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Passive sampling in support of biota monitoring of hydrophobic substances under the Water Framework Directive
No full textInternational audienceThis paper presents an approach to apply aquatic passive sampling (PS) in regulatory chemical water quality monitoring in Europe. Absorption-based passive sampling is well developed and suitable for the sampling of hydrophobic chemicals, some of which are European Water Framework Directive priority substances with Environmental Quality Standards (EQS) derived for biota. Considering a chemical activity approach to chemical risk assessment, we propose equilibrium concentration in lipids (from passive water sampling) as a reference value for measured concentrations in biota. Through existing PS-fish datasets, we show a growing body of evidence supporting the use of lipid-based contaminant concentrations at equilibrium with water derived from PS as a conservative proxy of levels of these chemicals in fish. We propose a procedure that includes PS as a first, animal-free screening step of a tiered approach, followed by more conventional fish analyses when PS indicates these are needed to confirm EQSbiota exceedance. This paper reviews fish-passive sampler datasets, provides a reasoning for the proposed procedure and discusses how to broadly put it into monitoring practice. PS offers the possibility of well-defined standardised monitoring approaches that can help overcome the natural variability challenges associated with measurements in biota across member states and simplify EQSbiota compliance
Caractérisation des frayères potentielles d’ombles chevalier (Salvelinus umbla) dans le lac de Sainte-Croix.
No full textMotifs de semis, traits et proportions d'espèces pour la gestion agroécologique des adventices dans les associations légumineuse-céréale
No full textEvaluation de technique innovantes avec des essais réels et virtuels (simulations).Ce volume fait suite au carrefour de l'innovation Inrae, organisé par Inrae, Agreenium et l'Institut Agro Dijon, les 26 et 27 novembre 2024 de restitution du projet sur les Connaissances et outils pour des démarches préventives et opérationnelles en gestion agroécologique des adventices (COPRAA).International audienceL'objectif de cette étude était d'évaluer par simulation avec le modèle FLORSYS, paramétré et évalué préalablement, les effets, en l'absence de stress azoté ou hydrique, d'associations bispécifiques légumineuse-céréale sur la dynamique des adventices et la production des cultures. Sept proportions d'espèces, neuf motifs spatiaux de semis et quatre mélanges (triticale-féverole, blé-féverole, blé-pois, orge-pois) ont été comparés aux cultures pures. Les simulations montrent que (1) les associations orgepois et triticale-féverole contrôlent le mieux les adventices, (2) le motif alternant un rang de céréale et un rang de légumineuse, d'une part, et les proportions d'espèces avec deux tiers de céréales, d'autre part, maximisent les rendements et minimisent les pertes dues aux adventices, (3) la biomasse adventice en association est supérieure ou égale à celle en céréale pure mais toujours inférieure à celle en légumineuse pure et, (4) l'association bénéficie surtout aux légumineuses grâce à la compétition exercée sur les adventices par la céréale associée
Individual and combined effects of design and inter-operator variability on stream ecological assessment
No full textInternational audienceIn the context of long-term monitoring of stream ecological quality at large spatial extent, it is important to assess the overall reliability of a biotic index and to mitigate its uncertainty to ensure the effectiveness of stakeholder assessments and decisions. Only few studies have focused on the uncertainties associated to both the design of the method used to assess ecological status and the different steps of biological data acquisition. In this study we investigated the uncertainty associated with the design of a multimetric index (i.e., the uncertainty related to index parameter values because of the development dataset characteristics and calculation method), as well as the field data uncertainty because of inter-operator variability (i.e., associated with the sampling, sorting and identification steps of the applied protocol). We examined how the combined sources of uncertainty propagate to the index values and the final ecological assessment of water bodies. For this study, we focused on the I2M2, a multimetric index based on benthic macroinvertebrate assemblages and used to assess the ecological quality of French wadeable streams in the context of the European Water Framework Directive. We have shown that inter-operator variability was always the main source of uncertainty. The uncertainty related to the index design remained very limited. This study has highlighted the importance of robust index design combined with standardisation of the field and laboratory steps for the overall reliability of a biotic index, especially for long-term, spatially extensive monitoring of stream ecological health
Guidance framework to apply best practices in ecological data analysis: lessons learned from building Galaxy-Ecology
