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Intense efforts have been devoted to describe the biochemical pathway of plant sulphur (S) assimilation from sulphate. However, essential information on metabolic regulation of S assimilation is still lacking, such as possible interactions between S assimilation, photosynthesis and photorespiration. In particular, does S assimilation scale with photosynthesis thus ensuring sufficient S provision for amino acids synthesis? This lack of knowledge is problematic because optimization of photosynthesis is a common target of crop breeding and furthermore, photosynthesis is stimulated by the inexorable increase in atmospheric CO2. Here, we used high-resolution 33S and 13C tracing technology with NMR and LC-MS to access direct measurement of metabolic fluxes in S assimilation, when photosynthesis and photorespiration are varied via the gaseous composition of the atmosphere (CO2, O2). We show that S assimilation is stimulated by photorespiratory metabolism and therefore, large photosynthetic fluxes appear to be detrimental to plant cell sulphur nutrition., Cyril Abadie and Guillaume Tcherkez tested whether the metabolic flux associated with sulfur assimilation effectively scales with photosynthesis by measuring metabolic fluxes in sulfur assimilation. This study suggests that photorespiratory metabolism stimulates sulfur assimilation.

he relationship between detritivore diversity and decomposition can provide information on how biogeochemical cycles are affected by ongoing rates of extinction, but such evidence has come mostly from local studies and microcosm experiments. We conducted a globally distributed experiment (38 streams across 23 countries in 6 continents) using standardised methods to test the hypothesis that detritivore diversity enhances litter decomposition in streams, to establish the role of other characteristics of detritivore assemblages (abundance, biomass and body size), and to determine how patterns vary across realms, biomes and climates. We observed a positive relationship between diversity and decomposition, strongest in tropical areas, and a key role of abundance and biomass at higher latitudes. Our results suggest that litter decomposition might be altered by detritivore extinctions, particularly in tropical areas, where detritivore diversity is already relatively low and some environmental stressors particularly prevalent., This study was part of the DecoDiv project conducted by the GLoBE network (www.globenetwork.es), which is coordinated by L. B. Most research was based on crowdfunding (details on specific funding sources at each region are given in Supplementary Information). Project coordination was funded by Basque Government funds (Ref. IT951-16) to the Stream Ecology Group (UPV/EHU, Spain).

Background: Tree species represent 20% of the vascular plant species worldwide and they play a crucial role in the global functioning of the biosphere. The Mediterranean Basin is one of the 36 world biodiversity hotspots, and it is estimated that forests covered 82% of the landscape before the first human impacts, thousands of years ago. However, the spatial distribution of the Mediterranean biodiversity is still imperfectly known, and a focus on tree species constitutes a key issue for understanding forest functioning and develop conservation strategies. Methods: We provide the first comprehensive checklist of all native tree taxa (species and subspecies) present in the Mediterranean-European region (from Portugal to Cyprus). We identified some cases of woody species difficult to categorize as trees that we further called “cryptic trees”. We collected the occurrences of tree taxa by “administrative regions”, i.e. country or large island, and by biogeographical provinces. We studied the species-area relationship, and evaluated the conservation issues for threatened taxa following IUCN criteria. Results: We identified 245 tree taxa that included 210 species and 35 subspecies, belonging to 33 families and 64 genera. It included 46 endemic tree taxa (30 species and 16 subspecies), mainly distributed within a single biogeographical unit. The countries with the highest tree richness are Greece (146 taxa), Italy (133), Albania (122), Spain (155), Macedonia (116), and Croatia (110). The species-area relationship clearly discriminated the richest central-eastern (Balkans) and northern (Alpine and Cevenno-Pyrenean) biogeographical provinces, against the five western provinces in the Iberian Peninsula. We identified 44 unrecognized “cryptic trees”, representing 21% of the total trees. Among the 245 taxa identified, 19 are considered to be threatened (15 CR + EN + VU) or near threatened (4 NT) by IUCN. Conclusions: The Mediterranean-European region includes an unsuspectedly high number of tree taxa, almost 200 tree taxa more than in the central European region. This tree diversity is not distributed evenly and culminates in the central-eastern part of the Mediterranean region, whereas some large Tyrrhenian islands shelter several narrow endemic tree taxa. Few taxa are recognized as threatened in the IUCN Red list, and the vulnerability of these species is probably underestimated. French Foundation for Research on Biodiversity (FRB). Centre for Synthesis and Analysis of Biodiversity data ANR-11-LABX-0061

International audience; Estimates of cumulative plastic inputs into the oceans are expressed in hundred million tons, whereas the total mass of microplastics afloat at sea is 3 orders of magnitude below this. This large gap is evidence of our ignorance about the fate of plastics, as well as transformations and sinks in the oceans. One of the current challenges consists of identifying and quantifying plastic particles at the microscale, the small microplastics (SMP, 25–1000 μm). The aim of the present study is to investigate SMP concentration in count and in mass at the sea surface in the North Atlantic subtropical gyre during the sea campaign Expedition 7th Continent. After isolation, SMP were characterized by micro-Fourier-transform infrared spectroscopy. Microplastic distribution was modeled by a wind-driven vertical mixing correction model taking into account individual particle properties (dimension, shape and density). We demonstrate that SMP buoyancy is significantly decreased compared to the large microplastics (LMP, 1–5 mm) and consequently more susceptible to vertical transport. The uncorrected LMP concentration in count was between 13 000 and 174 000 pieces km–2, and was between 5 and 170 times more abundant for SMP. With a wind-driven vertical mixing correction, we estimated that SMP were 300 to 70 000 times more abundant than LMP. When discussing this in terms of weight after correction, LMP concentrations were between 50 and 1000 g km–2, and SMP concentrations were between 5 and 14 000 g km–2.

Altres ajuts: these projects are co-funded by European regional development fund (ERDF / FEDER, 2007-2013). Recent studies suggest that carbon (C) is stored in the topsoil of pastures established after deforestation. However, little is known about the long-term capacity of tropical pastures to sequester C in different soil layers after deforestation. Deep soil layers are generally not taken into consideration or are underestimated when C storage is calculated. Here we show that in French Guiana, the C stored in the deep soil layers contributes significantly to C stocks down to a depth of 100 cm and that C is sequestered in recalcitrant soil organic matter in the soil below a depth of 20 cm. The contribution of the 50-100 cm soil layer increased from 22 to 31 % with the age of the pasture. We show that long-term C sequestration in C4 tropical pastures is linked to the development of C3 species (legumes and shrubs), which increase both inputs of N into the ecosystem and the C:N ratio of soil organic matter. The deep soil under old pastures contained more C3 carbon than the native forest. If C sequestration in the deep soil is taken into account, our results suggest that the soil C stock in pastures in Amazonia would be higher with sustainable pasture management, in particular by promoting the development of legumes already in place and by introducing new species.

