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1. Short- and Long-term Responses of Nematode Communities to Predicted Rainfall Reduction in Mediterranean Forests

Author

Pablo Homet, Jean-Marc Ourcival, Eduardo Gutiérrez, Jara Domínguez-Begines, Luis Matías, Oscar Godoy, Lorena Gómez-Aparicio, Universidad de Sevilla. Departamento de Biología Vegetal y Ecología, Ministerio de Ciencia, Innovación y Universidades (MICINN). España, European Commission. Fondo Social Europeo (FSO), Analyses et Expérimentations pour les Ecosystèmes (AnaEE), Ministerio de Economía y Competitividad (MINECO). España, Observatoire de REcherche Montpelliérain de l’Environnement (OSU OREME), Ministerio de Ciencia, Innovación (España), European Commission, Agencia Estatal de Investigación (España), Universidad de Sevilla, Ministerio de Economía y Competitividad (España), French national research infrastructure, Homet, Pablo, Ourcival, J. M., Domínguez Begines, J., Matías Resina, Luis, Godoy, Óscar, and Gómez Aparicio, Lorena

Subjects
Protect, restore and promote sustainable use of terrestrial ecosystems, sustainably manage forests, combat desertification, and halt and reverse land degradation and halt biodiversity loss, Rainfall exclusion, Soil food web, Resistance, Soil Science, Climate change, Precipitation, Experimental drought, Microbiology, Soil fauna
Abstract

5 figuras.- 1 tabla.- This article is in Press, Journal Pre-proof, Climate change is a fundamental process affecting terrestrial ecosystems. However, there is relatively little knowledge about its impacts on soil communities, with a large degree of uncertainty regarding their resistance to predicted alterations in temperature and, particularly, precipitation. Moreover, most studies exploring the response of soil biota to predicted rainfall reduction have focused on mesic environments and soil microbes, which limit our ability to find general patterns across ecosystems and soil organisms. In this study, we analysed the impact of predicted climate change scenarios of rainfall reduction on soil food webs of Mediterranean water-limited forests using nematodes as bioindicators. We took advantage of replicated rainfall exclusion infrastructures (30% exclusion) established in Quercus forests of southern Spain in 2016 (2-year exclusion) and of southern France in 2003 (15-year exclusion) to explore the sensitivity of the soil food web to predicted reductions at short- and long-term scales. Rainfall reduction had large negative short-term effects on nematode abundance, particularly of lower trophic groups (bacterivores and fungivores). Rainfall reduction had also consistent short- and long-term impacts on community composition (decrease of fungivores, marginal increase of omnivores) and nematode-based indicators of soil food web structure (higher maturity and structure index, lower prey:predator ratio). These results can be considered indicative of a low resistance of the soil food web to rainfall reductions predicted by climate change. Overall, our findings demonstrate the sensitivity of water-limited forests to further reductions in soil water availability, which might substantially alter their soil communities and likely affect the many ecosystem processes that they control., This study was funded by the MICINN projects INTERCAPA (CGL2014-56739-R) and MICROFUN (RTI2018-094394-B-I00). P.H. was supported by a FPI-MICINN grant. L.M. was supported by the fellowship IV2 from VI-PPIT (Univ. Sevilla) and the project PID2019-108288RA-I00 (MINECO). OG acknowledges financial support provided by the Spanish Ministry of Economy and Competitiveness (MINECO) and by the European Social Fund through the Ramón y Cajal Program (RYC-2017-23666). Puéchabon is supported by the OSU OREME (UMS 3282) and the French national research infrastructure ANAEE-France (ANR-11-INBS-0001).

Published
2023

2. Meteorological and climatic variables predict the phenology of Ixodes ricinus nymph activity in France, accounting for habitat heterogeneity

