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1. Pesticide Residues in French Soils: Occurrence, Risks, and Persistence

Author: Claire Froger, Claudy Jolivet, Hélène Budzinski, Manon Pierdet, Giovanni Caria, Nicolas P. A. Saby, Dominique Arrouays, Antonio Bispo, Info&Sols (Info&Sols), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Earth and Planetary Observation Centre (EPOC), University of Stirling, Interactions Sol Plante Atmosphère (UMR ISPA), Ecole Nationale Supérieure des Sciences Agronomiques de Bordeaux-Aquitaine (Bordeaux Sciences Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire d'Analyses des Sols (LAS), Laboratoire Avancé de Spectroscopie pour les Intéractions la Réactivité et l'Environnement - UMR 8516 (LASIRE), and Institut de Chimie du CNRS (INC)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)
Subjects: [SDE]Environmental Sciences, Environmental Chemistry, General Chemistry
Abstract: International audience
Published: 2023

2. Numerical Evaluation of Circuit Model for Fast Computational Analysis of Resonant Wireless Power Transfer System

Author: F. M. Freitas, I. V. Soares, L. Krähenbühl, A. Bréard, C. Vollaire, S. T. M. Gonçalves, U. C. Resende, Centro Federal de Educação Tecnológica de Minas Gerais (CEFET-MG), Institut d'Électronique et des Technologies du numéRique (IETR), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Nantes Université - pôle Sciences et technologie, Nantes Université (Nantes Univ)-Nantes Université (Nantes Univ), Ampère, Département Automatique pour l'Ingénierie des Systèmes (AIS), Ampère (AMPERE), École Centrale de Lyon (ECL), Université de Lyon-Université de Lyon-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-École Centrale de Lyon (ECL), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and Ampère, Département Energie Electrique (EE)
Subjects: Circuit model, magnetic metamaterial, resonance, [SPI.NRJ]Engineering Sciences [physics]/Electric power, wireless power transfer, near field coupling, LC metamaterial, Electrical and Electronic Engineering, Electronic, Optical and Magnetic Materials
Abstract: International audience; This paper proposes a circuit model to calculate the current along printed coils used in Resonant Wireless Power Transfer. It considers a system composed of a metamaterial and two coplanar coils, transmitter and receiver, respectively. First, a circuit model for the system is presented. Then, an analytical model is proposed to calculate the self-inductance of printed inductors, their characteristic resistance, and the mutual inductance between coils. The proposed formulation for calculating the mutual inductance between inductors is based on Neumann’s formula. The practical results validate the model precision, obtaining a maximum deviation of approximately 8%, 3%, and 3%, respectively. Due to the generality of this approach, it can also be applied to more complex structures such as metasurfaces. The proposed 3-D models proved to be ideal for modeling the printed inductor. Furthermore, this model proved to be computationally more efficient for analyzing large systems when compared to commercial full-wave simulation software, with a reduction in the computational time larger than three orders of magnitude.
Published: 2023

3. FAIR-Checker: supporting digital resource findability and reuse with Knowledge Graphs and Semantic Web standards

Author: Gaignard, Alban, Rosnet, Thomas, de Lamotte, Frédéric, Lefort, Vincent, Devignes, Marie-Dominique, Nantes Université (Nantes Univ), Theories and Approaches of Genomic Complexity (TAGC), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut Français de Bioinformatique (IFB-CORE), Institut National de Recherche en Informatique et en Automatique (Inria)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), Méthodes et Algorithmes pour la Bioinformatique (MAB), Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Laboratoire Lorrain de Recherche en Informatique et ses Applications (LORIA), Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), unité de recherche de l'institut du thorax UMR1087 UMR6291 (ITX), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Nantes Université - UFR de Médecine et des Techniques Médicales (Nantes Univ - UFR MEDECINE), Nantes Université - pôle Santé, Nantes Université (Nantes Univ)-Nantes Université (Nantes Univ)-Nantes Université - pôle Santé, and Nantes Université (Nantes Univ)-Nantes Université (Nantes Univ)
Subjects: [INFO.INFO-IR]Computer Science [cs]/Information Retrieval [cs.IR], [INFO.INFO-WB]Computer Science [cs]/Web, Bioschemas, [INFO]Computer Science [cs], [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], SPARQL, SHACL, FAIR, Schema.org
Abstract: International audience; The current rise of Open Science and Reproducibility in the Life Sciences requires the creation of rich, machine-actionable metadata in order to better share and reuse biological digital resources such as datasets, bioinformatics tools, training materials, etc. For this purpose, FAIR principles have been defined for both data and metadata and adopted by large communities, leading to the definition of specific metrics. However, automatic FAIRness assessment is still difficult because computational evaluations frequently require technical expertise and can be time-consuming. As a first step to address these issues, we propose FAIR-Checker , a web-based tool to assess the FAIRness of metadata presented by digital resources. FAIR-Checker offers two main facets: a “Check” module providing a thorough metadata evaluation and recommendations, and an “Inspect” module which assists users in improving metadata quality and therefore the FAIRness of their resource. FAIR-Checker leverages Semantic Web standards and technologies such as SPARQL queries and SHACL constraints to automatically assess FAIR metrics. Users are notified of missing, necessary, or recommended metadata for various resource categories. We evaluate FAIR-Checker in the context of improving the FAIRification of individual resources, through better metadata, as well as analyzing the FAIRness of more than 25 thousand bioinformatics software descriptions.
Published: 2023

4. Widening the landscape of transcriptional regulation of green algal photoprotection

Author: Marius Arend, Yizhong Yuan, M. Águila Ruiz-Sola, Nooshin Omranian, Zoran Nikoloski, Dimitris Petroutsos, Bioinformatics Group, Institute of Biochemistry and Biology, University of Potsdam, Systems Biology and Mathematical Modeling Group, Max-Planck-Institute of Molecular Plant Physiology, Dynamique du protéome et biogenèse du chloroplaste (ChloroGenesis), Physiologie cellulaire et végétale (LPCV), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Grenoble Alpes (UGA), The Human Frontiers Science Program (project RGP0046/2018), The Prestige Marie-Curie co-financing grant PRESTIGE-2017-1-0028, The International Max Planck Research School ‘Primary Metabolism and Plant Growth at the Max Planck Institute of Molecular Plant Physiology, ANR-18-CE20-0006,MetaboLIGHT,Regulation de la photosynthèse par la Lumière et le métabolisme chez les algues(2018), ANR-15-IDEX-0002,UGA,IDEX UGA(2015), ANR-17-EURE-0003,CBH-EUR-GS,CBH-EUR-GS(2017), and Universidad de Sevilla. Departamento de Bioquímica Vegetal y Biología Molecular
Subjects: MESH: Chlamydomonas reinhardtii, Multidisciplinary, [SDV]Life Sciences [q-bio], General Physics and Astronomy, MESH: Carbon, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, General Chemistry, MESH: Carbon Dioxide, MESH: Chlamydomonas, MESH: Gene Expression Regulation, General Biochemistry, Genetics and Molecular Biology, MESH: Photosynthesis
Abstract: Availability of light and CO2, substrates of microalgae photosynthesis, is frequently far from optimal. Microalgae activate photoprotection under strong light, to prevent oxidative damage, and the CO2 Concentrating Mechanism (CCM) under low CO2, to raise intracellular CO2 levels. The two processes are interconnected; yet, the underlying transcriptional regulators remain largely unknown. Employing a large transcriptomic data compendium of Chlamydomonas reinhardtii’s responses to different light and carbon supply, we reconstruct a consensus genome-scale gene regulatory network from complementary inference approaches and use it to elucidate transcriptional regulators of photoprotection. We show that the CCM regulator LCR1 also controls photoprotection, and that QER7, a Squamosa Binding Protein, suppresses photoprotection- and CCM-gene expression under the control of the blue light photoreceptor Phototropin. By demonstrating the existence of regulatory hubs that channel light- and CO2-mediated signals into a common response, our study provides an accessible resource to dissect gene expression regulation in this microalga.
Published: 2023

5. Migration of surface-associated microbial communities in spaceflight habitats

Author: Daniele Marra, Thodoris Karapantsios, Sergio Caserta, Eleonora Secchi, Malgorzata Holynska, Simon Labarthe, Bastien Polizzi, Sandra Ortega, Margaritis Kostoglou, Christophe Lasseur, Ioannis Karapanagiotis, Sigolene Lecuyer, Arnaud Bridier, Marie-Françoise Noirot-Gros, Romain Briandet, 'Federico II' University of Naples Medical School, Aristotle University of Thessaloniki, Department of Civil, Environmental and Geomatic Engineering [ETH Zürich] (D-BAUG), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), ESA - ESTEC (Netherlands), Institut de Chimie de la Matière Condensée de Bordeaux (ICMCB), Université de Bordeaux (UB)-Institut Polytechnique de Bordeaux-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Mathématiques de Besançon (UMR 6623) (LMB), Centre National de la Recherche Scientifique (CNRS)-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC), Institut Pascal (IP), Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne (UCA)-Institut national polytechnique Clermont Auvergne (INP Clermont Auvergne), Université Clermont Auvergne (UCA)-Université Clermont Auvergne (UCA), Laboratoire Interdisciplinaire de Physique [Saint Martin d’Hères] (LIPhy ), Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA), Laboratoire de Fougères - ANSES, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and Elsevier
Subjects: Space flight, Biofilm, Microgravity, Transcriptomic, Adaptation, Evolution, Control, [SDV]Life Sciences [q-bio], Cell Biology, Molecular Biology, Applied Microbiology and Biotechnology, Microbiology
Abstract: Astronauts are spending longer periods locked up in ships or stations for scientific and exploration spatial missions. The International Space Station (ISS) has been inhabited continuously for more than 20 years and the duration of space stays by crews could lengthen with the objectives of human presence on the moon and Mars. If the environment of these space habitats is designed for the comfort of astronauts, it is also conducive to other forms of life such as embarked microorganisms. The latter, most often associated with surfaces in the form of biofilm, have been implicated in significant degradation of the functionality of pieces of equipment in space habitats. The most recent research suggests that microgravity could increase the persistence, resistance and virulence of pathogenic microorganisms detected in these communities, endangering the health of astronauts and potentially jeopardizing long-duration manned missions. In this review, we describe the mechanisms and dynamics of installation and propagation of these microbial communities associated with surfaces (spatial migration), as well as long-term processes of adaptation and evolution in these extreme environments (phenotypic and genetic migration), with special reference to human health. We also discuss the means of control envisaged to allow a lasting cohabitation between these vibrant microscopic passengers and the astronauts., Biofilm, 5, ISSN:2590-2075
Published: 2023

6. Light-independent regulation of algal photoprotection by CO2 availability

Author: M. Águila Ruiz-Sola, Serena Flori, Yizhong Yuan, Gaelle Villain, Emanuel Sanz-Luque, Petra Redekop, Ryutaro Tokutsu, Anika Küken, Angeliki Tsichla, Georgios Kepesidis, Guillaume Allorent, Marius Arend, Fabrizio Iacono, Giovanni Finazzi, Michael Hippler, Zoran Nikoloski, Jun Minagawa, Arthur R. Grossman, Dimitris Petroutsos, Dynamique du protéome et biogenèse du chloroplaste (ChloroGenesis), Physiologie cellulaire et végétale (LPCV), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Grenoble Alpes (UGA), Light Photosynthesis & Metabolism (Photosynthesis), Department of Plant Biology [Carnegie] (DPB), Carnegie Institution for Science, Universidad de Córdoba = University of Córdoba [Córdoba], National Institute for Basic Biology [Okazaki] (NIBB), Graduate University for Advanced Studies [Hayama] (SOKENDAI), Max Planck Institute of Molecular Plant Physiology (MPI-MP), Max-Planck-Gesellschaft, University of Potsdam = Universität Potsdam, The Human Frontiers Science Program through the funding of the project RGP0046/2018, Prestige Marie-Curie co-financing grant PRESTIGE-2017-1-0028, The International Max Planck Research School 'Primary Metabolism and Plant Growth' at the Max Planck Institute of Molecular Plant Physiology, The program ‘Plan Propio UCO’ from University of Cordoba, The Carnegie Institution for Science and the Department of Energy, DE-SC0019417, The Marie Curie Initial Training Network Accliphot FP7-PEPOPLE-2012-ITN, The Japan Society for the Promotion of Science, JSPS, for the grants-in-Aid for Scientific Research, KAKENHI, 21H04778 and 21H05040, The German Research Foundation DFG HI 739/9.2, ANR-18-CE20-0006,MetaboLIGHT,Regulation de la photosynthèse par la Lumière et le métabolisme chez les algues(2018), ANR-17-EURE-0003,CBH-EUR-GS,CBH-EUR-GS(2017), ANR-15-IDEX-0002,UGA,IDEX UGA(2015), and European Project: 751039,UNREDE
Subjects: MESH: Chlamydomonas reinhardtii, Multidisciplinary, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, MESH: Photosystem II Protein Complex, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], General Physics and Astronomy, MESH: Proteins, General Chemistry, MESH: Carbon Dioxide, General Biochemistry, Genetics and Molecular Biology, MESH: Photosynthesis
Abstract: Photosynthetic algae have evolved mechanisms to cope with suboptimal light and CO2 conditions. When light energy exceeds CO2 fixation capacity, Chlamydomonas reinhardtii activates photoprotection, mediated by LHCSR1/3 and PSBS, and the CO2 Concentrating Mechanism (CCM). How light and CO2 signals converge to regulate these processes remains unclear. Here, we show that excess light activates photoprotection- and CCM-related genes by altering intracellular CO2 concentrations and that depletion of CO2 drives these responses, even in total darkness. High CO2 levels, derived from respiration or impaired photosynthetic fixation, repress LHCSR3/CCM genes while stabilizing the LHCSR1 protein. Finally, we show that the CCM regulator CIA5 also regulates photoprotection, controlling LHCSR3 and PSBS transcript accumulation while inhibiting LHCSR1 protein accumulation. This work has allowed us to dissect the effect of CO2 and light on CCM and photoprotection, demonstrating that light often indirectly affects these processes by impacting intracellular CO2 levels.
Published: 2023

7. Survey of ticks and tick-borne pathogens in wild chimpanzee habitat in Western Uganda

Author: Lacroux, Camille, Bonnet, Sarah, Pouydebat, Emmanuelle, Buysse, Marie, Rahola, Nil, Rakotobe, Sabine, Okimat, John-Paul, Duron, Olivier, Koual, Rachid, Asalu, Edward, Krief, Sabrina, Éco-Anthropologie (EA), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Kibale National Park, Mécanismes Adaptatifs et Evolution (MECADEV), La Phocéenne de Cosmétique, Écologie et Émergence des Pathogènes Transmis par les Arthropodes / Ecology and Emergence of Arthropod-borne Pathogens, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Département Santé Animale (DEPT SA), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM), Biologie moléculaire et immunologie parasitaires et fongiques (BIPAR), École nationale vétérinaire - Alfort (ENVA)-Laboratoire de santé animale, sites de Maisons-Alfort et de Normandie, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Uganda Wildlife Authority (UWA), The Great Ape Conservation Project, the Fondation Ensemble, the Fondation pour la Nature et l’Homme, the Fondation Prince Albert II and the Fonds Français pour l’Environnement Mondial provided financial support for the research conducted at Sebitoli. La Phocéenne de Cosmétique and the Association Nationale de la Recherche et de la Technologie provided funds for the PhD scholarship of Camille Lacroux. This work has benefited from ‘Investissements d’Avenir’ managed by the French Agence Nationale de la Recherche (ANR, Laboratoire d’Excellence CEBA, ref. ANR-10-LABX-25-01)., and ANR-10-LABX-0025,CEBA,CEnter of the study of Biodiversity in Amazonia(2010)
Subjects: Vector-borne pathogens, Borrelia, Cryptoplasma, Ehrlichia, MESH: Rickettsia, MESH: Ixodidae, Piroplasmids, MESH: Ixodes, MESH: Tick-Borne Diseases, Infectious Diseases, Ticks, Amblyomma, [SDE]Environmental Sciences, Apes, Kibale, Parasitology, MESH: Tick Infestations, Rickettsia, MESH: Uganda
Abstract: Background Ticks and tick-borne pathogens significantly impact both human and animal health and therefore are of major concern to the scientific community. Knowledge of tick-borne pathogens is crucial for prescription of mitigation measures. In Africa, much research on ticks has focused on domestic animals. Little is known about ticks and their pathogens in wild habitats and wild animals like the endangered chimpanzee, our closest relative. Methods In this study, we collected ticks in the forested habitat of a community of 100 chimpanzees living in Kibale National Park, Western Uganda, and assessed how their presence and abundance are influenced by environmental factors. We used non-invasive methods of flagging the vegetation and visual search of ticks both on human team members and in chimpanzee nests. We identified adult and nymph ticks through morphological features. Molecular techniques were used to detect and identify tick-borne piroplasmids and bacterial pathogens. Results A total of 470 ticks were collected, which led to the identification of seven tick species: Haemaphysalis parmata (68.77%), Amblyomma tholloni (20.70%), Ixodes rasus sensu lato (7.37%), Rhipicephalus dux (1.40%), Haemaphysalis punctaleachi (0.70%), Ixodes muniensis (0.70%) and Amblyomma paulopunctatum (0.35%). The presence of ticks, irrespective of species, was influenced by temperature and type of vegetation but not by relative humidity. Molecular detection revealed the presence of at least six genera of tick-borne pathogens (Babesia, Theileria, Borrelia, Cryptoplasma, Ehrlichia and Rickettsia). The Afrotopical tick Amblyomma tholloni found in one chimpanzee nest was infected by Rickettsia sp. Conclusions In conclusion, this study presented ticks and tick-borne pathogens in a Ugandan wildlife habitat whose potential effects on animal health remain to be elucidated. Graphical Abstract
Published: 2023

