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Five new species of Miridiba Reitter, 1902 are described from Laos and illustrated: Miridiba (Pledina) brancuccii sp. nov., Miridiba (Pledina) laotica sp. nov., Miridiba (Pledina) phousanensis sp. nov., Miridiba (Pledina) phupanensis sp. nov., Miridiba (Pledina) rasoria sp. nov., Cinq nouvelles espèce du genre Miridiba Reitter, 1902 sont décrites du Laos et illustrées : Miridiba (Pledina) brancuccii sp. nov., Miridiba (Pledina) laotica sp. nov., Miridiba (Pledina) phousanensis sp. nov., Miridiba (Pledina) phupanensis sp. nov., Miridiba (Pledina) rasoria sp. nov.

The genus Hystatoderes Lameere, 1917 is reviewed and the species present in Vietnam are treated. The genus remained monotypic for a long time with H. weissi (Lameere, 1915) as the only species. However, further studies of recent material have differentiated three species within the genus, which are described and illustrated here. An identification key for male and female is provided. Hystatoderes vitalisi Lameere, 1917 is relieved from synonymy with H. weissi and considered a good species. The genus Laokaya Pic, 1928 is proposed as a junior synonym of Hystatoderes and its only species Laokaya vitalisi Pic, 1928 as a junior synonym of H. vitalisi. Hystatoderes antonkozlovi sp. nov. from Central Vietnam is described. The male of H. weissi is described for the first time. An updated list of species composing the genus Hystatoderes is given., Le genre Hystatoderes Lameere, 1917 est revu et les espèces présentes au Vietnam sont traitées. Le genre est resté longtemps monotypique avec comme seule espèce H. weissi (Lameere, 1915). De nouvelles études sur du matériel récent ont permis de différencier trois espèces dans le genre, qui sont décrites et illustrées ici. Une clé d’identification pour les mâles et femelles est fournie. Hystatoderes vitalisi Lameere, 1917 est relevé de la synonymie avec H. weissi et considéré comme une bonne espèce. Le genre Laokaya Pic, 1928 est proposé comme synonyme junior de Hystatoderes et son unique espèce Laokaya vitalisi Pic, 1928 comme synonyme junior d’Hystatoderes vitalisi. Une espèce nouvelle, H. antonkozlovi sp. nov., est décrite du centre du Vietnam. Le mâle de H. weissi est décrit pour la première fois. Une liste actualisée des espèces composant le genre Hystatoderes est donnée.

Sphallopataroides gen. nov, Sphallopataroides pirreanus sp. nov., and Pseudosparna iolandae sp. nov. are described from Panama. New country records from Panama are provided: Leptostylus armatus Monné & Hoffmann, Sphallopataroides gen. nov., Sphallopataroides pirreanus sp. nov., et Pseudosparna iolandae sp. nov. sont descrits du Panama. De nouvelles mentions nationales du Panama sont fournies: Leptostylus armatus Monné & Hoffmann, 1981; Atrypanius cinerascens (Bates, 1864); et Colobothea chemsaki Giesbert, 1979.

Three new species from Sao Tome and Principe are described, illustrated and compared with known species: Litargus (Litargus) cauquili sp. nov., Litargus (Litargus) bacchiolellii sp. nov. and Litargus (Litargus) ingleberti sp. nov. The species Litargus (Litargus) unicolor Grouvelle, 1914 is newly recorded from Sao Tome., Trois nouvelles espèces de Sao Tomé et Principe sont décrites, illustrées et comparées aux espèces connues les plus proches : Litargus (Litargus) cauquili sp. nov., Litargus (Litargus) bacchiolellii sp. nov. et Litargus (Litargus) ingleberti sp. nov. L'espèce Litargus (Litargus) unicolor Grouvelle, 1914 est nouvellement signalée de Sao Tomé.

International audience

The following species are newly recorded: Anthrenus (Anthrenops) eichleri Kadej & Háva, 2006 (Azerbaijan); Anthrenus (Anthrenops) coloratus Reitter, 1881 (Nepal); Anthrenus (Anthrenus) indicus Kadej, Háva & Kalík, 2007 (Pakistan); Anthrenus (Anthrenus) oceanicus Fauvel, 1903 (Singapore); Aethriostoma undulata Motschulsky, 1858 (Singapore); Anthrenus (Anthrenus) pfefferi Kalík, 1954 (Croatia); Apsectus dichromus Beal, 1959 (Peru); Attagenus quadritinctus Reitter, 1889 (Azerbaijan); Dermestes (Dermestes) cernyi Háva, 2009 (Kyrgyzstan); Dermestes (Dermestinus) intermedius intermedius Kalík, 1951 (Serbia); Orphilus africanus Háva, 2005 (Tunisia); Orphinus (Orphinus) rihai Háva, 2015 (Myanmar); Orphinus (Curtophinus) thailandicus Háva, 2012 (Myanmar); Phradonoma nobile (Reitter, 1881) (Mexico: Baja California); Thaumaglossa tonkinea Pic, 1916 (Laos); Trinodes schawalleri Háva, 2019 (South Africa: Transvaal); Trogoderma sternale sternale Jayne, 1882 (U.S.A.: Maine)., Les espèces suivantes sont nouvellement enregistrées : Anthrenus (Anthrenops) eichleri Kadej & Háva, 2006 (Azerbaïdjan) ; Anthrenus (Anthrenops) coloratus Reitter, 1881 (Népal) ; Anthrenus (Anthrenus) indicus Kadej, Háva & Kalík, 2007 (Pakistan) ; Anthrenus (Anthrenus) oceanicus Fauvel, 1903 (Singapour) ; Aethriostoma undulata Motschulsky, 1858 (Singapour) ; Anthrenus (Anthrenus) pfefferi Kalík, 1954 (Croatie) ; Apsectus dichromus Beal, 1959 (Pérou) ; Attagenus quadritinctus Reitter, 1889 (Azerbaïdjan) ; Dermestes (Dermestes) cernyi Háva, 2009 (Kirghizistan) ; Dermestes (Dermestinus) intermedius intermedius Kalík, 1951 (Serbie) ; Orphilus africanus Háva, 2005 (Tunisie) ; Orphinus (Orphinus) rihai Háva, 2015 (Myanmar) ; Orphinus (Curtophinus) thailandicus Háva, 2012 (Myanmar) ; Phradonoma nobile (Reitter, 1881) (Mexique : Baja California) ; Thaumaglossa tonkinea Pic, 1916 (Laos) ; Trinodes schawalleri Háva, 2019 (Afrique du Sud : Transvaal) ; Trogoderma sternale sternale Jayne, 1882 (États-Unis : Maine).

