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18 Jan 2022
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Machine learning models based on molecular descriptors to predict human and environmental toxicological factors in continental freshwater

Predicting characterization factors of chemical substances from a set of molecular descriptors based on machine learning algorithms

Recommended by ORCID_LOGO based on reviews by Patrice Couture, Sylvain Bart, Dominique Lamonica and 2 anonymous reviewers

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

Machine learning models based on molecular descriptors to predict human and environmental toxicological factors in continental freshwaterRémi Servien, Eric Latrille, Dominique Patureau, Arnaud Hélias<p style="text-align: justify;">It is a real challenge for life cycle assessment practitioners to identify all relevant substances contributing to the ecotoxicity. Once this identification has been made, the lack of corresponding ecotoxicity facto...Aquatic ecotoxicology, Ecosystem Health, Environmental pollution, ModellingSandrine CHARLES2021-07-21 09:09:50 View
02 May 2024
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Maternal body condition affects the response of larval spined toads' faecal microbiome to a widespread contaminant

Effects of AMPA on Bufo spinosus microbiota

Recommended by based on reviews by Fabrice Martin-Laurent, Lauris Evariste and 1 anonymous reviewer

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

 

Maternal body condition affects the response of larval spined toads' faecal microbiome to a widespread contaminantSabrina Tartu, Nicolas Pollet, Isabelle Clavereau, Gauthier Bouchard, Francois Brischoux<p>Glyphosate’s primary metabolite, aminomethylphosphonic acid (AMPA), is the most detected pollutant in surface waters. Recent studies have raised concerns about its toxicity, yet underlying mechanisms remain poorly understood. A disruption of th...Aquatic ecotoxicology, Environmental pollutionMarie-Agnès Coutellec Lauris Evariste, Fabrice Martin-Laurent2023-12-19 10:32:45 View
29 Jul 2024
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Molecular response to multiple trace element contamination of the European sardine

Molecular-level responses highlight physiological stress in muscle and liver tissue of apparently healthy European sardine specimen

Recommended by ORCID_LOGO and ORCID_LOGO based on reviews by Sophie Prud'homme, Roberta Bettinetti and 1 anonymous reviewer

Fish is an essential component of healthy human diets and the preservation of fish stocks and other marine resources is included as a target of Sustainable Development Goal 14 ‘Conserve and sustainably use the Oceans, Sea and Marine Resources for Sustainable Development’ (UNEP). However, several fish stocks remain in sub-optimal (or worse) conditions due to overfishing and a range of stressors including chemical pollution. Chemical pollution can result in high level of chemicals in fish making it unsuitable for human consumption. Furthermore, the occurrence of chemical-related physiological stress in otherwise apparently healthy fish requires additional research efforts. In natural environments, further complexity arises from fish being simultaneously exposed to multiple contaminants/stressors as opposed to laboratory investigation usually dealing with one or very few contaminants/stressors at a time (Schäfer et al., 2023).

Beauvieux et al. (2024) examined the possible role of accumulation of multiple elements on the physiological status of first-year-of-life specimen of European sardine collected in the Gulf of Lions (northeastern Mediterranean Sea) as a contributing factor to the declining sardine population observed in the region since 2008. The ultimate objective of the paper was to identify potential biomarkers of stress in fish otherwise not exhibiting any anomalies in body condition, in agreement with the principles of chemical stress ecology put forward by van der Brink (2008). 

Out of a total of 105 specimen, individuals were selected according to the lowest (n = 14) or highest (n = 15) levels of contamination and subject to proteomic analysis of liver and red muscle tissues.  A first Principal component analysis on all specimen highlighted the possible influence of the Rhone river as a source of geogenic and anthropogenic elements to the Gulf of Lions. 

A second PCA performed only on specimen selected from proteomics analysis allowed to identify three elemental mixtures possibly responsible for the observed physiological effects. Proteomic analysis in liver and muscle tissue identified both similarities and differences in the pathways involved in response to stress. More in detail, the expression patterns of Myosin and Myomesin were downregulated in red muscle for highly exposed specimen, which suggests possible effects of elemental accumulation on the locomotion abilities of Mediterranean sardines. Pathways involved in lipid metabolism and immune processes were up-regulated in liver, pointing to increased energetic costs for maintaining the overall fish homeostasis in presence of metal contamination. It is interesting to note that these effects were observed at concentrations below the legal thresholds for human consumption (except for As), albeit such thresholds are available only for a limited number of elements (Cd, Pb, Cd, As and inorganic Sn) (EU, 2023).