8. CusProSe: a customizable protein annotation software with an application to the prediction of fungal secondary metabolism genes

Author: Oliveira, Leonor, Chevrollier, Nicolas, Dallery, Jean-Felix, O’connell, Richard, Lebrun, Marc-Henri, Viaud, Muriel, Lespinet, Olivier, Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), BIOlogie et GEstion des Risques en agriculture (BIOGER), Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Herbifun project 16-CE20-0023-01 ANR, ANR-17-EURE-0007,SPS-GSR,Ecole Universitaire de Recherche de Sciences des Plantes de Paris-Saclay(2017), and AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: Multidisciplinary, [SDV]Life Sciences [q-bio], Annotation, polyketide synthase, [SDE]Environmental Sciences, Software
Abstract: We report here a new application, CustomProteinSearch (CusProSe), whose purpose is to help users to search for proteins of interest based on their domain composition. The application is customizable. It consists of two independent tools, IterHMMBuild and ProSeCDA. IterHMMBuild allows the iterative construction of Hidden Markov Model (HMM) profiles for conserved domains of selected protein sequences, while ProSeCDA scans a proteome of interest against an HMM profile database, and annotates identified proteins using user-defined rules. CusProSe was successfully used to identify, in fungal genomes, genes encoding key enzyme families involved in secondary metabolism, such as polyketide synthases (PKS), non-ribosomal peptide synthetases (NRPS), hybrid PKS-NRPS and dimethylallyl tryptophan synthases (DMATS), as well as to characterize distinct terpene synthases (TS) sub-families. The highly configurable characteristics of this application makes it a generic tool, which allows the user to refine the function of predicted proteins, to extend detection to new enzymes families, and may also be applied to biological systems other than fungi and to other proteins than those involved in secondary metabolism.
Published: 2023

9. Profils chimiques des glandes à venin chez les reines, les fondatrices, les gynes pré-hivernantes et les ouvrières du frelon Vespa velutina nigrithorax

Author: Berville, Laurence, Lucas, Christophe, Haouzi, Mélissa, Khalil, Ali, Gévar, Jérémy, Bagnières, A.G., Darrouzet, Éric, Institut de recherche sur la biologie de l'insecte UMR7261 (IRBI), Université de Tours (UT)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS), Université de Tours (UT), École nationale vétérinaire, agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS), Institut d'écologie et des sciences de l'environnement de Paris (iEES Paris ), Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), This study received funding from the Centre-Val deLoire region, in the form of French regional grants forour FRELON and FRELON 2 projects, as well as fromVeto-pharma and the French administrative depart-ment of La Manche. The TQ-MS was funded by theregion Centre-Val de Loire (APR-IA 2012)., and Berville, Laurence
Subjects: [SDE] Environmental Sciences, Invasive species, Glande à venin, Espèces invasives, Venom gland, Building and Construction, Frelon à pattes jaunes, Communication chimique, Chemical communication, [SDE.BE] Environmental Sciences/Biodiversity and Ecology, Vespidae, Yellow-legged hornet, [SDE]Environmental Sciences, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Electrical and Electronic Engineering
Abstract: Invasive species are permanently modifying the distribution and diversity of native species worldwide. For nearly two decades, a hornet, Vespa velutina nigrithorax (Hymenoptera: Vespidae), has been spreading in Europe. Due to its marked invasiveness, this yellow-legged hornet is of great economic and ecological concern, mainly because of the damage it causes to insects in general and bees in particular. Current management methods are sparse and ineffective. Naturally produced by insects, semio-chemicals have been proposed as integrated management tools in this context, either for disruption or mass trapping, as an alternative tool to conventional nonselective traps. Here, we focused on the venom gland, which produces the alarm pheromone. In previous studies, individuals showed marked diversity in their chemical profiles. However, to successfully conduct targeted pheromone-based trapping, the hornet's chemical ecology must be thoroughly characterized. Therefore, it was necessary to better understand the chemical composition of the alarm pheromone of not only workers but also other V. v. nigrithorax females. First, we evaluated the differences in venom gland profiles between the four types of females: queens, foundresses, pre-winter gynes, and workers. Next, we experimentally explored the venom gland profiles of V. velutina nigrithorax workers and pre-wintering gynes by in vivo and in vitro approaches. We found 13 new compounds in the venom gland, of which 9 were identified (chain lengths: C8 to C12). Two compounds were found exclusively in reproductive females. Profiles differed among pre-wintering gynes, foundresses, and queens but not between pre-wintering gynes and workers. This result indicates that the chemical signature of the female venom gland changes over the course of life history: from pre-wintering gynes to foundresses to queens., Les espèces invasives modifient en permanence la répartition et la diversité des espècesindigènes dans le monde entier. Depuis près de vingt ans, un frelon originaire d’Asie du Sud-Est,Vespa velutina nigrithorax (Hymenoptera : Vespidae), se répand en Europe. En raison de son caractèreinvasif marqué, ce frelon à pattes jaunes suscite de vives inquiétudes sur le plan économique etécologique, principalement en raison des dégâts qu’il cause aux insectes en général et aux abeillesen particulier. Les méthodes de gestion actuelles sont rares et inefficaces. Naturellement produits parles insectes, les produits sémio-chimiques ont été proposés comme outils de gestion intégrée. Dansce contexte, soit pour la perturbation, soit pour le piégeage de masse, en tant qu’outil alternatif auxpièges non sélectifs conventionnels. Ici, nous nous sommes concentrés sur la glande à venin, quiproduit la phéromone d’alarme. Des études antérieures ont montré que les femelles présentaientune variabilité dans les profils chimiques. Cependant, pour mener à bien un piégeage ciblé à basede phéromones, l’écologie chimique du frelon doit être caractérisée de manière approfondie. Il étaitdonc nécessaire de mieux comprendre la composition chimique de la phéromone d’alarme nonseulement des ouvrières, mais également des autres femelles de V. v. nigrithorax. Tout d’abord, nousavons examiné les différences dans les profils des glandes à venin entre les quatre types de femelles :les reines, les fondatrices, les gynes pré-hivernantes et les ouvrières. Ensuite, nous avons exploréexpérimentalement les profils des glandes à venin des ouvrières de V. velutina nigrithorax et des gynespré-hivernantes par des approches in vivo et in vitro. Nous avons constaté la présence de 13 nouveauxcomposés dans la glande à venin, dont 9 ont été identifiés (longueur des chaînes : C8 à C12). Deuxcomposés ont été trouvés exclusivement chez les femelles reproductrices. Les profils diffèrent entreles gynes pré-hivernantes, les fondatrices et les reines, mais pas entre les gynes pré-hivernantes et lesouvrières. Ce résultat indique que la signature chimique de la glande à venin femelle évolue au coursde l’histoire de vie : des gynes pré-hivernantes aux fondatrices, en passant par les reines.
Published: 2023

10. Cuticle architecture and mechanical properties: a functional relationship delineated through correlated multimodal imaging

Author: Nicolas Reynoud, Nathalie Geneix, Angelina D’Orlando, Johann Petit, Jeremie Mathurin, Ariane Deniset-Besseau, Didier Marion, Christophe Rothan, Marc Lahaye, Bénédicte Bakan, Unité de recherche sur les Biopolymères, Interactions Assemblages (BIA), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), BioInformatique et BioStatistiques (BIBS), Centre International de Recherche en Infectiologie (CIRI), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Biologie du fruit et pathologie (BFP), Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut de Chimie Physique (ICP), Institut de Chimie du CNRS (INC)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), INRAE and Region Pays de la Loire (Fr)., and ANR-21-CE11-0035,COPLAnAR,COPLAnAR : cartography corrélative pour élucider les relations structure-propriétés de la cuticule des plantes(2021)
Subjects: hyperspectral, plant cuticle, Solanum lycopersicum, Physiology, nanomechanical, AFM PF-QNM, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, correlated multimodal imaging, Plant Science, Raman
Abstract: Cuticle are multifunctional hydrophobic biocomposites that protect aerial organs of plants. Along plant development, plant cuticle must accommodate different mechanical constraints combining extensibility and stiffness, the corresponding structure-function relationships are unknown. Recent data showed a fine architectural tuning of the cuticle architecture and the corresponding chemical clusters along fruit development which raise the question of their impact on the mechanical properties of the cuticle.We investigated the in-depth nanomechanical properties of tomato fruit cuticle from early development to ripening, in relation to chemical and structural heterogeneities by developing a correlative multimodal imaging approach.Unprecedented sharps heterogeneities were evidenced with the highlighting of an in-depth mechanical gradient and a ‘soft’ central furrow that were maintained throughout the plant development despite the overall increase in elastic modulus. In addition, we demonstrated that these local mechanical areas are correlated to chemical and structural gradients.This study shed light on a fine tuning of mechanical properties of cuticle through the modulation of their architecture, providing new insight for our understanding of structure-function relationships of plant cuticle and for the design of biosinpired material.
Published: 2023

11. Debris-flow surges of a very active alpine torrent: a field database

Author: Suzanne Lapillonne, Firmin Fontaine, Frédéric Liebault, Vincent Richefeu, Guillaume Piton, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université Grenoble Alpes (UGA), Institut des Géosciences de l’Environnement (IGE), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Grenoble Alpes (UGA)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), Laboratoire sols, solides, structures - risques [Grenoble] (3SR), Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), ANR-11-LABX-0030,TEC XXI,Ingénierie de la Complexité : la mécanique et ses interfaces au service des enjeux sociétaux du 21iè(2011), and ANR-10-LABX-0056,OSUG@2020,Innovative strategies for observing and modelling natural systems(2010)
Subjects: [SPI.GCIV.RISQ]Engineering Sciences [physics]/Civil Engineering/Risques, General Earth and Planetary Sciences, [PHYS.PHYS.PHYS-GEO-PH]Physics [physics]/Physics [physics]/Geophysics [physics.geo-ph], [PHYS.MECA.MEFL]Physics [physics]/Mechanics [physics]/Fluid mechanics [physics.class-ph], [SDU.STU.GM]Sciences of the Universe [physics]/Earth Sciences/Geomorphology
Abstract: This paper presents a methodology to analyse debris flows focusing at the surge scale rather than the full scale of the debris-flow event, as well as its application to a French site. Providing bulk surge features like volume, peak discharge, front height, front velocity and Froude numbers allows for numerical and experimental debris-flow investigations to be designed with narrower physical ranges and thus for deeper scientific questions to be explored. We suggest a method to access such features at the surge scale that can be applied to a wide variety of monitoring stations. Requirements for monitoring stations for the methodology to be applicable include (i) flow height measurements, (ii) a cross-section assumption and (iii) a velocity estimation. Raw data from three monitoring stations on the Réal torrent (drainage area: 2 km2, southeastern France) are used to illustrate an application to 34 surges measured from 2011 to 2020 at three monitoring stations. Volumes of debris-flow surges on the Réal torrent are typically sized at a few thousand cubic metres. The peak flow height of surges ranges from 1 to 2 m. The peak discharge range is around a few dozen cubic metres per second. Finally, we show that Froude numbers of such surges are near critical.
Published: 2023

12. Ileal Digestibility of Nitrogen and Amino Acids in Human Milk and an Infant Formula as Determined in Neonatal Minipiglets

Author: Charton, Elise, Henry, Gwénaële, Cahu, Armelle, Le Gouar, Yann, Dahirel, Patrice, Moughan, Paul, Montoya, Carlos, Bellanger, Amandine, Dupont, Didier, Le Huërou-Luron, Isabelle, Deglaire, Amélie, Science et Technologie du Lait et de l'Oeuf (STLO), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Rennes Angers, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Nutrition, Métabolismes et Cancer (NuMeCan), Université de Rennes (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Riddet Institute and Massey Institute of Food Science and Technology, Massey University, Centre d'Investigation Clinique [Rennes] (CIC), Université de Rennes (UR)-Hôpital Pontchaillou-Institut National de la Santé et de la Recherche Médicale (INSERM), Hôpital Sud [CHU Rennes], CHU Pontchaillou [Rennes], and This work was supported by the Brittany Region, France (Grant ARED, 1318) and L’institut Agro Rennes-Angers. Financial support was also provided by the Riddet Institute, a New Zealand Centre of Research Excellence (CoRE), and the Catalyst Fund of the New Zealand Ministry of Business, Innovation and Employ-ment (MBIE).
Subjects: Nutrition and Dietetics, infant nutrition, multiple hydrolysis, true digestibility, digestible indispensable AA score tryptophan, Infant formula, human milk, Medicine (miscellaneous), tryptophan, bioavailability, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition
Abstract: International audience; Background: Infant formula (IF) has to provide at least the same amount of amino acids (AAs) as human milk (HM). AA digestibility in HM and IF was not studied extensively, with no data available for tryptophan digestibility. Objectives: The present study aimed to measure the true ileal digestibility (TID) of total nitrogen and AAs in HM and IF to estimate AA bioavailability using Yucatan mini-piglets as an infant model. Methods: Twenty-four 19-day-old piglets (males and females) received either HM or IF for 6 days or a protein-free diet for 3 days, with cobalt-EDTA as an indigestible marker. Diets were fed hourly over 6 h before euthanasia and digesta collection. Total N, AA, and marker contents in diets and digesta were measured to determine the TID. Unidimensional statistical analyses were conducted. Results: Dietary N content was not different between HM and IF, while true protein was lower in HM (À4 g/L) due to a 7-fold higher nonprotein N content in HM. The TID of total N was lower (P < 0.001) for HM (91.3 AE 1.24%) than for IF (98.0 AE 0.810%), while the TID of amino acid nitrogen (AAN) was not different (average of 97.4 AE 0.655%, P ¼ 0.272). HM and IF had similar (P > 0.05) TID for most of the AAs including tryptophan (96.7 AE 0.950%, P ¼ 0.079), except for some AAs (lysine, phenylalanine, threonine, valine, alanine, proline, and serine), with small significant difference (P < 0.05). The first limiting AA was the aromatic AAs, and the digestible indispensable AA score (DIAAS) was higher for HM (DIAAS HM ¼ 101) than for IF (DIAAS IF ¼ 83). Conclusion: HM, compared to IF, had a lower TID for total N only, whereas the TID of AAN and most AAs, including Trp, was high and similar. A larger proportion of non-protein N is transferred to the microbiota with HM, which is of physiological relevance, although this fraction is poorly considered for IF manufacturing.
Published: 2023

13. Biotic and abiotic drivers of aquatic plant communities in shallow pools and wallows on the sub-Antarctic Iles Kerguelen

