In fish, the gut microbiome plays a crucial role in homeostasis and health and is affected by several organic and inorganic environmental contaminants. Amphidromous fish are sentinel species, particularly exposed to these stressors. We used whole metagenome sequencing to characterize the gut microbiome of wild European eels (Anguilla anguilla) at a juvenile stage captured from three sites with contrasted pollution levels in term of heavy metals and persistent organic pollutants. The objectives were to identify what parameters could alter the gut microbiome of this catadromous fish and to explore the potential use of microbiota as bioindicators of environment quality. We identified a total of 1079 microbial genera. Overall, gut microbiome was dominated by Proteobacteria, Firmicutes and Actinobacteria. Alpha and beta diversity were different amongst sites and could be explained by a reduced number of environmental and biological factors, specifically the relative abundance of fish preys in eels’ diet, PCB101, γHCH (lindane), transnonachlor and arsenic. Furthermore, we identified a series of indicator taxa with differential abundance between the three sites. Changes in the microbial communities in the gut caused by environmental pollutants were previously undocumented in European eels. Our results indicate that microbiota might represent another route by which pollutants affect the health of these aquatic sentinel organisms.

The impact of microplastics (MP) has attracted much attention from the scientific community and many laboratory assessments have been made of their effects on aquatic organisms. To produce MP from real environmental plastic waste, which would enable more realistic experiments, we used plastic pearl farming equipment from French Polynesian lagoons. Here, the pearl oyster Pinctada margaritifera could encounter MP coming from their breakdown in its surrounding environment. We tested an established method based on mechanical cryogenic grinding and liquid sieving. Our desired size range was 20–60 μm, corresponding to the optimal particle size ingested by P. margaritifera. The protocol was effective, generating MP particles of 20–60 μm (∼17,000–28,000 MP μg−1), but also produced too many smaller particles. The peak in the desired size range was thus flattened by the many small particles <3 μm (∼82,000–333,000 MP μg−1; 53–70% of total analysed particles), visible at the limit of Coulter counter analysis (cut-off point: 2 μm). Laser diffraction analysis (cut-off point: 0.4 μm) provided greater detail, showing that ∼80–90% of the total analysed particles were <1 μm. Diverging particle size distributions between those expected based on sieving range and those really observed, highlight the need to perform fine-scaled particle size distribution analyses to avoid underestimating the number of small micro- and nanoplastics (MNP) and to obtain an exact estimation of the fractions produced. Size and microstructure characterization by scanning electron microscopy suggested spontaneous particle self-assembly into crystal superstructures, which is the supposed cause of the divergence we observed. Overall, our results emphasize that particle self-assembly is a technical hurdle requiring further work and highlight the specific need to finely characterize the size distribution of MNP used in ecotoxicological experiments to avoid overestimating effects.

We measured phytoplankton primary production and heterotrophic bacterial activities on microplastics and seawater in the Northwestern Mediterranean Sea during two 3-month spring periods over 2 consecutive years. Microorganisms growing on a 5 mm diameter low density polyethylene films (LDPE; 200 μm thick) faced two contrasting conditions depending on the year. Spring 2018 was characterized by consistent nutrient inputs and bloom development. In spring 2019, nutrient inputs and bloom were low. For the first time, we observed a clear coupling between primary production and heterotrophic prokaryote production on microplastics during both years, but with different intensity between years that reflected the crucial role of the trophic environmental conditions (nutrient supply) in shaping microbial activities on plastics. We found that high primary production on plastics could support the whole (net autotrophy) or the majority of the bacterial carbon demand needed for heterotrophic activities, supplemented by other carbon sources if surrounding waters are highly productive. We propose that microbial activity on plastics influences the microbial community in the surrounding seawater, especially when the environmental conditions are less favorable. An illustrative image of the role of plastics in the environment could be that of an inverter in an electrical circuit that mitigates both positive and negative variations. Our results highlight the potential role of the plastisphere in shaping biogeochemical cycles in the context of increasing amounts of plastic particles in the marine environment.