No full textInternational audienceNumerous conceptual frameworks exist for best practices in research data and analysis (e.g., Open Science and FAIR principles). In practice, there is a need for further progress to improve transparency, reproducibility, and confidence in ecology. Here, we propose a practical and operational framework for researchers and experts in ecology to achieve best practices for building analytical procedures from individual research projects to production-level analytical pipelines. We introduce the concept of atomization to identify analytical steps that support generalization by allowing us to go beyond single analyses. The term atomization is employed to convey the idea of single analytical steps as “atoms” composing an analytical procedure. When generalized, “atoms” can be used in more than a single case analysis. These guidelines were established during the development of the Galaxy-Ecology initiative, a web platform dedicated to data analysis in ecology. Galaxy-Ecology allows us to demonstrate a way to reach higher levels of reproducibility in ecological sciences by increasing the accessibility and reusability of analytical workflows once atomized and generalized
Highly Pathogenic Clade 2.3.4.4b H5N1 Influenza Virus in Seabirds in France, 2022–2023
No full textInternational audienceIn 2022, a very high number of wild bird deaths associated with the detection of highly pathogenic (HP) H5 avian influenza virus (AIV) lineage Gs/GD/96, clade 2.3.4.4b viruses were unusually observed in Europe between May and September, whereas prior to 2022 most of these HP H5 AIVs detected in wild birds in Europe were almost all detected between October and March and few between April and September. In France, wild birds affected by this virus during this unusual period were mainly seabirds, including larids and sulids. Although the abnormal mortalities in larids and sulids were reported simultaneously, sequencing of the complete genomes of the viruses identified in these seabirds showed that sulids are mainly infected with genotype EA‐2020‐C, whereas larids are mainly infected with genotype EA‐2022‐BB. The identification of these two genotypes, therefore, confirmed that there was no direct link between the abnormal mortality observed in sulids and the abnormal mortality observed in larids. These two seabird mortality events can also be distinguished by the evolutionary pattern of the number of detections. Indeed, sulid mortality associated with the EA‐2020‐C genotype was observed in France only between July and September, corresponding to a single epidemic wave, whereas larid mortality associated with the EA‐2022‐BB genotype began in France and Europe in May 2022 and then this genotype continued to spread among larids in France in the form of several successive epidemic waves until at least September 2023
Abundance and reproduction behavior data for waterbirds ( Anatidae , Rallidae , Charadriiforms , Podicipediforms ) breeding in European France based on a probability sampling design
No full textInternational audienceAbstract Appropriate management of wildlife requires sound knowledge and high‐quality data about species distributions, abundance, and trends in numbers. From a legal standpoint, Article 12 of the European “Birds” Directive requires Member States to report on breeding populations sizes. Acquiring such data is difficult owing to the wide distribution of most species and the multispecies nature of surveys. We relied on a stratified two‐stage spatial sampling design to assess breeding population size of waterbirds in European France. The data come from 2428 grid cells of 500 m × 500 m surveyed by territory or spot mapping three times at one‐month interval between 15 March and 15 June during the springs of 2021 or 2022. Individual bird location within each grid cell and their breeding behavior were recorded. A total of 6938 grid cell visits were undertaken, yielding 64,731 observations accounting for 132,292 individuals. These data are primarily aimed to assess the breeding population size of the 25 most common waterbirds (the population size estimates will be presented in a future article). However, because the location and time of observation of all individuals, as well as their behavior, are recorded, questions such as intra‐ and interspecific distribution rules, or habitat selection processes, can be addressed with this dataset too. As observers were also incited to record all other species among Anatidae, Rallidae, Charadriiforms and Podicipediforms, this dataset also provides robust original data on exotic and rare birds. The detailed Metadata and complete data set are available in MetaCat in JaLTER at https://jalter.diasjp.net/data/ERDP-2025-02
A la rencontre des singes de Guyane
No full textNational audienceLa Guyane compte 8 espèces de primates, qui présentent des enjeux de conservation et de gestion différents. Sept sont présents sur tout le territoire, mais leur abondance locale est liée à des facteurs environnementaux et anthropiques
Analyse comparative des dispositifs pour deux suivis nationaux couvrant les oiseaux prairiaux : L'Observatoire National de l'Ecosystème Prairie de Fauche (ONEPF) et le Suivi Temporel des Oiseaux Communs (STOC)
