TE, Payet J, Schuhmacher M, van de Meent D, Hauschild MZ (2008) USEtox—the UNEP-SETAC toxicity model: recommended characterisation factors for human toxicity and freshwater ecotoxicity in life cycle impact assessment. The International Journal of Life Cycle Assessment, 13, 532. https://doi.org/10.1007/s11367-008-0038-4

Servien R, Latrille E, Patureau D, Hélias A (2022) Machine learning models based on molecular descriptors to predict human and environmental toxicological factors in continental freshwater. bioRxiv, 2021.07.20.453034, ver. 6 peer-reviewed and recommended by Peer Community in Ecotoxicology and Environmental Chemistry. https://doi.org/10.1101/2021.07.20.453034

Servien R, Mamy L, Li Z, Rossard V, Latrille E, Bessac F, Patureau D, Benoit P (2014) TyPol – A new methodology for organic compounds clustering based on their molecular characteristics and environmental behavior. Chemosphere, 111, 613–622. https://doi.org/10.1016/j.chemosphere.2014.05.020

Ponds, as small freshwater ecosystems, are particularly vulnerable due to their limited size. Yet they are often overlooked in research, possibly because they are considered less important (Biggs et al., 2017). Shallow water bodies support higher biodiversity than larger aquatic ecosystems. Peri-urban areas, characterized by a blend of agricultural and urban land uses, are dynamic and constantly evolving landscapes with diverse activities and stakeholders (Zoomers et al., 2017); as such, they are referred to as "restless landscapes" or zones of continual transformation (Zoomers et al., 2017). They often harbor neglected ecosystems, and despite their ecological importance, ponds and wetlands in peri-urban areas remain relatively underexplored (Wanek et al., 2021). Furthermore, these areas may experience increased contaminant inputs, which are regarded as one of the 12 major threats to freshwater biodiversity (Reid et al., 2019).

In this context, Hulot et al. (2025) monitored 12 peri-urban ponds in the Île-de-France region (near Paris, France) to investigate the relationships between land use, pollutant concentrations in water and sediment, and macroinvertebrate distribution. The originality of this work lies in its multidisciplinary and integrated approach, combining ecological and chemical analyses. While assessing agricultural, urban, grassland, and forest landscapes surrounding each pond, this study aimed to understand how contaminants constrain macroinvertebrate communities. The authors hypothesized that i) ponds in grassland and forest environments support higher local diversity than those in agricultural or urban areas, ii) rare and pollution-sensitive species significantly contribute to regional diversity, and iii) contaminants in water and sediment influence the distribution of macroinvertebrate morphotaxa.

This study provides numerous novel results. Specifically, it demonstrates that fluctuations in morphotaxa composition are predominantly driven by species replacement rather than by disparities in species richness. This pattern was largely attributed to the high prevalence of pollutant-tolerant species in certain ponds. In addition, community compositions appeared to be influenced by sediment levels of pharmaceuticals, water conductivity, and ammonium concentrations. In summary, ponds located in peri-urban areas are subject to a range of human-induced disturbances, and these results suggest that these disturbances lead to chronic and varied contamination, which in turn affects the composition of morphotaxa communities.

These findings establish a clear connection between local pollution and ecological composition, a crucial aspect for effective conservation and restoration efforts on peri-urban ponds.

References

Biggs, J., S. von Fumetti, Kelly-Quinn M. (2017). The importance of small waterbodies for biodiversity and ecosystem services: implications for policy makers. Hydrobiologia 793(1): 3-39 625. https://doi.org/10.1007/s10750-016-3007-0

Hulot, F.D., Hanot, C., Nélieu, S., Lamy, I., Karolak, S., Delarue, G., Baudry E., (2024) Do macroinvertebrate abundance and community structure depend on the quality of ponds located in peri-urban areas? ver.3 peer-reviewed and recommended by PCI Ecotoxicology and Environmental Chemistry. https://hal.science/hal-04850220v1

Reid, A. J., A. K. Carlson, I. F. Creed, E. J. Eliason, P. A. Gell, P. T. J. Johnson, 712 K. A. Kidd, T. J. MacCormack, J. D. Olden, S. J. Ormerod, J. P. Smol, W. W. Taylor, K. Tockner, J. C. Vermaire, D. Dudgeon, Cooke, S. J. 2019. Emerging threats and persistent conservation challenges for freshwater biodiversity. Biological Reviews 94(3):849-873. https://doi.org/10.1111/brv.12480