International audience | In 2020 two main French research institutes, INRA and IRSTEA, merged to form INRAE the French National Research Institute for Agriculture, Food and Environment. This was a timely opportunity to update the ecotoxicology delineations and to identify new key issues to be developedat INRAE, notably by including aquatic ecosystems biodiversity and public policies as new research priorities, and for the French ECOTOX Network of terrestrial and aquatic ecotoxicology supported by INRAE (https://www6.inrae.fr/ecotox/) to address new research and development topics.Within this context, the ecotoxicology of the soil:water continuum (SWC) was chosen as the theme of the 7th seminar of the ECOTOX Network held as a 2-day webinar in November 2020. This special issue proposes a selection of some of the presented studies, covering subjects from terrestrial to aquatic ecotoxicology, including experimental and modelling approaches, to finally tentatively describe what could stand for SWC ecotoxicology in the Anthropocene context.

International audience | The evaluation of soil quality requires the use of robust methods to assess biologically based indicators. Among them, enzyme activities are used for several decades, but there is a clear need to update their measurement methods for routine use, in combining feasibility, accuracy, and reliability. To this end, the platform Biochem-Env optimized a miniaturized method to measure enzyme activities in soils using colorimetric substrates in micro-well plates. The standardization of the method was carried out within the framework of ISO/TC 190/SC 4/WG 4 "Soil quality - Biological methods" workgroup, recommending an inter-laboratory evaluation for the publication of a full ISO standard. That evaluation, managed by the platform, was based on the measurement, in six soils of contrasted physicochemical properties, of the ten soil enzyme activities described in the standard. Eight laboratories were involved in the validation study. Only 2.7% of outliers were identified from the analyses of the whole dataset. The repeatability and reproducibility of the method were determined by computing, respectively, the intra-laboratory (CVr,) and inter-laboratory (CVR) coefficients of variation for each soil and enzyme. The mean CVr ranged from 4.5% (unbuffered phosphatase) to 9.9% (alpha-glucosidase), illustrating a reduced variability of enzyme activities within laboratories. The mean CVR ranged from 13.8% (alkaline phosphatase) to 30.9% (unbuffered phosphatase). Despite this large CVR noticed for unbuffered phosphatase, the method was repeatable, reproducible, and sensitive. It also proved to be applicable for measuring enzyme activities in different types of soils. These results have been found successful by ISO/TC 190/SC4 and resulted in the publication of ISO 20130:2018 standard.

International audience | The effect of wastewater irrigation on the diversity and composition of bacterial communities of soil mesocosms planted with lettuces was studied over an experiment made of five cultivation campaigns. A limited effect of irrigation with either raw or treated wastewater was observed in both alpha-diversity and beta-diversity of soil bacterial communities. However, the irrigation with wastewater fortified with a complex mixture of fourteen relevant chemicals at 10 mu g/L each, including pharmaceutical, biocide, and pesticide active substances, led to a drift in the composition of soil bacterial community. One hundred operational taxonomic units (OTUs) were identified as responsible for changes between treated and fortified wastewater irrigation treatments. Our findings indicate that under a realistic agronomical scenario, the irrigation of vegetables with domestic (treated or raw) wastewater has no effect on soil bacterial communities. Nevertheless, under the worst-case scenario tested here (i.e., wastewater fortified with a mixture of chemicals), non-resilient changes were observed suggesting that continuous/repeated irrigation with wastewater could lead to the accumulation of contaminants in soil and induce changes in bacterial communities with unknown functional consequences.

International audience | Insects play many important roles in nature due to their diversity, ecological role, and impact on agriculture or human health. They are directly influenced by environmental changes and in particular anthropic activities that constitute an important driver of change in the environmental characteristics. Insects face numerous anthropogenic stressors and have evolved various detoxication mechanisms to survive and/or resist to these compounds. Recent studies highligted the pressure exerted by xenobiotics on insect life-cycle and the important role of insect-associated bacterial microbiota in the insect responses to environmental changes. Stressor exposure can have various impacts on the composition and structure of insect microbiota that in turn may influence insect biology. Moreover, bacterial communities associated with insects can be directly or indirectly involved in detoxification processes with the selection of certain microorganisms capable of degrading xenobiotics. Further studies are needed to assess the role of insect-associated microbiota as key contributor to the xenobiotic metabolism and thus as a driver for insect adaptation to polluted habitats.