xxx, 335 p. [EN]The biogeochemical cycles describe the matter and energy flux between ecosystems in the Earth System. However, climate change, human population growth and other global change hazards alter the natural balance of these cycles. Within this context, understanding which mechanisms control the mass transfer, and assessing their spatial and temporal evolution becomes necessary to balance a sustainable development with the environmental protection. In the biogeochemical cycles the relative importance of the different factors involved changes with the spatial and temporal scales used for their evaluation, creating the need of tools capable of integrating these factors for analysis. Commonly, these tools involve modelling.With regards to biogeochemical cycling research, focus has been pointed to the Critical Zone, a part of the environment comprising from the ground surface to the consolidated rock. Is within this zone where the geochemical cycle interacts with the biogeochemical cycles through the physical and chemical weathering processes. Weathering conditions the chemical composition of the aquatic environments through the liberation of products from the solid phase. In the continental zone, rivers act not only as reaction matrix in the Critical Zone, but also as a vector of transport for those products from the hydrographic basin to other environments, such as lakes or oceans. At the local level, this matter transfer is of interest for ecological analysis both at the river and wetland scale; while at the global scale, these processes impact on the oceanic and atmospheric composition in geological scales.The main objective of this work is to evaluate the role of chemical weathering in the biogeochemical cycles, paying special attention to the major ions derived from rocks through the modelling of this process at different spatial and temporal scales. In particular, a global-to-local and static-to-dynamic approach has been followed.At the beginning of this work, there existed several modelling tools capable of assessing the chemical weathering using a mechanistic approach, however, its application to large spatial and temporal scales is conditioned to the availability of input data and computing resources. As an alternative, there were other empirical models applicable at the global scale. Taking as starting point the most recent studies, and after the evaluation of 1751 river compositions, in this work we have been able to confirm that hydrology, lithology, and soil are the most relevant factors at the global scale regarding chemical weathering. Indeed, its implication on each major ion liberation has been proved, allowing the yield of the first global scale maps of specific fluxes derived from rocks, as well as the comparison of hotspots between ions. At the global scale, 3374·106 Mg·y-1 dissolved matter is yielded from rocks, where 58% is Ca2+, 24% is Na+, 15% is Mg2+, and 3% is K+ with respect to the cation flux, and a 74% is alkalinity, 18% is SO42-, and 8% is Cl- with regards to the anion flux.Besides, a more detailed analysis at a local scale case study (the Deba river basin, Gipuzkoa, Basque Country) has been accomplished, paying attention to the processes responsible of the chemical composition of the waters, as well as to the hydrological effect on the temporal evolution of the exports to the ocean. In this catchment, the effect of evaporitic springs and gypsum deposits in one of its headwaters has been shown to have a great impact on the stream water chemical composition down to the outlet. This study has also permitted to highlight the advantages of combining punctual sampling information with continuous registries to evaluate the temporal evolution of the system. Identifying the moments after the flood events as those with the greatest relative dissolved exports to the ocean within the year.Once the main processes governing the chemical composition of water in this study were identified, the application of the global model to the basin scale has been performed through the coupling of the model to the physically-based hydrological model (SWAT). Such assessment has allowed to evaluate the possibilities and limitations of the models in local scales, both under a static and a dynamic approach. The model allows to obtain results with a mean discrepancy of 13% with respect to reality, when the effects of point sources (such as the evaporitic springs and gypsum deposits) do not condition the ionic composition.Acknowledging the limitations at the local scale, the model has been again applied at the global scale, aiming to evaluate not only the spatial distribution of the chemical weathering derived fluxes, but the impact of this process on the global carbon cycle under a climate change context. The results from this simulation have allowed to see that the potential impacts derived from the climate change on the hydrological balance will increase between 8 to 13% the CO2 consumption rates derived from the chemical weathering of rocks, but its growth will not been nor spatially nor temporally homogeneous.The results from this PhD thesis have allowed to the assess the role of chemical weathering at the global scale, specially on the carbon cycle. Future research should focus on improving the model configuration and integrating the results from other studies following a local-to-global approach. [ES]Los ciclos biogeoquímicos describen el flujo de materia y energía entre los ecosistemas del Sistema Tierra. Sin embargo, el cambio climático, el aumento de la población y otras amenazas del cambio global alteran el equilibrio natural de estos ciclos. En este contexto se vuelve necesario tanto entender qué mecanismos controlan la transferencia de materia, como estimar su evolución espacial y temporal, para poder equilibrar un desarrollo sostenible con la protección del medioambiente. La relevancia de distintos factores involucrados en los distintos ciclos biogeoquímicos cambia con respecto a la escala temporal y espacial utilizada para su evaluación, creando la necesidad de herramientas capaces de integrar dichos factores para poder llevar a cabo su análisis. Generalmente, estas herramientas implican trabajo de modelización.Con relación a la investigación en los ciclos biogeoquímicos, la atención se ha centrado en la Zona Crítica, un espacio del ecosistema que comprende desde la superficie del suelo hasta la roca consolidada. Es en esta zona donde los ciclos geoquímicos interaccionan con los ciclos biogeoquímicos a través de la alteración física y química. La alteración condiciona la composición química de los entornos acuáticos tras la liberación de productos de la fase rocosa. En la zona continental, los ríos actúan no únicamente como matriz de reacción en la Zona Crítica, sino también como vector de transporte de esos productos desde la cuenca hidrográfica hacia otros entornos, como lagos u océanos. A nivel local, esta transferencia de materia resulta de interés para análisis ecológicos tanto a nivel de río como a nivel de estuario, mientras que a nivel global el impacto de estos procesos afecta a la composición de los océanos e incluso de la atmósfera en escalas geológicas.El objetivo principal de este trabajo es evaluar el papel de la erosión química en los ciclos biogeoquímicos, prestando especial atención a los iones mayoritarios derivados de las rocas, a través del modelado de este proceso a diferentes escalas espaciales y temporales. En particular, se ha seguido un enfoque espacial de global-a-local y temporal de estático-a-dinámico.Al inicio de este trabajo, existían varias herramientas de modelización capaces de evaluar la erosión química desde un punto de vista físico y termodinámico, sin embargo, su aplicación a grandes escalas espaciales y temporales se ve condicionada por disponibilidad de datos de entrada y de recursos de computación. Como alternativa, también constaban otros modelos de base empírica que permitían su aplicación a escala global. Tomando como referencia los estudios más actuales, y tras la evaluación de la composición de 1751 ríos en este trabajo, se ha podido confirmar que la hidrología, la litología y el suelo son los factores más relevantes a nivel global respecto a la erosión química. También se ha podido constatar que su implicación en la liberación de cada ion mayoritario de la roca es diferente, permitiendo obtener los primeros mapas a nivel global de flujos específicos derivados de la roca, así como la comparación de puntos calientes de cada ion. A nivel global, 3374·106 Mg·año-1 de material disuelto se libera de las rocas, siendo un 58% Ca2+, un 24% Na+, un 15% Mg2+, y un 3% K+ respecto al flujo de cationes, y un 74% alcalinidad, un 18% SO42-, y un 8% Cl- respecto al flujo de aniones.Paralelamente, se ha realizado un análisis más detallado de un caso local (la cuenca del río Deba, Gipuzkoa, País Vasco) prestando atención a los procesos condicionantes de la composición química de las aguas, así como al efecto de la hidrología sobre la evolución temporal de los flujos al océano. En esta cuenca destaca el importante efecto que ejercen las fuentes de evaporitas y los depósitos de yesos en una de las partes de cabecera, que condicionan fuertemente la química de las aguas hasta la desembocadura. Este estudio también ha permitido subrayar la ventaja de combinar muestreos puntuales con registros en continuo para evaluar la evolución temporal del sistema. Identificando los momentos después de las crecidas como los de mayores exportaciones disueltas relativas al océano a lo largo del año.Una vez identificados los procesos determinantes de la composición química del agua en este caso de estudio, se ha trasladado la aplicación del modelo global hasta la escala de cuenca mediante la integración de dicho modelo a un modelo hidrológico de base física (SWAT). Este estudio ha permitido evaluar las posibilidades y las limitaciones del modelo en escalas locales, tanto de forma estática como dinámica. El modelo permite obtener unos resultados con una discrepancia media respecto a la realidad del 13% siempre que los efectos puntuales (como las fuentes de evaporitas y los depósitos de yesos) no condicionen la presencia de iones mayoritarios.Conocidas las limitaciones que pueden existir a escalas locales, el modelo se ha aplicado a escala global nuevamente, tratando de evaluar no sólo la distribución espacial de los flujos derivados de la erosión química, sino el impacto que este proceso genera sobre el ciclo global del carbono bajo un contexto de cambio climático. Los resultados de la simulación nos han permitido ver que los potenciales impactos derivados del cambio climático en la hidrología aumentarán globalmente entre un 8 y un 13% las tasas de consumo de CO2 por la erosión de las rocas, pero su aumento no será uniforme ni espacial ni temporalmente.Los resultados de esta tesis doctoral permiten evaluar el papel de la erosión química a la escala global, especialmente en el ciclo del carbono. Investigación futura debería centrarse en mejorar la configuración del modelo e integrar los resultados de otros estudios con enfoques local-a-global. [FR]Les cycles biogéochimiques décrivent le flux de matière et d'énergie entre les environnements du système Terre. Cependant, le changement climatique, l'augmentation de la population et d'autres menaces du changement global altèrent l'équilibre naturel de ces cycles. Dans ce contexte, il devient nécessaire de comprendre quels mécanismes contrôlent le transfert de matière et estimer son évolution spatiale et temporelle, pour équilibrer le développement durable avec la protection de l'environnement. L¿importance relative des différents facteurs intervenant évoluant par rapport à l'échelle temporelle et spatiale utilisée pour leur évaluation, crée la nécessité des outils capables d'intégrer ces facteurs afin de réaliser les analyses. Normalement, ces outils utilisent la modélisation.Par rapport à la recherche des cycles biogéochimiques, une attention est dirigée sur la Zone Critique, une zone de l¿environnement allant de la surface du sol à la roche consolidée. C'est dans cette zone que les cycles géochimiques interagissent avec les cycles biogéochimiques par l¿altération physique et chimique. C¿est l¿altération qui conditionne la composition des milieux aquatiques après la libération des produits par la phase rocheuse. Dans la zone continentale, les rivières agissent non seulement comme matrice de réaction dans la zone critique, mais aussi comme vecteur de transport de ces produits du bassin hydrographique vers d'autres environnements, tels que les lacs ou les océans. Au niveau local, ce transfert de matière présente un intérêt pour les analyses écologiques à la fois au niveau des fleuves et des estuaires, tandis qu'au niveau global ces processus affectent la composition des océans et même l'atmosphère à l'échelle géologique.L'objectif principal de ce travail est d'évaluer le rôle de l'érosion chimique dans les cycles biogéochimiques, en accordant une attention particulière aux ions majoritaires dérivés des roches, à travers la modélisation de ce processus à différentes échelles spatiales et temporelles. En particulier, une approche spatiale globale-locale et temporelle statique-dynamique a été suivie.Au début de ce travail, il y avait plusieurs outils de modélisation capables d'évaluer l'érosion chimique d'un point de vue physique et thermodynamique, cependant, son application à de grandes échelles spatiales et temporelles est conditionnée par la disponibilité des données d'entrée et des ressources informatiques. Comme alternative, il y avait aussi d'autres modèles empiriques qui permettaient son application à l'échelle mondiale. En prenant comme référence les études les plus récentes et après l'évaluation de la composition chimique de 1751 rivières dans ce travail, il a été possible de confirmer que l'hydrologie, la lithologie et le sol sont les facteurs les plus pertinents à l'échelle mondiale en ce qui concerne l¿altération chimique. Il a également été vérifié que leur implication dans la libération de chaque ion majeur de la roche est différente, permettant d'obtenir les premières cartes globales d'écoulements spécifiques dérivés de la roche, ainsi que la comparaison des points chauds de chaque ion. À l'échelle mondiale, 3374·106 Mg·an-1 de matière dissoute sont libérés des roches, soit 58% de Ca2+, 24% de Na+, 15% de Mg2+ et 3% de K+ par rapport au flux de cations et 74% d'alcalinité, 18% SO42- et 8% Cl- en ce qui concerne le flux d'anions.Parallèlement, une étude plus détaillée a été réalisée dans un cas d¿étude local (le bassin versant de Deba, Gipuzkoa, Pays Basque), en prêtant attention aux processus de conditionnement de la composition chimique des eaux, ainsi qu'à l'effet de l'hydrologie sur l'évolution temporelle des écoulements vers l'océan. Dans ce bassin, se distingue l'effet important exercé par les sources d'évaporites et les dépôts de gypse dans l'une des parties de tête, qui conditionnent fortement la chimie jusqu'à l¿exutoire. Cette étude a également mis en évidence l'avantage de combiner des échantillonnages ponctuels avec des enregistrements continus pour évaluer l'évolution temporelle du système. En identifiant les moments après les crues comme ceux de plus grande exportation d¿éléments dissous relatifs vers l'océan tout au long de l'année.Une fois les processus déterminants identifiés issus de la composition chimique de l'eau dans cette étude de cas, l'application du modèle global a été transférée à l'échelle du bassin en intégrant ce modèle dans un modèle physique hydrologique (SWAT). Cette étude a permis d'évaluer les possibilités et les limites du modèle à l'échelle locale, à la fois statiquement et dynamiquement. Le modèle permet d'obtenir des résultats avec un écart moyen de 13% par rapport à la réalité, tant que les effets ponctuels (tels que les sources d'évaporites et les dépôts de gypse) ne conditionnent pas la présence d'ions majoritaires.Connaissant les limitations qui peuvent exister à l'échelle locale, le modèle a été appliqué à nouveau à l'échelle mondiale, essayant d'évaluer non seulement la distribution spatiale des flux issus de l'érosion chimique, mais l'impact que ce processus génère sur le cycle global de carbone dans un contexte de changement climatique. Les résultats de la simulation nous ont permis de voir que les impacts potentiels dérivés du changement climatique sur l'hydrologie augmenteraient globalement les taux de consommation de CO2 de 8 à 13% en raison de l'érosion des roches, mais leur augmentation ne serait pas uniforme ni spatiale ni temporairement.Les résultats de cette thèse de doctorat nous ont permis d'évaluer le rôle de l'érosion chimique à l'échelle mondiale, notamment dans le cycle du carbone. Les recherches futures devraient se concentrer sur l'amélioration de la configuration du modèle et l'intégration des résultats d'autres études aux approches locales à mondiales.