No full textThe degradation of permanent grasslands and the associated decline in biodiversity are critical issues in France. In order to monitor changes in the ecological status of grasslands, the Observatoire National de l'Ecosystème Prairie de Fauche (ONEPF) was set up in 2001, focusing on the monitoring of bird populations associated with these environments. However, it was put on hold in 2021 to redefine its objectives and explore the possibility of synergy with other national schemes. The aim of this study is to compare ONEPF with the Temporal Monitoring of Common Birds (STOC) in order to assess their complementarity in terms of monitoring trends in grassland bird abundance. The two protocols adopt a relatively similar field methodology. To carry out this work, three aspects were analysed: the spatio-temporal coverage of the stations, the landscape composition of the stations studied and the comparison of abundance trends modelled using data from the two systems. The analysis includes a total of 944 ONEPF stations and 5186 STOC stations, covering the period from 2003 to 2021.Comparative analyses highlight that the objectives of the STOC and ONEPF monitoring systems differ fundamentally, leading to major disparities in the landscapes and geographical areas monitored. There is very little spatial overlap between the two systems. The overlap in ecological contexts is also limited: a comparison of the landscapes monitored by the two systems shows that STOC mainly monitors fragmented grasslands, with little representation of hay meadows, whereas ONEPF focuses on larger expanses of hay meadows on a local and landscape scale.A comparison of the abundances and species richness captured by each system reveals that the averages for the target species are significantly higher at the ONEPF stations than at the STOC stations. This can be explained by the fact that ONEPF targets very specific species, which are often under-represented in STOC data, due to their affinity with particular habitats such as large hay meadows. The results show that by concentrating on these specific environments, ONEPF provides more robust estimates of abundance trends for most of the observatory's target species, accompanied by narrower confidence intervals. On the other hand, the STOC provides less accurate estimates for species that depend on grassland environments.La dégradation des prairies permanentes et le déclin de la biodiversité associée sont des enjeux critiques en France. Afin de suivre l’évolution de l’état écologique des prairies, l'Observatoire National de l’Ecosystème Prairie de Fauche (ONEPF) a été mis en place en 2001, axé sur le suivi des populations d’oiseaux inféodés à ces milieux. Cependant, il a été mis en pause en 2021 pour redéfinir ses objectifs et explorer la possibilité d'une synergie avec d'autres dispositifs nationaux. Cette étude vise à comparer l’ONEPF avec le Suivi Temporel des Oiseaux Communs (STOC) afin d’évaluer leur complémentarité en matière de suivi des tendances d’abondance des oiseaux prairiaux. Les deux protocoles adoptent une méthodologie terrain relativement similaire. Pour réaliser ce travail, trois aspects ont été analysés : le recouvrement spatio-temporel des stations, la composition paysagère des stations étudiées et la comparaison des tendances d’abondance modélisées à partir des données des deux dispositifs. L’analyse inclut un total de 944 stations de l’ONEPF et 5186 stations du STOC, couvrant la période de 2003 à 2021.Les analyses comparatives soulignent que les objectifs des dispositifs de suivi STOC et ONEPF diffèrent fondamentalement, entraînant d'importantes disparités dans les paysages et les zones géographiques suivies. En effet, le recouvrement spatial entre les deux dispositifs est très limité. Le recoupement des contextes écologiques est également limité : la comparaison des paysages suivis par les deux dispositifs montre que le STOC suit principalement des prairies fragmentées, avec une faible représentation des prairies de fauche, tandis que l'ONEPF se concentre sur de plus vastes étendues de prairies de fauche aux échelles locales et paysagères.La comparaison des abondances et richesses spécifique captées par chaque dispositif révèle que les moyennes des espèces cibles sont significativement plus élevées dans les stations de l’ONEPF que dans celles du STOC. Cela s'explique par le fait que l’ONEPF cible des espèces très spécifiques, souvent sous-représentées dans les données du STOC, en raison de leur affinité avec des habitats particuliers tels que les grandes prairies de fauche. Les résultats montrent ainsi que l’ONEPF, en se concentrant sur ces milieux spécifiques, fournit des estimations de tendance d’abondance plus robustes pour la plupart des espèces cibles de l’observatoire, accompagnées d'intervalles de confiance plus étroits. En revanche, le STOC présente des estimations moins précises pour les espèces inféodées aux milieux prairiaux
Rapport de campagnes. Retour sur les missions PatriNat de suivi DCSMM des espèces non indigènes 2024
No full textResponsables de l’étude : Cécile Massé et Suzie HumbertChef de l’équipe en charge du programme : Anne SouquièreContributeurs et experts mobilisés : Saint-Malo : Anne-Laure Janson, Marine Delessalle (PatriNat) Loïc Legoff, Henri Vandame (MNHN), Alice Landais (Région Bretagne) ; Golfe du Lion : Pierre Bourlard, Noëmie Michez, Bruno Ferrari, Gilles Esposito (PNM du Golfe du Lion) ; Corse : Alexandre Crispi, Axel Priouzeau, Cédric Minicucci (PNM du Cap Corse et Agriate) ; Arcachon : Vaea Bujan (UMR EPOC), Laurent Letort, Anne-Karima Bohi (CNRS), ainsi que l’ensemble des gestionnaires des sites concernés.Ce rapport de campagnes a pour objectif de présenter le détail des missions effectuées en 2024 dans le cadre de la mise en œuvre du programme de surveillance DCSMM des espèces non indigènes (Descripteur 2).Selon le plan proposé par la coordination des programmes de surveillance, les missions sont réalisées dans les sous-régions marines Mers Celtiques, Golfe de Gascogne Sud et Méditerrannée Occidentale dans les zones à risque d’introduction d’espèces non indigènes.Ce programme de surveillance est toujours en phase de développement et de mise en œuvre opérationnelle et fait l’objet d’un travail de mise au point d’une stratégie nationale et par façade