Author

Phrutsamon Wongnak, Séverine Bord, Maude Jacquot, Albert Agoulon, Frédéric Beugnet, Laure Bournez, Nicolas Cèbe, Adélie Chevalier, Jean-François Cosson, Naïma Dambrine, Thierry Hoch, Frédéric Huard, Nathalie Korboulewsky, Isabelle Lebert, Aurélien Madouasse, Anders Mårell, Sara Moutailler, Olivier Plantard, Thomas Pollet, Valérie Poux, Magalie René-Martellet, Muriel Vayssier-Taussat, Hélène Verheyden, Gwenaël Vourc’h, Karine Chalvet-Monfray, Unité Mixte de Recherche d'Épidémiologie des maladies Animales et zoonotiques (UMR EPIA), 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), Mathématiques et Informatique Appliquées (MIA-Paris), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Biologie, Epidémiologie et analyse de risque en Santé Animale (BIOEPAR), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Boehringer Ingelheim Animal Health, Partenaires INRAE, Laboratoire de la rage et de la faune sauvage de Nancy (LRFSN), Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Unité de recherche Comportement et Ecologie de la Faune Sauvage (CEFS), Ecosystèmes forestiers (UR EFNO), Biologie moléculaire et immunologie parasitaires et fongiques (BIPAR), École nationale vétérinaire d'Alfort (ENVA)-Laboratoire de santé animale, sites de Maisons-Alfort et de Dozulé, 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)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Agroclim (AGROCLIM), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Mathématiques et Informatique Appliquées (MIA Paris-Saclay), École nationale vétérinaire, agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), 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), Animal, Santé, Territoires, Risques et Ecosystèmes (UMR ASTRE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Most tick observatories were supported by the CC-EID and Climatick projects: 'Adaptation of Agriculture and Forests to Climate Change' metaprogramme of the French National Research Institute for Agriculture, Food and Environment (INRAE). The observatory of Les Bordes was installed and equipped by the Centre Val-de-Loire region, the Loiret and the French National Forest Office. We also would like to thank the TEMPO French Network (https://tempo.pheno.fr/) for providing resources to support this study. The Les Bordes site belongs to the French national research infrastructure, ANAEE-F (http://www.anaee-france.fr/fr/), and is also included in the SOERE TEMPO (https://tempo.pheno.fr/).The Les Bordes site is also part of the framework of the ZAL (LTSER Zone Atelier Loire) and the GIS Coop network (https://www6.inra.fr/giscoop/), which is supported by the French Ministry for Agriculture and Food. This study was partially funded by EU grant 874850 MOOD and is catalogued as MOOD 040. The contents of this publication are the sole responsibility of the authors and do not necessarily reflect the views of the European Commission. Finally, PW is grateful for a grant from the Association Nationale de la Recherche et de la Technologie, bourse CIFRE (no 2019/0393)., European Project: 874850,H2020-SC1-2019-Single-Stage-RTD,MOOD(2020), and École nationale vétérinaire - Alfort (ENVA)-Laboratoire de santé animale, sites de Maisons-Alfort et de Dozulé

Subjects
Ecological epidemiology, Nymph, 2. Zero hunger, Lyme Disease, Multidisciplinary, Ixodes, Ixodes ricinus ticks, [SDV]Life Sciences [q-bio], Forests, 15. Life on land, Habitat characteristics, Phenological patterns, 13. Climate action, Questing activity, Meteorological conditions, Animals, Humans, Seasons, Entomology, Ecosystem, Ecological modelling
Abstract

Ixodes ricinus ticks (Acari: Ixodidae) are the most important vector for Lyme borreliosis in Europe. As climate change might affect their distributions and activities, this study aimed to determine the effects of environmental factors, i.e., meteorological, bioclimatic, and habitat characteristics on host-seeking (questing) activity of I. ricinus nymphs, an important stage in disease transmissions, across diverse climatic types in France over 8 years. Questing activity was observed using a repeated removal sampling with a cloth-dragging technique in 11 sampling sites from 7 tick observatories from 2014 to 2021 at approximately 1-month intervals, involving 631 sampling campaigns. Three phenological patterns were observed, potentially following a climatic gradient. The mixed-effects negative binomial regression revealed that observed nymph counts were driven by different interval-average meteorological variables, including 1-month moving average temperature, previous 3-to-6-month moving average temperature, and 6-month moving average minimum relative humidity. The interaction effects indicated that the phenology in colder climates peaked differently from that of warmer climates. Also, land cover characteristics that support the highest baseline abundance were moderate forest fragmentation with transition borders with agricultural areas. Finally, our model could potentially be used to predict seasonal human-tick exposure risks in France that could contribute to mitigating Lyme borreliosis risk.

Published
2022
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3. Assessing the accuracy and robustness of a process-based model for coffee agroforestry systems in Central America

Author

Elias de Melo Virginio Filho, Olivier Roupsard, Peter Läderach, Mirna Barrios, Oriana Ovalle-Rivera, Bruno Rapidel, Marcel van Oijen, Centro Agronómico Tropical de Investigación y Enseñanza - Tropical Agricultural Research and Higher Education Center (CATIE), International Center for Tropical Agriculture [Colombie] (CIAT), Consultative Group on International Agricultural Research [CGIAR] (CGIAR), Centre for Ecology and Hydrology [Edinburgh] (CEH), Natural Environment Research Council (NERC), LMI IESOL Intensification Ecologique des Sols Cultivés en Afrique de l’Ouest [Dakar] (IESOL), Institut de recherche pour le développement (IRD [Sénégal]), 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 SupAgro, 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), Centro Agronómico Tropical de Investigación y Enseñanza [Nicaragua] (CATIE), Performance des systèmes de culture des plantes pérennes (UPR Système de pérennes), Caf'Adapt project, Fontagro/RF-1027, CGIAR Research Program on Climate Change, Agriculture and Food Security (CCAFS) with the support from CGIAR Fund Donors and through bilateral funding agreements, French national research infrastructure ANAEE-F (http://www.anaeefrance.fr/fr/), European project CAFNET (EuropAid/121998/C/G), CATIE-PROCAGICA-IICA-UE project, BBSRC through GCRF project SEACAF (BB/S01490X/1)., ANR-10-STRA-0003,ECOSFIX,Services écosystémiques des racines – redistribution hydrique, séquestration du carbone et fixation du sol(2010), ANR-13-AGRO-0005,MACACC,Modélisation pour l'accompagnement des ACteurs, vers l'Adaptation des Couverts pérennes ou agroforestiers aux Changements globaux(2013), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and 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)