International audience; The COVID-19 pandemic has led to a resurgence of the debate on whether host-parasite interactions should evolve towards avirulence. In this review, we first show that SARS-CoV-2 virulence is evolving, before explaining why some expect the mortality caused by the epidemic to converge towards that of human seasonal alphacoronaviruses. Leaning on existing theory, we then include viral evolution into the picture and discuss hypotheses explaining why the virulence has increased since the beginning of the pandemic. Finally, we mention some potential scenarios for the future.

The collection of animal position data via GPS tracking devices has increased in quality and usage in recent years. Animal position and movement, although measured discretely, follows the same principles of kinematic motion, and as such, the process is inherently continuous and differentiable. I demonstrate the functionality and visual elegance of smoothing spline models. I discuss the challenges and benefits of implementing such an approach, and I provide an analysis of movement and social interaction of seven jaguars inhabiting the Taiamã Ecological Station, Pantanal, Brazil, a region with the highest known density of jaguars. In the analysis, I derive measures for pairwise distance, cooccurrence, and spatiotemporal association between jaguars, borrowing ideas from density estimation and information theory. These measures are feasible as a result of spline model estimation, and they provide a critical tool for a deeper investigation of cooccurrence duration, frequency, and localized spatio‐temporal relationships between animals. In this work, I characterize a variety of interactive relationships between pairs of jaguars, and I particularly emphasize the relationships in movement of two male–female and two male–male jaguar pairs exhibiting highly associative relationships., I propose the use of smoothing spline models to explore animal movement and social interaction. I propose temporal‐state density estimation and localized mutual information measures to characterize behavior and strength of association between jaguars on a refined and unified time grid. I provide further characterization of time‐dependent male–male and female–male relationships in this region, an important step in determining conservation policy for an endangered neotropical predator.

Although parasite infection and pollution are common threats facing wild populations, the response of the gut microbiota to the joint impact of these stressors remains largely understudied. Here, we experimentally investigated the effects of exposure to Polycyclic Aromatic Hydrocarbons (PAHs) and infection by a common acanthocephalan intestinal parasite (Pomphorhynchus sp.) on the gut microbial flora of a freshwater fish, the European chub (Squalius cephalus). Naturally infected or uninfected individuals were exposed to PAHs at environmentally realistic concentrations over a five-week period. Characterization of the gut bacterial community through 16S rRNA gene amplicon sequencing revealed that parasitic infection was a more structuring factor of bacterial diversity and composition than PAH exposure. Specifically, chub infected by Pomphorhynchus sp. harbored significantly less evenly represented gut bacterial communities than the uninfected ones. In addition, substantial changes in sequence abundance were observed within the main bacterial phyla, including the Firmicutes, Fusobacteriota, Actinobacteriota, and Proteobacteria. Again, these compositional changes correlated with host infection with Pomphorhynchus sp., confirming its pivotal role in gut microbial assemblage. Overall, these results highlight the importance of defining the parasitic status of individuals when conducting microbial ecotoxicological analyses at the digestive tract level, as this should lead to better understanding of microbiota modulations and help to identify microbial markers specifically associated with chemicals.

The role of earthworms on biogeochemical carbon cycling is a major knowledge gap resulting from the difficulty of isolating and exploring the effects provided by the diversity of organisms. In this study, we investigated the effect of six earthworm species belonging to three ecological categories on soil organic carbon (SOC) mineralisation. To this end, we produced casts with the six species using subsoil material with low SOC content and miscanthus litter. Cast were subjected to laboratory ageing for 140 days. During this process, we monitored physicochemical parameters, CO2 emissions and determined the micro-scale organisation of the casts’ particulate organic matter and pores using X-ray tomography.Our results showed contrasting properties of fresh casts from the 3 main ecological categories, in accordance with the earthworm species’ morphological or behavioral strategies, indicating that those were maintained in artificial environments. However, species-specific changes in cast properties throughout ageing increased intragroup variability among ecological categories. As a result we observed earthworm species-specific evolution of CO2 mineralisation rates during casts ageing. We found that at least half of the variability in CO2 emissions was explained by cast microstructural changes, related to the spatial arrangement between particulate organic matter, porosity, and mineral particles. We conclude that earthworm species-specific traits may play a role in organic carbon protection through their impact on microstructural cast properties.