International audience; General context: Intra-specific diversity plays a key role in species' response to climate change (CC) and their ability to adapt locally through plastic response and/or response to selection. However, the CC velocity is likely to exceed the natural adaptation potential of most species and populations. One solution is to use assisted migration to bring genetic diversity from a region already subject to the expected future climate and therefore able to survive in the new region. Objective: We investigate how the consideration of existing intra-specific variability (due to local adaptation and to plasticity) affects the past and future prediction of vulnerability in beech. Methods: We used CASTANEA, a process-based model, able to simulate carbon and water fluxes for different species, to assess the vulnerability of beech stands across Europe. The simulation design include several climatic scenarios of the past and the future under CC, with or without within-stand trait variability, and one with assisted migration (allowing the whole range off variation everywhere). We accounted for the genetic variability in three major adaptive traits: (1) the date of budburst (TBB), related to vulnerability to late frosts, (2) the percentage of loss of conductance (PLC), related to vulnerability to cavitation and (3) water use efficiency (WUE), related to vulnerability to carbon starvation. Results: We found that the vulnerability of the optimal average tree in a stand with trait variation is lower than that of stands without variation. In addition, with intra-specific variability, the species distribution is larger, especially in the south of Europe. Finally, in the future under CC, migrated trees are able to grow under conditions further north of the area and contribute to reduce the expected vulnerability without assisted migration.

National audience; Recent interest for microgeographic adaptation, i.e. adaptation at spatial scales compatible with substantial amount of gene dispersal, offers to reconsider the scale at which evolution occurs (Richardson et al. 2014). Whether gene flow is constraining or facilitating local adaptation at this fine spatial scale remains an unresolved question. Too important gene flow would overwhelm the effects of natural selection and decrease local adaptation along environmental gradients. Conversely, gene flow, and particularly long-distance dispersal events, could play a major role in resupplying the genetic variation of populations and favouring the spread of beneficial alleles (Kremer et al. 2012). Hence, the high dispersal capacities of trees are often assumed to be the main process maintaining the large levels of genetic variation measured in their natural populations. However, evidences for microgeographic adaptation and the quantitative assessment of the impact of gene flow on adaptive genetic variation are still limited in most temperate trees. Here, we sampled 60 open-pollinated families of European beech (Fagus sylvatica L.) from three natural plots, spreading along a short elevation gradient (∼1.5 km) at the warm margin of this species distribution. We analysed the phenotypic and genotypic data of ∼2,300 seedlings grown in a common garden. We focused on 11 potentially adaptive traits with significant heritabilities (Gauzere et al. 2016) and tested for signature of local selection on quantitative trait differentiation. We then identified the offspring likely originating from local or distant pollen immigration events and quantified the role of gene flow in increasing locally the additive variance of traits under selection. We found a significant signal of adaptive differentiation among plots separated by less than one kilometre, with local selection acting on growth and phenological traits. We found that trees in the plots at high elevation, experiencing the lowest temperature conditions, flushed earlier and had a higher height and diameter growth in our common garden than trees from the plot at low elevation. Beech populations originating from higher longitude or elevation have also been shown to be genetically earlier in provenance tests, suggesting that these populations evolved phenological traits promoting a longer vegetation period. At this southern margin of the species, the reduced allocation to stem growth at the low elevation plot is likely an adaptive response to drought, which has previously been described by comparing marginal vs central beech populations. Consistently with theoretical expectations, our results suggest a beneficial effect of pollen dispersal by increasing the genetic diversity for these locally differentiated traits. These effects were quantitatively high, with more than twice higher genetic variance for immigrant than local offspring, although with large standard errors around estimates. Our results highlight that local selection is an important evolutionary force in natural tree populations, and provide a strong evidence that adaptive genetic differentiation can occur despite high gene flow. For the two genetically differentiated traits, our analyses suggested a beneficial effect of pollen dispersal by increasing genetic diversity after one episode of reproduction. The findings suggest that conservation and management interventions to facilitate movement of gametes along short ecological gradients would boost genetic diversity of individual tree populations, and thereby enhance their adaptive potential.

