Biology subjects

Geffard, O.

Publications and source records attributed to Geffard, O..

7 recordsLinked to original sources

bioRxiv2026

Uncovering aquatic toxicity as a specific stressor among multiple environmental drivers affecting the functional structure of French stream macroinvertebrate communities

O_LISince recent years, freshwater ecosystems such as rivers are subjected to increasing pressures from human-induced drivers of changes, including chemical contamination, warming and nutrient enrichment. Among those, toxic chemicals are particularly concerning, as aquatic contamination is strongly increasing but their effects on ecosystem structure and functioning remain poorly understood and difficult to predict. Yet, those are expected to impact freshwater ecological communities, notably through selecting species exhibiting particular biological traits. A growing literature tested predictions on the effects of multiple environmental drivers, including chemicals, on the functional structure of macroinvertebrate communities, but disentangling the respective influences of the different drivers on the observed patterns usually remains challenging. C_LIO_LIHere, we used multivariate analyses with variation partitioning to estimate the independent and combined effects of toxic contamination, water temperature and nutrient load on the species abundances and biological traits of macroinvertebrate communities in 76 French streams. Toxic contamination was quantified based on the Gammarus feeding inhibition indicator recorded during repeated in situ biotests. We then compared trait responses with expectations from a priori predictions derived from the literature, and looked at the link between taxon turnover and taxonomic and functional diversity metrics using linear models. C_LIO_LIOur results suggest that, when considered independently, each driver had specific impact on invertebrate taxa and biological traits, with different consequences on community composition and diversity. Notably, we showed significant changes in taxonomic composition linked to toxicity, associated with the reduction of both taxonomical and functional richness, but no significant effect on biological trait composition. In contrast, temperature and moreover nutrient load strongly effected traits, but with variables associations with diversity metrics depending on driver. Finally, when all three drivers were considered in combination, patterns were similar to those observed for temperature, suggesting dominance rather than additive effects between drivers. C_LIO_LIOur study reveals particular negative impacts of toxicity on macroinvertebrate communities in contrast with other drivers, which highlights the potential risk posed by contaminants for freshwater biodiversity. C_LI

ecology↗

bioRxiv2024

Key gut microbiota components and functions in an aquatic keystone species across diets assessed by metaproteomics

The gut microbiota plays a crucial role in maintaining host fitness and modulating contaminant toxicity-related responses. However, information on how the gut microbiota of sentinel species responds to environmental factors is limited. In this study, we characterized the gut microbial community and its functions under normal, contaminant-free conditions by examining the effects of different diets over a 10-day period (alder leaf, carrot, spinach, and protein-rich granules) on the amphipod Gammarus fossarum, commonly used in bioassays for ecotoxicity assessment of contaminated rivers. Metaproteomic analysis of intestine samples enabled taxonomic characterization of the gut microbiota from this millimetric animal, assignment of biological functions to each microbial entity, and functional analysis of host proteins. The most abundant microbes detected in the gut belong to 37 bacterial and 5 fungal genera. Functional analyses of host and microbial proteins revealed complementary metabolic activities, allowing the degradation of complex polysaccharides such as cellulose and chitin. Diet was found to shape microbial community structure, with foodborne microorganisms strongly influencing structural changes during short-term feeding in amphipods. These microorganisms remained viable post-ingestion and contributed to food digestion. Functional stability was maintained across different diets, although the protein-rich granules diet induced functional shifts in both the host and its microbiota, reflecting their adaptation to a novel nutrient source. Finally, we identified a core microbiota driving key gut functions, less affected by dietary variations. These findings are significant for future ecotoxicological and biomonitoring investigations, leveraging the microbiomes of these sentinel animals as pivotal targets.

molecular biology↗

bioRxiv2024

Proteogenomic reconstruction of organ-specific metabolic networks in an environmental sentinel species, the amphipod Gammarus fossarum