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Phosphatidylinositol 4-kinases (PI4Ks) are the first enzymes that commit phosphatidylinositol into the phosphoinositide pathway. Phosphoinositides (PPI), minor components of plasma membrane, are the phosphorylated derivatives of phosphatidylinositol (PI), such as phosphatidylinositol-4-phosphate (PI4P) and phosphatidylinositol-4,5-bisphosphate (PI(4,5)P2). In the Arabidopsis thaliana genome, twelve putative PI4K isoforms have been identified. Eight belong to type-II (AtPI4Kγ1-8), and four belong to type-III (AtPI4Kα1 and α2 and AtPI4Kβ1 and β2).To study the role of PI4Ks, I have worked with a double mutant defective plant in both the PI4Kβ genes. I show that the Arabidopsis thaliana pi4kβ1β2 double mutant exhibits several root phenotypes: impaired root growth, a lower sensitivity of roots to exogenous IAA (indole-3-acetic acid), impaired gravistimulation, and misshapen root hair growth. These changes appeared to coincide with a less stable actin cytoskeleton and an alteration in intracellular trafficking dynamics in pi4kβ1β2 roots. The content of bioactive auxin in the pi4kβ1β2 roots was similar to that in wild-type ones. Yet, an enhanced auxin-conjugating activity was detected and the auxin level reporter DII-VENUS did not respond to exogenous auxin in pi4kβ1β2 mutant. These data, therefore, link altered PI4K activity to the modification of vesicular trafficking and actin filaments organization one the one hand to altered auxin response likely due to alteration in auxin homeostasis one the other hand.The second part of my thesis was related to the Blumeria graminis (Bgh) interaction with pi4kβ1β2 double mutant. It is known that Arabidopsis has non-host resistance to Bgh. It means that plants build a special resistance structure - papillae - that acts as a barrier between fungi and plant cells. The pi4kβ1β2 double mutant showed an enhanced successful penetration of Bgh 24 hpi. The sid2 mutation affects the ISOCHORISMATE SYNTHASE 1 gene necessary for the synthesis of salicylic acid (SA). A similar defect in penetration resistance was seen in sid2/pi4kβ1β2, indicating the SA-independent character of this phenomenon. Deficiency of PI4Kbetas led to decreased accumulation of PI4P level in papillae. During pathogen attack, plenty of phospholipids and proteins were shown to accumulate in papillae. My hypothesis was that PI4Ks are essential for plant successful defense against Bgh, and more specifically for the formation of a successful papilla.The third part of my thesis concerns the mechanism leading to a constitutively active immunity in pi4kβ1β2 double mutant. In 4-week-old pi4kβ1β2 plants, an accumulation SA occurs. This SA accumulation was shown to be responsible for the dwarf stature of 4-week-old pi4kβ1β2 plants. The question is therefore to understand why the immunity system is constitutively switched on. The immunity system could be activated through cell-membrane or nuclear localized receptors. To study the role of type β PI4Ks in the regulation of defense mechanisms, I first crossed the pi4kβ1β2 double mutant with several mutants affected in different receptors or regulators of immunity. The use of different types of receptors or regulators of immunity will cover a wide range of pathways associated with the both - cell-surface and intracellular immunity. As a control, I used the sid2/pi4kβ1β2 triple mutant that does not accumulate SA, in contrast to pi4kβ1β2 plants. For phenotype describing rosette size was measured. After that typical immunity features were tested: resistance level to hemibiotroph Pseudomonas syringae pv tomato DC3000, PR1 expression and callose accumulation level. If any of these receptors/regulators is upstream to SA accumulation, I hoped to obtain a reverted plant phenotype with wild-type features. The dwarf pi4kβ1β2 phenotype was preserved for all mutants except one - wrky70/pi4kβ1β2, which indicates a possible role of WRKY70 factor in the constitutive SA accumulation., Les phosphatidylinositol 4-kinases (PI4K) sont les premières enzymes qui engagent le phosphatidylinositol dans la voie des phosphoinositides. Dans le génome d'Arabidopsis thaliana, douze isoformes putatives de PI4K ont été identifiées. Huit appartiennent au type II (AtPI4Kγ1-8) et quatre appartiennent au type III (AtPI4Kα1 et α2 et AtPI4Kβ1 et β2).Pour étudier le rôle des PI4K, j'ai travaillé avec une plante double mutante défectueuse dans les deux gènes PI4Kβ. J’ai montré que le double mutant d'Arabidopsis thaliana pi4kβ1β2 présente plusieurs phénotypes racinaires: une croissance racinaire altérée, une moindre sensibilité des racines à l'IAA exogène (acide indole-3-acétique), une gravistimulation altérée et une croissance des poils. Ces changements semblaient coïncider avec un cytosquelette d'actine moins stable et une altération de la dynamique du trafic intracellulaire dans les racines pi4kβ1β2. La teneur en auxine bioactive dans les racines pi4kβ1β2 était similaire à celle des racines de type sauvage. Ces données relient donc l'activité PI4K altérée à la modification du trafic vésiculaire et de l'organisation des filaments d'actine d'une part, et à la réponse altérée de l'auxine probablement due à l'altération de l'homéostasie de l'auxine d'autre part.La deuxième partie de ma thèse portait sur l'interaction de Blumeria graminis (Bgh) avec le double mutant pi4kβ1β2. On sait qu'Arabidopsis a une résistance non hôte à Bgh. Papilles - qui agit comme une barrière entre les champignons et les cellules végétales. Le double mutant pi4kβ1β2 a montré une meilleure pénétration de Bgh 24 hpi, donc une moindre résistance de la plante. La mutation sid2 touche le gène ISOCHORISMATE SYNTHASE 1nécessaire à la synthèse d’acide salicylique (SA). Un défaut similaire de résistance à la pénétration a été observé dans sid2/pi4kβ1β2, indiquant le caractère indépendant de SA de ce phénomène. La carence en PI4Kbetas a entraîné une diminution de l'accumulation du niveau de PI4P dans les papilles. Au cours de l'attaque pathogène, il a été démontré que de nombreux phospholipides et protéines s'accumulent dans les papilles. Mon hypothèse était que les PI4K sont essentielles pour une défense réussie des plantes contre la Bgh, et plus spécifiquement pour la formation d'une papille efficace.La troisième partie de ma thèse concerne le mécanisme conduisant à une immunité constitutivement active chez le double mutant pi4kβ1β2. Chez les plantes pi4kβ1β2 âgées de 4 semaines, une accumulation de SA. Cette accumulation de SA s'est avérée responsable de la stature naine des plantes pi4kβ1β2 âgées de 4 semaines. La question est donc de comprendre pourquoi le système immunitaire est constitutivement enclenché. Le système immunitaire pourrait être activé par l'intermédiaire de récepteurs localisés dans la membrane cellulaire ou solubles. Pour étudier le rôle des PI4K de type β dans la régulation des mécanismes de défense, j'ai d'abord croisé le double mutant pi4kβ1β2 avec plusieurs mutants affectés dans différents récepteurs ou régulateurs de l'immunité. Comme témoin, j'ai utilisé le triple mutant sid2/pi4kβ1β2 qui n'accumule pas de SA, contrairement aux plantes pi4kβ1β2. Pour le phénotype décrivant la taille de la rosette a été mesurée. Après cela, les caractéristiques typiques de l'immunité ont été testées : niveau de résistance à l'hémibiotrophe Pseudomonas syringae pv tomato DC3000, expression de PR1 et niveau d'accumulation de callose. Si l'un de ces récepteurs/régulateurs est en amont de l'accumulation de SA, j'espérais obtenir un phénotype végétal inversé avec des caractéristiques de type sauvage. Le phénotype nain pi4kβ1β2 a été préservé pour tous les mutants sauf un - wrky70/pi4kβ1β2_ ce qui indique un rôle possible du facteur de transcription WRKY70 dans l'accumulation constitutive de SA.