Subjects
0106 biological sciences, Yield, Mean squared error, F08 - Systèmes et modes de culture, Agroforesterie, 01 natural sciences, Modelling, symbols.namesake, [SDV.SA.SF]Life Sciences [q-bio]/Agricultural sciences/Silviculture, forestry, Robustness (computer science), Calibration, Production (economics), Agroforestry systems, 2. Zero hunger, Méthode statistique, Agroforestry, U10 - Informatique, mathématiques et statistiques, Modélisation des cultures, Bayesian calibration, Forestry, Markov chain Monte Carlo, 04 agricultural and veterinary sciences, Coffea arabica, 15. Life on land, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, Bayesian statistics, Variable (computer science), Rendement des cultures, Théorie bayésienne, Agriculture and Soil Science, 040103 agronomy & agriculture, symbols, 0401 agriculture, forestry, and fisheries, Environmental science, Scale (map), Agronomy and Crop Science, 010606 plant biology & botany
Abstract

International audience; Coffee is often grown in production systems associated with shade trees that provide different ecosystem services. Management, weather and soil conditions are spatially variable production factors. CAF2007 is a dynamic model for coffee agroforestry systems that takes these factors as inputs and simulates the processes underlying berry production at the field scale. There remain, however, uncertainties about process rates that need to be reduced through calibration. Bayesian statistics using Markov chain Monte Carlo algorithms is increasingly used for calibration of parameter-rich models. However, very few studies have employed multi-site calibration, which aims to reduce parameter uncertainties using data from multiple sites simultaneously. The main objectives of this study were to calibrate the coffee agroforestry model using data gathered in long-term experiments in Costa Rica and Nicaragua, and to test the calibrated model against independent data from commercial coffee-growing farms. Two sub-models were improved: calculation of flowering date and the modelling of biennial production patterns. The modified model, referred to as CAF2014, can be downloaded at 10.5281/zenodo.3608877. Calibration improved model performance (higher R-2, lower RMSE) for Turrialba (Costa Rica) and Masatepe (Nicaragua), including when all experiments were pooled together. Multi-site and single-site Bayesian calibration led to similar RMSE. Validation on new data from coffee-growing farms revealed that both calibration methods improved simulation of yield and its bienniality. The thus improved model was used to test the effect of N fertilizer and shade in different locations on coffee yield.

Published
2020
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4. Le mélange des espèces réduit la sensibilité à la sécheresse du pin sylvestre (Pinus sylvestris L.) et du chêne (Quercus robur L., Quercus petraea (Matt.) Liebl.) - L'approvisionnement en eau et la fertilité du site modifient l'effet de mélange

Author

Steckel, M., del Río, Macarena, Heym, M., Aldea, J., Bielak, K., Brazaitis, G., Cerny, J., Coll, L., Collet, Catherine, Ehbrecht, M., Jansons, A., Nothdurft, A., Pach, M., Pardos, M., Ponette, Quentin, Reventlow, D.O.J., Sitko, R., Svoboda, M., Vallet, Patrick, Wolff, B., Pretzsch, Hans, TECHNICAL UNIVERSITY OF MUNICH DEU, Partenaires IRSTEA, Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA), UNIVERSITY OF VALLADOLID AND INIA MADRID ESP, Swedish University of Agricultural Sciences (SLU), SGGW WARSAW UNIVERSITY OF LIFE SCIENCES POL, Vytautas Magnus University - Vytauto Didziojo Universitetas (VDU), FORESTRY AND GAME MANAGEMENT RESEARCH INSTITUTE JILOVISTE CZE, UNIVERSITY OF LLEIDA ESP, SILVA (SILVA), AgroParisTech-Université de Lorraine (UL)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), GEORG AUGUST UNIVERSITAT GOTTINGEN DEU, LATVIAN STATE FOREST RESARCH INSTITUTE SILAVA SALASPILS LVA, University of Natural Resources and Life Sciences (BOKU), UNIVERSITY OF AGRICULTURE KRAKOW POL, Centro de Investigacion Forestal (INIA-CIFOR), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria = National Institute for Agricultural and Food Research and Technology (INIA), Université Catholique de Louvain = Catholic University of Louvain (UCL), UNIVERSITY OF COPENHAGEN DNK, Technical University in Zvolen (TUZVO), CZECH UNIVERSITY OF LIFE SCIENCES SUCHDOL CZE, Laboratoire des EcoSystèmes et des Sociétés en Montagne (UR LESSEM), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université Grenoble Alpes (UGA), Ecosystèmes forestiers (UR EFNO), European Union as part of the ERA-Net SUMFOREST project REFORM -Mixed species forest management, German Federal Ministry of Food and Agriculture (BMEL) through the Federal Office for Agriculture and Food (BLE) : 2816ERA02S, Research Council of Lithuania (LMTLT): S-SUMFOREST-17-1, Ecofor, Allenvi, French national research infrastructure ANAEE-F, European Project: 778322,H2020-EU.1.3.3.,CARE4C (2018), Universität für Bodenkultur Wien = University of Natural Resources and Life [Vienne, Autriche] (BOKU), and Eberswalde University for Sustainable Development (HNE)