Author: Douce, Pauline, Mermillod‐blondin, Florian, Simon, Laurent, Dolédec, Sylvain, Eymar‐dauphin, Pauline, Renault, David, Sulmon, Cécile, Vallier, Félix, Bittebiere, Anne-Kristel, Équipe 1 - Biodiversité et Adaptation dans les Hydrosystèmes (BAH), Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés (LEHNA), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-École Nationale des Travaux Publics de l'État (ENTPE)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-École Nationale des Travaux Publics de l'État (ENTPE)-Centre National de la Recherche Scientifique (CNRS), Équipe 3 - Écologie, Évolution, Écosystemes Souterrains (E3S), Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), and Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Habitat, Plant community structure, Spatio-temporal variability, Seasonality, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, Aquatic plants, Ponds, General Agricultural and Biological Sciences
Abstract: International audience; In the sub-Antarctic region, climate change is particularly rapid, while their freshwater ecosystems, such as ponds, host plant species with limited spatial distributions. These particular systems and their plant communities remain however poorly known and the context of their changing habitat calls for deeper insights into these systems. We performed an extensive survey of 45 ponds over three locations of the Iles Kerguelen during the winter and summer seasons of two years, which included the measurement of 12 abiotic parameters and the assessment of the plant community composition. Overall, our results showed that Iles Kerguelen ponds are shallow freshwater ecosystems harbouring species-poor plant communities with high even- ness, of which structure did not vary among the sampled locations. Three different habitats were identified among ponds in relation with nutrient supply by marine animals, which ultimately influenced plant community structure and cover. We highlight that these habitats are mostly determined by water depth, nutrients, and temperature (mean and variance). Present plant community composition was more strongly correlated with plant community composition in the previous year than with abiotic conditions. Overall, this study provides new knowledge on the aquatic plant communities and the functioning of Iles Kerguelen freshwater ecosystems, which can serve as a basis for future studies dealing with the impact of climate change in the sub-Antarctic region.
Published: 2023

14. Architecture and yield relationship in hazelnut tree

Author: Grisafi, Francesca, Farinelli, Daniela, Costes, Evelyne, Boudon, Frédéric, Durand, Jean-Baptiste, Tombesi, S., Università cattolica del Sacro Cuore = Catholic University of the Sacred Heart [Roma] (Unicatt), Università degli Studi di Perugia = University of Perugia (UNIPG), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université de Montpellier (UM), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Serra, S., and Lauri, P.-É.
Subjects: Nut, Branching, Shoot length, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Horticulture, Corylus avellana, [SDV.SA.HORT]Life Sciences [q-bio]/Agricultural sciences/Horticulture, Hazel
Abstract: International audience; Yield reduction over the years is a phenomenon that affects many fruit tree species, including hazel (Corylus avellana). Studying plant architecture could provide useful information for improving crop management, such as pruning, to reduce the impact of yield reductions. This study aimed to compare the relationship between bud composition and shoot length in hazel shoots. The experiment was carried out in January 2020 and 2021 in Deruta, Perugia (Italy). In 2020, 120 1-year-old shoots of C. avellana 'Tonda di Giffoni' were sampled. In 2021, the same observations were performed on lateral and apical 1-year-old shoots that had burst from parental buds in spring 2020. Depending on its length, each shoot was sorted into four categories: short (Sh) when shorter than 5 cm, medium (Me) when between 5 and 20 cm, long (Lo) when between 20 and 40 cm, and very long (VLo) when longer than 40 cm. For each shoot, shoot length, axillary and apical bud fate was recorded at each node: vegetative bud, latent bud, catkin, and mixed bud (V, B, C, and M, respectively). Percentage of lateral mixed buds was higher in longer shoots than in shorter ones while that of vegetative buds remained constant whatever the length. Fruit set, computed as the ratio between the number of nuts and the number of mixed buds, was significantly higher in Lo and VLo shoots. It was observed that the length of lateral proleptic shoots, developed in 2021, was related to the length of the bearer shoot from which it was developed. Proleptic lateral Sh shoots were the most frequent among all length categories while longer proleptic shoots (Lo and VLo) were originated only from Lo and VLo shoots. Managing tree architecture, considering a good balance between long and short shoots, and mixed and vegetative buds, could help control and prevent yield decrease in hazelnut trees.
Published: 2023

15. pH-Dependent Changes in Structural Stabilities of Bt Cry1Ac Toxin and Contrasting Model Proteins following Adsorption on Montmorillonite

Author: Wenqiang Zhao, Céline Poncet-Legrand, Siobhan Staunton, Hervé Quiquampoix, Ecologie fonctionnelle et biogéochimie des sols et des agro-écosystèmes (UMR Eco&Sols), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Chinese Academy of Agricultural Sciences (CAAS), Sciences Pour l'Oenologie (SPO), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), and This work was supported by the ERASMUS MUNDUS Action 2 PANACEA program (2012-2647/001-001-EMA2), the National Natural Science Foundation of China (31870607), and the Youth Innovation Promotion Association of the Chinese Academy of Sciences (2019363).
Subjects: α-chymotrypsin, adsorption, differential scanning calorimetry (DSC), bovine serum albumin (BSA), [SDE]Environmental Sciences, structural stability, Environmental Chemistry, General Chemistry, [SDV.SA.SDS]Life Sciences [q-bio]/Agricultural sciences/Soil study, Cry1Ac protein
Abstract: International audience; The environmental fate of insecticidal Cry proteins, including time-dependent conservation of biological properties, results from their structural stability in soils. The complex cascade of reactions involved in biological action requires Cry proteins to be in solution. However, the pH-dependent changes in conformational stability and the adsorption–desorption mechanisms of Cry protein on soil minerals remain unclear. We used Derjaguin–Landau–Verwey–Overbeek (DLVO) calculation and differential scanning calorimetry to interpret the driving forces and structural stabilities of Cry1Ac and two contrasting model proteins adsorbed by montmorillonite. The structural stability of Cry1Ac is closer to that of the “hard” protein, α-chymotrypsin, than that of the “soft” bovine serum albumin (BSA). The pH-dependent adsorption of Cry1Ac and α-chymotrypsin could be explained by DLVO theory, whereas the BSA adsorption deviated from it. Patch-controlled electrostatic attraction, hydrophobic effects, and entropy changes following protein unfolding on a mineral surface could contribute to Cry1Ac adsorption. Cry1Ac, like chymotrypsin, was partly denatured on montmorillonite, and its structural stability decreased with an increase in pH. Moreover, small changes in the conformational heterogeneity of both Cry1Ac and chymotrypsin were observed following adsorption. Conversely, adsorbed BSA was completely denatured regardless of the solution pH. The moderate conformational rearrangement of adsorbed Cry1Ac may partially explain why the insecticidal activity of Bt toxin appears to be conserved in soils, albeit for a relatively short time period.
Published: 2023

16. Digital agriculture in Europe and in France: which organisations can boost adoption levels?

Author: Véronique Bellon-Maurel, Isabelle Piot-Lepetit, Nina Lachia, Bruno Tisseyre, Technologies et Méthodes pour les Agricultures de demain (UMR ITAP), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Institut Convergences Agriculture Numérique #DigitAg, Institut National de Recherche en Sciences et Technologies pour l'Environnement et l'Agriculture (IRSTEA), Montpellier Interdisciplinary center on Sustainable Agri-food systems (Social and nutritional sciences) (UMR MoISA), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Centre International de Hautes Etudes Agronomiques Méditerranéennes - Institut Agronomique Méditerranéen de Montpellier (CIHEAM-IAMM), Centre International de Hautes Études Agronomiques Méditerranéennes (CIHEAM)-Centre International de Hautes Études Agronomiques Méditerranéennes (CIHEAM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, and ANR-16-CONV-0004,DIGITAG,Institut Convergences en Agriculture Numérique(2016)
Subjects: digital agriculture, green deal, [SDV.SA.AGRO]Life Sciences [q-bio]/Agricultural sciences/Agronomy, innovation use, Digitalization, Plant Science, [SHS.ECO]Humanities and Social Sciences/Economics and Finance, innovation adoption, Digital agriculture Innovation ecosystems Green deal Farm-to-Fork Innovation adoption Innovation use Digitalization #DigitAg, #DigitAg, Farm-to-Fork, [INFO.INFO-ET]Computer Science [cs]/Emerging Technologies [cs.ET], digitalisation, innovation ecosystems, Agronomy and Crop Science
Abstract: International audience; This paper presents the way the digital transformation of the agricultural sector is implemented in Europe and in France. It describes the main European and national strategies, the structure of research and innovation initiatives, and the investment in capacity building to foster innovation, adoption and use. More specifically, the French research and innovation ecosystem on digital agriculture is described. The actors involved come from different organisations, such as research and higher educational institutes, government agencies, agricultural technology (AgTech) companies, farmer unions etc., and work together by means of associations (e.g. Robagri), networks (e.g. RMT Naexus, DigiFermes, Fermes Leader), or living labs (e.g. Occitanum) on both digital technology assessment and co-design. Additionally, support is devoted to capacity building (e.g. Le Mas numérique, Mobilab) and a better understanding of the drivers of adoption and use of digital technologies (e.g. FrOCDA). Among these various organisations, #DigitAg, the Digital Agriculture Convergence Lab, has been created to foster interdisciplinary research on digital agriculture. All these initiatives aim to use digital technologies to support the European Green Deal, Farm-to-Fork and Biodiversity strategies as well as the French orientation towards more agroecological practices for safer and more sustainable food systems. Even though this organisational ecosystem is developing fast, the objective of encouraging the coevolution of both digital and green transformations is not without challenges that still need to be overcome, either through new research, innovations, initiatives or collaborations between the actors involved.
Published: 2023

17. Floral resource maps: a tool to explain flower-visiting insect abundance at multiple spatial scales

Author: Audrey Alignier, Nathan Lenestour, Emma Jeavons, Joan van Baaren, Stéphanie Aviron, Léa Uroy, Claire Ricono, Cécile Le Lann, Biodiversité agroécologie et aménagement du paysage (UMR BAGAP), Ecole supérieure d'Agricultures d'Angers (ESA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Rennes Angers, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de biologie végétale Yves Rocher, Dynamiques et écologie des paysages agriforestiers (DYNAFOR), École nationale supérieure agronomique de Toulouse (ENSAT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and This work was supported by the Zone Atelier Armorique. Audrey Alignier has received research support for the FLORAG project (2020) and Nathan Lenestour’s internship, and Stéphanie Aviron has received research support for the DIVAG project (2019).
Subjects: [SDV.EE]Life Sciences [q-bio]/Ecology, environment, Ecology, Pollinators, Geography, Planning and Development, Floral resource, Wild bees, Domestic bees, Functional landscape, Nature and Landscape Conservation
Abstract: International audience; Context : Flower-visiting insects depend on floral resource availability from both cultivated and semi-natural habitats in agricultural landscapes. Landscape studies exploring insect abundance mainly focus on land cover maps without considering plant species within. Highlighting the functional role of landscapes through the potential floral resources they provide is an overlooked innovative approach. Objectives : We aimed to identify traits of floral communities that are important, across several spatial scales, for explaining the abundance of flower-visiting insects. Mapping and quantifying potential floral resources according to their attractivity, accessibility and profitability in both crop and non-crop habitats was performed to gain insights into flower-vising insect requirements. Methods : We translated land-cover maps of 39 landscapes of 250 m, 500 m and 1000 m radius into potential floral resource maps, using pre-existing vegetation surveys and floral traits databases. In the centres of the landscapes, the abundance of flower-visiting insect groups (domestic and wild bees, bumblebees and hoverflies) were recorded in organic winter cereal fields. We then fitted Generalized Linear Models (GLMs) to investigate the effects of flower trait variables (pre-selected with conditional random forests) at both field and landscape scales on the abundance of each flower-visiting insect group. Results : Floral resource maps explained the abundances of flower-visiting insect groups. Small wild bees (< 1 cm) responded positively to the relative amount of attractive and accessible floral resources at 250 m. The abundance of domestic bees and bumblebees was positively correlated with the relative amount of high nectar producing plants at 1000 m. The abundance of hoverflies was positively influenced by the relative amount of actinomorphic flowers (i.e., those with radial symmetry), at 1000 m.Conclusion : Resource maps could explain flower-visiting insect abundances, identify which category of floral resources organisms require, and determine in which habitat types these resources prevail. These results open a new research area related to managing the environment by optimising floral resources for flower-visiting insect conservation and pollination maintenance.
Published: 2023

18. Acclimation limits for embolism resistance and osmotic adjustment accompany the geographical dry edge of Mediterranean species

Author: Asaf Alon, Shabtai Cohen, Régis Burlett, Uri Hochberg, Victor Lukyanov, Ido Rog, Tamir Klein, Hervé Cochard, Sylvain Delzon, Rakefet David‐Schwartz, Institute of Plant Sciences, Volcani Center, Institute of Plant Science, Institute of Soil, Water and Environmental Sciences, Agricultural Research Organization - the Volcani Center, Biodiversité, Gènes & Communautés (BioGeCo), Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Weizmann Institute of Science [Rehovot, Israël], Laboratoire de Physique et Physiologie Intégratives de l’Arbre en environnement Fluctuant (PIAF), and Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Clermont Auvergne (UCA)
Subjects: climate change, hydraulic failure, drought resistance, [SDE]Environmental Sciences, osmotic adjustment, tree hydraulics, hydraulic safety margins, Ecology, Evolution, Behavior and Systematics
Abstract: Survival and growth of woody species in the Mediterranean are mainly restricted by water availability. We tested the hypothesis that Mediterranean species acclimate their xylem vulnerability and osmotic potential along a precipitation gradient.We studied five predominant co-occurring Mediterranean species; Quercus calliprinos, Pistacia palaestina, Pistacia lentiscus, Rhamnus lycioides and Phillyrea latifolia, over two summers at three sites. The driest of the sites is the distribution edge for all the five species. We measured key hydraulic and osmotic traits related to drought resistance, including resistance to embolism (psi(50)) and the seasonal dynamics of water and osmotic potentials.The leaf water potentials (psi(l)) of all species declined significantly along the summer, reaching significantly lower psi(l) at the end of summer in the drier sites. Surprisingly, we did not find plasticity along the drought gradient in psi(50) or osmotic potentials. This resulted in much narrower hydraulic safety margins (HSMs) in the drier sites, where some species experienced significant embolism.Our analysis indicates that reduction in HSM to null values put Mediterranean species in embolism risk as they approach their hydraulic limit near the geographical dry edge of their distribution.
Published: 2023

19. Brassica napus Drought–Induced 22-kD Protein (BnD22) Acts Simultaneously as a Cysteine Protease Inhibitor and Chlorophyll-Binding Protein

Author: Youssef Bouargalne, Florian Guilbaud, David Macherel, Olivier Delalande, Carole Deleu, Françoise Le Cahérec, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Université de Rennes (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Rennes Angers, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Rennes Angers, IRHS - Équipe SMS (Source and sink Metabolism and Stress responses) (IRHS-SMS), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université d'Angers (UA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Rennes Angers, Institut de Génétique et Développement de Rennes (IGDR), Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), program 'Investments for the Future', a PhD grant from the French Research Ministry 'Ministere de l'Enseignement Superieur et de la Recherche (MESR)' [ANR-11-BTBR-0004], Brittany regional authority [ANR-11-BTBR-0004], and ANR-11-BTBR-0004,RAPSODYN,Optimisation de la teneur et du rendement en huile chez le colza cultivé sous contrainte azotée(2011)
Subjects: Inhibition constant, Subcellular localization, Physiology, Water-soluble chlorophyll proteins (WSCP), Kunitz-type protease inhibitors, Papain, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Cell Biology, Plant Science, General Medicine, Brassica napus (oilseed rape)
Abstract: Class II water-soluble chlorophyll proteins (WSCPs) from Brassicaceae are non-photosynthetic proteins that bind with chlorophyll (Chl) and its derivatives. The physiological function of WSCPs is still unclear, but it is assumed to be involved in stress responses, which is likely related to their Chl-binding and protease inhibition (PI) activities. Yet, the dual function and simultaneous functionality of WSCPs must still be better understood. Here, the biochemical functions of Brassica napus drought–induced 22-kDa protein (BnD22), a major WSCP expressed in B. napus leaves, were investigated using recombinant hexahistidine-tagged protein. We showed that BnD22 inhibited cysteine proteases, such as papain, but not serine proteases. BnD22 was able to bind with Chla or Chlb to form tetrameric complexes. Unexpectedly, BnD22–Chl tetramer displays higher inhibition toward cysteine proteases, indicating (i) simultaneous Chl-binding and PI activities and (ii) Chl-dependent activation of PI activity of BnD22. Moreover, the photostability of BnD22–Chl tetramer was reduced upon binding with the protease. Using three-dimensional structural modeling and molecular docking, we revealed that Chl binding favors interaction between BnD22 and proteases. Despite its Chl-binding ability, the BnD22 was not detected in chloroplasts but rather in the endoplasmic reticulum and vacuole. In addition, the C-terminal extension peptide of BnD22, which cleaved off post-translationally in vivo, was not implicated in subcellular localization. Instead, it drastically promoted the expression, solubility and stability of the recombinant protein.
Published: 2023