International audience; Microbes in the atmosphere have broad ecological impacts, including the potential to trigger precipitation through species and strains that act as ice nucleation particles. To characterize spatiotemporal trends of microbial assemblages in precipitation we sequenced 16S (bacterial) and 18S (fungal) rRNA gene amplicon libraries collected from 72 precipitation events in three US states (Idaho, Louisiana, and Virginia) over four seasons. We considered these data from the perspective of a novel metacommunity framework. In agreement with our heuristic, we found evidence for distinct mechanisms underlying the composition and diversity of bacterial and fungal assemblages in precipitation. Specifically, we determined that: 1) bacterial operational taxonomic unit (OTU) composition of precipitation was strongly associated with macroscale drivers including season and high altitude characteristics of storms; 2) fungal OTU composition was strongly correlated with mesoscale drivers including particular spatial locations; 3) β‐diversity (heterogeneity of taxa among samples) for both bacteria and fungi was largely maintained by turnover of taxa; however, 4) bacterial assemblages had higher contributions to total β‐diversity from nestedness (i.e., lower richness assemblages were largely taxonomic subsets of richer assemblages), due to losses of taxa during dispersal, particularly among potential ice nucleation active bacteria; and 5) fungal assemblages had higher contributions to total β‐diversity from turnover due to OTU replacement. Spatiotemporal trends in precipitation‐borne metacommunities allowed delineation of a large number of statistically significant indicator taxa for particular sites and seasons, including trends for bacteria that are potentially ice nucleation active. Our findings advance understanding regarding the dispersion of aerosolized microbes via wet deposition, and the development of theory concerning potential assembly rules for bioaerosol assemblages.

The sudden interruption of recurring larch budmoth (LBM; Zeiraphera diniana or griseana Gn.) outbreaks across the European Alps after 1982 was surprising, because populations had regularly oscillated every 8–9 years for the past 1200 years or more. Although ecophysiological evidence was limited and underlying processes remained uncertain, climate change has been indicated as a possible driver of this disruption. An unexpected, recent return of LBM population peaks in 2017 and 2018 provides insight into this insect’s climate sensitivity. Here, we combine meteorological and dendrochronological data to explore the influence of temperature variation and atmospheric circulation on cyclic LBM outbreaks since the early 1950s. Anomalous cold European winters, associated with a persistent negative phase of the North Atlantic Oscillation, coincide with four consecutive epidemics between 1953 and 1982, and any of three warming-induced mechanisms could explain the system’s failure thereafter: (1) high egg mortality, (2) asynchrony between egg hatch and foliage growth, and (3) upward shifts of outbreak epicentres. In demonstrating that LBM populations continued to oscillate every 8–9 years at sub-outbreak levels, this study emphasizes the relevance of winter temperatures on trophic interactions between insects and their host trees, as well as the importance of separating natural from anthropogenic climate forcing on population behaviour. Electronic supplementary material The online version of this article (10.1007/s00442-019-04585-9) contains supplementary material, which is available to authorized users.

Résumé; Allis shad (Alosa alosa) populations showed important decline among last decades, and it is assumed that the species' distribution area has restricted. In some watersheds, the status of the species is preocupating, however this remains poorly explained. In the Gironde-Garonne-Dordogne system (SW France), its decline leads to the adoption of a fishery moratorium in 2008. Despite this measure, local populations don't show signs of a recovering. One hypothesis consists in the unefficiency of the recruitment process: indeed, young-of-the-year Allis shad are exposed to many pressures during their downstream migration, such as hypoxia (low water oxygen concentration). In the Gironde estuary, hypoxic events are frequent in summertime, and can consist in episodes of several days with water O2 saturations under 30%. In addition, hypoxic events are thought to be even more severe and frequent in the future, according to most of climate change scenarios. Such low O2 availability could threaten young Allis shad, and as a consequence, this could condition their migration success. To our knowledge, if authors have suggested that 3-months old Allis shad show lower resistance to hypoxia at higher temperature, the abilities of younger developmental stages (larval and migrating stages) have never been studied. Here we meant to describe tolerance range of 10, 30, 60 and 90-days old Allis shad to oxythermic stress, by conducting behavioural analysis at individual scale in decreasing water oxygen saturation conditions (from 100 to 30%), at temperatures 18, 22, or 26°C. By this study, we aimed to bring useful information on the importance of oxythermic conditions for Allis shad in both larvae reintroduction purposes and juvenile migration success.

Résumé; Allis shad (Alosa alosa) populations have shown an important decline throughout thelast few decades, and it is assumed that the species’ distribution area has been restricted. In the Gironde-GaronneDordogne system (GGD, SW France), its decline leads to the adoption of a fishery moratorium in 2008. Despite this measure, locally no signs of recovery are observed. One hypothesis consists of the inefficiency of the recruitment process: young-of-the-year Allis shad are exposed to many pressures during their downstream migration, such as hypoxia. In the GGD system, hypoxic events are frequent in summertime (periods of several days with water O2 saturations under 30%). Those events are thought to become more severe andfrequent according to most climate change scenarios. Such low O2 availability could threaten young Allis shadby altering their migration success. If authors have suggested that 3-months old Allis shad show lower resistance to hypoxia at highertemperature, the abilities of younger development stages have never been studied. Here we meant to describe tolerance range of 10, 30, 60 and 90-days oldAllis shad to oxythermic stress by conducting behavioural analysis at an individual scale in decreasing water oxygen saturation conditions (from 100 to 30%), at four temperatures (18, 22, 26°C for 10, 30 days-old ; 22, 26, 28°C for 60, 90 days-old). By this study, we aimed to bring useful information on the importance of oxythermic conditions for Allis shad in both larvae reintroduction purposes and juvenile migration success

International audience

Annual radial growth and latewood formation increase during the period 1966–2015 in Larix cajanderi Mayr. and Pinus sylvestris L. along a latitudinal gradient on Siberian permafrost. Warmer temperatures and precipitation at the onset of the growth season favor growth in both species. A vast area of Siberian boreal forest is covered by continuous permafrost, where tree radial growth is strongly limited by low temperatures. Understanding how climate controls Siberian conifer growth is critical in order to predict their response to ongoing climate change. To explore variations in the radial growth and earlywood/latewood formation of Pinus sylvestris L. and Larix cajanderi Mayr. trees along a climate gradient within the continuous permafrost zone in Central Yakutia (Russia), a region experiencing accelerated warming. We evaluated spatiotemporal differences in tree-ring and latewood width among sites by using generalized additive mixed models. Pearson’s correlations were used to analyze the effect of local climate (temperature, precipitation) and drought (SPEI) on the formation of earlywood and latewood. Both conifers showed increased radial growth in recent decades. Radial growth was controlled by temperature and precipitation in both species along the gradient, with earlier precipitation events being critical for the formation of wide rings. Although temperature is considered as the main limiting factor triggering tree growth in the continuous permafrost zone, our results showed that water availability also plays a key role in radial tree growth even in the coldest sites.