The complexity of food webs and how it depends on environmental variables is a long-standing question in ecology. Food-chain length depends on many factors, such as productive space, disturbance and spatial processes. It is not clear though how food-chain length should vary with adaptive evolutionary changes of the constitutive species. Assuming that each trophic level is subject to a competition-colonization trade-off, we model the adaptive evolution of their colonization rates and its consequences on equilibrium occupancies and food-chain length. When colonization rates are allowed to evolve, longer food chains can persist. Extinction, perturbation and habitat loss all affect the evolutionary-stable colonization rates, but trade-off strength (costs of dispersal) has a major role: weaker trade-offs yield longer chains. Our results suggest a strong link between within-trophic level competition, spatial occupancies and food-chain length. Although these eco-evo dynamics partly alleviate the constraint on food-chain length in metacommunities, we show it is no magic bullet: the highest, most vulnerable, trophic levels are also those that least benefit from evolution. Our model generates qualitative predictions regarding how trait evolution affects the response of communities to disturbance and habitat loss. This highlights the importance of eco-evolutionary dynamics at metacommunity level in determining food-chain length.

Thermo-hydroregulation strategies involve concurrent changes in functional traits related to energy, water balance and thermoregulation and play a key role in determining life-history traits and population demography of terrestrial ectotherms. Local thermal and hydric conditions should be important drivers of the geographical variation of thermo-hydroregulation strategies, but we lack studies that examine these changes across climatic gradients in different habitat types. Here, we investigated intraspecific variation of morphology and thermo-hydroregulation traits in the widespread European common lizard (Zootoca vivipara louislantzi) across a multidimensional environmental gradient involving independent variation in air temperature and rainfall and differences in habitat features (access to free-standing water and forest cover). We sampled adult males for morphology, resting metabolic rate, total and cutaneous evaporative water loss and thermal preferences in 15 populations from the rear to the leading edge of the distribution across an elevational gradient ranging from sea level to 1750 m. Besides a decrease in adult body size with increasing environmental temperatures, we found little effect of thermal conditions on thermo-hydroregulation strategies. In particular, relict lowland populations from the warm rear edge showed no specific ecophysiological adaptations. Instead, body mass, body condition and resting metabolic rate were positively associated with a rainfall gradient, while forest cover and water access in the habitat throughout the season also influenced cutaneous evaporative water loss. Our study emphasizes the importance of rainfall and habitat features rather than thermal conditions for geographical variation in lizard morphology and physiology.

Présentation du dispositif Observatoire de l'environnement nocturne (CNRS) et Observatoire de l'environnement nocturne de La Réunion (CNRS/Parc national de La Réunion) aux services internes du Parc national de La Réunion.

International audience; La connaissance de la biodiversité des organismes dans les milieux urbains est un enjeu majeur pour la compréhension de la résilience de nos écosystèmes en ville. Aujourd’hui, le développement de trames qui visent à maintenir et à reconstituer un réseau d’échanges d’espèces terrestres, aquatiques et nocturnes (vertes, bleues ou noires) contribue à la protection de cette diversité, notamment en améliorant les espaces dits naturels, mais aussi en offrant des continuités écologiques indispensables pour le maintien et la stabilité des communautés d’organismes.

International audience

International audience; Within the framework of a Franco-Lebanese mission in the area of Tyre (Lebanon), we were able to improve our knowledge of the relative sea level variations on its maritime facade. Two fish tanks were discovered near the southern and northern capes of the ancient rocky island of Tyre. Both fish tanks were cut into a Pleistocene sandstone bedrock. Small water inflow and outflow channels, also cut into the sandstone bedrock, help to better understand and constrain the variations in relative sea level during ancient times in this area. The first results show that these Roman fish tanks were affected by a relative sea-level rise of ca. 0.50 m. This 0.50 m rise is usually observed around the Circum-Mediterranean since the Roman period. In other words, no tectonic movement appears to have affected this area since Roman times.

International audience; The biology and ecology of benthic fauna from extreme environments, such as the hadal zone (> 6,000 m depth), is scarce due to the difficulties of access, exploration, and work logistics. The few exploration cruises of bottom settings have shown that benthic foraminifera, and meiofauna in general, display high abundances in the sediments, indicating that these organisms present unique adaptations and interactions to extreme conditions (e. g. high hydrostatic pressure, limitation of calcite and organic matter, etc.). As such, new species to science have also been reported. The Peru-Chile trench represents the deepest ecosystem in the South Pacific. It has been explored only on three occasions describing it as a eutrophic environment with high biomass of meiofauna. For foraminifera, only species reports have been published, being the ecology neglected. In this study, we aimed to determine the community structure (abundance, diversity, spatial and vertical distribution) of the foraminifera collected from 6 stations in the Atacama trench in the SONNE Cruise during 2018. We compared the taxa features to granulometry and proxies of food, organic matter source, and oxygenation. Dissolved oxygen at all trench stations penetrated 3-5 cm into the sediments and TOC was 0.5-1.3 %. The grain size was mainly silt-rich. The presence of 120 morphospecies, many of them soft-walled, is reported. The community was dominated by large specimens (>500 µm), and small specimens (63-150 µm) were rare. The bulk of the community concentrated in the first centimeter of sediment despite all the trench stations were fully oxygenated. However, different assemblages were found in the 6 analyzed stations. We argue if these community differences are generated by the gradient of organic matter nature or the presence/abundance of meiofaunal/macrofaunal predators. Our results contribute to the knowledge of ecology and diversity of foraminifera from the Atacama Trench and give insight to the role of this group in the benthic food webs in hadal settings.

