Conception d'un système modulaire de collecte de données embarqué sur le drone marin PAMELI

International audienceThe PAMELI project (Multidimensional Autonomous Platform for Interdisciplinary Littoral Exploration) focuses on the repeated observation of environmental parameters such as physico-chemical parameters of the water column (Ph, salinity, conductivity), water depth and precise altimetry using a marine drone. This project first developed in Pertuis Charentais, since July 2018. One of the challenges of this project is to design an information system for data collection that is robust, reliable and flexible, ie to guarantee the good conditions for archiving and replaying data according to FAIR principles (Findable, Accessible, Interoperable and Reusable).This poster details the solutions put in place in an embedded information system to ensure this level of data quality requirements, and to meet the constraints of this embedded system (low energy resources, no Internet access, sensors removable, scalable and heterogeneous in their mode of communication). In particular, it shows how the operators of the drone can visualize the collected data in real time to intervene quickly in case of failure, or record annotations during the mission of the drone that will adjust the data qualification methods.Le projet PAMELI (Plateforme Autonome Multicapteurs pour l'Exploration Littorale Interdisciplinaire) porte sur l'observation répétée des paramètres environnementaux tels que les paramètres physico-chimiques de la colonne d'eau (Ph, salinité, conductivité), la profondeur d'eau et l'altimétrie précise à l'aide d'un drone marin. Ce projet se développe dans un premier temps dans les Pertuis Charentais, depuis juillet 2018. Un des enjeux de ce projet est de concevoir un système d'information pour la collecte des données qui soit robuste, fiable et flexible, i.e. permettant de garantir les bonnes conditions d'archivage et de rediffusion des données suivant les principes du FAIR (Findable, Accessible, Interoperable and Reusable). Ce poster détaille donc les solutions mises en place dans un système d’information embarqué pour assurer ce niveau d’exigences concernant la qualité des données, et de répondre aux contraintes de ce système embarqué (faibles ressources énergétiques, pas d’accès Internet, capteurs amovibles, évolutifs et hétérogènes dans leur mode de communication). En particulier, il montre comment les opérateurs du drone peuvent visualiser les données collectées en temps réel pour intervenir rapidement en cas de panne, ou enregistrer des annotations durant la mission du drone qui permettront d’ajuster les méthodes de qualification des données

Impact of human activities on the spatio-seasonal dynamics of plankton diversity in drained marshes and consequences on eutrophication

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Prospections géophysiques multi-méthodes et multi-échelles du site Néolithique du Pontet à Saint-Nazaire-sur-Charente (Charente-Maritine, France)

International audienceLe site du Pontet est localisé à proximité de l’estuaire de la Charente. Il est accolé à une paléo-falaise formant le versant d’une petite vallée. Il a été découvert en 2009 par E. Bouchet sur des clichés aériens montrant la présence de quatre fossés discontinus attribués au Néolithique récent. Son étude est intégrée au PCR « Dynamique d’occupation et d’exploitation du sel dans les golfes charentais, du Néolithique à l’Age du Fer » car il pourrait être associé à des activités de production de sel.Une campagne de prospection magnétique à haute résolution a été effectuée sur l’ensemble site en employant un protocole original de cartographie magnétique. La carte résultante est de grande qualité. Elle précise le tracé des fossés de l’enceinte et met en évidence deux autres enceintes, une imposante entrée avec des « pinces de crabe », des fosses et des trous de poteau. Ces données ont été complétées par des cartes et des sections de résistivité électrique. Le tout a été confronté à un modèle numérique de surface à haute résolution réalisé par photogrammétrie via un drone pour mettre en évidence la microtopographie et la géomorphologie de la vallée.L’ensemble de ces données pose de solides bases préliminaires à une étude du site par les méthodes d’exploration archéologique plus conventionnelles. Les prospections géophysiques ont ainsi permis de cibler une zone de fouille correspondant à un alignement de quatre fosses qui interrogeaient l’équipe sur leur fonction (production de sel ?)