20. Climatology of low-level clouds over Western equatorial Africa based on ground observations and satellites

Author: Champagne, Olivier, Aellig, R., Fink, A.H., Philippon, Nathalie, Camberlin, Pierre, Moron, V., Knippertz, P., Seze, G., van der Linden, R., Institut des Géosciences de l’Environnement (IGE), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Grenoble Alpes (UGA)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), Université Grenoble Alpes (UGA), Institute of Meteorology and Climate Research, Karlsruhe Institute of Technology (KIT), Biogéosciences [UMR 6282] (BGS), Université de Bourgogne (UB)-Centre National de la Recherche Scientifique (CNRS), Centre européen de recherche et d'enseignement des géosciences de l'environnement (CEREGE), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Collège de France (CdF (institution))-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire de Météorologie Dynamique (UMR 8539) (LMD), Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-École des Ponts ParisTech (ENPC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Département des Géosciences - ENS Paris, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL), and ANR-19-CE01-0021,DYVALOCCA,Dynamique, variabilité et effets bioclimatiques des nuages bas sur la façade Atlantique de l'Afrique Centrale(2019)
Subjects: Cloud cover, Climatology, Atmospheric Science, Atmosphere, [SDU.STU.CL]Sciences of the Universe [physics]/Earth Sciences/Climatology, Africa, Surface observations, Satellite observations
Abstract: The tropical cloud forest ecosystem in Western Equatorial Africa (WEA) is known to be sensitive to the presence of an extensive and persistent low-level stratiform cloud deck during the long dry season from June to September (JJAS). Here we present a new climatology of the diurnal cycle of the low-level cloud cover from surface synoptic stations over WEA during JJAS 1971–2019. For the period JJAS 2008–2019, we also utilized estimates of cloudiness from four satellite products, namely the Satellite Application Facility on Support to Nowcasting and Very Short Range Forecasting (SAFNWC) cloud classification, the Day and Night Microphysical Schemes (DMS/NMS) and cross-sections from CALIPSO and CloudSat (2B-GEOPROF-LIDAR). A comparison with surface stations reveals that the NMS at night together with SAFNWC at daytime yield the smallest biases. The climatological analysis reveals that low-level clouds persist during the day over the coastal plains and windward side of the low mountain ranges. Conversely, on their leeward sides, i.e. over the plateaus, a decrease of the low-level cloud frequency is observed in the afternoon, together with a change from stratocumulus to cumulus. At night, the low-level cloud deck reforms over this region with the largest cloud occurrence frequencies in the morning. Vertical profiles from 2B-GEOPROF-LIDAR reveal cloud tops below 3000 m even at daytime. The station data and the suitable satellite products form the basis to better understand the physical processes controlling the clouds and to evaluated cloudiness from reanalyses and models.
Published: 2023

21. A new genus and species of the damsel-dragonfly family Burmaphlebiidae (Odonata: Epiproctophora)

Author: Corentin Jouault, André Nel, Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Géosciences Rennes (GR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)
Subjects: Kachin, taxonomy, Insecta, Insect Science, [SDE]Environmental Sciences, Cretaceous, Ecology, Evolution, Behavior and Systematics, Amber
Abstract: International audience; Bilebullephlebia legendrei n. gen., n. sp. is described, illustrated, and placed into the small epiproctophoran family Burmaphlebiidae. This family was previously known from the mid-Cretaceous Kachin amber by two monotypic genera, but the new fossil shows that its diversity is underestimated. At least one additional genus with an enigmatic wing venation remains to be described from the same deposit. Nothing is known about the genitalia configuration of the Burmaphlebiidae but new fossils are expected to clarify the position of the family which is currently only discussed in light of wing venation characters.
Published: 2023

22. The evolutionary history of the Central Asian steppe-desert taxon Nitraria (Nitrariaceae) as revealed by integration of fossil pollen morphology and molecular data

Author: Amber Woutersen, Phillip E Jardine, Daniele Silvestro, Raul Giovanni Bogotá-Angel, Hong-Xiang Zhang, Niels Meijer, Johannes Bouchal, Natasha Barbolini, Guillaume Dupont-Nivet, Andreas Koutsodendris, Alexandre Antonelli, Carina Hoorn, Institute for Biodiversity and Ecosystem Dynamics (IBED), Westfälische Wilhelms-Universität Münster = University of Münster (WWU), Université de Fribourg = University of Fribourg (UNIFR), University of Gothenburg (GU), Universidad Distrital Francisco Jose de Caldas [Bogota], Chinese Academy of Sciences [Xi’an], Senckenberg Institute, University of Vienna [Vienna], Stockholm University, University of Bergen (UiB), Géosciences Rennes (GR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), University of Potsdam = Universität Potsdam, Universität Heidelberg [Heidelberg] = Heidelberg University, Departement of Computer of Science University of Oxford, University of Oxford, Swiss National Science Foundation (SNSF) (PCEFP3_187012, FN-1749), Swedish Research Council, CAS President's International Fellowship Initiative (2018VBA0038), and European Project: 649081,H2020,ERC-2014-CoG,MAGIC(2015)
Subjects: desert -Eurasian steppe -light microscopy -phylogeny -SEM -Tibetan Plateau, [SDU.STU.ST]Sciences of the Universe [physics]/Earth Sciences/Stratigraphy, Plant Science, [SDU.STU.PG]Sciences of the Universe [physics]/Earth Sciences/Paleontology, Ecology, Evolution, Behavior and Systematics
Abstract: The transition from a greenhouse to an icehouse world at the Eocene-Oligocene Transition (EOT) coincided with a large decrease of pollen from the steppe-adapted genus Nitraria. This genus, now common along the Mediterranean coast, Asia and Australia, has a proposed coastal origin and a geographically widespread fossil record. Here we investigated the evolution, taxonomic diversity and morphological disparity of Nitraria throughout the Cenozoic by integrating extant taxa and fossil palynological morphotypes into a unified phylogenetic framework based on both DNA sequences and pollen morphological data. We present the oldest fossil pollen grain of Nitraria, at least 53 Myr old. This fossil was found in Central Asian deposits, providing new evidence for its origin in this area. We found that the EOT is an evolutionary bottleneck for Nitraria, coinciding with retreat of the proto-Paratethys Sea, a major global cooling event and a turnover in Central Asian steppe vegetation. We infer the crown age of modern Nitraria spp. to be significantly younger (Miocene) than previously estimated (Palaeocene). The diversity trajectory of Nitraria inferred from extant-only taxa differs markedly from one that also considers extinct taxa. Our study demonstrates it is therefore critical to apply an integrative approach to fully understand the plant evolutionary history of Nitrariaceae.
Published: 2023

23. Does short food supply chain participation improve farm economic performance? A meta‐analysis

Author: Chiaverina, Pierre, Drogué, Sophie, Jacquet, Florence, Lev, Larry, King, Robert, Montpellier Interdisciplinary center on Sustainable Agri-food systems (Social and nutritional sciences) (UMR MoISA), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Centre International de Hautes Etudes Agronomiques Méditerranéennes - Institut Agronomique Méditerranéen de Montpellier (CIHEAM-IAMM), Centre International de Hautes Études Agronomiques Méditerranéennes (CIHEAM)-Centre International de Hautes Études Agronomiques Méditerranéennes (CIHEAM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Oregon State University (OSU), University of Minnesota System, and This work was financially supported by the French Region Occitanie (# 20007393/ALDOCT – 001034).
Subjects: Meta-analysis, JEL: Q - Agricultural and Natural Resource Economics • Environmental and Ecological Economics/Q.Q1 - Agriculture/Q.Q1.Q13 - Agricultural Markets and Marketing • Cooperatives • Agribusiness, Economics and Econometrics, Farmers, JEL: Q - Agricultural and Natural Resource Economics • Environmental and Ecological Economics/Q.Q1 - Agriculture/Q.Q1.Q14 - Agricultural Finance, Income, [SHS.ECO]Humanities and Social Sciences/Economics and Finance, Economic performance, Short food supply chains, Agronomy and Crop Science
Abstract: International audience; Many researchers, policy makers and food activists view Short Food Supply Chains (SFSC) as attractive levers for improving farm income and the sustainability of farming systems. However, the empirical evidence documenting the association between SFSC participation and farm economic performance has been mixed. In this study, through a meta-analysis using a logistic regression, we identify key factors to explain differences between studies that find better economic performance in SFSC and those that do not. Our meta-analysis consists of 48 studies published in English and French from 2000 to 2022 that examine the economic performance of farms engaged in SFSC. Based on far more empirical evidence than previous reviews, we find that the relationship between SFSC participation and farmer income remains ambiguous. More specifically the findings indicate that the reported effect of SFSC on a farm economic performance varies depending on location and the indicator used to capture the economic performance of farms. Studies conducted in Europe are more likely to report higher farmer income as are studies that use profit satisfaction metrics rather than measures of gross or net income. We also emphasize the need to interpret the reported results cautiously because few are based on causal inference methods. Furthermore, the very few studies that account for selection bias often do so with inadequate corrections.
Published: 2023

24. Aluminum-induced colloidal destabilization of iron-organic matter nanoaggregates

Author: Anthony Beauvois, Delphine Vantelon, Jacques Jestin, Aurélien Dupont, Valérie Briois, Erwan Paineau, Thomas Bizien, Alice Pradel, Mélanie Davranche, Géosciences Rennes (GR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), Synchrotron SOLEIL (SSOLEIL), Centre National de la Recherche Scientifique (CNRS), Laboratoire Léon Brillouin (LLB - UMR 12), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), LLB - Matière molle et biophysique (MMB), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Biosit : biologie, santé, innovation technologique (SFR UMS CNRS 3480 - INSERM 018), Université de Rennes (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Laboratoire de Physique des Solides (LPS), Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), INSU : Initiative Structurante EC2CO – BIOHEFECT, and Dubigeon, Isabelle
Subjects: XAS, [SDU.STU.GC]Sciences of the Universe [physics]/Earth Sciences/Geochemistry, Geochemistry and Petrology, aluminum, [SDU.STU.GC] Sciences of the Universe [physics]/Earth Sciences/Geochemistry, Ferrihydrite, humic acid, SAXS
Abstract: International audience; The structural organization of heterogeneous and multiphase natural aggregates depends on the biophysicochemical conditions prevailing in the environment, with major ions playing a crucial role. In this study, the impact of aluminum (Al) on iron-organic matter (Fe-OM) aggregates was investigated since Al can interact with OM and can be incorporated in Fe-oxyhydroxides or adsorbed on their surface. Mimetic environmental Fe-OM-Al aggregates were synthesized at various [Fe] and [Al] with a constant [OM]. At low [Al+Fe], Fe-OM-Al aggregates exhibit a colloidal behavior. Within the aggregates, Fe is present as Fe(III)-oligomers and ferrihydrite-like nanoparticles whereas Al forms monomers, oligomers and small polymers, all bound to OM. The Al and Fe phases interacted with each other. At high [Fe+Al], the Fe(III)-oligomers and Al monomers/oligomers polymerized which increases the size and quantity of the ferrihydrite-like nanoparticles and Al polymers and then branched out the OM, resulting in a large settling network. The effect of Al on the Fe-OM aggregates structure could also have an impact on the fate of pollutants. The occurrence of Al amorphous hydroxides and the increase in ferrihydrite-like nanoparticles lead to a higher availability of surface reactive sites and subsequently to an increase in the sorption capacity of the Fe-OM aggregates for pollutants that exhibit a greater affinity for minerals than for organics.
Published: 2023

25. Temperature, productivity, and habitat characteristics collectively drive lake food web structure

Author: Camille Leclerc, Nathalie Reynaud, Pierre‐Alain Danis, Florentina Moatar, Martin Daufresne, Christine Argillier, Philippe Usseglio‐Polatera, Valérie Verneaux, Nicolas Dedieu, Victor Frossard, Arnaud Sentis, Risques, Ecosystèmes, Vulnérabilité, Environnement, Résilience (RECOVER), Aix Marseille Université (AMU)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Pôle Écla - écosystèmes lacustres (ECLA), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Office français de la biodiversité (OFB), Office français de la biodiversité (OFB), RiverLy - Fonctionnement des hydrosystèmes (RiverLy), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire Interdisciplinaire des Environnements Continentaux (LIEC), Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Terre et Environnement de Lorraine (OTELo), Institut national des sciences de l'Univers (INSU - CNRS)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Chrono-environnement (UMR 6249) (LCE), Centre National de la Recherche Scientifique (CNRS)-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC), Centre Alpin de Recherche sur les Réseaux Trophiques et Ecosystèmes Limniques (CARRTEL), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and ANR-19-CE02-0001,EcoTeBo,Conséquences écologiques des changements de taille induit par la température(2019)
Subjects: trophic ecology, Global and Planetary Change, productivity, Ecology, aquatic ecosystem, habitat, Environmental Chemistry, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, climate, freshwater ecosystem, General Environmental Science
Abstract: International audience; While many efforts have been devoted to understand variations in food web structure among terrestrial and aquatic ecosystems, the environmental factors influencing food web structure at large spatial scales remain hardly explored. Here, we compiled biodiversity inventories to infer food web structure of 67 French lakes using an allometric niche-based model and tested how environmental variables (temperature, productivity, and habitat) influence them. By applying a multivariate analysis on 20 metrics of food web topology, we found that food web structural variations are represented by two distinct complementary and independent structural descriptors. The first is related to the overall trophic diversity, whereas the second is related to the vertical structure. Interestingly, the trophic diversity descriptor was mostly explained by habitat size (26.7% of total deviance explained) and habitat complexity (20.1%) followed by productivity (dissolved organic carbon: 16.4%; nitrate: 9.1%) and thermal variations (10.7%). Regarding the vertical structure descriptor, it was mostly explained by water thermal seasonality (39.0% of total deviance explained) and habitat depth (31.9%) followed by habitat complexity (8.5%) and size (5.5%) as well as annual mean temperature (5.6%). Overall, we found that temperature, productivity, and habitat characteristics collectively shape lake food web structure. We also found that intermediate levels of productivity, high levels of temperature (mean and seasonality), as well as large habitats are associated with the largest and most complex food webs. Our findings, therefore, highlight the importance of focusing on these three components especially in the context of global change, as significant structural changes in aquatic food webs could be expected under increased temperature, pollution, and habitat alterations.
Published: 2023

26. Growth–defence trade-off in rice: fast-growing and acquisitive genotypes have lower expression of genes involved in immunity