Subjects
Drought stress, SPEI, Resilience, Recovery, education, fungi, Resistance, [SDE]Environmental Sciences, food and beverages, Complementarity, Facilitation, Ecological gradient
Abstract

[Departement_IRSTEA]Territoires [TR1_IRSTEA]SEDYVIN; International audience; Tree species mixing has been widely promoted as a promising silvicultural tool for reducing drought stress. However, so far only a limited number of species combinations have been studied in detail, revealing inconsistent results. In this study, we analysed the effect of mixing Scots pine and oak (pedunculate oak and sessile oak) trees on their drought response along a comprehensive ecological gradient across Europe. The objective was to improve our knowledge of general drought response patterns of two fundamental European tree species in mixed versus monospecific stands. We focused on three null hypotheses: (HI) tree drought response does not differ between Scots pine and oak, (HII) tree drought response of Scots pine and oak is not affected by stand composition (mixture versus monoculture) and (HIII) tree drought response of Scots pine and oak in mixtures and monocultures is not modified by tree size or site conditions. To test the hypotheses, we analysed increment cores of Scots pine and oak, sampled in mixed and monospecific stands, covering a wide range of site conditions. We investigated resistance (the ability to maintain growth levels during drought), recovery (the ability to restore a level of growth after drought) and resilience (the capacity to recover to pre-drought growth levels), involving sitespecific drought events that occurred between 1976 and 2015. In monocultures, oak showed a higher resistance and resilience than Scots pine, while recovery was lower. Scots pine in mixed stands exhibited a higher resistance, but also a lower recovery compared with Scots pine in monocultures. Mixing increased the resistance and resilience of oak. Ecological factors such as tree size, site water supply and site fertility were found to have significant effects on the drought response. In the case of Scots pine, resistance was increased by tree size, while recovery was lowered. Resistance of oak increased with site water supply. The observed mixing effect on the tree drought response of Scots pine and oak was in some cases modified by the site conditions studied. Positive mixing effects in terms of resistance and resilience of oak increased with site water supply, while the opposite was found regarding recovery. In contrast, site fertility lessened the positive mixing effect on the resistance of Scots pine. We hypothesise that the observed positive mixing effects under drought mainly result from waterand/or light-related species interactions that improve resource availability and uptake according to temporal and spatial variations in environmental conditions.

Published
2020
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5. A systems biology view of wood formation in Eucalyptus grandis trees submitted to different potassium and water regimes

Author

Mônica T. Veneziano Labate, Fabien Mounet, Marie Morel, Jacqueline Grima-Pettenati, Marie Denis, Raphael Ployet, Mathias Christina, Jean-Paul Laclau, Gilles Chaix, Thais Regiani Cataldi, Carlos Alberto Labate, Mario Tomazello Filho, Bénédicte Favreau, Hélène San Clemente, Laboratoire de Recherche en Sciences Végétales (LRSV), Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Interactions Sol Plante Atmosphère (ISPA), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Supérieure des Sciences Agronomiques de Bordeaux-Aquitaine (Bordeaux Sciences Agro), Auteur indépendant, Aide à la Décision pour une Médecine Personnalisé - Laboratoire de Biostatistique, Epidémiologie et Recherche Clinique - EA 2415 (AIDMP), Université de Montpellier (UM)-Université Montpellier 1 (UM1), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), University of São Paulo, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Interactions Sol Plante Atmosphère (UMR ISPA), Université Montpellier 1 (UM1)-Université de Montpellier (UM), Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Régulation et Dynamique de la Formation du Bois, Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Ecofor, Allenvi, French National Research Infrastructure ANAEE-F, Centre National pour la Recherche Scientifique (CNRS), French Laboratory of Excellence project 'TULIP' : ANR-10-LABX-41, ANR-11-IDEX-0002-02, Agropolis Fondation : 1203-003, ANR-10-LABX-372 0001-01, CAPES : 017/13, CNPq : 444793/2014-3, 014/2012, FAPESP : 2013/25642-5, Ministere de l'Education Nationale, de l'Enseignement Superieur et de la Recherche, ANR-11-IDEX-0002,UNITI,Université Fédérale de Toulouse(2011), and ANR-10-LABX-0001,AGRO,Agricultural Sciences for sustainable Development(2010)