Ecological observations based on functional gene sequencing are sensitive to the amplicon processing method

Until recently, the de facto method for short-read-based amplicon reconstruction was a sequence similarity threshold approach (operational taxonomic units [OTUs]). This has changed with the amplicon sequence variant (ASV) method where distributions are fitted to abundance profiles of individual genes using a noise-error model. While OTU-based approaches are still useful for 16S rRNA/18S rRNA genes, where thresholds of 97% to 99% are used, their use for functional genes is still debatable as there is no consensus on clustering thresholds. Here, we compare OTU- and ASV-based reconstruction approaches and taxonomy assignment methods, the naive Bayesian classifier (NBC) and Bayesian lowest common ancestor (BLCA) algorithm, using a functional gene data set from the microbial nitrogen-cycling community in the Brouage mudflat (France). A range of OTU similarity thresholds and ASVs were used to compare amoA (ammonia-oxidizing archaea [AOA] and ammonia-oxidizing bacteria [AOB]), nxrB, nirS, nirK, and nrfA communities between differing sedimentary structures. Significant effects of the sedimentary structure on weighted UniFrac (WUniFrac) distances were observed for AOA amoA when using ASVs, an OTU at a threshold of 97% sequence identity (OTU-97%), and OTU-85%; AOB amoA when using OTU-85%; and nirS when using ASV, OTU-90%, and OTU-85%. For AOB amoA, significant effects of the sedimentary structures on UniFrac distances were observed when using OTU-97% but not ASVs, and the inverse was found for nrfA. Interestingly, conclusions drawn for nirK and nxrB were consistent between amplicon reconstruction methods. We also show that when the sequences in the reference database are related to the environment in question, the BLCA algorithm leads to more phylogenetically relevant classifications. However, when the reference database contains sequences more dissimilar to the ones retrieved, the NBC obtains more information

Influence of habitat quality and diversity on two populations of Eurasian curlew (Numenius arquata) with contrasting dynamics in Western France

Like most shorebirds in Europe, breeding populations of Eurasian curlew (Numenius arquata) are suffering from habitat loss and degradation mainly caused by changes in agricultural practices. In Deux-Sèvres (France), the number of pairs has gradually declined since the early 2000s in the main, historical breeding site, while a new breeding site has appeared recently 80 kilometres further north with increasing number of pairs through the survey period. Many wheat fields and rare dry grasslands are found in the north, whereas the landscape in the south is mainly composed of tillage plots, hay meadows, and pastures. This study aims to highlight differences in food availability and quality between the two areas. Sample series of ground-dwelling and vegetation-dwelling invertebrates were carried out during three key stages of the species breeding cycle with pitfall traps and sweep nets. Dry grasslands in the north were found to be the most favourable habitat in terms of prey availability for adults and for chicks during the brood-rearing period. Moreover, hay meadows and pastures in the south seemed to be resource-abundant feeding habitats. Therefore, the habitats of the northern site seem to offer a greater abundance of invertebrates and thus a potentially larger food resource than the southern one. It follows that the northern site likely offers better breeding conditions, especially for the growth of chicks. An increase in the area of dry grasslands in the north and the establishment of adapted agricultural management in the south would be favourable for the conservation of local curlew populations

Influence of environmental gradients on the distribution of benthic resources available for shorebirds on intertidal mudflats of Yves Bay, France

International audienceThe case study of Yves Bay (Pertuis Charentais, France) highlighted links between environmental gradients (i.e. sediment characteristics and emersion time) and prey distribution and availability for the two most numerous shorebird species overwintering in Yves Bay: the red knot Calidris canutus and the dunlin Calidris alpina. Two hundred and fifty-two stations were sampled on a predetermined 250 m regular grid covering the intertidal mudflats of this major wintering site in France for east-Atlantic migratory shorebirds. The distribution of principal benthic species abundance and biomass was modelled along two environmental gradients: sediment structure (particularly pronounced north–south sand-mud gradient) and emersion time. The effect of emersion time combined with sedimentary structure strongly explained abundances and biomasses of the main prey for C. canutus and C. alpina in the bay (Cerastoderma edule, Hydrobia ulvae, Macoma balthica, Scrobicularia plana, and Nephtys hombergii). This study highlighted prey species-specific spatial segregation/overlapping as well as spatial interferences in the trophic niche of the two shorebirds