Author: Felix de Tombeur, Rémi Pélissier, Ammar Shihan, Koloina Rahajaharilaza, Florian Fort, Lucie Mahaut, Taïna Lemoine, Sarah J Thorne, Sue E Hartley, Delphine Luquet, Denis Fabre, Hans Lambers, Jean-Benoît Morel, Elsa Ballini, Cyrille Violle, Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), The University of Western Australia (UWA), Plant Health Institute of Montpellier (UMR PHIM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, University of Antananarivo, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, and University of Sheffield [Sheffield]
Subjects: plant functional trait, plant defence, Physiology, [SDV]Life Sciences [q-bio], silicon, rice (Oryza sativa), Plant Science, plant economics spectrum, intraspecific variation, growth-defence trade-off, silica, Defence gene, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, plant immunity
Abstract: Plant ecologists and molecular biologists have long considered the hypothesis of a trade-off between plant growth and defence separately. In particular, how genes thought to control the growth–defence trade-off at the molecular level relate to trait-based frameworks in functional ecology, such as the slow–fast plant economics spectrum, is unknown. We grew 49 phenotypically diverse rice genotypes in pots under optimal conditions and measured growth-related functional traits and the constitutive expression of 11 genes involved in plant defence. We also quantified the concentration of silicon (Si) in leaves to estimate silica-based defences. Rice genotypes were aligned along a slow–fast continuum, with slow-growing, late-flowering genotypes versus fast-growing, early-flowering genotypes. Leaf dry matter content and leaf Si concentrations were not aligned with this axis and negatively correlated with each other. Live-fast genotypes exhibited greater expression of OsNPR1, a regulator of the salicylic acid pathway that promotes plant defence while suppressing plant growth. These genotypes also exhibited greater expression of SPL7 and GH3.2, which are also involved in both stress resistance and growth. Our results do not support the hypothesis of a growth–defence trade-off when leaf Si and leaf dry matter content are considered, but they do when hormonal pathway genes are considered. We demonstrate the benefits of combining ecological and molecular approaches to elucidate the growth–defence trade-off, opening new avenues for plant breeding and crop science.
Published: 2023

27. Trait‐dependent diversification in angiosperms: Patterns, models and data

Author: Andrew J. Helmstetter, Rosana Zenil-Ferguson, Hervé Sauquet, Sarah P. Otto, Marcos Méndez, Mario Vallejo-Marin, Jürg Schönenberger, Concetta Burgarella, Bruce Anderson, Hugo de Boer, Sylvain Glémin, Jos Käfer, Centre de Synthèse et d’Analyse sur la Biodiversité (CESAB), Fondation pour la recherche sur la Biodiversité (FRB), University of Kentucky (UK), University of New South Wales [Sydney] (UNSW), University of British Columbia [Vancouver], Universidad Rey Juan Carlos [Madrid] (URJC), Uppsala University, University of Vienna [Vienna], Stellenbosch University, Natural History Museum [Oslo], University of Oslo (UiO), Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Diversité, adaptation, développement des plantes (UMR DIADE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM), and Fondation pour la recherche sur la biodiversité
Subjects: phylogenetics, flowering plants, macroevolution, trait evolution, speciation, BiSSE, extinction, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], [SDE.BE]Environmental Sciences/Biodiversity and Ecology, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, Ecology, Evolution, Behavior and Systematics
Abstract: Variation in species richness across the tree of life, accompanied by the incredible variety of ecological and morphological characteristics found in nature, has inspired many studies to link traits with species diversification. Angiosperms are a highly diverse group that has fundamentally shaped life on earth since the Cretaceous, and illustrate how species diversification affects ecosystem functioning. Numerous traits and processes have been linked to differences in species richness within this group, but we know little about how these interact and their relative importance. Here, we synthesized data from 152 studies that used state-dependent speciation and extinction (SSE) models on angiosperm clades. Intrinsic traits related to reproduction and morphology were often linked to diversification but a set of universal drivers did not emerge as traits did not have consistent effects across clades. Importantly, dataset properties were correlated to SSE model results - trees that were larger, older, or less well-sampled tended to yield trait-dependent outcomes. We compared these properties to recommendations for SSE model use and provide a set of best practices to follow when designing studies and reporting results. Finally, we argue that SSE model inferences should be considered in a larger context incorporating species’ ecology, demography and genetics.
Published: 2023

28. A major genetic locus in neighbours controls changes of gene expression and susceptibility in intraspecific rice mixtures

Author: Rémi Pélissier, Aurélie Ducasse, Elsa Ballini, Julien Frouin, Cyrille Violle, Jean‐Benoit Morel, Plant Health Institute of Montpellier (UMR PHIM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, ANR-16-IDEX-0006,MUSE,MUSE(2016), and European Project: 639706,H2020,ERC-2014-STG,CONSTRAINTS(2015)
Subjects: indirect genetic effect, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, modulation of disease by neighbours, Physiology, rice, [SDV]Life Sciences [q-bio], transcriptomic, Plant Science, transcriptomic response toneighbour
Abstract: International audience; Reports indicate that intraspecific neighbours alter the physiology of focal plants, and with a few exceptions, their molecular responses to neighbours are unknown. Recently, changes in susceptibility to pathogen resulting from such interactions were demonstrated, a phenomenon called neighbour-modulated susceptibility (NMS). However, the genetics of NMS and the associated molecular responses are largely unexplored. Here, we analysed in rice the modification of biomass and susceptibility to the blast fungus pathogen in the Kitaake focal genotype in the presence of 280 different neighbours. Using genome-wide association studies, we identified the loci in the neighbour that determine the response in Kitaake. Using a targeted transcriptomic approach, we characterized the molecular responses in focal plants co-cultivated with various neighbours inducing a reduction in susceptibility. Our study demonstrates that NMS is controlled by one major locus in the rice genome of its neighbour. Furthermore, we show that this locus can be associated with characteristic patterns of gene expression in focal plant. Finally, we propose an hypothesis where Pi could play a role in explaining this case of NMS. Our study sheds light on how plants affect the physiology in their neighbourhood and opens perspectives for understanding plant-plant interactions.
Published: 2023

29. Faecal Short-chain Fatty Acid and Early Introduction of Foods in the First 200 Days of Infant’s Life in the District of Abidjan (Ivory Coast)

Author: Mouroufie Abo Kouadio Jerome, Silué Fatogoma Etienne, Coulibaly Ngolo David, Muriel Thomas, PEPKE Fréderic, Coxam Véronique, Kati-Coulibaly Seraphin, FAYE-KETTE Hortense, MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Paris Center for Microbiome Medicine, Unité de Nutrition Humaine (UNH), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Clermont Auvergne (UCA), Laboratory of Nutrition and Pharmacology [Abidjan, Côte d’Ivoire] (UFR-Biosciences), Université Félix Houphouët-Boigny (UFHB), Institut Pasteur de Côte d'Ivoire, and Réseau International des Instituts Pasteur (RIIP)
Subjects: gut microbiota, infants, [SDV.MHEP.PHY]Life Sciences [q-bio]/Human health and pathology/Tissues and Organs [q-bio.TO], [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, General Medicine, infants early diet diversification gut microbiota, early diet diversification, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology
Abstract: Dosage of short chain fatty acids (SCFAs) according to food diet showed that the content of acetate was high in newborn feaces. Infants receiving food supplements have a complex and diverse gut microbiota. Moreover, the results show that infants from poor districts have an abundant concentration of SCFAs in their faeces compared to those living in places with a relatively high standard of living. Among infants receiving milk, the highest proportion of SCFA is acetate in breastfed infants (BF) at a rate of 15.025 ± 2.23 μmol/g, followed by propionate in infants receiving mixed feeding (BF+FF), at a rate of 13.58 ± 1.03 μmol/g and butyrate in infants taking mixed feeding at a rate of 0.32 ± 0.72 μmol/g. However, among infants starting early diet diversification, acetate is higher in infants receiving milk formula and diet diversification (FF+FD) with a concentration of 25.4 ± 0 μmol/g, followed by propionate (2.36 ± 0 μmol/g) in infants receiving mixed feeding (BF+FF) and butyrate in those fed with (BF+FD). Partial breastfeeding is associated with a higher proportion of acetate, butyrate and propionate. The study of the correlation between the different SCFAs produced and the ASV (Variants of Microbial Amplicon Sequences) of the intestinal community of the child, shows that acetate is positively correlated with Bifidobacterium and negatively with Streptococcus and Escherichia-Shigella. Propionate is positively correlated with Bifido bacterium and negatively with Escherichia-Shigella. Similarly, butyrate is positively correlated with Bifidobacterium and negatively with Escherichia-Shigella.
Published: 2023

30. Genetic variability and plasticity of plant allometry

Author: François Vasseur, Cyrille Violle, Brian J. Enquist, Denis Vile, Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), Écophysiologie des Plantes sous Stress environnementaux (LEPSE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), University of Arizona, Santa Fe Institute, Association Nationale de la Recherche et de la Technologie, Grant/Award Number: 0398/2009-09 42 008, H2020 European Research Council, Grant/Award Number: ERC-StG-2020-949843 PHENOVIGOUR, Région Occitanie Pyrénées-Méditerranée, Grant/Award Number: FEDER FSE IEJ 2014- 2020, ANR-17-CE02-0018,AraBreed,Exploration des réponses évolutives des plantes à des changements environnementaux à la lumière des théories écologiques : un test expérimental chez l'espèce modèle Arabidopsis thaliana(2017), and European Project: 639706,H2020,ERC-2014-STG,CONSTRAINTS(2015)
Subjects: high temperature, [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, water stress, Arabidopsis thaliana, intraspecific trait variability, plasticity, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, growth rate, metabolic scaling theory, Ecology, Evolution, Behavior and Systematics
Abstract: International audience; The metabolic scaling theory (MST) predicts quasi-universal trait-size relationships in plants, characterised by a unique allometric exponent within and across large taxonomic scales. However, recent studies have identified variability in allometric relationships, without a clear understanding of the modulating role played by genetic variation and environment.Here, we investigated (1) the allometric relationships for two central traits of MST, namely total leaf area and plant growth rate, in the model species Arabidopsis thaliana, (2) the variability of plant allometries between genotypes and (3) the plastic responses of plant allometries under water deficit, high temperature and their interaction.Using a population of 120 genotypes, we found that intraspecific allometries adhered on average with MST predictions. However, a broad variability but a moderate plasticity in the allometric exponents was observed across genotypes and environments. Allometric exponents were impacted significantly, yet weakly, by water deficit, but not by high temperature. Moreover, genotypes that deviated from MST predictions exhibited more plasticity in trait-size relationships than genotypes that followed MST predictions.Our study suggests that plant allometry is genetically variable and might be related to different adaptive strategies to cope with stressing conditions. Thus, our results highlights the need of assessing trait-size relationships within species to understand the mechanisms of plant adaptation to contrasted environments.
Published: 2023

31. Molecular phylogenetics shed light on polyploid speciation in gorses (Ulex, Fabaceae: Genisteae) and on the origin of the invasive Ulex europaeus

Author: Bellot, Sidonie, Dias, Paula M.B., Affagard, Marc, Ainouche, Malika-Lily, Misset, Marie-Thérèse, Aïnouche, Abdelkader, Royal Botanic Gardens [Kew], Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), research unit UMR-CNRS 6553 Ecobio at the University of Rennes-1, CNRS (INEE, UMR CNRS 6553 Ecobio), and University of Rennes-1 (France)
Subjects: matK, rps12, autopolyploidy, Plant Science, ITS, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, trnK, molecular dating, allopolyploidy, Ecology, Evolution, Behavior and Systematics, ETS
Abstract: Hybridization and polyploidy are key evolutionary forces in plant diversification, and their co-occurrence in the context of allopolyploid speciation is often associated with increased ability to colonize new environments and invasiveness. In the genus Ulex (Fabaceae), the European gorse (Ulex europaeus subsp. europaeus) is the only invasive and the only polyploid that has recently spread in different eco-geographical regions across the world. Understanding what confers such ecological advantages to this species, compared to its diploid and polyploid congeners, first requires clarification of the ecogeographical and evolutionary context of its formation. To achieve this, the geographical distributions of all Ulex spp. were estimated from species occurrence records, and phylogenetic analyses including all Ulex spp. were performed based on four nuclear (ITS and ETS nrDNA) and plastid (rps12 intron and trnK-matK) regions. The resulting trees were dated using a secondary calibration. Patterns of DNA sequence variation and dated phylogenetic trees were then interpreted in light of previous knowledge of chromosome numbers in Ulex to infer past events of polyploid speciation in the genus. We show that: (1) most current Ulex spp. radiated in the Iberian Peninsula during the past 1–2 Myr; (2) the history of Ulex was punctuated by multiple whole-genome duplication events; and (3) U. europaeus subsp. europaeus is the only gorse taxon that was formed by hybridization of two well-differentiated lineages (which separated c. 5 Mya) with wide climatic ranges (currently represented by Ulex minor and Ulex europaeus subsp. latebracteatus), possibly contributing to the invasive nature and wider climatic range of U. europaeus subsp. europaeus. These findings provide a much-needed evolutionary framework in which to explore the adaptive consequences of genome mergers and duplication in Ulex.
Published: 2023

32. The F-box protein UFO controls flower development by redirecting the master transcription factor LEAFY to new cis-elements

Author: Philippe Rieu, Laura Turchi, Emmanuel Thévenon, Eleftherios Zarkadas, Max Nanao, Hicham Chahtane, Gabrielle Tichtinsky, Jérémy Lucas, Romain Blanc-Mathieu, Chloe Zubieta, Guy Schoehn, François Parcy, Régulateurs du développement de la fleur (Flo_RE ), Physiologie cellulaire et végétale (LPCV), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Grenoble Alpes (UGA), Institut de biologie structurale (IBS - UMR 5075), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA), Integrated Structural Biology Grenoble (ISBG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-European Molecular Biology Laboratory [Grenoble] (EMBL)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA), European Synchroton Radiation Facility [Grenoble] (ESRF), StructDev (StructDev), ANR-10-INBS-0005,FRISBI,Infrastructure Française pour la Biologie Structurale Intégrée(2010), ANR-17-EURE-0003,CBH-EUR-GS,CBH-EUR-GS(2017), ANR-17-CE20-0014,UbiFlor,Comment l'ubiquitination permet à LEAFY de créer les fleurs(2017), and ANR-10-LABX-0049,GRAL,Grenoble Alliance for Integrated Structural Cell Biology(2010)
Subjects: UFO, flower development, Arabidopsis, Plant Science, [SDV.BDD]Life Sciences [q-bio]/Development Biology, transcription factor, LEAFY
Abstract: International audience; In angiosperms, flower development requires the combined action of the transcription factor LEAFY (LFY) and the ubiquitin ligase adaptor F-box protein, UNUSUAL FLORAL ORGANS (UFO), but the molecular mechanism underlying this synergy has remained unknown. Here we show in transient assays and stable transgenic plants that the connection to ubiquitination pathways suggested by the UFO F-box domain is mostly dispensable. On the basis of biochemical and genome-wide studies, we establish that UFO instead acts by forming an active transcriptional complex with LFY at newly discovered regulatory elements. Structural characterization of the LFY-UFO-DNA complex by cryo-electron microscopy further demonstrates that UFO performs this function by directly interacting with both LFY and DNA. Finally, we propose that this complex might have a deep evolutionary origin, largely predating flowering plants. This work reveals a unique mechanism of an F-box protein directly modulating the DNA binding specificity of a master transcription factor.
Published: 2023

33. Validation of the IMPACT-III Questionnaire in French Children With Inflammatory Bowel Disease

Author: Jérémy Vanhelst, Laurent Béghin, Elodie Drumez, Djamal Djeddi-Dine, Dominique Tuck, Stéphanie Coopman, Frédéric Gottrand, Delphine Ley, Equipe 3: EREN- Equipe de Recherche en Epidémiologie Nutritionnelle (CRESS - U1153), Université Sorbonne Paris Nord-Centre de Recherche Épidémiologie et Statistique Sorbonne Paris Cité (CRESS (U1153 / UMR_A_1125 / UMR_S_1153)), Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-Université Sorbonne Paris Cité (USPC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-Université Sorbonne Paris Cité (USPC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institute for Translational Research in Inflammation - U 1286 (INFINITE (Ex-Liric)), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille), CHU Lille, Evaluation des technologies de santé et des pratiques médicales - ULR 2694 (METRICS), Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille), CHU Amiens-Picardie, Périnatalité et Risques Toxiques - UMR INERIS_I 1 (PERITOX), Institut National de l'Environnement Industriel et des Risques (INERIS)-Université de Picardie Jules Verne (UPJV)-CHU Amiens-Picardie, and Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)
Subjects: Pediatrics, Perinatology and Child Health, Gastroenterology, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology
Abstract: International audience; Objectives: This study assessed the reliability and validity of the IMPACT-III questionnaire, a health-related quality of life (HRQoL) instrument, in French children with inflammatory bowel disease (IBD).Methods: Eighty-four children and adolescents (45 boys, aged 14.3 ± 2.7 years) were included in a validation study of the IMPACT-III questionnaire. Patients completed 2 questionnaires for measuring HRQoL: the IMPACT-III and the Pediatric Quality of Life Inventory 4.0 Generic Core Scale (PedsQL). Internal consistency was assessed using Cronbach α. Factor analysis was performed on data from the IMPACT-III to help construct domains. Concurrent validity was assessed by calculating Spearman correlation coefficients.Results: Cronbach α for the PedsQL total score was good (0.89). The most robust factor solution was a 3-domain structure: (a) Concerns, (b) Body Image and Physical Condition, and (c) Symptoms and Socializing. All domains had good reliability (0.674-0.863). Only 2 items had to be removed. Discriminant validity was demonstrated by significant differences ( P < 0.001) in median IMPACT-III scores between inactive and active disease for the total score (83.3 vs 72.0), and for Concerns ( P < 0.002) and Symptoms and Socializing ( P < 0.001).Conclusions: These results suggest that IMPACT-III appears to be a useful instrument for measuring HRQoL in French children with IBD.
Published: 2023