Subjects
0106 biological sciences, 0301 basic medicine, K50 - Technologie des produits forestiers, SECA, Physiology, tree physiology, Gene regulatory network, Biomass, Plant Science, drought, 01 natural sciences, Trees, transcriptomics, [SDV.SA.SF]Life Sciences [q-bio]/Agricultural sciences/Silviculture, forestry, Cell Wall, Gene Regulatory Networks, Plant Proteins, Eucalyptus, Wood production, wood traits, Systems Biology, system biology, potassium, metabolomics, Phenotype, Propriété technologique, Metabolome, Besoin en eau, gene network, Secondary cell wall, secondary cell wall, wood, Eucalyptus grandis, abiotic stress, F60 - Physiologie et biochimie végétale, Biology, 03 medical and health sciences, Bois, Metabolomics, Xylem, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Botany, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Abiotic stress, Water, 15. Life on land, saccharification, 030104 developmental biology, Transcriptome, Transcription Factors, 010606 plant biology & botany, F04 - Fertilisation
Abstract

International audience; Wood production in fast-growing Eucalyptus grandis trees is highly dependent on both potassium (K) fertilization and water availability but the molecular processes underlying wood formation in response to the combined effects of these two limiting factors remain unknown. E. grandis trees were submitted to four combinations of K-fertilization and water supply. Weighted gene co-expression network analysis and MixOmics-based co-regulation networks were used to integrate xylem transcriptome, metabolome and complex wood traits. Func- tional characterization of a candidate gene was performed in transgenic E. grandis hairy roots. This integrated network-based approach enabled us to identify meaningful biological pro- cesses and regulators impacted by K-fertilization and/or water limitation. It revealed that modules of co-regulated genes and metabolites strongly correlated to wood complex traits are in the heart of a complex trade-off between biomass production and stress responses. Nested in these modules, potential new cell-wall regulators were identified, as further con- firmed by the functional characterization of EgMYB137. These findings provide new insights into the regulatory mechanisms of wood formation under stressful conditions, pointing out both known and new regulators co-opted by K-fertilization and/or water limitation that may potentially promote adaptive wood traits.

Published
2019
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6. MYO1C stabilizes actin and facilitates the arrival of transport carriers at the Golgi complex

Author

Capmany, Anahi, Yoshimura, Azumi, Kerdous, Rachid, Caorsi, Valentina, Lescure, Aurianne, Del Nery, Elaine, Coudrier, Evelyne, Goud, Bruno, Schauer, Kristine, Compartimentation et dynamique cellulaires (CDC), Institut Curie [Paris]-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Université Paris sciences et lettres (PSL), BioImaging Cell and Tissue Core Facility (PICT-IBiSA), Institut Curie [Paris], Centre National de la Recherche Scientifique (CNRS)-Institut Curie [Paris]-Université Pierre et Marie Curie - Paris 6 (UPMC), This work was supported by Labex CelTisPhyBio [ANR-10-LBX-0038] and Université de Recherche Paris Sciences et Lettres [ANR-10-IDEX-0001-02 PSL], as well as grants from Agence Nationale de la Recherche [#2010 BLAN 122902], the European Research Council [project 339847 ‘MYODYN’], Centre National de la Recherche Scientifique and Institut Curie., We acknowledge the following people for providing materials: Franck Perez, Ana-Maria Lennon-Duménil, Eija Jokitalo, Michael Schell and Woo Keun Song for plasmids, and Buzz Baum for the myosin library. We thank Tarn Duong for advice on statistical analysis and kernel density estimation, Sarah Tessier for the siRNA screening technical assistance, and and Patricia Davidson for critical reading of the manuscript. We greatly acknowledge the Cell and Tissue Imaging Facility (PICT-IBiSA, PICT-EM and PICT-IBiSA) and Nikon Imaging Center, Institut Curie (Paris), member of the French National Research Infrastructure France-BioImaging (ANR10-INBS-04).

Subjects
MYOSIN1, Otras Ciencias Biológicas, [SDV]Life Sciences [q-bio], MYO18A, GOLGI APPARATUS, macromolecular substances, MYO6, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Myosin1, Cell Line, purl.org/becyt/ford/1 [https], Ciencias Biológicas, MYH9, Myosin Type I, MYOSIN IIA, RAB6, Cell Movement, Rab6, Humans, Myosin IIA, purl.org/becyt/ford/1.6 [https], PLECKSTRIN HOLOLOGY DOMAIN, ARP2/3, Pleckstrin holology domain, Actins, Actin Cytoskeleton, Protein Transport, Rab11, Golgi apparatus, RAB11, Arp2/3, CIENCIAS NATURALES Y EXACTAS
Abstract