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International audience; An emerging research axis of the STEEP team (steep.inria.fr) of Inria (Grenoble, France) intends to contribute to the design, evaluation and debate of socio-technical alternatives for the future (e.g., horizon 2050). “Expert” quantitative modeling makes it possible to guarantee the biophysical coherence of narratives (regarding flows of materials, energy and human work) and to tackle complex issues (e.g. trade-offs between social and environmental criteria, trade-offs between geographical scales…) (Giampietro et al, 2021 ; Courtonne, 2016). In order for these alternatives to emerge in a democratic manner, the team is currently involved in both “expert modeling” and “participatory modeling” (where groups of citizens identify what they wish to model and create and evaluate their own alternatives). This communication will focus on the latest developments on the “expert” side.We define a socio-technical alternative as a consistent arrangement of modes of production and modes of consumption. This includes biophysical and socio-political dimensions, but for the time being the emphasis is laid on the circulation of material, energy and human work between sectors and down to final consumption.

International audience

This paper introduces an approach for land cover pixel-based classification from massive satellite image time series scale using Gaussian Processes. Sparse methods combined with variational inference allow the learning of large scale Gaussian Process. Using a spatiospectro-temporal covariance function can help to take into account all the structure of the data. Experimental results conducted on a national scale data-set show that our method is effective and close to several state-of-the-art approaches (random forest and deep learning methods)., Cet article présente une approche permettant la classification pixellaire de séries temporelles d'images satellites massives à partir de processus gaussiens. Notre modèle s'appuie sur des processus gaussiens variationnels parcimonieux associés à des fonctions de covariance spatio-spectro-temporelles. Les résultats expérimentaux réalisés sur un jeu de données à l'échelle nationale montrent que notre méthode est efficace et comparable à des approches de l'état de l'art (forêt d'arbres décisionnels et méthodes d'apprentissage profond).

International audience

L'écopastoralisme est une pratique de gestion écologique en plein essor, dont les bienfaits pour le maintien ou la restauration des milieux naturels ont été largement démontrés. Mais cette solution alternative de gestion obtient-elle les mêmes résultats sur des milieux fortement anthropisés et artificialisés ? Une étude menée sur les digues artificielles du Rhône de la réserve de chasse de Donzère-Mondragon s'est intéressée aux impacts des différents troupeaux sur les communautés végétales d’écosystèmes récents. Grâce à un suivi botanique sur plusieurs années, les scientifiques ont pu démontrer que la gestion par les herbivores s'avérait efficace pour maintenir l'ouverture des milieux et augmenter significativement le nombre et la diversité des espèces par rapport à l’absence de gestion ou aux interventions mécaniques.

International audience; Human papillomaviruses (HPVs), the most oncogenic virus known to humans, are often associated with Herpes Simplex Virus-2 (HSV-2) infections. The involvement of the latter in cervical cancer is controversial but its longterm infections might modulate the mucosal microenvironment in a way that favors carcinogenesis. We know little about coinfections between HSV-2 and HPVs, and studying the immunological and microbiological dynamics in the early stages of these infections may help identify or rule out potential interactions. We report two cases of concomitant productive, although asymptomatic, HSV-2 and HPV infections in young women (aged 20 and 25). The women were followed up for approximately a year, with clinical visits every two months and weekly self-samples. We performed quantitative analyses of their HSV-2 and HPV viral loads, immunological responses (IgG and IgM antibodies and local cytokines expression profiles), vaginal microbiota composition, as well as demographic and behavior data. We detect interactions between virus loads, immune response, and the vaginal microbiota, which improve our understanding of HSV-2 and HPVs' coinfections and calls for further investigation with larger cohorts.

International audience

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International audience

International audience; Designing agroforestry systems is a complex task due to the numerous elements and their multiple interactions. Co-design workshops are useful to overcome these difficulties by gathering people from different disciplines. But these workshops use tools that do not provide a standardised representation of agroforestry systems nor the provision of ecosystem services. Our objective is thus to develop a conceptual information framework based on graphs that allows modeling the agroforestry system and its ecosystem functions. In the first step, we infer a topological graph from the position of the physical objects representing system components: trees, crops, tree lines, and their spatial relationships (e.g. adjacency, inclusion...). We represent then the relationship between ecosystem structure and functioning as a graph. Applying graph technics such as subgraph research, we can estimate whether a specific system (graph) can support a specific ecosystem function (subgraph). This results in a new graph-based model to describe both the spatial and functional relationships between elements of agroforestry systems. Figure 1 illustrates the different steps to apply this model to a simple agroforestry system: 1. Create a system mock-up with physical objects 2. Acquire the scene by a camera and identify physical objects 3. Automatically extract the topological graph 4. Perform subgraphs research to identify functions 5. Visualize the scene with both realistic trees and schematic representations of ecosystem functions In the future, this work will be combined with augmented reality to visualize the agroforestry system and the production of ecosystem services directly on the physical mock-up. Thus, our work will improve the efficiency of co-design workshop by (i) formalizing the knowledge on the relationship between structure and function in agroforestry systems and, by (ii) sharing this information with non-specialists in a visual way, while allowing intuitive interaction through the physical mock-up. Thus, the designed system answers farmer's needs better.