Although stressors other than trace elements could contribute to the observed molecular responses, as acknowledged by the authors themselves, Beauvieux et al. (2024) show that biological responses at lower levels of biological organization can provide both early-warning indications of potential adverse effects in the long term and better understanding of drivers of population decline. By advancing our knowledge of the physiological responses to trace elements and identifying potential biomarkers, this study lays the groundwork for more effective monitoring and conservation strategies. Further studies addressing the combined effects of multiple environmental stressors remain essential to develop holistic approaches to marine ecosystem management and species conservation. 

References

Beauvieux A., Fromentin J.-M., Saraux C., Romero D., Couffin N., Brown A., Metral L., Bertile F., Schull Q. (2024). Molecular response to multiple trace element contamination of the European sardine. bioRxiv, ver. 4 peer-reviewed and recommended by Peer Community in Ecotoxicology and Environmental Chemistry. https://doi.org/10.1101/2024.02.16.580673  

EU (2023). Commission Regulation (EU) 2023/915. https://eur-lex.europa.eu/eli/reg/2023/915/oj/eng

Schäfer R. B., Jackson M., Juvigny-Khenafou N., Osakpolor S. E., Posthuma L., Schneeweiss A., Spaak J., & Vinebrooke R. (2023). Chemical Mixtures and Multiple Stressors: Same but Different? Environmental Toxicology and Chemistry, 42(9), 1915-1936, https://doi.org/10.1002/etc.5629

UNEP: https://sdgs.un.org/goals

Van den Brink P. J. (2008). Ecological Risk Assessment: From Book-Keeping to Chemical Stress Ecology. Environmental Science & Technology, 42(24), 8999-9004. https://doi.org/10.1021/es801991c 

Molecular response to multiple trace element contamination of the European sardineAnaïs Beauvieux, Jean-Marc Fromentin, Claire Saraux, Diego Romero, Nathan Couffin, Adrien Brown, Luisa Metral, Fabrice Bertile, Quentin Schull<p>In marine ecosystems, the presence of trace elements resulting from anthropogenic activities has raised concerns regarding their potential effects on marine organisms. This study delves into the intricate relationship between trace element cont...Biomarkers, Environmental pollution, Marine ecotoxicologyDavide Anselmo Luigi Vignati2024-02-22 16:24:52 View
22 Jul 2023
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No evidence for an effect of chronic boat noise on the fitness of reared water fleas

Noise impact in Daphnia magna

Recommended by ORCID_LOGO based on reviews by Marie-Agnès Coutellec and 1 anonymous reviewer

Our ability to anticipate and estimate how pollution affects biota is of paramount importance in the field of ecotoxicology. Impact of chemical pollution by metals, drugs or pesticides was widely studied in different species using acute and chronic scenarios. While environmental factors such as temperature are also often considered, noise is largely ignored in these models despite the knowledge of its detrimental effects in vertebrates. Studies of noise impacts included behavior and fitness endpoints and showed no effect to death depending on intensity, frequency and the distance from the noise source (Peng et al., 2015). Nonetheless, the impact of noise in biota is not well-understood, which impairs its effective mitigation. 

Noise or acoustic pollution due to boat traffic produce low-frequency stationary noise. It is a pervasive and ubiquitous pollutant found in aquatic ecosystems. In this context, Prosnier et al. (2023) addresses how intermittent and random noise impacted Daphnia magna, a representative of zooplankton model, widely used in ecotoxicology. Endpoints of lifespan and clonal offspring production were measured in the presence or absence of motorboat noises, in animals reared from birth to death. Noise consisted in a playlist of 15 sounds of motorboat recorded in the Grangent lake (Loire, France). Their intensity ranged from 0 to -25 dB Re 1 μPa by 5 dB to create 75 sounds from 103 to 150 dB RMS Re 1 μPa – a range of levels occurring in lakes. Treatment had no effect on analyzed endpoints, contrary to a continuous broadband noise (100-20,000 Hz) that caused higher survival and fecundity, and reduced speed of motion compared to control (Prosnier et al., 2022). Data point that temporal (continuous, regular, random) and frequency of noise are instrumental for its effects. 