In this study, we aimed to identify the myosin motor proteins that control trafficking at the Golgi complex. In addition to the known Golgi-associated myosins MYO6, MYO18A and MYH9 (myosin IIA), we identified MYO1C as a novel player at the Golgi in a human cell line. We demonstrate that depletion of MYO1C induces Golgi complex fragmentation and decompaction. MYO1C accumulates at dynamic structures around the Golgi complex that colocalize with Golgi-associated actin dots. MYO1C depletion leads to loss of cellular F-actin, and Golgi complex decompaction is also observed after inhibition or loss of the actin-related protein 2/3 complex, Arp2/3 (also known as ARPC). We show that the functional consequence of MYO1C depletion is a delay in the arrival of incoming transport carriers, both from the anterograde and retrograde routes. We propose that MYO1C stabilizes actin at the Golgi complex, facilitating the arrival of incoming transport carriers at the Golgi.This article has an associated First Person interview with the first author of the paper. Fil: Capmany, Anahi. Institute Curie; Francia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza; Argentina. Universidad Nacional de Cuyo. Facultad de Ciencias Medicas. Instituto de Inmunologia; Argentina Fil: Yoshimura, Azumi. Institute Curie; Francia Fil: Kerdous, Rachid. Institute Curie; Francia Fil: Caorsi, Valentina. Abbelight; Francia Fil: Lescure, Aurianne. Institute Curie; Francia Fil: Nery, Elaine Del. Institute Curie; Francia Fil: Coudrier, Evelyne. Institute Curie; Francia Fil: Goud, Bruno. Institute Curie; Francia Fil: Schauer, Kristine. Institute Curie; Francia

Published
2019
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7. Automatic high-frequency measurements of full soil greenhouse gas fluxes in a tropical forest

Author

E. A. Courtois, C. Stahl, B. Burban, J. Van den Berge, D. Berveiller, L. Bréchet, J. L. Soong, N. Arriga, J. Peñuelas, I. A. Janssens, Department of Biology, University of Antwerp (UA), Laboratoire Ecologie, Evolution, Interactions des Systèmes amazoniens (LEEISA), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Guyane (UG)-Centre National de la Recherche Scientifique (CNRS), Ecologie des forêts de Guyane (UMR ECOFOG), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-AgroParisTech-Université de Guyane (UG)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Ecologie Systématique et Evolution (ESE), Université Paris-Sud - Paris 11 (UP11)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS), Lawrence Berkeley National Laboratory [Berkeley] (LBNL), Universitat Autònoma de Barcelona (UAB), Investissement d'Avenir' [ANR-10-LABX-25-01, ANR-11-INBS-0001], Ecofor, French national research infrastructure, ANAEE-F, 'investissement d'avenir' grant from the Agence Nationale de la Recherche (CEBA) [ANR-10-LABX-25-01], Antwerp University (Methusalem funding), ICOS-Belgium, Fonds Wetenschappelijk Onderzoek (FWO), U.S. Department of Energy [DE-AC02-05CH11231], Allenvi, European Project: 610028,EC:FP7:ERC,ERC-2013-SyG,IMBALANCE-P(2014), and Courtois, Elodie Alice

Subjects
Spectrum analyzer, rain-forest, nitrous-oxide, 010504 meteorology & atmospheric sciences, [SDV]Life Sciences [q-bio], lcsh:Life, spatial variation, Atmospheric sciences, 01 natural sciences, Methane, land-use change, chemistry.chemical_compound, Flux (metallurgy), lcsh:QH540-549.5, Meteorology & Atmospheric Sciences, Ecosystem, biogeochemical controls, Biology, Ecology, Evolution, Behavior and Systematics, 0105 earth and related environmental sciences, Earth-Surface Processes, Physics, lcsh:QE1-996.5, n2o, emissions, chamber measurements, co2, respiration, 04 agricultural and veterinary sciences, Nitrous oxide, Biological Sciences, 15. Life on land, lcsh:Geology, Climate Action, Chemistry, lcsh:QH501-531, TheoryofComputation_MATHEMATICALLOGICANDFORMALLANGUAGES, chemistry, Closure (computer programming), 13. Climate action, Greenhouse gas, Carbon dioxide, Earth Sciences, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, Environmental science, lcsh:Ecology, Environmental Sciences
Abstract

Measuring in situ soil fluxes of carbon dioxide (CO2), methane (CH4), and nitrous oxide (N2O) continuously at high frequency requires appropriate technology. We tested the combination of a commercial automated soil CO2 flux chamber system (LI-8100A) with a CH4 and N2O analyzer (Picarro G2308) in a tropical rainforest for 4 months. A chamber closure time of 2 min was sufficient for a reliable estimation of CO2 and CH4 fluxes (100 % and 98.5 % of fluxes were above minimum detectable flux – MDF, respectively). This closure time was generally not suitable for a reliable estimation of the low N2O fluxes in this ecosystem but was sufficient for detecting rare major peak events. A closure time of 25 min was more appropriate for reliable estimation of most N2O fluxes (85.6 % of measured fluxes are above MDF ± 0.002 nmol m−2 s−1). Our study highlights the importance of adjusted closure time for each gas.