La compréhension du déterminisme des émissions de N2O, troisième gaz à effet de serre d’origine anthropique, constitue un enjeu environnemental majeur. Ce manuscrit présente les travaux de recherche réalisés dans le cadre d’un stage de Master 2 à l’INRA (Orléans) sur l’étude du lien entre dynamique des émissions de N2O et fonctionnement hydrique d’un sol cultivé fertilisé. Cette étude a été réalisée sur une maquette expérimentale de sol de 10 m², mise en pente sous un simulateur de pluie. Les émissions de N2O ont été mesurées pendant 70 jours en 16 points de la maquette, à l’aide d’une chambre mobile et d’un spectromètre laser SPIRIT. Les variables du sol (substrats azotés, pH, masse volumique, teneur en eau) ont été mesurées en amont, milieu et aval du dispositif au cours de l’expérimentation. Sur toutes les zones, un premier pic d’émission a été observé en réponse à une pluie de 24 mm consécutive à un apport en substrat azoté – deux conditions favorisant la dénitrification -, et un second pic, plus faible, a été observé après une pluie de 8 mm. La dynamique des processus hydriques (écoulements latéraux, accumulation d’eau en bas de pente), explique des émissions plus fortes en aval., Understanding the dynamics of N2O emissions, the third anthropogenic greenhouse gas, is a major environmental issue. This manuscript presents the research work carried out as part of a Master 2 internship at INRA (Orléans). It deals with the analysis of the relationships between N2O emissions dynamics, and hydric functioning of a cultivated and fertilised soil. A 10 m² sloped soil model was installed under a rain simulator. N2O emissions were measured for 70 days at 16 points of the model, using a fast-box chamber and a SPIRIT laser spectrometer. Soil characteristics (nitrogen, pH, bulk density, water content) were measured upstream, mid- and downstream during the experiment. On all points, a first N2O peak was observed after a 24 mm rainfall following a nitrogen application - two conditions favoring denitrification -, and a second but lower peak was observed after a 8 mm rainfall. The dynamics of the water processes (lateral flows, accumulation of water at the bottom of the slope), explains stronger emissions at the downstream position.

Article en open access; International audience; In this study, we report the development of a set of 15 polymorphic microsatellite markers for the box tree moth, Cydalima perspectalis (Walker), a highly invasive insect in Europe causing significant damage to natural and ornamental Buxus trees. The markers were characterized for four distant populations in both its native (China, two populations) and invasive ranges (Czech Republic and Turkey, one population each). The number of alleles ranged from 2 to 12. No marker significantly deviated from the Hardy-Weinberg equilibrium for all the populations sampled. These microsatellite markers are promising tools for further studies on the invasive pathways and dispersal pattern of the box tree moth in Europe.

Recycling organic waste products in agriculture is a potential route for the dispersion of pharmaceutical residues in the environment. In this study, the concentrations of thirteen pharmaceuticals and the personal care product triclosan (PPCPs) were determined in different environmental matrices from long-term experimental fields amended with different organic waste products (OWPs), including sludge, composted sludge with green wastes, livestock effluents and composted urban wastes applied at usual agricultural rates. PPCP concentrations were different in OWPs, varying from a few micrograms to milligrams per kilogram dry matter or per litre for slurry. OWPs from sludge or livestock effluents primarily contained antibiotics, whereas composted urban wastes primarily contained anti-inflammatory compounds. PPCP contents in soils amended for several years were less than a few micrograms per kilogram. The most persistent compounds (fluoroquinolones, carbamazepine) were quantified or detected in soils amended with sludge or composted sludge. In soils amended with composted municipal solid waste, carbamazepine was quantified, and fluoroquinolones, ibuprofen and diclofenac were sometimes detected. The small increases in fluoroquinolones and carbamazepine in soils after individual OWP applications were consistent with the fluxes from the applied OWP. The measured concentrations of pharmaceuticals in soil after several successive OWP applications were lower than the predicted concentrations because of degradation, strong sorption to soil constituents and/or leaching. Dissipation half-lives (DT50) were approximately 750–2500, 900 and < 300 days for fluoroquinolones, carbamazepine and ibuprofen, respectively, in temperate soils and < 350 and < 80 days for fluoroquinolones and doxycycline, respectively, in tropical soils. Detection frequencies in soil leachates were very low (below 7%), and concentrations ranged from the limits of detection (0.002–0.03 μg/L) and exceptionally to 0.27 μg/L. The most frequently detected pharmaceuticals were carbamazepine and ibuprofen. Based on the risk quotient, the estimated ecotoxicological risks for different soil organisms were low.

Nitrous acid (HONO) fluxes were measured above an agricultural field site near Paris during different seasons. Above bare soil, different crops were measured using the aerodynamic gradient (AG) method. Two LOPAPs (LOng Path Absorption Photometer) were used to determine the HONO gradients between two heights. During daytime mainly positive HONO fluxes were observed, which showed strong correlation with the product of the NO2 concentration and the long wavelength UV light intensity, expressed by the photolysis frequency J(NO2). These results are consistent with HONO formation by photosensitized heterogeneous conversion of NO2 on soil surfaces as observed in recent laboratory studies. An additional influence of the soil temperature on the HONO flux can be explained by the temperature-dependent HONO adsorption on the soil surface. A parameterization of the HONO flux at this location with NO2 concentration, J(NO2), soil temperature and humidity fits reasonably well all flux observations at this location.

Aim: The winemaking sector in Portugal is of major socio-economic relevance, significantly contributing to the national exports and sustaining many wine-related activities, including oenotourism. Portuguese viticultural regions present a wide range of edaphoclimatic conditions with remarkable regional specificities, thus contributing to the individuality of their wines. Owing to the strong influence of climate and weather factors on grapevines, climate change may drive significant impacts on Portuguese viticulture.Methods and results: Climatic projections for the next decades in Portugal highlight an overall warming and drying trend of the grapevine growing season, potentially resulting in modifications in phenology, growth, development, yields and eventually wine characteristics and typicity. Furthermore, the current viticultural suitability of each region is projected to undergo significant changes, suggesting a reshaping of the optimal conditions for viticulture throughout the country. In order to sustain high quality levels and affordable yield regularity, cost-effective, appropriate and timely adaptation measures must be implemented by the sector.Conclusion: The most recent scientific studies covering the potential impacts of climate change on Portuguese viticulture are herein presented.Significance and impact of the study: Possible adaptation measures against these threats are also discussed, foreseeing their integration into decision support systems by stakeholders and decision-makers.

Unpublished chemical and isotopic data taken in November 1992 from the three major Saharan aquifers, namely the Continental Intercalaire (CI), the Complexe Terminal (CT) and the phreatic aquifer (Phr), were integrated with original samples in order to chemically and isotopically characterize the largest Saharan aquifer system and investigate the processes through which groundwaters acquire their mineralization. Instead of classical Debye–Hückel extended law, a specific interaction theory (SIT) model, recently incorporated in PHREEQC 3.0, was used. Inverse modeling of hydrochemical data constrained by isotopic data was used here to quantitatively assess the influence of geochemical processes: at depth, the dissolution of salts from the geological formations during upward leakage without evaporation explains the transitions from CI to CT and to a first end member, a cluster of Phr (cluster I); near the surface, the dissolution of salts from sabkhas by rainwater explains another cluster of Phr (cluster II). In every case, secondary precipitation of calcite occurs during dissolution. All Phr waters result from the mixing of these two clusters together with calcite precipitation and ion exchange processes. These processes are quantitatively assessed by the PHREEQC model. Globally, gypsum dissolution and calcite precipitation were found to act as a carbon sink.

International audience; Altitude lakes are weakly impacted by human activities. This makes them choice ecosystems to understand how biological communities are impacted by natural factors. This question was addressed to littoral benthic diatoms, a largely used ecological indicator. We wanted to know if benthic diatoms in lakes are more impacted by local varying factors (altitude, lake depth...) or regional varying factors (geology). The study area takes place in the Northern French Alps. Littoral benthic diatoms of 63 natural lakes situated between 1350 and 2700 m · a.s.l. were sampled. Two categories of communities were observed: one of deep and lower altitude lakes and one of higher altitude and shallower lakes. In each category, communities were characterized and were corresponding to particular lake types: lakes dominated by a particular geology, lakes with a water level fluctuation, turbid lakes,... Communities did not show a spatial structure. We observed that local factors were more important than regional factors. Indeed, the study area displayed a mixed geology even at a local level. On another hand, altitude a local varying factor determines freezing period a determining item of high-altitude lake functioning.