International audience | Abstract France is the first pesticide-consuming country in Europe. Glyphosate is the most used pesticide worldwide and glyphosate is detected in the general population of industrialized countries, with higher levels found in farmers and children. Little data was available concerning exposure in France. Our objective was to determine glyphosate levels in the French general population and to search for an association with seasons, biological features, lifestyle status, dietary habits, and occupational exposure. This study includes 6848 participants recruited between 2018 and 2020. Associated data include age, gender, location, employment status, and dietary information. Glyphosate was quantified by a single laboratory in first-void urine samples using ELISA. Our results support a general contamination of the French population, with glyphosate quantifiable in 99.8% of urine samples with a mean of 1.19 ng/ml + / − 0.84 after adjustment to body mass index (BMI). We confirm higher glyphosate levels in men and children. Our results support glyphosate contamination through food and water intake, as lower glyphosate levels are associated with dominant organic food intake and filtered water. Higher occupational exposure is confirmed in farmers and farmers working in wine-growing environment. Thus, our present results show a general contamination of the French population with glyphosate, and further contribute to the description of a widespread contamination in industrialized countries.

International audience | The main objective of this study was to improve our knowledge on the responses of fish populations to multistress (diffuse pollution and warming waters) in estuaries. Adult flounders were caught in two estuaries in the Eastern English Channel: the heavily polluted Seine estuary vs the moderately contaminated Canche estuary. Fish samplings were conducted in January just before the reproduction period, and in July when gonads were at rest. The overall rise in coastal winter water temperatures detected over the Channel impairs the flounder's phenology of reproduction in the two estuaries, inducing a delay of maturation process and probably also spawning. The higher liver histopathology index in Seine vs Canche could be the consequence of the fish exposition to a complex cocktail of contaminants in a strongly industrialized estuary. Higher levels of neurotoxicity, gill lipid peroxidation, and liver EROD activity were observed in Seine vs Canche. Furthermore, a possible impairment in mitochondrial metabolism was suggested in the Seine flounder population. We confirmed in this study the potential role of two membrane lipids (sphingomyelin and phosphatidylserine) in the resistance towards oxidative stress in Seine and Canche. Finally, we suggest that the Seine flounder population (and possibly the connected Eastern English Channel flounder populations over the French Coast) could be seriously impacted in the future by multistress: higher winter temperatures and chemical contamination.

International audience | Organic waste (OW) reuse in agriculture is a common practice fostered by benefits in terms of waste recycling and crop production. However, OW amendments potentially affect the fate of pesticide spread on fields to protect the crops from pests and weeds. The influence of OW on the sorption, degradation, and leaching of pesticides is generally studied for each mechanism separately under artificial laboratory conditions. Our study aims at evaluating the balance of these mechanisms under more realistic conditions to clarify the influence of three common OW amendments on the fate, in soil, of the widely used herbicide S-Metolachlor. We performed leaching experiments in large undisturbed soil cores amended with raw sewage sludge, composted sludge, and digested pig slurry (digestate), respectively. We monitored S-Metolachlor and its two main metabolites MET-OA and MET-ESA in the leachates during a succession of 10 rainfall events over 126 days. We also quantified the remaining S-Metolachlor and metabolites in the soil at the end of the experiments. S-Metolachlor leaching didn't exceed 0.1% of the applied dose with or without OW amendment. Despite a soil organic carbon increase of 3 to 32%, OW amendments did not significantly affect the amount of S-Metolachlor that leached through the soil (0.01 to 0.1%) nor its transformation rate (6.0 to 8.6%). However, it affected the degradation pathways with an increase of MET-OA relative to MET-ESA formed after OW amendment (28 to 54%) compared to the controls (8%). Concentration of S- Metolachlor and metabolites in the leachates of all treatments greatly exceeded the regulatory limit for groundwater intended for human consumption in Europe. These high concentrations were probably the consequence of preferential macropore flow. Colloids had comparable levels in the leachates after S-Metolachlor application. Dissolved organic carbon was also comparable in the controls, digestate, and sludge treatments but was 65% higher in the compost-amended cores. These results, along with a great variability among replicates inherent to experiments performed under realistic conditions, partly explain the limited impact of OW on the transport of S-Metolachlor.