Wanek, A., C. L. M. Hargiss, J. Norland, Ellingson, N. 2021. Assessment of water quality in ponds across the rural, peri-urban, and urban gradient. Environmental Monitoring and Assessment 193: 694. https://doi.org/10.1007/s10661-021-09471-7

Zoomers, A., F. van Noorloos, K. Otsuki, G. Steel, van Westen, G. 2017. The Rush for Land in anUrbanizing World: From Land Grabbing Toward Developing Safe, Resilient, and Sustainable Cities and Landscapes. World Dev 92:242-252. https://doi.org/10.1016/j.worlddev.2016.11.016

The overall pollution of air, water, and soil is currently recognized as one of the five main drivers of biodiversity loss (IPBES 2019). Among chemicals, pesticides play a significant role in this global crisis, as recently re-assessed at the scale of France (Pesce et al. 2023). In this context, although parent molecules are subject to national and international regulations, based on a priori ecological risk assessment (e.g., REACH) as well as monitoring in some environments (see e.g., pesticides classified in the priority list of substances by the Water Frame Directive), pesticide metabolites are rarely considered. In the case of the widely used herbicide glyphosate, a particular concern is rising about its primary metabolite, aminomethylphosphonic acid (AMPA), due to its persistence and overlooked toxicity. 

Amphibians are the most threatened class of vertebrates on earth, with two in every five species considered threatened with extinction (IUCN Red List). While this overall decline has multiple causes, the contribution of pesticides is suspected to be significant in some regions.

In this context, Tartu et al. (2024) studied the effects of AMPA on the gut microbiota of the spined toad, Bufo spinosus. This work complements a previous study which showed embryo mortality, oxidative stress, deformities at hatching, and delayed development (Tartu et al. 2022). Using a common garden experiment based on populations from contrasted habitats (agricultural vs woodland, same as in the previous study), the authors captured breeding pairs and collected the eggs laid in the laboratory. These were exposed to 0.4 µg/L AMPA during embryonic and larval development. Individual microbiota was analysed non-invasively, i.e., using the faeces collected in treatment vessels. Bacterial biodiversity was genetically assessed (16S rRNA). The community biomass and taxonomic structure were analysed as a function of chemical treatment, mother and father body condition (fat vs thin), as well as population of origin. 

As a primary effect, AMPA reduced the microbial biomass. Furthermore, a significant interaction was detected between AMPA and mother condition on the community structure and composition. This alteration, observed in « fat » females only, was reflected through a significant decrease in Bacteroidota and a significant increase in Actinobacteriota (the latter being consistent with the ability of some species in this phylum to use AMPA as a source of phosphorus). The higher sensitivity of tadpoles from females in better condition seems counterintuitive, since better body condition is expected to be associated with higher fitness (and possibly higher ability to face chemical stress), the authors discuss this in the light of the literature (which shows that microbiome-fitness relationships are not often evidenced in natural populations), and hypothesize that these females in better conditions host a microbiota that may be more efficient, yet also more sensitive to AMPA. Not ruling out other possible factors ignored in their study, in particular genotypic effects, the authors further discuss the importance of maternally transmitted effects via the microbiota. 

Altogether, the results published by Tartu et al. (2024) provide important new findings on AMPA toxicity to amphibian microbiota, and also confirm the occurrence of vertical transmission of the microbiota from mother to progeny in this vertebrate class.

References 

IPBES (2019). Global assessment report on biodiversity and ecosystem services of the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services. E. S. Brondizio, J. Settele, S. Díaz, and H. T. Ngo (editors). IPBES secretariat, Bonn, Germany. 1148 pages. https://doi.org/10.5281/zenodo.3831673

Pesce, S., Mamy, L., Sanchez, W., et al. (2023). Main conclusions and perspectives from the collective scientific assessment of the effects of plant protection products on biodiversity and ecosystem services along the land–sea continuum in France and French overseas territories. Environ Sci Pollut Res . https://doi.org/10.1007/s11356-023-26952-z

Tartu, S., Renoirt, M., Cheron, M., Gisselmann, L.-L., Catoire, S., Brischoux, F. (2022). Did decades of glyphosate use have selected for resistant amphibians in agricultural habitats? Environ. Pollut. 310, 119823. https://doi.org/10.1016/j.envpol.2022.119823

Tartu, S., Pollet, N., Clavereau, I., Gauthier Bouchard, G., Brischoux, F. (2024). Maternal body condition affects the response of larval spined toads’ faecal microbiome to a widespread contaminant. bioRxiv,  ver. 2 peer-reviewed and recommended by Peer Community in Ecotoxicology and Environmental Chemistry. https://doi.org/10.1101/2023.12.18.572122