A review of operational methods of variational and ensemble-variational data assimilation

Variational and ensemble methods have been developed separately by various research and development groups and each brings its own benefits to data assimilation. In the last decade or so various ways have been developed to combine these methods, especially with the aims of improving the background error covariance matrices and of improving efficiency. The field has become confusing, even to many specialists, and so there is now a need to summarise the methods in order to show how they work, how they are related, what benefits they bring, why they have been developed, how they perform, and what improvements are pending. This paper starts with a reminder of basic variational and ensemble techniques and shows how they can be combined to give the emerging ensemble-variational (EnVar) and hybrid methods. A key part of the paper includes details of how localisation is commonly represented. There has been a particular push to develop four-dimensional methods that are free of linearised forecast models. This paper attempts to provide derivations of the formulations of most popular schemes. These are otherwise scattered throughout the literature or absent. It builds on the nomenclature used to distinguish between methods, and discusses further possible developments to the methods, including the representation of model error

Individual and mixture acute toxicity of model pesticides chlordecone and pyriproxyfen in the estuarine copepod Eurytemora affinis

International audienceDue to the increase in the use of phytosanitary products during the last few decades, the importance to study the effect of pesticide mixtures has been established. In this study, we investigated the acute toxicity of two model insecticides, chlordecone (CLD) and pyriproxyfen (PXF), alone and in mixtures, in the estuarine copepod Eurytemora affinis. After 48 h of exposure, the relative LC50 were 73.24 and 131.61 μg/L for PXF and CLD, respectively. The lower concentration tested (10 μg/L) did not affect the mortality of E. affinis whatever the considered chemical compound. To understand the interaction between compounds in mixture, the results were fitted to the concentration addition, Vølund, and Hewlett models. The best fit was obtained with the Hewlett model, suggesting a synergistic effect of the mixture

Susceptibility of the Non-Targeted Crustacean Eurytemora affinis to the Endocrine Disruptor Tebufenozide: A Transcriptomic Approach

Copepods are zooplanktonic crustaceans ubiquitously widespread in aquatic systems. Although they are not the target, copepods are exposed to a wide variety of pollutants such as insect growth regulators (IGRs). The aim of this study was to investigate the molecular response of a non-targeted organism, the copepod Eurytemora affinis, to an IGR. Adult males and females were exposed to two sub-lethal concentrations of tebufenozide (TEB). Our results indicate a sex-specific response with a higher sensitivity in males, potentially due to a differential activation of stress response pathways. In both sexes, exposure to TEB triggered similar pathways to those found in targeted species by modulating the transcription of early and late ecdysone responsive genes. Among them were genes involved in cuticle metabolism, muscle contraction, neurotransmission, and gametogenesis, whose mis-regulation could lead to moult, locomotor, and reproductive impairments. Furthermore, genes involved in epigenetic processes were found in both sexes, which highlights the potential impact of exposure to TEB on future generations. This work allows identification of (i) potential biomarkers of ecdysone agonists and (ii) further assessment of putative physiological responses to characterize the effects of TEB at higher biological levels. The present study reinforces the suitability of using E. affinis as an ecotoxicological model

The endocrine-disrupting effect and other physiological responses of municipal effluent on the clam Ruditapes decussatus

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The copepod Eurytemora affinis as a relevant species to assess estuarine sediment toxicity: Effects on gene expression and swimming behavior

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Controversial use of vitellogenin as a biomarker of endocrine disruption in crustaceans: New adverse pieces of evidence in the copepod Eurytemora affinis

International audienceIn recent years, the interest in the use of vitellogenin (VTG) as a biomarker of endocrine disruption in fish has led to VTG being considered as a potential tool in invertebrates. Among aquatic invertebrate models in ecotoxicology, the copepods are considered as reference species in marine, estuarine and freshwater ecosystems. In this context, we identified a VTG cDNA in Eurytemora affinis. The Ea-VTG2 cDNA is 5416bp in length with an open reading frame (ORF) of 5310bp that encodes a putative protein of 1769 amino acids residues. Phylogenetic analysis confirmed the hypothesis of a VTG duplication event before the emergence of the copepod species. The analysis of the Ea-VTG2 expression by qPCR in males and females according to their reproductive stages allowed transcript basal levels to be determined. The expression pattern revealed a gradual increase of transcript levels during maturation in females. Important inter-sex differences were observed with a VTG level in males ranging from about 1900- to 6800-fold lower than in females depending on their stage. Moreover, the protein was only detected in ovigerous females. The inducibility of Ea-VTG2 by chemicals was studied in males exposed to either a model of endocrine disruptor in vertebrates i.e. 4-nonylphenol (4-NP) or a crustacean hormone i.e. Methyl Farnesoate (MF), and in males sampled from a multi-contaminated estuary. No induction was highlighted. The VTG should not be considered as an appropriate biomarker in E. affinis as previously suggested for other crustaceans

Decoupled responses of the copepod Eurytemora affinis transcriptome and its microbiota to dissolved copper exposure

International audienceChemical contamination is a common threat to biota thriving in estuarine and coastal ecosystems. Of particular importance is that trace metals tend to accumulate and exert deleterious effects on small invertebrates such as zooplankton, which are essential trophic links between phytoplankton and higher-level consumers in aquatic food webs. Beyond the direct effects of the contamination, we hypothesized that metal exposure could also affect the zooplankton microbiota, which in turn might further impair host fitness. To assess this assumption, copepods (Eurytemora affinis) were sampled in the oligo-mesohaline zone of the Seine estuary and exposed to dissolved copper (25 µg.L−1) over a 72-hour time period. The copepod response to copper treatment was assessed by determining transcriptomic changes in E. affinis and the alteration of its microbiota. Unexpectedly, very few genes were differentially expressed in the copper-treated copepods compared to the controls for both male and female samples, while a clear dichotomy between sex was highlighted with 80% of the genes showing sex-biased expression. In contrast, copper increased the taxonomic diversity of the microbiota and resulted in substantial compositional changes at both the phyla and genus levels. Phylogenetic reconstruction of the microbiota further suggested that copper mitigated the phylogenetic relatedness of taxa at the basal tree structure of the phylogeny, whereas it strengthened it at the terminal branches. Increased terminal phylogenetic clustering in the copper-treated copepods coincided with higher proportions of bacterial genera previously identified as copper resistant (e.g., Pseudomonas, Acinetobacter, Alkanindiges, Colwellia) and a higher relative abundance of the copAox gene encoding a periplasmic inducible multi-copper oxidase. The enrichment in micro-organisms likely to perform copper sequestration and/or enzymatic transformation processes, underlines the need to consider the microbial component during evaluation of the vulnerability of zooplankton to metallic stress