34. The Expanding Menagerie of Prunus-Infecting Luteoviruses

Author: Maryam Khalili, Thierry Candresse, Igor Koloniuk, Dana Safarova, Yoann Brans, Chantal Faure, Marine Delmas, Sébastien Massart, Miguel A. Aranda, Kadriye Caglayan, Veronique Decroocq, Pavlina Drogoudi, Miroslav Glasa, George Pantelidis, Milan Navratil, François Latour, Josef Spak, Jaroslava Pribylova, Daniel Mihalik, Francesco Palmisano, Antonella Saponari, Tomas Necas, Jiri Sedlak, Armelle Marais, Biologie du fruit et pathologie (BFP), Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institute of Plant Molecular Biology, Biological Centre, Czech Academy of Sciences [Prague] (CAS), Palacky University Olomouc, Centre Technique Interprofessionnel des Fruits et Légumes (CTIFL), Unité Expérimentale Arboricole (UE ARBO), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), TERRA, Gembloux Agro-Bio Tech, Consejo Superior de Investigaciones Científicas [Spain] (CSIC), Hatay Mustafa Kemal University, Ellinikos Georgikos OrGanismos-DIMITRA (ELGO -DIMITRA), Slovak Academy of Science [Bratislava] (SAS), Institute of Biology, Ss Cyril and Methodius University in Skopje, Agricultural Research and Experimentation Centre 'Basile Caramia', Mendel University in Brno (MENDELU), Vyzkumny A Slechtitelsky Ustav Ovocnarsky, This study was funded by the European Union through the Horizon 2020 Marie Skłodowska-Curie Actions Innovative Training Network (H2020 MSCA- 60 ITN) project 'INEXTVIR' (Grant agreement number 813542). The ChLVA research part was financed by Academy of Sciences of the Czech Republic support (RVO60077344). The plant indexing biological tests conducted by CTIFL were funded by INTERFEL (Fresh fruit and 68vegetable interprofessional association). D. Safarova and M. Navratil have received support from the Ministry of Agriculture of the Czech Republic, National Agency for Agricultural Research (Project no. QK1920124). M. Glasa and D. Mihálik have received support from the Slovak Research & Development Agency (project APVV-18-0005), European Project: H2020 MSCA-60 ITN, and European Project: 813542,INEXTVIR
Subjects: biological indexing, Stone fruit, [SDV]Life Sciences [q-bio], Luteovirus, geographical distribution, HTS, Plant Science, Pathogen Detection, Agronomy and Crop Science, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy
Abstract: International audience; Members of the genus Luteovirus are responsible for economically destructive plant diseases worldwide. Over the past few years, three luteoviruses infecting Prunus trees have been characterized. However, the biological properties, prevalence, and genetic diversity of those viruses have not yet been studied. High throughput sequencing of samples of various wild, cultivated, and ornamental Prunus species enabled the identification of four novel species in the genus Luteovirus for which we obtained complete or nearly complete genomes. Besides, we identified another new putative species recovered from Sequence Read Archive data. Furthermore, we conducted a survey on peach-infecting luteoviruses in eight European countries. Analyses of 350 leaf samples collected from germplasm, production orchards, and private gardens showed that peach-associated luteovirus (PaLV), nectarine stem pitting-associated virus (NSPaV), and a novel luteovirus, peach-associated luteovirus 2 (PaLV2), are present in all countries, while the most prevalent virus was NSPaV, followed by PaLV. An analysis of the genetic diversity of these viruses was also conducted. Moreover, the biological indexing on GF305 peach indicator plants demonstrated that PaLV and PaLV2, like NSPaV, are transmitted by graft at relatively low rates. No clear viral symptoms have been observed either in graft-inoculated GF305 indicators, or in different peach tree varieties observed in an orchard. The data generated during this study provide a broader overview of the genetic diversity, geographical distribution and prevalence of peach-infecting luteoviruses, and suggest these viruses are likely asymptomatic in peach under most circumstances.
Published: 2023

35. Assessing French departments’ spending efficiency over time

Author: Kassoum Ayouba, Marie-Line Duboz, Julie Le Gallo, Territoires (Territoires), AgroParisTech-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Clermont Auvergne (UCA), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre de REcherches sur les Stratégies Economiques (UR 3190) (CRESE), Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC), Université Bourgogne Franche-Comté [COMUE] (UBFC), Centre d'Economie et de Sociologie Rurales Appliquées à l'Agriculture et aux Espaces Ruraux (CESAER), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Dijon, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Institut Agro Dijon, and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)
Subjects: Local governments, Efficacité, Economics and Econometrics, JEL: H - Public Economics/H.H2 - Taxation, Subsidies, and Revenue/H.H2.H21 - Efficiency • Optimal Taxation, [QFIN]Quantitative Finance [q-fin], Contextual variables, JEL: C - Mathematical and Quantitative Methods/C.C1 - Econometric and Statistical Methods and Methodology: General/C.C1.C14 - Semiparametric and Nonparametric Methods: General, Efficiency, JEL: H - Public Economics/H.H5 - National Government Expenditures and Related Policies/H.H5.H50 - General, JEL: C - Mathematical and Quantitative Methods/C.C6 - Mathematical Methods • Programming Models • Mathematical and Simulation Modeling/C.C6.C61 - Optimization Techniques • Programming Models • Dynamic Analysis, Dépenses, Variables contextuelles, Expenditures, Collectivités locales, Modèle conditionnel, Conditional model
Abstract: International audience
Published: 2023

36. Soil transfer impacts restored soil profiles and hydrodynamic properties

Author: Bulot, Adeline, Bourru, Elise, Ruy, Stéphane, Dutoit, Thierry, Biodiversité agroécologie et aménagement du paysage (UMR BAGAP), Ecole supérieure d'Agricultures d'Angers (ESA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Rennes Angers, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Institut méditerranéen de biodiversité et d'écologie marine et continentale (IMBE), Avignon Université (AU)-Aix Marseille Université (AMU)-Institut de recherche pour le développement [IRD] : UMR237-Centre National de la Recherche Scientifique (CNRS), Syndicat Mixte du Bassin de Thau – 328, Quai des Moulins, 34200 S`ete, France, Environnement Méditerranéen et Modélisation des Agro-Hydrosystèmes (EMMAH), and Avignon Université (AU)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: Cambisol, Reconstituted technosoil, [SDE]Environmental Sciences, Haplic, Soil hydrological properties, Dry grassland, Ecological restoration
Abstract: International audience; Natural and semi-natural grasslands, particularly dry grasslands, are high-value biodiversity hotspots in Europe and major challenges for ecological conservation and restoration. Soil transfer has been used successfully to restore dry grassland ecosystems (soil and vegetation), but should only be applied as a last resort and where an undegraded ecosystem has previously independently been earmarked for destruction. Assessing overall restoration success means taking soil recovery into account as well as vegetation regeneration. In Mediterranean regions and under global warming, soil hydrodynamic properties are the most critical limiting factors for the restoration of dry ecosystems. This study analyses soil physico-chemical parameters and hydrodynamic properties in reconstructed soils after soil transfer following a petrol land spill. Six years after soil transfer and compared to the surrounding soil reference steppe, the horizons of the soil transfer treatments were significantly less colonised by plant roots and showed very few biological activities and earthworm galleries. Then, their porosity was also significantly lower. Hydrodynamic properties continue to differ significantly between the restored site and the surrounding reference steppe ecosystem. There is also less available soil water and water drains faster in all soil transfer treatments. This can be explained by significant higher finer grain size (clays, silt), chemical elements (N, P, K), and plant cover for soil transfer treatments but significant, lower levels of organic matterdue to mechanical soil compaction during soil spreading. The soil transfer treatment involving full reconstitution of the three main soil layers yields the most encouraging results. However, the question arises of whether long-term vegetation recovery might be compromised by soil hydrological dysfunction under global warming.
Published: 2023

37. Combining multi-spectral data with statistical and deep-learning models for improved exoplanet detection in direct imaging at high contrast

Author: Flasseur, Olivier, Bodrito, Théo, Mairal, Julien, Ponce, Jean, Langlois, Maud, Lagrange, Anne-Marie, Centre de Recherche Astrophysique de Lyon (CRAL), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Models of visual object recognition and scene understanding (WILLOW), Département d'informatique - ENS Paris (DI-ENS), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Inria de Paris, Institut National de Recherche en Informatique et en Automatique (Inria), Apprentissage de modèles à partir de données massives (Thoth), Inria Grenoble - Rhône-Alpes, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire Jean Kuntzmann (LJK), Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), Université Grenoble Alpes (UGA), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS), Center for Data Science, New York University [New York] (NYU), NYU System (NYU)-NYU System (NYU), Laboratoire d'études spatiales et d'instrumentation en astrophysique = Laboratory of Space Studies and Instrumentation in Astrophysics (LESIA), Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire de Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Institut de Planétologie et d'Astrophysique de Grenoble (IPAG), Centre National d'Études Spatiales [Toulouse] (CNES)-Observatoire des Sciences de l'Univers de Grenoble (OSUG ), Institut national des sciences de l'Univers (INSU - CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Grenoble Alpes (UGA)-Météo-France -Institut national des sciences de l'Univers (INSU - CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Grenoble Alpes (UGA)-Météo-France, The work of OF, ML, and AML was supported in part by the EuropeanResearch Council (ERC) under the European Union’s Horizon 2020 researchand innovation program (COBREX, n° 885593). The work of TB and JP wassupported in part by the Inria/NYU collaboration, the Louis Vuitton/ENS chair on artificial intelligence and the French Agence Nationale de la Recherche (ANR) as part of the Investissements d’avenir program (PRAIRIE 3IAInstitute, n° 19-P3IA-0001). The work of JM was supported in part by theERC (SOLARIS, n° 714381) and by the ANR (3IA MIAI, n° 19-P3IA-0003)., ANR-19-P3IA-0001,PRAIRIE,PaRis Artificial Intelligence Research InstitutE(2019), ANR-19-P3IA-0003,MIAI,MIAI @ Grenoble Alpes(2019), European Project: 885593,COBREX, and European Project: 714381,H2020,SOLARIS(2017)
Subjects: Earth and Planetary Astrophysics (astro-ph.EP), FOS: Computer and information sciences, [PHYS]Physics [physics], Computer Science - Machine Learning, [STAT.AP]Statistics [stat]/Applications [stat.AP], Multi-variate data, [PHYS.ASTR.EP]Physics [physics]/Astrophysics [astro-ph]/Earth and Planetary Astrophysics [astro-ph.EP], Matched filter, FOS: Physical sciences, Correlated data, [INFO.INFO-NE]Computer Science [cs]/Neural and Evolutionary Computing [cs.NE], Machine Learning (cs.LG), [INFO.INFO-AI]Computer Science [cs]/Artificial Intelligence [cs.AI], [STAT]Statistics [stat], Detection, [STAT.ML]Statistics [stat]/Machine Learning [stat.ML], Supervised deep learning, Astrophysics - Instrumentation and Methods for Astrophysics, [PHYS.ASTR]Physics [physics]/Astrophysics [astro-ph], Instrumentation and Methods for Astrophysics (astro-ph.IM), [STAT.ME]Statistics [stat]/Methodology [stat.ME], [PHYS.PHYS.PHYS-DATA-AN]Physics [physics]/Physics [physics]/Data Analysis, Statistics and Probability [physics.data-an], Astrophysics - Earth and Planetary Astrophysics
Abstract: Exoplanet detection by direct imaging is a difficult task: the faint signals from the objects of interest are buried under a spatially structured nuisance component induced by the host star. The exoplanet signals can only be identified when combining several observations with dedicated detection algorithms. In contrast to most of existing methods, we propose to learn a model of the spatial, temporal and spectral characteristics of the nuisance, directly from the observations. In a pre-processing step, a statistical model of their correlations is built locally, and the data are centered and whitened to improve both their stationarity and signal-to-noise ratio (SNR). A convolutional neural network (CNN) is then trained in a supervised fashion to detect the residual signature of synthetic sources in the pre-processed images. Our method leads to a better trade-off between precision and recall than standard approaches in the field. It also outperforms a state-of-the-art algorithm based solely on a statistical framework. Besides, the exploitation of the spectral diversity improves the performance compared to a similar model built solely from spatio-temporal data., accepted to EUSIPCO 2023
Published: 2023

38. Structural studies of the deacylated glycolipids and lipoteichoic acid of Lactococcus cremoris 3107

Author: Ruiz-Cruz, Sofía, Sadovskaya, Irina, Mahony, Jennifer, Grard, Thierry, Chapot-Chartier, Marie-Pierre, van Sinderen, Douwe, Vinogradov, Evguenii, Transfrontalière BioEcoAgro - UMR 1158 (BioEcoAgro), Université d'Artois (UA)-Université de Liège-Université de Picardie Jules Verne (UPJV)-Université du Littoral Côte d'Opale (ULCO)-Université de Lille-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-JUNIA (JUNIA), Université catholique de Lille (UCL)-Université catholique de Lille (UCL), Biochimie des Produits Aquatiques (BPA), Université du Littoral Côte d'Opale (ULCO)-Transfrontalière BioEcoAgro - UMR 1158 (BioEcoAgro), Université catholique de Lille (UCL)-Université catholique de Lille (UCL)-Université d'Artois (UA)-Université de Liège-Université de Picardie Jules Verne (UPJV)-Université du Littoral Côte d'Opale (ULCO)-Université de Lille-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-JUNIA (JUNIA), University College Cork (UCC), MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institute for Biological Science, and National Research Council of Canada (NRC)
Subjects: Lactococcus cremoris 3107, [SDV]Life Sciences [q-bio], Lactic acid bacteria, Glycolipids, Lipoteichoic acid, Cell walls, NMR
Abstract: International audience; Lactococcus cremoris and Lactococcus lactis are among the most extensively exploited species of lactic acid bacteria in dairy fermentations. The cell wall of lactococci, like other Gram-positive bacteria, possesses a thick peptidoglycan layer, which may incorporate cell wall polysaccharides (CWPS), wall teichoic acids (WTA), and/or lipoteichoic acids (LTA).In this study, we report the isolation, purification and structural analysis of the carbohydrate moieties of glycolipids (GL) and LTA of the L. cremoris model strain 3107. Chemical structures of these compounds were studied by chemical methods, NMR spectroscopy and positive and negative mode ESI MS. We found that the LTA of strain 3107 is composed of short chains of 1,3-polyglycerol phosphate (PGP), attached to O-6 of the non-reducing glucose of the kojibiose-Gro backbone of the glycolipid anchor. Extraction of cells with cold TCA afforded the detection of 1,3-glycerol phosphate chains randomly substituted at O-2 of glycerol by D-Ala. Unlike the LTA of L. lactis strains studied to date, the PGP backbone of the LTA of L. cremoris 3107 did not carry any glycosyl substitution. The deacylated glycolipid fraction contained the free kojibiose-Gro oligosaccharide, identical to the backbone of the GL anchor of LTA, and its shorter fragment α-Glc-1-Gro. These OS may have originated from the GL precursors of LTA biosynthesis.
Published: 2023