Metabolic pathways are targets of environmental contaminants underlying a large variability of toxic effects throughout biodiversity. However, the systematic reconstruction of metabolic pathways remains limited in environmental sentinel species due to the lack of available genomic data in many taxa of animal diversity. In order to improve the knowledge of the metabolism of sentinel species, in this study we used a multi-omics approach to reconstruct the most comprehensive map of metabolic pathways for a crustacean model in biomonitoring, the amphipod Gammarus fossarum. We revisited the assembly of RNA-seq data by de novo approaches drastically reducing RNA contaminants and transcript redundancy. We also acquired extensive mass spectrometry shotgun proteomic data on several organs from G. fossarum males and females to identify organ-specific metabolic profiles. The G. fossarum metabolic pathway reconstruction (available through the metabolic database GamfoCyc) was performed by adapting the genomic tool CycADS and we identified 377 pathways representing 7,630 annotated enzymes, 2,610 enzymatic reactions and the expression of 858 enzymes was experimentally validated by proteomics. Our analysis shows organ-specific metabolic profiles, such as an elevated abundance in enzymes involved in ATP biosynthesis and fatty acid beta-oxidation indicative of the high-energy requirement of the gills, or the key anabolic and detoxification role of the hepatopancreatic caeca, as exemplified by the specific expression of the retinoid biosynthetic pathways and glutathione synthesis. In conclusion, the multi-omics data integration performed in this study provides new resources to investigate metabolic processes in crustacean amphipods and their role in mediating the effects of environmental contaminant exposures in sentinel species.

molecular biology↗

bioRxiv2023

Concomitant investigation of crustacean amphipods lipidome and metabolome during molting stage by Zeno SWATH Data-Independent Acquisition coupled with Electron Activated Dissociation and machine learning

BackgroundDIA (Data-Independent Acquisition) is a powerful technique in Liquid Chromatography coupled with high-resolution tandem Mass Spectrometry (LC-MS/MS) in metabolomics and lipidomics, for comprehensive profiling of molecules in biological samples. It provides unbiased coverage, improved reproducibility, and quantitative accuracy compared to Data-Dependent Acquisition (DDA). Combined with the Zeno trap and Electron-Activated Dissociation (EAD), DIA enhances data quality and structural elucidation compared to conventional fragmentation under CID. These tools were applied to study the lipidome and metabolome of the freshwater amphipod Gammarus fossarum, successfully discriminating stages and highlighting significant biological features. Despite being underused, DIA, along with the Zeno trap and EAD, holds great potential for advancing research in the omics field. ResultsDIA combined with the Zeno trap enhances detection reproducibility compared to conventional DDA, improving fragmentation spectra quality and putative identifications. LC coupled with Zeno-SWATH-DIA methods were used to study molecular changes in reproductive cycle of female gammarids. Multivariate data analysis including Principal Component Analysis and Partial Least Square Discriminant Analysis successfully identified statistically significant features responsible for group segregation. EAD fragmentation helped to identify unknown features and to confirm their molecular structure using fragmentation spectra DB annotation or machine learning. EAD database matching accurately annotated five glycerophospholipids, including the position of double bonds on fatty acid chain moieties. SIRIUS database predicted structures of unknown features based on experimental fragmentation spectra to compensate for database incompleteness. SignificanceReproducible detection of features and confident identification of putative compounds are pivotal stages within analytical pipelines. The DIA approach combined with Zeno pulsing and EAD synergistically enhances detection sensitivity while providing orthogonal fragmentation information, thereby facilitating a comprehensive and insightful exploration of pertinent biological molecules associated with the reproductive cycle of gammarids. The developed methodology holds great promises for identifying biomarkers of significance in the field of environmental assessment. HighlightsO_LIAdvancements in Data-Independent-Acquisition methods for lipidomics and metabolomics. C_LIO_LIZeno pulsing improves sensitivity in fragment detection and compound identification. C_LIO_LIComprehensive structure elucidation of lipids and metabolites using EAD fragmentation. C_LI

biochemistry↗

bioRxiv2023

Assimilation efficiencies and elimination rates of trace metals accumulated by trophic pathway in Gammarus fossarum