Prioritization of introduction pathways is seen as an important component of the management of biological invasions. We address whether established alien plants, mammals, freshwater fish and terrestrial invertebrates with known ecological impacts are associated with particular introduction pathways (release, escape, contaminant, stowaway, corridor and unaided). We used the information from the European alien species database DAISIE (www.europe-aliens.org) supplemented by the EASIN catalogue (European Alien Species Information Network), and expert knowledge. Plants introduced by the pathways release, corridor and unaided were disproportionately more likely to have ecological impacts than those introduced as contaminants. In contrast, impacts were not associated with particular introduction pathways for invertebrates, mammals or fish. Thus, while for plants management strategies should be targeted towards the appropriate pathways, for animals, management should focus on reducing the total number of taxa introduced, targeting those pathways responsible for high numbers of introductions. However, regardless of taxonomic group, having multiple introduction pathways increases the likelihood of the species having an ecological impact. This may simply reflect that species introduced by multiple pathways have high propagule pressure and so have a high probability of establishment. Clearly, patterns of invasion are determined by many interacting factors and management strategies should reflect this complexity

Since the early 1990s, ash dieback due to the invasive ascomycete Hymenoscyphus fraxineus is threatening Fraxinus excelsior in most of its natural range. Previous studies reported significant levels of genetic variability in susceptibility in F. excelsior either in field or inoculation experiments. The present study was based on a field experiment planted in 1995, 15 years before onset of the disease. Crown and collar status were monitored on 777 trees from 23 open-pollinated progenies originating from three French provenances. Health status was modeled using a Bayesian approach where spatiotemporal effects were explicitly taken into account. Moderate narrow-sense heritability was found for crown dieback (h2 = 0.42). This study is first to show that resistance at the collar level is also heritable (h2 = 0.49 for collar lesions prevalence and h2 = 0.42 for their severity) and that there is significant genetic correlation (r = 0.40) between the severities of crown and collar symptoms. There was no evidence for differences between provenances. Family effects were detected, but computing individual breeding values showed that most of the genetic variation lies within families. In agreement with previous reports, early flushing correlates with healthier crown. Implications of these results in disease management and breeding are discussed.

International audience

The amount and spatial distribution of foliage in a tree canopy have fundamental functions in ecosystems as they affect energy and mass fluxes through photosynthesis and transpiration. They are usually described by the Leaf Area Index (LAI) and the Leaf Area Density (LAD), which can be measured through a variety of methods, including voxel-based methods applied to LiDAR point clouds. A theoretical study recently compared the numerical errors arising from different voxel-based estimation methods for Plant Area Density (PAD) based on Beer’s law-based, contact frequency and Maximum-Likelihood Estimation, showing that the bias-corrected Maximum Likelihood Estimator was theoretically the most efficient. However, this earlier study i) ignored wood volumes; ii) neglected vegetation clumping inside the voxel; iii) ignored instrument characteristics in terms of effective footprint, iv) was limited to a single viewpoint. In practice, retrieving LAD from PAD is not straightforward, vegetation is not randomly distributed in volumes of interest, beams are divergent and forestry plots are usually sampled from more than one viewpoint, to mitigate the effect of occlusion. In the present short communication, we extend the previous efficient formulation to actual field conditions to i) account for the presence of both wood volumes and wood hits, ii) rigorously include correction terms for vegetation and instrument characteristics, iii) integrate multiview data. A numerical comparison with other methods commonly used to combine information from different viewpoints led to error reduction, especially in poorly-explored volumes, which are frequent in actual canopies. Beyond its concision, completeness and efficiency, this new formulation -which can be applied to multiview TLS, but also UAV LiDAR scanning - can help reducing errors in LAD estimation.

International audience

Résumé; International audience

International audience; The number of invasive alien pest and pathogen species affecting ecosystem functioning, human health and economies has increased dramatically over the last decades. Discoveries of invasive pests and pathogens previously unknown to science or with unknown host associations yet damaging on novel hosts highlights the necessity of developing novel tools to predict their appearance in hitherto naive environments. The use of sentinel plant systems is a promising tool to improve the detection of pests and pathogens before introduction and to provide valuable information for the development of preventative measures to minimize economic or environmental impacts. Though sentinel plantings have been established and studied during the last decade, there still remains a great need for guidance on which tools and protocols to put into practice in order to make assessments accurate and reliable. The sampling and diagnostic protocols chosen should enable as much information as possible about potential damaging agents and species identification. Consistency and comparison of results are based on the adoption of common procedures for sampling design and sample processing. In this paper, we suggest harmonized procedures that should be used in sentinel planting surveys for effective sampling and identification of potential pests and pathogens. We also review the benefits and limitations of various diagnostic methods for early detection in sentinel systems, and the feasibility of the results obtained supporting National Plant Protection Organizations in pest and commodity risk analysis.

National audience

International audience

résumé résumérésumé; International audience

International audience

Adaptation des forêts au changement climatique : menaces et opportunités. 2. journée scientifique du projet environnemental CLIMIBIO

Sequential cropping (also known as multiple or double cropping) is a common feature, particularly for tropical regions, where the crop seasons are largely dictated by the main wet season such as the Asian summer monsoon (ASM). The ASM provides the water resources for crops grown for the whole year, thereby influencing crop production outside the ASM period. Land surface models (LSMs) typically simulate a single crop per year, however, in order to understand how sequential cropping influences demand for resources, we need to simulate all of the crops grown within a year in a seamless way. In this paper we implement sequential cropping in a branch of the Joint UK Land Environment Simulator (JULES) and demonstrate its use at Avignon, a site that uses the sequential cropping system and provides over 15-years of continuous flux observations which we use to evaluate JULES with sequential cropping. In order to implement the method in future regional simulations where there may be large variations in growing conditions, we apply the same method to four locations in the North Indian states of Uttar Pradesh and Bihar to simulate the rice--wheat rotation and compare model yields to observations at these locations. JULES is able to simulate sequential cropping at Avignon and the four India locations, representing both crops within one growing season in each of the crop rotations presented. At Avignon the maxima of LAI, above ground biomass and canopy height occur at approximately the correct time for both crops. The magnitudes of biomass, especially for winter wheat, are underestimated and the leaf area index is overestimated. The JULES fluxes are a good fit to observations (r-values greater than 0.7), either using grasses to represent crops or the crop model, implying that both approaches represent the surface coverage correctly. For the India simulations, JULES successfully reproduces observed yields for the eastern locations, however yields are under estimated for the western locations. This development is a step forward in the ability of JULES to simulate crops in tropical regions, where this cropping system is already prevalent, while also providing the opportunity to assess the potential for other regions to implement it as an adaptation to climate change.