39. Drivers of PES effectiveness: Some evidence from a quantitative meta-analysis

Author: Saint-Cyr, Legrand D.F., Védrine, Lionel, Legras, Sophie, Le Gallo, Julie, Bellassen, Valentin, Centre d'Economie et de Sociologie Rurales Appliquées à l'Agriculture et aux Espaces Ruraux (CESAER), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Dijon, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Territoires (Territoires), AgroParisTech-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Clermont Auvergne (UCA), and European Project: 770747,LIFT
Subjects: Economics and Econometrics, additionality, [QFIN]Quantitative Finance [q-fin], Payment for Environmental Services PES, effectiveness, General Environmental Science
Abstract: International audience; Payments for Environmental or Ecosystem Services (PES) schemes have become a popular tool to addressenvironmental degradation and to promote sustainable management of ecosystem services. We use metaregressionanalysis on a sample of 110 individual studies to investigate the determinants of the environmentaleffectiveness, defined as the probability to increase environmental services (ES) provision, of about 149 PESschemesimplemented worldwide. We find that increased effectiveness of PES schemes is strongly associatedwith periodical third-party monitoring, generic reference design and to a lesser extent results-based payments.We further study the determinants of PES additionality, defined as direct changes in ES provision induced by thePES scheme, compared to a baseline without PES, on a smaller sample of 41 studies from which we could obtainthe necessary data. The results confirm the role of certain design variables, such as monitoring type, and raise apotential trade-off between enrolment and additionality in the assessment of PES effectiveness.
Published: 2023

40. Making technological innovations accessible to agricultural water management: Design of a low-cost wireless sensor network for drip irrigation monitoring in Tunisia

Author: Paul Vandôme, Crystele Leauthaud, Simon Moinard, Oliver Sainlez, Insaf Mekki, Abdelaziz Zairi, Gilles Belaud, Gestion de l'Eau, Acteurs, Usages (UMR G-EAU), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Bureau de Recherches Géologiques et Minières (BRGM) (BRGM)-Institut de Recherche pour le Développement (IRD)-AgroParisTech-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Département Environnements et Sociétés (Cirad-ES), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Technologies et Méthodes pour les Agricultures de demain (UMR ITAP), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut National de Recherche en Génie Rural Eaux et Forêts (INRGREF), and Ecole Nationale du Génie Rural, des Eaux et des Forêts (ENGREF)-Institution de la Recherche et de l'Enseignement Supérieur Agricoles [Tunis] (IRESA)
Subjects: Internet of things (IoT), Agricultural water management, [SDE]Environmental Sciences, Drip irrigation monitoring, Low cost soil moisture sensor, LoRa network, Wireless sensor network
Abstract: International audience; Unsustainable use of water resources and climate change will exacerbate the existing tensions surrounding resources, especially in the Mediterranean context. Despite investments in costly modern equipment, the performance of irrigated agriculture remains below expectations, notably because of the lack of available water data and the limited use of decision support tools. Although a variety of soil moisture sensors are available on the market, they are not widely used by the agricultural community because of their high cost and complexity. Access to information at an unprecedented level, via easily accessible low-cost and low-tech sensors, may be a major lever for improved identification of achievable gains in performance, and to guide actors toward efficient water management. To explore this hypothesis, an open source wireless soil moisture sensor, low-energy and economically and technically accessible, was developed. The tool was designed according to water users’ requirements and applied to a Tunisian irrigation scheme subject to major water use efficiency issues. The functioning of the wireless sensor network was tested on pilot plots over a growing season and compared with commercial sensors. A single parameter calibration can be performed in either the laboratory or the field. This low-cost sensor can be used for real-time irrigation monitoring and as a decision-making tool for water management.
Published: 2023

41. Docosahexaenoic acid and etanercept could reduce functional and metabolic alterations during collagen-induced arthritis in rats without any synergistic effect

Author: Léger, Thibault, Brun, Aurélien, Lanchais, Kassandra, Rigaudière, Jean-Paul, Briat, Arnaud, Guitton, Yann, Marchand, Fabien, Tournadre, Anne, Capel, Frédéric, Unité de Nutrition Humaine (UNH), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Clermont Auvergne (UCA), Imagerie Moléculaire et Stratégies Théranostiques (IMoST), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Clermont Auvergne (UCA), Laboratoire d'étude des Résidus et Contaminants dans les Aliments (LABERCA), École nationale vétérinaire, agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Neuro-Dol (Neuro-Dol), Centre d’Infection et d’Immunité de Lille - INSERM U 1019 - UMR 9017 - UMR 8204 (CIIL), Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Centre National de la Recherche Scientifique (CNRS), Université Clermont Auvergne (UCA), Centre de Recherche en Nutrition Humaine d'Auvergne (CRNH d'Auvergne), and Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: [SDV]Life Sciences [q-bio]
Abstract: International audience
Published: 2023

42. Spatiotemporal distribution of zooplankton in relation to some abiotic variables in the waters of the Kribian Atlantic coast (South Cameroon)

Author: Gabriel Bertrand Zambo, Rachelle Biloa Essomba, Rodrigue Dongmo Nanfack, François Desire Edoa Owona, Eric Kueppo Kouedeum, Paul Bertrand Nangou Sob, Piscart Christophe, Serge Hubert Togouet Zébazé, Université de Yaoundé I, Université de Douala, Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), and Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Zooplanktonic, Physicochemical, Kribian, Coast, General Medicine, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography
Abstract: A research to study the zooplanktonic population in relation to some abiotic variables of the Kribian coast waters was conducted from July to December 2020 following a monthly sampling in six (6) selected sites. The physicochemical parameters were determining out using standard methods. Concerning the zooplankton, the water was collected at the surface, in the trophogenic and tropholytic layers, then filtered through a 64 µm plankton sieve and the retentate was fixed with 96% alcohol. Identification and counting were done in the laboratory using a Wild M5 binocular loupe, appropriate keys and works. The physicochemical results showed a very good oxygenation of the waters (91.85 ± 3.87%), basic pH (8.43 ± 0.54 U.C), a low salinity and conductivity of respectively 13.04 ± 3.92 g/L and 23.07±4.23 µS/cm characteristic of the haline domains and a temperature of 28.66 ± 1.35°C. With regard to nutrients, the values recorded showed a progressive enrichment of the water in nitrate (2.2±1.81mg/L) and a low concentration in orthophosphate (0.25±0.41mg/L). the zooplankton community haboured, 54 taxa belonging to 3 major groups (Copepoda, Cladocera, Ciliate) and other Zooplankton, 24 families and 29 genera were recorded. The Copepod group dominated the taxonomic richness with 34 taxa (62.96% of total richness), followed by Tintinidae with 4 taxa (7.4%), Cladocera with 1 marine taxa (1.9%) and 15 taxa for other zooplankton (27.8%). Quantitatively, Copepods were once again the most abundant group in the population, with an average of 78.3% of the total zooplankton abundance. The dominant copepod taxa in terms of abundance were those of the families of: Paracalanidae (mean abundance: 116 ind/L) and Oithonidae (mean abundance: 99ind/L).
Published: 2023

43. Drought survival and recovery in grasses: Stress intensity and plant–plant interactions impact plant dehydration tolerance

Author: Karim Barkaoui, Florence Volaire, Agrosystèmes Biodiversifiés (UMR ABSys), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre International de Hautes Etudes Agronomiques Méditerranéennes - Institut Agronomique Méditerranéen de Montpellier (CIHEAM-IAMM), Centre International de Hautes Études Agronomiques Méditerranéennes (CIHEAM)-Centre International de Hautes Études Agronomiques Méditerranéennes (CIHEAM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Département Performances des systèmes de production et de transformation tropicaux (Cirad-PERSYST), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), Département agronomie et sciences de l'environnement pour les agroécosystèmes (AgroEcoSystem), and Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: senescence, Tolérance à la sécheresse, Physiology, [SDV]Life Sciences [q-bio], F60 - Physiologie et biochimie végétale, Festuca arundinacea, Plant Science, Poaceae, relative yield, Déshydratation, intraspecific variability, lethal drought, Physiologie végétale, Résistance à la sécheresse, drought acclimation, drought recovery, H50 - Troubles divers des plantes, Dactylis glomerata, leaf meristem
Abstract: The data that support the findings of this study are openly available in figshare at https://doi.org/10.6084/m9.figshare.21834459.; International audience; Plant dehydration tolerance confers drought survival in grasses, but the mortality thresholds according to soil water content (SWC), vapour pressure deficit (VPD) and plant-plant interactions are little explored. We compared the dehydration dynamics of leaf meristems, which are the key surviving organs, plant mortality, and recovery of Mediterranean and temperate populations of two perennial grass species, Dactylis glomerata and Festuca arundinacea, grown in monocultures and mixtures under a low-VPD (1.5 kPa) versus a high-VPD drought (2.2 kPa). The lethal drought index (LD 50), that is, SWC associated with 50% plant mortality, ranged from 2.87% (ψs = −1.68 MPa) to 2.19% (ψs = −4.47 MPa) and reached the lowest values under the low-VPD drought. Populations of D. glomerata were more dehydration-tolerant (lower LD 50), survived and recovered better than F. arundinacea populations. Plant-plant interactions modified dehydration tolerance and improved post-drought recovery in mixtures compared with monocultures. Water content as low as 20.7%-36.1% in leaf meristems allowed 50% of plants to survive. We conclude that meristem dehydration causes plant mortality and that drought acclimation can increase dehydration tolerance. Genetic diversity, acclimation and plant-plant interactions are essential sources of dehydration tolerance variability to consider when predicting drought-induced mortality.
Published: 2023

44. Continuum from microplastics to nanoplastics: effects of size and source on the estuarine bivalve Scrobicularia plana

Author: Isabelle Métais, Oihana Latchere, Coraline Roman, Hanane Perrein-Ettajani, Mohammed Mouloud, Didier Georges, Thybaud Audroin, Charlotte Catrouillet, Julien Gigault, null Agnès-Feurtet-Mazel, Magalie Baudrimont, Amélie Châtel, Université Catholique de l'Ouest (UCO), Géosciences Rennes (GR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), Environnements et Paléoenvironnements OCéaniques (EPOC), Observatoire aquitain des sciences de l'univers (OASU), Université Sciences et Technologies - Bordeaux 1 (UB)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Sciences et Technologies - Bordeaux 1 (UB)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), and TROPHIPLAST, funded by the French national agency ANSES (grant agreement 2018/1/017).
Subjects: [SDU.STU.GC]Sciences of the Universe [physics]/Earth Sciences/Geochemistry, Health, Toxicology and Mutagenesis, [SDE]Environmental Sciences, Environmental Chemistry, General Medicine, Pollution
Abstract: International audience; Plastic has been largely detected in estuarine environments and represents major concern towards aquatic living organisms. The present study evaluates the impact of microplastics (MPs) and nanoplastics (NPs) under realistic exposure conditions. Scrobicularia plana individuals were exposed to low concentrations (0.008, 10, and 100 µg L−1) of environmental MPs and NPs as well as to standard PS NPs, as a comparison condition. The aim of this study was to understand the ecotoxicological effects of environmental plastic particles on S. plana gills and digestive glands but also to compare the effects of plastic polymers size in order to highlight if the size could induce different toxicity profiles within this model organism, at different levels of biological organization. Results showed a differential induction of detoxification enzymes (CAT, GST), immunity (AcP), DNA damage processes as well as a differential effect on behavior and condition index of animals depending upon the type of plastic, the size, the concentration tested, and the type of organ. This study underlines the necessity of testing (i) plastics collected from the environment as compared to standard ones and (ii) the effect of size using plastics coming from the same batch of macrosized plastics. This study concludes on the future need directions that plastic-based studies must take in order to be able to generate a large quantity of relevant data that could be used for future regulatory needs on the use of plastic.
Published: 2023

45. A systemic approach to grapevine decline diagnosed using three key indicators: plant mortality, yield loss and vigour decrease

Author: Anne MEROT, Guillaume Coulouma, Nathalie Smits, Elsa Robelot, Christian Gary, Lucia Guerin-Dubrana, Jouanel Poulmach, Xavier Burgun, Anne Pellegrino, Marc Fermaud, Agrosystèmes Biodiversifiés (UMR ABSys), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre International de Hautes Etudes Agronomiques Méditerranéennes - Institut Agronomique Méditerranéen de Montpellier (CIHEAM-IAMM), Centre International de Hautes Études Agronomiques Méditerranéennes (CIHEAM)-Centre International de Hautes Études Agronomiques Méditerranéennes (CIHEAM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Laboratoire d'étude des Interactions Sol - Agrosystème - Hydrosystème (UMR LISAH), Institut de Recherche pour le Développement (IRD)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Santé et agroécologie du vignoble (UMR SAVE), Université de Bordeaux (UB)-Institut des Sciences de la Vigne et du Vin (ISVV)-Ecole Nationale Supérieure des Sciences Agronomiques de Bordeaux-Aquitaine (Bordeaux Sciences Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Chambre d'Agriculture de l'Hérault (CA 34), Institut Français de la Vigne et du Vin (IFV), Écophysiologie des Plantes sous Stress environnementaux (LEPSE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, and Plan National Dépérissement Viticole (PNDV) / France Agrimer
Subjects: vine mortality, diagnosis, dieback, [SDV]Life Sciences [q-bio], yield loss, vigour, Horticulture, decline, indicators, Food Science
Abstract: International audience; Grapevine decline, a major global viticulture issue, is defined as a multi-year decrease in vine productivity and/or increase in vine mortality. Although grapevine trunk diseases are one of the most studied causes, the decline is multifactorial and associated with more than 70 factors, including abiotic and biotic hazards. With so many factors to consider, the phenomenon is difficult to understand. Our study aims to make it easier to determine and assess grapevine decline by focusing on three key indicators: yield, mortality and vegetative vigour. We investigated the relationships between these indicators from both a temporal and spatial perspective to propose a set of diagnostic indicators. Thus, we conducted a winegrower survey, a historical analysis of grapevine decline and field measurements of the abovementioned indicators on plot networks in three major French winegrowing regions (see graphical abstract): Bordeaux, Cognac and Languedoc. We found that winegrowers' perceptions of decline were consistent with an objective characterisation based on field measurements of the indicators. Although vine mortality progressively spread over the years, neither the survey nor the historical analysis showed a direct link between decline and yield loss. Rather, large yearly fluctuations in yield, which did not systematically decrease over time, account for this finding. As a result, the mortality rate and the normalised difference vegetation index (NDVI) indicators were shown to be earlier indicators of grapevine decline than yield loss (addressed from the yield achievement ratio, YAR). We performed a multifactorial analysis of the overall data set from the three regions to deepen our understanding of the diversity of declining situations and the underlying environmental and management factors contributing to decline. Finally, two ground-based NDVI indicators and an image-analysis methodology using aerial photographs were proposed as easy-to-obtain indicators of grapevine decline. NDVI indicators were linearly correlated with both the YAR and mortality rate. This study provides a better understanding and promising tools for the early diagnosis of grapevine decline.
Published: 2023

46. Cognitive performance is associated with glomerular filtration rate in patients with chronic kidney disease: results from the CKD-REIN cohort