To improve the assessment of metal toxicity in aquatic organisms, it is important to consider the different uptake pathways (i.e. trophic or aqueous). The bioaccumulation of dissolved metals such as Cd and Zn in gammarids is beginning to be well described. However, there are very few data on the contribution of the dietary pathway, and its associated toxicokinetic parameters. Among these, the assimilation efficiency (AE) is an essential parameter for the implementation of models that take the trophic pathway into account. This study aims to estimate the assimilation efficiencies and elimination rates of two types of food, i.e. alder leaves and chironomid larvae, contaminated with three metals (Ag, Cd and Zn) of major concern for the Water Framework Directive (WFD). The pulse-chase-feeding method was used. Gammarids were fed with alder leaves or chironomid larvae previously contaminated with 110mAg, 109Cd or 65Zn, for a short period of time (1 to 5 hours), followed by an elimination phase of 14 days. At different time points, the gammarids were placed alive on the gamma detector to individually quantify whole body concentrations of 110mAg, 109Cd or 65Zn. Our results indicate that: i) Cd has the highest assimilation efficiency (39% for leaves and 19% for larvae), followed by Zn (15% for leaves and 9% for larvae) and Ag (5% for leaves); ii) for Cd and Zn, the AE were higher when gammarids were fed with leaves than with larvae; iii) the elimination rates of metals seem to depend more on the food matrix than on the metal assimilated; and thus iv) the biological half-life calculated from the kes is 5.1 days for Ag, between 4.9 and 13 days for Cd and between 3.8 and 13 days for Zn.

physiology↗

bioRxiv2022

Generic solving of physiologically-based kinetic models in support of next generation risk assessment due to chemicals

Increasing the confidence in using in vitro and in silico model-based data to aid the chemical risk assessment process is one, if not the most, important challenge currently facing regulatory authorities. A particularly crucial concern is to fully take advantage of scientifically valid Physiologically-Based Kinetic (PBK) models. Nevertheless, risk assessors remain still unwilling in employing PBK models within their daily work. Indeed, PBK models are not often included in current official guidance documents. In addition, most users have limited experience in using modelling in general. So, the complexity of PBK models, together with a lack to evaluation methods of their performances, certainly contributes to their under-use in practical risk assessment. This paper proposes an innovative and unified modelling framework, in both the writing of PBK equations as matrix ordinary differential equations (ODE), and in its exact solving simply expressed with matrix products. This generic PBK solution allows to consider as many as state-variables as needed to quantify chemical absorption, distribution, metabolism and excretion processes within living organisms when exposed to chemical substances. This generic PBK model makes possible any compartmentalisation to be considered, as well as all appropriate inter-connections between compartments and with the external medium. We first introduce our PBK modelling framework, with all intermediate steps from the matrix ODE to the exact solution. Then we apply this framework to bioaccumulation testing, before illustrating its concrete use through complementary case studies in terms of species, compounds and model complexity. O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY

pharmacology and toxicology↗

bioRxiv2020

Shotgun lipidomics and mass spectrometry imaging unveil diversity and dynamics in lipid composition in Gammarus fossarum

Sentinel species are playing an indispensable role in monitoring environmental pollution in aquatic ecosystems. Many pollutants found in water prove to be endocrine disrupting chemicals that could cause disruptions in lipid homeostasis in aquatic species. A comprehensive profiling of the lipidome of these species is thus an essential step towards understanding the mechanism of toxicity induced by pollutants. We here extensively examined both the composition and spatial distribution of lipids in freshwater crustacean Gammarus fossarum. The baseline lipidome of gammarids of different gender and reproductive stage was established by high throughput shotgun lipidomics. Spatial lipid mapping by high resolution mass spectrometry imaging led to the discovery of sulfate-based lipids in hepatopancreas and their accumulation in mature oocytes. We uncovered in G. fossarum a diverse and dynamic lipid composition that deepens our understanding of the biochemical changes during development and which could serve as a reference for future ecotoxicological studies.

biochemistry↗