Published
2019
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8. Fertilization increases the functional specialization of fine roots in deep soil layers for young Eucalyptu s grandis trees

Author

Ivanka Rosada De Oliveira, Yann Nouvellon, Jean-Paul Laclau, Joannès Guillemot, Jean-Pierre Bouillet, Christophe Jourdan, Claude Plassard, Paulo Cesar Ocheuze Trivelin, José Leonardo de Moraes Gonçalves, Bruno Bordron, Cassio Hamilton Abreu-Junior, Agnès Robin, Universidade de São Paulo (USP), Ecologie fonctionnelle et biogéochimie des sols et des agro-écosystèmes (UMR Eco&Sols), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA), Universidade Estadual Paulista Júlio de Mesquita Filho = São Paulo State University (UNESP), Centro de Energia Nuclear na Agricultura (CENA ), University of São Paulo (USP), SOERE F-ORE-T (granted by Ecofor, Allenvi and the French National Research Infrastructure ANAEEF (http://www.anaee-france.fr/fr/), FAPESP Thematic Project (2010/16623-9), Intens&fix Project (ANR-2010-STRA-004-03), ANR-11-INBS-0001,ANAEE-FR,ANAEE-Services(2011), ANR-10-STRA-0004,Intens&Fix,Intensification écologique des écosystèmes de plantations forestières. Modélisation biophysique et évaluation socio-économique de l'association d'espèces fixatrices d'azote(2010), UMR Eco&Sols, IRD, and Universidade Estadual Paulista (Unesp)

Subjects
0106 biological sciences, 01 natural sciences, RAIZ, Human fertilization, Nutrient, Profondeur, Sol sableux, Transport des substances nutritives, Leaching (agriculture), Nutrient uptake potential, Chemistry, Engrais phosphaté, 15N, Forestry, Enracinement, Analyse de tissu foliaire, Eucalyptus, Plantation forestière, Sandy tropical soil, Soil horizon, Eucalyptus grandis, Engrais potassique, Randomized block design, chemistry.chemical_element, Management, Monitoring, Policy and Law, 010603 evolutionary biology, Fertilisation, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Nature and Landscape Conservation, Topsoil, Engrais azoté, Phosphorus, 15. Life on land, Deep fine roots, Rubidium, K10 - Production forestière, F61 - Physiologie végétale - Nutrition, Agronomy, Strontium, 010606 plant biology & botany, F04 - Fertilisation, Racine
Abstract

Made available in DSpace on 2018-12-11T16:52:33Z (GMT). No. of bitstreams: 0 Previous issue date: 2018-01-01 Functional specialization of fine roots was found for Eucalyptus grandis trees at harvesting age (6 years) on tropical soils. Aiming to elucidate whether functional specialization is a ubiquitous feature of eucalypts, we focused on its changes with ontogeny, tree nutrient status and soil depth. We studied the potential uptake of N, K and Ca by 2-year-old E. grandis trees, as a function of soil depth and NPK fertilization. We injected NO−3-15N, Rb+ (K+ analogue) and Sr2+ (Ca2+ analogue) tracers simultaneously in a solution at depths of 10, 50, 150 and 300 cm in a sandy Ferralsol soil. A complete randomized block design was set up with three replicates of paired trees per injection depth, in fertilized and non-fertilized plots. Recently expanded leaves were sampled at 70 days after tracer injection. Determination of foliar Rb, Sr concentrations and x(15N) allowed estimating the relative uptake potential (RUP) and the specific RUP (SRUP), defined as the ratio between RUP and fine root length density (RLD) in the corresponding soil layer. Various root traits were measured at each depth. Foliar N and K concentrations were higher in fertilized than in non-fertilized trees. The RUP of NO3 –-15N decreased sharply with soil depth and the highest values of the SRUP of NO3 –-15N were found at a depth of 50 cm. The RUP of Rb+ and Sr2+ did not change with soil depth, whilst the SRUP of Rb+ and Sr2+ were higher at the depth of 300 cm than in the topsoil, concomitant with an increase in root diameter and a decrease in root tissue density with depth. The SRUP of Rb+ and Sr2+ at a depth of 300 cm were on average 136 and 61% higher for fertilized trees than for non-fertilized trees, respectively. Fine roots of young E. grandis trees showed contrasting potential uptake rates with soil depth depending on the nutrient. Fertilization increased the uptake rate of Rb+ and Sr2+ by unit of root length in deep soil layers. Functional specialization of fine roots for cations of low mobility depending on depth previously shown at harvesting age also occurs in young E. grandis plantations and increases with fertilization application. This mechanism helps explaining very low amounts of cations lost by leaching in Eucalyptus plantations established in deep tropical soils, even in highly fertilized stands. USP-ESALQ CIRAD UMR Eco&Sols Eco&Sols Univ Montpellier CIRAD INRA IRD, Montpellier SupAgro UNESP Departamento de Solos e Recursos Ambientais Universidade Estadual Paulista ‘Júlio de Mesquita Filho’ USP-CENA INRA CIRAD IRD Montpellier SupAgro University of Montpellier UMR Eco&Sols UNESP Departamento de Solos e Recursos Ambientais Universidade Estadual Paulista ‘Júlio de Mesquita Filho’