One of the missions of Unesco’s intergovernmental scientific programme, Man and the Biosphere (MAB),is to support and encourage research activities. These activities are based in specific areas, the BiosphereReserves considered as model sites for the study and demonstration of integrated approaches toconservation and development. However, identifying scientific activities in Biosphere Reserves turned outto be more challenging than previously imagined. After reflecting upon the place of science at Unesco, theoriginality of the conceptualisation of this place within the MAB programme and the structural conditions of its implementation, we present different methods to identify the diversity of scientific activities withinFrench Biosphere Reserves. In a context of evolution and territorialisation of public action, this exploratorysurvey proposes a methodology allowing to come to grips with the complexity of scientific contributionswithin territorial projects whose aims are not purely academic., Le programme scientifique intergouvernemental Man and the Biosphere (MAB) de l’Unesco, dont l’une des missions est de soutenir et d’encourager les activités de recherche, s’appuie sur des territoires particuliers, les réserves de biosphère, définies comme des sites modèles d’étude et de démonstration des approches intégrées de la conservation et du développement. Pourtant, identifier les activités scientifiques dans ces réserves de biosphère se révèle bien plus complexe qu’il n’y paraît. Après avoir questionné la place de la science à l’Unesco, l’originalité de sa conceptualisation au sein du programme MAB et ses conditions structurelles de mise en œuvre, nous expérimentons et discutons,chemin faisant, différentes méthodes afin d’identifier la diversité des activités scientifiques au sein des réserves de biosphère françaises. Dans un contexte d’évolution et de territorialisation de l’action publique, cette enquête exploratoire propose in fine une méthodologie à même d’appréhender la complexité des contributions scientifiques au sein de projets de territoire dont les finalités ne sont pas purement académiques.

International audience

Morphological adjustment of small urban rivers is rarely studied especially in France. We propose an original hydrogeomorphological approach based on a detailed study of a whole catchment using field data acquired systematically all along the river: (i) channel cross-sections; (ii) riffle-pool sequences and(iii) obstacles to flow and stormwater discharges. Nine hydromorphological variables were used as a basis to classify the profiles (CAH/ACP). The classes were compared with 12 anthropogenic constraint variables to explain longitudinal morphological variability and to link morphology to pressures on this scale. The results showed an average incision of 0.50 m, an average widening of nearly 1 m, and heterogeneous distribution of the riffle-pool sequences (although not complete disappearance). Systematic analysis of within-channel forms revealed high morphological diversity, the absence of a linear relationship between the rate of urbanisation and incision/erosion, and the absence of longitudinal changes in response to urbanisation. The constraints identified are commonly observed in urbanised basins, but the variety of responses to the constraints makes it difficult to understand the system as a whole and prevents ecological restoration’s uniformity., L’ajustement morphologique des rivières urbaines est encore peu étudié. Cette étude propose une approche hydrogéomorphologique originale basée sur l’acquisition systématique et exhaustive de données de terrain sur le linéaire fluvial telles : (i) les sections transversales du chenal, (ii) lesalternances radier-mouille et (iii) les ouvrages transversaux et rejets d’eaux pluviales. Neuf de ces variables ont permis la classification des profils (CAH/ACP) en 5 classes hydromorphologiques. Cellesci ont été confrontées à douze variables de contrainte anthropiques afin d’expliquer la variabilité morphologique longitudinale et le lien entre les formes et les pressions. Les résultats montrent une incision moyenne d’environ 0,50 m, un élargissement moyen proche de 1 m, et une répartition hétérogène des séquences radiers-mouilles mais pas leur disparition. L’analyse systématique des formes intra-chenal a révélé une forte diversité morphologique, l’absence de relation linéaire entre taux d’urbanisation et incision/érosion, et l’absence d’évolution longitudinale d’un faciès « réponse àl’urbanisation ». Les contraintes identifiées sont communes aux bassins urbanisés, toutefois la diversité des réponses à ces contraintes complique l’appréhension de l’ensemble du système et s’oppose à l’uniformité de la restauration écologique.

International audience

We analyzed 324,734 SARS-CoV-2 variant screening tests from France enriched with 16,973 whole-genome sequences sampled during September 1, 2021-February 28, 2022. Results showed the estimated growth advantage of the Omicron variant over the Delta variant to be 105% (95% CI 96%-114%) and that of the BA.2 lineage over the BA.1 lineage to be 49% (95% CI 44%-52%). Quantitative PCR cycle threshold values were consistent with an increased ability of Omicron to generate breakthrough infections. Epidemiologic modeling shows that, in spite of its decreased virulence, the Omicron variant can generate important critical COVID-19 activity in hospitals in France. The magnitude of the BA.2 wave in hospitals depends on the level of relaxing of control measures but remains lower than that of BA.1 in median scenarios.