Background Grain yield of wheat is greatly associated with the population of wheat spikes, i.e., $$spike~number~\text {m}^{-2}$$spikenumberm-2. To obtain this index in a reliable and efficient way, it is necessary to count wheat spikes accurately and automatically. Currently computer vision technologies have shown great potential to automate this task effectively in a low-end manner. In particular, counting wheat spikes is a typical visual counting problem, which is substantially studied under the name of object counting in Computer Vision. TasselNet, which represents one of the state-of-the-art counting approaches, is a convolutional neural network-based local regression model, and currently benchmarks the best record on counting maize tassels. However, when applying TasselNet to wheat spikes, it cannot predict accurate counts when spikes partially present. Results In this paper, we make an important observation that the counting performance of local regression networks can be significantly improved via adding visual context to the local patches. Meanwhile, such context can be treated as part of the receptive field without increasing the model capacity. We thus propose a simple yet effective contextual extension of TasselNet—TasselNetv2. If implementing TasselNetv2 in a fully convolutional form, both training and inference can be greatly sped up by reducing redundant computations. In particular, we collected and labeled a large-scale wheat spikes counting (WSC) dataset, with 1764 high-resolution images and 675,322 manually-annotated instances. Extensive experiments show that, TasselNetv2 not only achieves state-of-the-art performance on the WSC dataset ($$91.01\%$$91.01% counting accuracy) but also is more than an order of magnitude faster than TasselNet (13.82 fps on $$912\times 1216$$912×1216 images). The generality of TasselNetv2 is further demonstrated by advancing the state of the art on both the Maize Tassels Counting and ShanghaiTech Crowd Counting datasets. Conclusions This paper describes TasselNetv2 for counting wheat spikes, which simultaneously addresses two important use cases in plant counting: improving the counting accuracy without increasing model capacity, and improving efficiency without sacrificing accuracy. It is promising to be deployed in a real-time system with high-throughput demand. In particular, TasselNetv2 can achieve sufficiently accurate results when training from scratch with small networks, and adopting larger pre-trained networks can further boost accuracy. In practice, one can trade off the performance and efficiency according to certain application scenarios. Code and models are made available at: https://tinyurl.com/TasselNetv2.

Les sols agricoles représentent près de 66 % des émissions anthropiques de protoxyde d’azote (N2O), 3ème gaz responsable de l’effet de serre additionnel. La variabilité des émissions mesurées au champ est élevée. La structure du sol impacte à la fois la production et le transport du N2O dans le profil de sol. L’objectif de cette thèse était de comprendre le rôle de l’état structural du sol sur la variabilité spatiale des émissions de N2O. La démarche utilisée associe deux types d’expérimentations en laboratoire - à l’échelle d’un bac de 0,3 m² x 0,1 m et sur une maquette de parcelle agricole de 10 m² x 0,3 m en sol nu - à un travail de modélisation intégrant des processus physiques, chimiques et biologiques dans le profil de sol et le ruissellement, le tout à une résolution temporelle fine. Ce travail a mis en évidence une hiérarchie entre les processus de production et de transport, qui évolue avec le temps et les conditions environnementales : dans des conditions favorables à la dénitrification, la production de N2O augmente avec la masse volumique en lien avec une augmentation de la part de porosité remplie d’eau, jusqu’à une certaine limite. Le modèle déterministe a montré que la dynamique de la pluie et du ruissellement associé modifie l’intensité et la dynamique des émissions de N2O, celles-ci étant plus tardives dans les zones avales recevant du ruissellement. Enfin, ce travail a confirmé la complexité du déterminisme des émissions de N2O et a permis de souligner l’intérêt de caractériser la structure du sol et les émissions à une haute résolution spatiale pour améliorer la qualité des modèles prédictifs., Agricultural soils account for 66 % of anthropogenic nitrous oxide emissions (N2O), the 3rd greenhouse gas emitted from anthropogenic activities. N2O emissions variability measured in-situ is quite high. Soil structure affects both N2O production processes and N2O movements through the soil profile. The main goal of this work was to understand the part of soil structure in soil N2O spatial variability. Two kinds of laboratory experiments were designed: rainfall experiments on soil trays of 0.3 m² x 0.1 m and on a 10 m² x 0.3 m box with a slope. A modelling approach with a short time step was combined, involving representation of physical, chemical and biological soil processes as well as a representation of surface runoff. This work highlighted a hierarchy between N2O production and N2O transportation processes, which evolve with time and environmental conditions: under conditions that favor denitrification, N2O production increases with soil bulk density due to an increase in the water-filled pore space, until a threshold limit. The deterministic modelling approach showed that rainfall dynamic and resulting runoff affect soil N2O emissions, those emissions occurring later downslope. Finally, this work highlighted the complexity of soil N2O emissions determinism and we pointed out that the description of soil structure at a high spatial resolution would be useful to improve modelling quality.

Projections of grapevine phenophases under future climate change scenarios are strategic decision support tools for viticulturists and wine producers. Several phenological models are tested for budburst, flowering, and veraison and for two main grapevine varieties (cv. Touriga Franca and Touriga Nacional) growing in the Douro Demarcated Region. Four forcing models (Growing degree-days, Richardson, Sigmoid, and Wang) and three dormancy models (Bidabe, Smoothed Utah and Chuine), with different parameterizations and combinations, are used. New datasets, combing phenology with weather station data, widespread over the Douro wine region, were used for this purpose. The eight best performing models and parameterizations were selected for each phenophase and variety, based on performance metrics. For both cultivars, results revealed moderate performances (0.4 &lt, R2 &lt, 0.7) for budburst, while high performances (R2 &gt, 0.7) were found for flowering and veraison, particularly when Growing degree-days or Sigmoid models are used, respectively. Climate change projections were based on a two-member climate model ensemble from the EURO-CORDEX project under RCP4.5. Projections depicted an anticipation of phenophase timings by 6, 8 or 10&ndash, 12 days until the end of the century for budburst, flowering, and veraison, respectively. The inter-model variability is of approximately 2&ndash, 4 days for flowering and veraison and 4&ndash, 6 days for budburst. These results establish grounds for the implementation of a decision support system for monitoring and short-term prediction of grapevine phenology, thus promoting a more efficient viticulture.

Standardized tools are needed to identify and prioritize the most harmful non-native species (NNS). A plethora of assessment protocols have been developed to evaluate the current and potential impacts of non-native species, but consistency among them has received limited attention. To estimate the consistency across impact assessment protocols, 89 specialists in biological invasions used 11 protocols to screen 57 NNS (2614 assessments). We tested if the consistency in the impact scoring across assessors, quantified as the coefficient of variation (CV), was dependent on the characteristics of the protocol, the taxonomic group and the expertise of the assessor. Mean CV across assessors was 40%, with a maximum of 223%. CV was lower for protocols with a low number of score levels, which demanded high levels of expertise, and when the assessors had greater expertise on the assessed species. The similarity among protocols with respect to the final scores was higher when the protocols considered the same impact types. We conclude that all protocols led to considerable inconsistency among assessors. In order to improve consistency, we highlight the importance of selecting assessors with high expertise, providing clear guidelines and adequate training but also deriving final decisions collaboratively by consensus

International audience

This article describes extreme indices maps (Data Cube, raster X Time) for different scenarios with a more important contribution to the sea level rise from Greenland and/or Antarctica during the 21st century under the Representative Concentration Pathway (RCP) 8.5 emission scenario. The indices are produced annually and globally with a resolution of 0.5° × 0.5° from 1951 to 2099. The data were generated by simulating daily maximum and minimum temperature and precipitation from the IPSL-CM5A-LR model from Coupled Model Intercomparison Project Phase 5 (CMIP5). These climatic data are unbiased and downscaled to the 0.5°x0.5 scale with the Cumulative Distribution Function transform (CDFt) and EWEMBI dataset compiled to support the bias correction of climate input data for ISIMIP. Finally, each extreme indice is computed on the unbiased data on each grid cell on all continents. Keywords: Ice sheet contribution, Climate change, Extreme events, Temperature, Precipitation, Global climate model

National audience; La restauration de la continuité écologique du fleuve Sélune (Manche) est un projet d’arasement de deux grands barrages (h. 36 et 16m) hydroélectriques sans précédent en Europe. Il est suivi par un programme scientifique (Selune-river-restoration.inra.fr) comprenant une analyse du reverdissement spontané d’un tronçon de 19km de long et 151ha (dimensions du premier lac de retenue disparu). Dès 2015, des baisses de niveaux successives ont dénoyé progressivement les plages de sédiments de l’ancienne vallée. Des travaux de gestion sédimentaire ont été conduits conjointement (creusement du lit mineur, stockage des sédiments par reprofilage localisé des berges) pour prévenir l’emportement des 700 000m3 de sédiments mobilisables. De fait, les vases exondées constituent des milieux pionniers ouverts à la recolonisation végétale. Les 4 années de suivi (2015-2018), état initial avant arasement, visaient à observer le patron spatial et la trajectoire des communautés végétales spontanées des points de vue structurel, taxonomique et fonctionnel. L’échantillonnage spécifique d’un site ayant subi une baisse de niveau automnale (2014), printanière (2017) et un remaniement artificiel automnal (2017) permet de comparer les réponses de la végétation (i) à la saison de la baisse de niveau et (ii) au remaniement. Dans tous les cas, la recolonisation est rapide, mais, les choix de gestion semblent influencer la composition et certaines fonctions des communautés. Ainsi, si des espèces pouvant fixer les rives sont présentes après chaque baisse, les communautés sont plus riches, diversifiées et les espèces de berges, plus abondantes suite à une baisse printanière. Le remaniement par le génie civil favorise une homogénéisation des communautés dominées par des annuelles ne se dispersant pas végétativement et restreint l’établissement d’espèces forestières. Cette perturbation forte (mélange des horizons, talutage, compactage) tardive est un retour à un état sensible (remise à nu) bouleversant le gain, après 2,5 ans de successions spontanées, de communautés typiques de berges aptes au maintien des sédiments. Les implications en matière de potentialités de restauration écologique passive de la vallée sont discutées.