Author: Pépin, Marion, Levassort, Hélène, Boucquemont, Julie, Lambert, Oriane, Alencar de Pinho, Natalia, Turinici, Monica, Helmer, Catherine, Metzger, Marie, Cheddani, Lynda, Frimat, Luc, Combe, Christian, Fouque, Denis, Laville, Maurice, Ayav, Carole, Liabeuf, Sophie, Jacquelinet, Christian, Teillet, Laurent, Stengel, Bénédicte, Massy, Ziad, Choukroun, Gabriel, Hôpital Ambroise Paré [AP-HP], Centre de recherche en épidémiologie et santé des populations (CESP), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Paul Brousse-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris-Saclay, Epidemiologie-Biostatistique [Bordeaux], Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Bordeaux Ségalen [Bordeaux 2], Laboratoire Interdisciplinaire de Recherche Appliquée en Economie de la Santé (LIRAES (URP_ 4470)), Université Paris Cité (UPCité), Bordeaux population health (BPH), Université de Bordeaux (UB)-Institut de Santé Publique, d'Épidémiologie et de Développement (ISPED)-Institut National de la Santé et de la Recherche Médicale (INSERM), Evolution, adaptation et comportement, Département écologie évolutive [LBBE], Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Hôpital Hôtel-Dieu [Paris], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Réseau Lorrain de prise en charge de l’insuffisance rénale chronique : Réseau NEPHROLOR (Nephrolor), Adaptation, mesure et évaluation en santé. Approches interdisciplinaires (APEMAC), Université de Lorraine (UL), Bioingénierie tissulaire (BIOTIS), Université de Bordeaux (UB)-Institut National de la Santé et de la Recherche Médicale (INSERM), Service de Néphrologie-transplantation-dialyse [Bordeaux], CHU Bordeaux [Bordeaux], Centre Hospitalier Lyon Sud [CHU - HCL] (CHLS), Hospices Civils de Lyon (HCL), Cardiovasculaire, métabolisme, diabétologie et nutrition (CarMeN), Université de Lyon-Université de Lyon-Hospices Civils de Lyon (HCL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre de Recherche en Nutrition Humaine Rhône-Alpes (CRNH-RA), Centre Hospitalier Universitaire de Saint-Etienne [CHU Saint-Etienne] (CHU ST-E)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-CHU Grenoble-Hospices Civils de Lyon (HCL)-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Grenoble Alpes (UGA), Service d'Epidémiologie et Evaluations Cliniques [CHRU Nancy] (Pôle S2R), Centre Hospitalier Régional Universitaire de Nancy (CHRU Nancy), Service de Néphrologie [CHRU Nancy], CHU Amiens-Picardie, Mécanismes physiopathologiques et conséquences des calcifications vasculaires - UR UPJV 7517 (MP3CV), Université de Picardie Jules Verne (UPJV)-CHU Amiens-Picardie, Chronic Kidney Disease - Réseau Epidémiologie et Information en Néphrologie (CKD REIN), Institut National de la Santé et de la Recherche Médicale (INSERM), Service Néphrologie/Dialyse [AP-HP Ambroise-Paré], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Ambroise Paré [AP-HP], Épidémiologie et recherches translationnelles sur les maladies rénales et cardiovasculaires (EPREC) (U1018 (Équipe 5)), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Paul Brousse-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris-Saclay-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Paul Brousse-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris-Saclay, and Service de Néphrologie-Dialyse-Transplantation [CHU Amiens-Picardie]
Subjects: cognition, Psychiatry and Mental health, renal medicine, epidemiology, Surgery, Neurology (clinical), [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology
Abstract: BackgroundChronic kidney disease (CKD) is associated with cognitive impairment in general population. We assessed the association between kidney and cognitive functions in patients with CKD and the influence of cardiovascular (CV) risk factors, and depression on this association.MethodsThe CKD-Renal Epidemiology and Information Network cohort included 3033 patients with CKD stages 3–4, followed for 5 years. Cognitive function was assessed with the Mini-Mental State Examination (MMSE) and estimated glomerular filtration rate (eGFR) with the CKD-Epidemiology Collaboration equation-creatinin formula. Evolution of the MMSE score over time and its association with baseline eGFR were investigated with linear mixed models. We assessed the risk of incident cognitive outcome (hospitalisation or death with relevant International Classification of Disease-10 codes), with a Cox proportional hazard model.ResultsThe mean age was 66.8, the mean eGFR was 33 mL/min/1.73 m2and 387 patients (13.0%) had an MMSE score below 24 at baseline. A 10 mL/min/1.73 m2decrement of baseline eGFR was associated with a mean MMSE decrease of 0.12 (95% CI 0.04 to 0.19) after adjustment for demographic characteristics, depression, CV risk factors and disease; but baseline eGFR was not associated with MMSE temporal evolution. HR for cognitive outcome during follow-up (median 2.01 years) associated with a 10 mL/min/1.73 m2decrement of baseline eGFR was 1.35 (1.07, 1.70) (p=0.01) after adjustment.ConclusionsIn patients with CKD, lower eGFR was associated with worse cognitive performance and incident cognitive events, independently of demographics, CV risk factors and depression.Trial registration numberNCT03381950.
Published: 2023

47. Land drainage functioning and hydrological impacts in rural catchments: model development and field experiments

Author: Daniel Zimmer, Julien Tournebize, Sami Bouarfa, Cyril Kao, Benoît Lesaffre, KIC Climat, Hydrosystèmes continentaux anthropisés : ressources, risques, restauration (UR HYCAR), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Gestion de l'Eau, Acteurs, Usages (UMR G-EAU), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Bureau de Recherches Géologiques et Minières (BRGM) (BRGM)-Institut de Recherche pour le Développement (IRD)-AgroParisTech-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), and Académie d'Agriculture de France
Subjects: Water quality, Subsurface drainage Waterlogged soil Modelling Boussinesq equation Peak flow Surface runoff Water quality, Peak flow, General Earth and Planetary Sciences, [SDU.STU.HY]Sciences of the Universe [physics]/Earth Sciences/Hydrology, Subsurface drainage, Surface runoff, Modelling, Waterlogged soil, Boussinesq equation, General Environmental Science
Abstract: International audience; The development of an integrated theory of subsurface drainage based on hydrology and hydrogeology concepts is presented. The historical context, the main hypothesis derived from the Boussinesq equation and the validation of the model predictions are discussed. Theoretical developments of this equation demonstrate that a single parameter (σ)-a combination of soil and drainage system properties-is sufficient for predicting the dynamics of subsurface drain flow rates. We also demonstrate that these drain flow rates are a function of the level of water replenishment in the system (classically the water table elevation), of the recharge intensity of the aquifer and of a buffer function related to the swelling or deflation of the water table shape during recharge events. For values of σ > 1, the buffer role of the water table is negligible. In that case approx. 13% of the water table recharge contributes to the flow rate, which is shown to explain the observed disconnection between water table elevations and peak flow rates at the outlet of classic agricultural drainage systems and to predict these peak flow rates accurately. A modelling approach based on this theory and validated experimentally (SIDRA model) allowed us to test the quality of the peak flow prediction. The SIDRA model also includes a surface runoff module and has been coupled to different modelling tools and used to analyse the impacts of subsurface drainage on water quality. The approach contributed towards the development of tools that helped to connect better the drainage systems to the hydrological functioning of watersheds.
Published: 2023

48. Fast and Bioorthogonal Release of Isocyanates in Living Cells from Iminosydnones and Cycloalkynes

Author: Maxime Ribéraud, Karine Porte, Arnaud Chevalier, Léa Madegard, Aurélie Rachet, Agnès Delaunay-Moisan, Florian Vinchon, Pierre Thuéry, Giovanni Chiappetta, Pier Alexandre Champagne, Grégory Pieters, Davide Audisio, Frédéric Taran, CEA- Saclay (CEA), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Service de Chimie Bio-Organique et de Marquage (SCBM), Médicaments et Technologies pour la Santé (MTS), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut de Chimie des Substances Naturelles (ICSN), Institut de Chimie du CNRS (INC)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Nanosciences et Innovation pour les Matériaux, la Biomédecine et l'Energie (ex SIS2M) (NIMBE UMR 3685), Institut Rayonnement Matière de Saclay (IRAMIS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL), New Jersey Institute of Technology [Newark] (NJIT), ANR-11-EQPX-0029,MORPHOSCOPE 2,Imagerie et reconstruction multiéchelles de la morphogenèse. (Plateforme d'innovation technologique et méthodologique pour l'imagerie in vivo et la reconstruction des dynamiques multiéchelles de la morphogenèse)(2011), ANR-10-INBS-0004,France-BioImaging,Développment d'une infrastructure française distribuée coordonnée(2010), ANR-11-IDEX-0003,IPS,Idex Paris-Saclay(2011), and ANR-19-CE06-0006,NanoClick,Micelles clivables par chimie bioorthogonale(2019)
Subjects: Colloid and Surface Chemistry, [SDV]Life Sciences [q-bio], General Chemistry, Biochemistry, Catalysis
Abstract: International audience; Bioorthogonal click and release reactions are powerful tools for chemical biology allowing, for example, the selective release of drugs in biological media, including inside animals. Here we developed two new families of iminosydnone mesoionic reactants that allow a bioorthogonal release of electrophilic species under physiological conditions. Their synthesis and reactivities as dipoles in cycloaddition reactions with strained alkynes have been studied in detail. Whereas the impact of the pH on the reaction kinetics was demonstrated experimentally, theoretical calculations suggest that the newly designed dipoles display reduced resonance stabilization energies compared to previously described iminosydnones explaining their higher reactivity. These mesoionic compounds react smoothly with cycloalkynes under physiological, copper-free reaction conditions to form a click pyrazole product together with a released alkyl-or aryl-isocyanate. With kinetic constants up to 1000 M-1 s-1 , this click and release reaction is among the fastest described to date, and represents the first bioorthogonal process allowing the release of isocyanate electrophiles inside living cells offering interesting perspectives in chemical biology.
Published: 2023

49. Modeled production, oxidation, and transport processes of wetland methane emissions in temperate, boreal, and Arctic regions

Author: Masahito Ueyama, Sara H. Knox, Kyle B. Delwiche, Sheel Bansal, William J. Riley, Dennis Baldocchi, Takashi Hirano, Gavin McNicol, Karina Schafer, Lisamarie Windham‐Myers, Benjamin Poulter, Robert B. Jackson, Kuang‐Yu Chang, Jiquen Chen, Housen Chu, Ankur R. Desai, Sébastien Gogo, Hiroki Iwata, Minseok Kang, Ivan Mammarella, Matthias Peichl, Oliver Sonnentag, Eeva‐Stiina Tuittila, Youngryel Ryu, Eugénie S. Euskirchen, Mathias Göckede, Adrien Jacotot, Mats B. Nilsson, Torsten Sachs, Osaka Metropolitan University, University of British Columbia [Vancouver], Lawrence Berkeley National Laboratory [Berkeley] (LBNL), Department of Environmental Science, Policy, and Management [Berkeley] (ESPM), University of California [Berkeley] (UC Berkeley), University of California (UC)-University of California (UC), US Geological Survey [Jamestown], United States Geological Survey [Reston] (USGS), Prairie and Northern Wildlife Research Centre, Environment and Climate Change Canada, Climate and Ecosystem Sciences Division, Research Faculty of Agriculture, Hokkaido University [Sapporo, Japan], University of Illinois [Chicago] (UIC), University of Illinois System, Department of Earth and Environmental Sciences [Chicago] (EAES), University of Illinois System-University of Illinois System, Rutgers University [Newark], Rutgers University System (Rutgers), Department of Earth and Environmental Science [Newark], Rutgers University System (Rutgers)-Rutgers University System (Rutgers), US Geological Survey [Menlo Park], NASA Goddard Space Flight Center (GSFC), Biospheric Sciences Laboratory, Department of Earth System Science [Stanford] (ESS), Stanford EARTH, Stanford University-Stanford University, Stanford University, Michigan State University System, University of Wisconsin-Madison, Department of Atmospheric and Oceanic Sciences [Madison], Université de Rennes (UR), Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), Shinshu University [Nagano], National Center for Agro-Meteorology, Helsingin yliopisto = Helsingfors universitet = University of Helsinki, Swedish University of Agricultural Sciences (SLU), Department of Forest Ecology and Management, Université de Montréal (UdeM), University of Eastern Finland, School of Forest Sciences, Seoul National University [Seoul] (SNU), Department of Landscape Architecture and Rural Systems Engineering, Institute of Arctic Biology, University of Alaska [Fairbanks] (UAF), Max Planck Institute for Biogeochemistry (MPI-BGC), Max-Planck-Gesellschaft, Institut des Sciences de la Terre d'Orléans - UMR7327 (ISTO), Bureau de Recherches Géologiques et Minières (BRGM) (BRGM)-Observatoire des Sciences de l'Univers en région Centre (OSUC), Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire de Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université d'Orléans (UO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire de Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université d'Orléans (UO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université d'Orléans (UO)-Centre National de la Recherche Scientifique (CNRS), Sol Agro et hydrosystème Spatialisation (SAS), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Rennes Angers, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), and German Research Centre for Geosciences - Helmholtz-Centre Potsdam (GFZ)
Subjects: multi-site synthesis, data-model fusion, Global and Planetary Change, Ecology, methane emissions, methane model, [SDE]Environmental Sciences, Environmental Chemistry, Eddy covariance, [SDU.ENVI]Sciences of the Universe [physics]/Continental interfaces, environment, Bayesian optimization, General Environmental Science
Abstract: International audience; Wetlands are the largest natural source of methane (CH4) to the atmosphere. The eddy covariance method provides robust measurements of net ecosystem exchange of CH4, but interpreting its spatiotemporal variations is challenging due to the co-occurrence of CH4 production, oxidation, and transport dynamics. Here, we estimate these three processes using a data-model fusion approach across 25 wetlands in temperate, boreal, and Arctic regions. Our data-constrained model—iPEACE—reasonably reproduced CH4 emissions at 19 of the 25 sites with normalized root mean square error of 0.59, correlation coefficient of 0.82, and normalized standard deviation of 0.87. Among the three processes, CH4 production appeared to be the most important process, followed by oxidation in explaining inter-site variations in CH4 emissions. Based on a sensitivity analysis, CH4 emissions were generally more sensitive to decreased water table than to increased gross primary productivity or soil temperature. For periods with leaf area index (LAI) of ≥20% of its annual peak, plant-mediated transport appeared to be the major pathway for CH4 transport. Contributions from ebullition and diffusion were relatively high during low LAI (
Published: 2023

50. Scaling of fractured rock flow. Proposition of indicators for selection of DFN based flow models

Author: Davy, Philippe, Le Goc, Romain, Darcel, Caroline, Selroos, Jan-Olof, Géosciences Rennes (GR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), Itasca Consultants, Swedish Nuclear Fuel and Waste Management Company, and Royal Institute of Technology [Stockholm] (KTH )
Subjects: Indicator, Percolation, General Earth and Planetary Sciences, [PHYS.MECA.MEFL]Physics [physics]/Mechanics [physics]/Fluid mechanics [physics.class-ph], Fracture network, [SDU.STU.HY]Sciences of the Universe [physics]/Earth Sciences/Hydrology, Crystalline rocks, Permeability, Scaling, General Environmental Science
Abstract: International audience; The objective of the paper is to better understand and quantify the flow structure in fractured rocks from flow logs, and to propose relevant indicators for validating, calibrating or even rejecting hydrogeological models. We first studied what the inflow distribution tells us about the permeability structure from a series of analyses: distribution of transmissivities as a function of depth, proportion of flowing sections as a function of section scale, and scaling of the arithmetically-averaged and geometrically-averaged permeability. We then define three indicators that describe few fundamental characteristics of the flow/permeability, whatever the scale: a percolation scale , the way permeability increases with scale above , and the variability of permeability. A 4th indicator on the representative elemental volume could in principle be defined but the data show that this volume/scale is beyond the 300 m investigated. We tested a series of numerical models built in three steps: the geo-DFN based on the observed fracture network, the open-DFN which is the part of the geo-DFN where fractures are open, and a transmissivity model applying on each fracture of the open-DFN (Discrete Fracture Network). The analysis of the models showed that the percolation scale is controlled by the open-DFN structure and that the percolation scale can be predicted from a scale analysis of the percolation parameter (basically, the third moment of the fracture size distribution that provides a measure of the network connectivity). The way permeability increases with scale above the percolation threshold is controlled by the transmissivity model and in particular by the dependence of the fracture transmissivity on either the orientation of the fractures via a stress-controlled transmissivity or their size or both. The comparison with data on the first two indicators shows that a model that matches the characteristics of the geo-DFN with an open fraction of 15% as measured adequately fits the data provided that the large fractures remain open and that the fracture transmissivity model is well selected. Most of the other models show unacceptable differences with data but other models or model combinations has still to be explored before rejecting them. The third indicator on model variability is still problematic since the natural data show a higher variability than the models but the open fraction is also much more variable in the data than in the models.
Published: 2023

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