11 pages, 8 figures, 2 tables.-- Data availability: Ocean Gene Atlas 2.0 is freely available and can be accessed via the following link: https://tara-oceans.mio.osupytheas.fr/ocean-gene-atlas/. Source code is available at GitLab repository: https://gitlab.osupytheas.fr/ocean_atlas/oga. Shotgun sequences are available at the European Nucleotide Archive (ENA, https://www.ebi.ac.uk/ena) under accession number PRJEB7988 (OM-RGCv1 and v2), PRJEB6609 (MATOU), PRJEB41575 (Tara Arctic metagenome co-assemblies) and PRJEB402 (EUK_SMAGs) (see Table 1). The predicted genes from the OM-RGC are available at ENA under the accession numbers ERZ094224 and ERZ096909 to ERZ097151, and the protein sequences are available at: ftp://ftp.genome.jp/pub/db/mgenes/Environmental/Tara.pep.gz. For OM-RGCv2, all data files can be found through BioStudies with the accession S-BSST297 and for the 530 Tara Arctic metagenome co-assemblies with S-BSST451. All MATOU, EUK_SMAGs, MGT and BAC_ARC_MAGs resources are available at http://www.genoscope.cns.fr/tara/. Registry of all the samples from the Tara Oceans Expedition (2009–2013) with environmental metadata are available at PANGAEA: https://doi.org/10.1594/PANGAEA.875582. For the Global Malaspina 2010 Expedition, all raw sequences are publicly available at both DOE's JGI Integrated Microbial Genomes and Microbiomes (IMG/MER) and the European Nucleotide Archive (ENA). Individual metagenome assemblies, annotation files, and alignment files can be accessed at IMG/MER. All accession numbers are listed at https://www.nature.com/articles/s42003-021-02112–2#MOESM4 in Supplementary Data 1. The metagenomic data can be found through ENA with accession number PRJEB44456 and the co-assembly for the MAG dataset construction with accession number PRJEB40454, the nucleotide sequence for each MAG and their annotation files can be found through BioStudies with accession S-BSST457 and also in the companion publication website at: https://malaspina-public.gitlab.io/malaspina-deep-ocean-microbiome/. The user manual is available at https://tara-oceans.mio.osupytheas.fr/ocean-gene-atlas/build/pdf/Ocean-Gene-Atlas_User_Manual.pd, Testing hypothesis about the biogeography of genes using large data resources such as Tara Oceans marine metagenomes and metatranscriptomes requires significant hardware resources and programming skills. The new release of the ‘Ocean Gene Atlas’ (OGA2) is a freely available intuitive online service to mine large and complex marine environmental genomic databases. OGA2 datasets available have been extended and now include, from the Tara Oceans portfolio: (i) eukaryotic Metagenome-Assembled-Genomes (MAGs) and Single-cell Assembled Genomes (SAGs) (10.2E+6 coding genes), (ii) version 2 of Ocean Microbial Reference Gene Catalogue (46.8E+6 non-redundant genes), (iii) 924 MetaGenomic Transcriptomes (7E+6 unigenes), (iv) 530 MAGs from an Arctic MAG catalogue (1E+6 genes) and (v) 1888 Bacterial and Archaeal Genomes (4.5E+6 genes), and an additional dataset from the Malaspina 2010 global circumnavigation: (vi) 317 Malaspina Deep Metagenome Assembled Genomes (0.9E+6 genes). Novel analyses enabled by OGA2 include phylogenetic tree inference to visualize user queries within their context of sequence homologues from both the marine environmental dataset and the RefSeq database. An Application Programming Interface (API) now allows users to query OGA2 using command-line tools, hence providing local workflow integration. Finally, gene abundance can be interactively filtered directly on map displays using any of the available environmental variables. Ocean Gene Atlas v2.0 is freely-available at: https://tara-oceans.mio.osupytheas.fr/ocean-gene-atlas/, French Government ‘Investissements d'Avenir’ programmes OCEANOMICS [ANR-11-BTBR-0008]; FRANCE GENOMIQUE [ANR-10-INBS-09-08]; Institut Français de Bioinformatique (IFB) [ANR-11-INBS-0013]; SeqDigger [ANR-19-CE45-0008]; AO-EMBRC [ANR-21-ESRE-0038]. Funding for open access charge: ANR [ANR-19-CE45-0008], With the institutional support of the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S)

International audience; The life of aquatic fauna in streams and rivers depends on hydrological variability with considerable emphasis on minimum discharge in flow regulated reaches. One of the methods used to define ecologically suitable minimum discharges is the physical habitat simulation method (habitat model) which converts the outputs of a hydrodynamic river model into habitat suitability for different aquatic taxa, based on their estimated hydraulic preferences. The application of this method requires the use of dedicated software. One of the current computer programs for habitat simulations in France (EVHA) is not technically up-to-date and had to be replaced. Much more than an update of existing software, HABBY is a new free and open-source program, which will be very useful to estimate ecological flows through aquatic habitat availability and suitability. Compatible with MS-Windows, macOS, and GNU/Linux, HABBY is developed in Python. It does not contain any internal hydrodynamic model but accepts, as inputs, the output files of several commonly used models. It also incorporates three statistical habitat models, including Estimhab, a popular statistical model in France. Moreover, a system of scripts helps to store past studies and facilitates the implementation of complex case studies.

International audience; Isothiazolinones are ubiquitous in our daily life; they are used as preservatives in cosmetics, household products and in building materials. These biocidal substances may be emitted inside house, inducing a potential risk for health, and released into the environment through wastewater or runoff, thus inducing a potential impact on aquatic ecosystems. The overall objective of this communication was to explore the isothiazolinone contamination of the continuum House-Sewer-River and to assess the induced risks for health and the aquatic life. The experimental results showed the ubiquity of isothiazolinones in indoor dust, urban water discharges and in the Seine River. Annual mass loads discharged into the Seine River were estimated using Monte Carlo method at both the conurbation and annual scales, they showed that wastewater discharges constitute the major entry pathway.