References

Peng, C., X. Zhao and G. Liu (2015). "Noise in the Sea and Its Impacts on Marine Organisms." Int J Environ Res Public Health 12(10): 12304-12323. https://doi.org/10.3390/ijerph121012304

Prosnier, L., E. Rojas and V. Médoc (2023). "No evidence for an effect of chronic boat noise on the fitness of reared water fleas." bioRxiv: 2022. ver. 4 peer-reviewed and recommended by Peer Community in Ecotoxicology and Environmental Chemistry. https://doi.org/10.1101/2022.11.20.517267

Prosnier, L., E. Rojas, O. Valéro and V. Médoc (2022). "Chronic noise unexpectedly increases fitness of a freshwater zooplankton." bioRxiv: 2022. https://doi.org/10.1101/2022.11.19.517212

No evidence for an effect of chronic boat noise on the fitness of reared water fleasLoïc Prosnier, Emilie Rojas, Vincent Médoc<p style="text-align: justify;">Among the numerous questions about human impacts on ecosystems, there is a growing interest for acoustic pollution. First studies on underwater acoustic pollution focused, and showed effects, on vertebrates’ behavio...Aquatic ecotoxicology, Ecosystem Health, Environmental pollution, Global changes, Life History, OtherClaudia Cosio2022-12-08 17:23:07 View
09 Dec 2022
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Soot and charcoal as reservoirs of extracellular DNA

New insights into eDNA sorption onto environmental carbonaceous materials

Recommended by based on reviews by Jérôme Duval and 1 anonymous reviewer

In recent years, the use of environmental DNA (eDNA) to investigate biodiversity has gained considerable interest (Thomsen and Willerslev, 2015; Mauvisseau et al., 2022). It allows for the indirect detection of species but it requires a sound understanding of eDNA behaviour and persistence in the environment. This is, however, a complex task because eDNA may be found in several states (e.g., dissolved, adsorbed, intracellular or intraorganellar), which display specific decay rates controlled by environmental factors (Harrisson et al., 2019; Mauvisseau et al. 2022). In the environment, dissolved DNA may interact with the surfaces of various sorbents, including mineral and organic particles/colloids. Current knowledge on eDNA sorption suggests that eDNA–sorbent interactions are controlled by electrostatics as well as inner-sphere complex formation (Mauvisseau et al., 2022). 

In this context, the work undertaken by Jelavic et al. (2022), focused on the adsorption of eDNA by lesser-investigated carbonaceous materials (CMs), namely soot and charcoal, as common non-mineral environmental surfaces. 

The authors aimed to study the adsorption capacity of soot and charcoal surfaces with respect to eDNA, in relation to solution parameters (i.e., pH, ionic strength, concentration/type of cations), time and eDNA length, under both non‐equilibrium and equilibrium conditions. Using such an approach, Jelavic et al. demonstrated the large adsorption capacities of CMs and the strong binding of DNA to these sorbents. The authors did not provide definitive conclusions on the mechanisms of eDNA sorption onto CMs. However, they provided new elements suggesting that, along with electrostatic interactions, hydrophobic interactions might play an important role in the adsorption of eDNA to CMs such as soot and charcoal. 

Altogether, the results presented in this paper highlight the relevance of CMs as sources of biodiversity information. In addition, it is likely that those results will also prove useful for the community to improve protocols for eDNA extraction from environmental samples that contain high fractions of CMs, e.g. urban soils. 

References

Harrison JB, Sunday JM, Rogers SM (2019) Predicting the fate of eDNA in the environment and implications for studying biodiversity. Proceedings of the Royal Society B: Biological Sciences, 286, 20191409. https://doi.org/10.1098/rspb.2019.1409

Jelavic S, Thygesen LG, Magnin V, Findling N, Müller S, Meklesh V, Sand KK (2022) Soot and charcoal as reservoirs of extracellular DNA. ChemRxiv, ver. 5 peer-reviewed and recommended by Peer Community in Ecotoxicology and Environmental Chemistry. https://doi.org/10.26434/chemrxiv-2021-9pz8c-v5

Mauvisseau Q, Harper LR, Sander M, Hanner RH, Kleyer H, Deiner K (2022) The Multiple States of Environmental DNA and What Is Known about Their Persistence in Aquatic Environments. Environmental Science & Technology, 56, 5322–5333. https://doi.org/10.1021/acs.est.1c07638

Thomsen PF, Willerslev E (2015) Environmental DNA – An emerging tool in conservation for monitoring past and present biodiversity. Biological Conservation, 183, 4–18. https://doi.org/10.1016/j.biocon.2014.11.019

Soot and charcoal as reservoirs of extracellular DNAStanislav Jelavic, Lisbeth Garbrecht Thygesen, Valerie Magnin, Nathaniel Findling, Sascha Müller, Viktoriia Meklesh, Karina Krarup Sand<p style="text-align: justify;">The vast potential of using sediment adsorbed DNA as a window to past and present biodiversity rely on the ability of solid surfaces to adsorb environmental DNA. However, a comprehensive insight into DNA adsorption ...Analytical Chemistry, Environmental chemistry, Environmental monitoringPierre LabadieAnonymous, Jérôme Duval2022-04-13 16:08:36 View