National audience

The European Union (EU) has recently published its first list of invasive alien species (IAS) of EU concern to which current legislation must apply. The list comprises species known to pose great threats to biodiversity and needs to be maintained and updated. Horizon scanning is seen as critical to identify the most threatening potential IAS that do not yet occur in Europe to be subsequently risk assessed for future listing. Accordingly, we present a systematic consensus horizon scanning procedure to derive a ranked list of potential IAS likely to arrive, establish, spread and have an impact on biodiversity in the region over the next decade. The approach is unique in the continental scale examined, the breadth of taxonomic groups and environments considered, and the methods and data sources used. International experts were brought together to address five broad thematic groups of potential IAS. For each thematic group the experts first independently assembled lists of potential IAS not yet established in the EU but potentially threatening biodiversity if introduced. Experts were asked to score the species within their thematic group for their separate likelihoods of i) arrival, ii) establishment, iii) spread, and iv) magnitude of the potential negative impact on biodiversity within the EU. Experts then convened for a 2‐day workshop applying consensus methods to compile a ranked list of potential IAS. From an initial working list of 329 species, a list of 66 species not yet established in the EU that were considered to be very high (8 species), high (40 species) or medium (18 species) risk species was derived. Here, we present these species highlighting the potential negative impacts and the most likely biogeographic regions to be affected by these potential IAS., We identified 66 species, that are currently absent from the EU, which pose a very high, high or medium threat to biodiversity and ecosystems. The species span a range of functional groups, with primary producers being numerically dominant. Escape from confinement is the pathway considered to be the most likely route of introduction for many species, particularly among plants and vertebrates.

The need to reconnect agriculture, environment, food, and health when addressing agrifood system transitions is widely acknowledged. However, most analytical frameworks, especially in the expanding literature about &ldquo, system approaches&rdquo, rely on impact-based approaches and, thus, tend to overlook ecological processes as well as social ones. This article aims at demonstrating that a territorial approach to agrifood system transitions is more appropriate to tackle the reconnection between agriculture, food, environment, and health than the larger scales (global or national food systems) or the smaller ones (such as those of alternative food systems) usually addressed in the literature. Co-elaborated by a sociologist, an ecologist, and a nutritionist, this article is based on a focused analysis of the literature that has addressed agrifood system transitions in the food and health sciences and in the social sciences and on the reflexive analysis of two past projects dealing with such transitions. It shows that a territorial approach allows including in the analysis the diverse agrifood systems&rsquo, components as well the ecological and social processes that may create functionalities for improving agrifood systems&rsquo, sustainability. This territorial approach is based on systemic and processual thinking and on a transdisciplinary perspective combining an objectification stance and a pragmatist constructivist one. It should allow actors and researchers to build a shared understanding of the transition processes within their shared territorial agrifood system, despite possibly different and diverging views.

The focus of this paper is to investigate the ability to assess the flow exchanges between the matrix and the conduits in two karstified watersheds (Aliou and Baget, Ari&egrave, ge, France) using the KarstMod modeling platform. The modeling is applied using hourly and daily time series. First, the flow dynamics between the conduit and the surrounding matrix are described on a rainfall event scale (i.e., a few days). The model allows us to describe a physical reality concerning the flow reversal between matrix and conduit when there is a significant rainfall event. Then, the long-term trends (i.e., inter-annual) in the matrix water level are evidenced using the moving average over shifting horizon method (MASH). The mean water level in the matrix dropped about 10% to 15% since the late 1960s. Also, the matrix recharge has been delayed from February in the late 1960s to April since the 1990s. Moreover, the contribution of the matrix in the total spring flow is estimated though mass balance. It is estimated that the annual matrix contribution in the total spring flow is about 3% and it can increase to up to 25% during periods with low rainfall.

National audience; Les jardins communs forestiers doivent être suivis, conservés, maintenus, voire étendus avec de nouvelles essences et doivent être bien renseignés et répertoriés dans les plans d’aménagements.Les résultats qui en sont issus doivent être diffusés et portés à la connaissance de tous, comme se proposent de le faire les projets en cours soutenus par le Ministère de l’Agriculture comme ESPERENSE , et MedForFutur, notamment. Les efforts de tous partenaires de la filière forestière française de recherche et développement pour se constituer en réseau (pour ce qui est des jardins communs, voir GEN4X et IN-Sylva et réfléchir à l’évolution de ces dispositifs pour prendre en compte les itinéraires sylvicoles, le potentiel offert par l’hybridation, la constitution de vergers à graines et îlots d’avenir, etc., vont aussi dans ce sens. Par ailleurs, les données issues de la gestion courante (suivis des coupes, régénérations et plantations par exemple) constituent aussi une ressource expérimentale d’une très grande richesse pour le choix des espèces et provenances, qui mérite d’être mieux tracée, archivée, valorisée (sommier électronique par exemple) et venir compléter les dispositifs de recherche classiques voir Fady et Scotti 2018 (Forêt Entreprise 240) et le blog.

International audience; The quantification of ozone by SIFT-MS was investigated in conditions suitable with an industrial emission context (high ozone demand, dry air/oxygen as the manufacturing gas of the ozone generator, and high humidity levels beyond saturation at room conditions). Ozone reacts with four negative precursor ions available in the SIFT-MS device (NO2–, O2–, HO–, and O–), each precursor ion having its specific domain of linearity. For a high ozone concentration range, only NO2– and O2– have resulted in a linear behavior (between 1 and 100 ppmv of O3 for NO2–, between 1 and 50 ppmv of O3 for O2–). No water interference was identified during ozone measurements by SIFT-MS using NO2– and O2– precursor ions, even with extreme humidity levels. The presence of nitrogen oxide contaminants (due to the use of dry air as the manufacturing gas of the ozone generator) affected the ozone quantification by SIFT-MS. It is critical for NO2– precursor ions, whose rate constant varied as a function of NO2 concentrations. With O2– precursor ion, ozone was successfully measured in the presence of nitrogen oxides; however, the secondary chemistry must be taken into account.

Partie 3 : Douglas-fir ecology; International audience

In the low Mediterranean basin, late spring and autumn rainfall events have the potential to increase discharge and transport substantial amounts of sediment soil (that is, the net soil erosion from a watershed). For the Alento River Basin (ARB), located in the low Tyrrhenian coast of Italy, we estimated changes of net erosion as dependent on the seasonality of antecedent soil moisture and its control on rainfall-runoff and erosivity. Based on rainfall and runoff erosivity sub-models, we developed a simplified model to evaluate basin-wide sediment yields on a monthly basis by upscaling point rainfall input. For the period 1951&ndash, 2018, the reconstruction of a time series of monthly net erosion data indicated a decreasing trend of the sediment yield after 1991. Revegetation and land abandonment that occurred in the last decades can explain such a decrease of net erosion, which occurred even when rainfall erosivity increased. This response, obtained at the basic scale, does not exclude that rapidly developing mesoscale convective systems, typically responsible for the heaviest and most destructive rainfall events in the ARB, can affect small catchments, which are the most vulnerable systems to storm-driven flash floods and soil erosion hazards during soil tilling in spring and at beginning of autumn.

Partie 3 : Douglas-fir ecology; International audience