International audience

International audience

International audience; The lipid fraction of birch pollen grains (BPGs) is not yet fully described, although pollen lipid molecules may play a role in the allergic immune response. The mechanisms by which atmospheric pollutants modify allergenic pollen grains (PGs) are also far from being elucidated despite high potential effects on allergic sensitization. This work is a contribution to a better description of the lipid profile (both external and cytoplasmic) of BPGs and of alterations induced by gaseous air pollutants. Several lipid extractions were performed using organic and aqueous solvents on BPGs following exposure to ozone and/or nitrogen dioxide and under conditions favoring the release of internal lipids. Ozone reacted with alkenes to produce aldehydes and saturated fatty acids, while nitrogen dioxide was shown to be unreactive with lipids. NO 2 exhibited a protective effect against the reactivity of alkenes with ozone, probably by competition for adsorption sites. The decreased reactivity of ozone during simultaneous exposure to NO 2 /O 3 raised the possibility of a Langmuir-Hinshelwood mechanism. Oxidation reactions induced by exposure of BPGs to ozone did not substantially modify the extraction of lipids by aqueous solvent, suggesting that the bioaccessibility of lipids was not modified by oxidation. On the contrary, the rupture of PGs appeared to be a key factor in enhancing the bioaccessibility of bioactive lipid mediators (linoleic and α-linolenic acids) in an aqueous solution. The internal lipid fraction of BPGs has specific characteristics compared with external lipids, with more abundant hexadecanoic acid, tricosanol, and particularly unsaturated fatty acids (linoleic and α-linolenic acids). Several mechanisms of action of gaseous pollutants on allergenic pollen were identified in this study: gaseous air pollutants can (i) modify the external lipid fraction by reactivity of alkenes, (ii) adsorb on the surface of PGs and be a source of oxidative stress after inhalation of PGs, and (iii) promote the release of cytoplasmic bioactive lipids by facilitating pollen rupture.

Bivalve predation by seabream has been observed worldwide and is a major concern for bivalve farmers. Farmed bivalve-seabream interactions must be better understood to ensure the sustainability of bivalve aquaculture. The objectives of this study were to characterize gilthead seabream Sparus aurata presence in a bivalve farm in Prevost Lagoon (Mediterranean Sea) using acoustic telemetry and to evaluate monthly losses of mussels Mytilus galloprovincialis and oysters Crassostrea gigas due to seabream predation over an 18 mo period inside the farm and at an unprotected experimental platform. Large (281 to 499 mm TL) seabream were more commonly detected in the bivalve farm than were small (200 to 280 mm TL) seabream. In contrast to small seabream, 90% of large seabream returned to and spent extended periods in the study area the following year, suggesting inter-annual site fidelity for large fish that used the bivalve farm as a feeding site. Signs of predation were observed on mussels and oysters throughout the year at the unprotected experimental platform. Farmers noted losses in the farm from April to September. Maximal losses (90 to 100%) were observed post-oyster ‘sticking’ and mussel socking. Despite the deployment of nets as mechanical protection to reduce predation, oyster losses represented 28% of the annual value of oysters sold while mussel losses were estimated at ca. 1%. These results suggest that bivalves must be protected by nets throughout the year to avoid predation, particularly post-handling. A collaboration between shellfish farmers and fishermen could be a sustainable solution for bivalve farming, by regularly fishing for seabream in farms, between tables and inside protective nets.

The current known distribution of Omura’s whale includes the tropical and warm temperate waters of the western Pacific, Indian, and Atlantic Oceans. Evidence of their presence in the Atlantic Ocean is based on beach cast specimens found on the coasts of Mauritania (North Atlantic) and Northeastern Brazil (South Atlantic). The present study characterizes the occurrence of this species in the São Pedro and São Paulo Archipelago (SPSPA), on the mid-Atlantic ridge between South America and Africa, based on autonomous recording systems. Acoustic signals were similar, but not identical, to B. omurai vocalizations recorded off the coast of Madagascar. Although these signals were recorded for only 11 months, there are peaks in vocal activity between May and June in the vicinities of SPSPA, suggesting either a shift in distribution within the Atlantic equatorial waters or seasonality in the species’ vocal behavior in this region. The first acoustic records of Omura’s whales in the Equatorial Atlantic suggest that these animals may also use deep-water habitats, in addition to the shallow-water habitat use observed in other regions., A atual distribuição conhecida da baleia-de-Omura (Balaenoptera omurai) inclui as águas tropicais e temperadas quentes dos oceanos Pacífico ocidental, Índico e Atlântico. A evidência de sua presença no oceano Atlântico baseia-se em espécimes encalhados encontrados em praias da Mauritânia (Atlântico Norte) e do Nordeste do Brasil (Atlântico Sul). O presente estudo caracteriza a ocorrência dessa espécie no Arquipélago de São Pedro e São Paulo (ASPSP), localizado sobre a Dorsal Mesoatlântica entre a América do Sul e a África, com base em sistemas de monitoramento acústico passivo. Os sinais acústicos detectados foram similares, mas não idênticos, às vocalizações de B. omurai gravadas na costa de Madagascar. Embora esses sinais tenham sido registrados por apenas 11 meses, há picos na atividade vocal entre maio e junho nas proximidades do ASPSP, sugerindo uma mudança na distribuição da espécie nas águas equatoriais do Atlântico ou uma sazonalidade no comportamento vocal nessa região. Os primeiros registros acústicos das baleias-de-Omura no Atlântico Equatorial sugerem que esses animais também podem utilizar habitats de águas profundas, além de habitats de águas rasas como observado em outras regiões.

International audience

International audience

International audience

International audience

International audience; Infectious disease transmission patterns in some outbreaks can be more heterogeneous than in others, with striking effects on the way epidemics unfold. Some studies show that the biological sources of heterogeneity may matter, but they tend to do so without controlling for the overall heterogeneity in the number of secondary cases caused by an infection. Here, we control for this important bias to explore the role of individual variation in infection duration and transmission rate on parasite emergence and spread. We simulate outbreaks using a stochastic SIR model, with and without parasite evolution. Consistently with existing studies, we show that the variance in the number of secondary infections has the strongest effect on outbreak emergence probability but has little effect on the epidemic dynamic once emergence is certain. The origin of heterogeneity also affects the probability of emergence, but its more striking effects are about properties of epidemics that do emerge. In particular, assuming more realistic variances in infection duration distributions lead to faster outbreaks and a higher peak of incidence. When the parasite requires evolutionary changes to be able to spread, the impact of heterogeneity depends on the underlying evolutionary model. If the parasite evolves within the host, decreasing the infection duration variance decreases the probability of emergence. These results show that using realistic distributions for infection duration is necessary to accurately capture the effect of individual heterogeneity on epidemiological dynamics, which has implications for the monitoring and control of infectious diseases, as well as data collection.