Published
2019
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9. Interannual and seasonal variations in ecosystem transpiration and water use efficiency in a tropical rainforest

Author

Fabien Wagner, Clément Stahl, Maricar Aguilos, Benoit Burban, Bruno Hérault, Kentaro Takagi, Camille Ziegler, Elodie A. Courtois, Damien Bonal, Sabrina Coste, Ecologie des forêts de Guyane (UMR ECOFOG), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-AgroParisTech-Université de Guyane (UG)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Institut National Polytechnique Félix Houphouët-Boigny, Laboratoire Ecologie, Evolution, Interactions des Systèmes amazoniens (LEEISA), Centre National de la Recherche Scientifique (CNRS)-Université de Guyane (UG)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Instituto Nacional de Pesquisas Espaciais (INPE), SILVA (SILVA), Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL)-AgroParisTech, Field Science Center for Northern Biosphere, Hokkaido University [Sapporo, Japan], French Ministry of Research, INRA, CNES, European Regional Development Fund (FEDER, 2007-2013), Ecofor, Allenvi, French national research infrastructure, ANAEE-F (ANAEE-France) [ANR-11-INBS-0001], Observatoire du Carbone en Guyane, Agence Nationale de la Recherche (CEBA) [ANR-10-LABX-25-01], Agence Nationale de la Recherche (ARBRE) [ANR-11-LABX-0002-01], and Bonal, Damien

Subjects
0106 biological sciences, Saison, F40 - Écologie végétale, 010504 meteorology & atmospheric sciences, water use efficiency, P40 - Météorologie et climatologie, F60 - Physiologie et biochimie végétale, [SDV]Life Sciences [q-bio], evapotranspiration, tropical rainforest, drought, radiation, Climate change, Atmospheric sciences, 01 natural sciences, Ecosystem model, Evapotranspiration, K01 - Foresterie - Considérations générales, Ecosystem, Forêt tropicale humide, Water-use efficiency, 0105 earth and related environmental sciences, Transpiration, Changement climatique, Forestry, lcsh:QK900-989, 15. Life on land, Évapotranspiration, 13. Climate action, Soil water, lcsh:Plant ecology, Écosystème forestier, Environmental science, 010606 plant biology & botany, Tropical rainforest
Abstract

International audience; Warmer and drier climates over Amazonia have been predicted for the next century with expected changes in regional water and carbon cycles. We examined the impact of interannual and seasonal variations in climate conditions on ecosystem-level evapotranspiration (ET) and water use efficiency (WUE) to determine key climatic drivers and anticipate the response of these ecosystems to climate change. We used daily climate and eddyflux data recorded at the Guyaflux site in French Guiana from 2004 to 2014. ET and WUE exhibited weak interannual variability. The main climatic driver of ET and WUE was global radiation (Rg), but relative extractable water (REW) and soil temperature (Ts) did also contribute. At the seasonal scale, ET and WUE showed a modal pattern driven by Rg, with maximum values for ET in July and August and for WUE at the beginning of the year. By removing radiation effects during water depleted periods, we showed that soil water stress strongly reduced ET. In contrast, drought conditions enhanced radiation-normalized WUE in almost all the years, suggesting that the lack of soil water had a more severe effect on ecosystem evapotranspiration than on photosynthesis. Our results are of major concern for tropical ecosystem modeling because they suggest that under future climate conditions, tropical forest ecosystems will be able to simultaneously adjust CO2 and H2O fluxes. Yet, for tropical forests under future conditions, the direction of change in WUE at the ecosystem scale is hard to predict, since the impact of radiation on WUE is counterbalanced by adjustments to soil water limitations. Developing mechanistic models that fully integrate the processes associated with CO2 and H2O flux control should help researchers understand and simulate future functional adjustments in these ecosystems.

Published
2019
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10. Nitrogen cycling in monospecific and mixed-species plantations of Acacia mangium and Eucalyptus at 4 sites in Brazil

Author

Florence Tardy, Jean-Pierre Bouillet, Jean-Paul Laclau, Marcelo Zacharias Moreira, D.R.M. Caldeira, José Leonardo de Moraes Gonçalves, Fernando Palha Leite, Carolina B. Brandani, Maureen Voigtlaender, Ranieri Ribeiro Paula, Didier Brunet, Universidade de São Paulo (USP), Universidade Estadual Paulista Júlio de Mesquita Filho = São Paulo State University (UNESP), Ecologie fonctionnelle et biogéochimie des sols et des agro-écosystèmes (UMR Eco&Sols), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA), Centro de Energia Nuclear na Agricultura (CENA ), University of São Paulo (USP), Celulose Nipo-Brasileira SA (CENIBRA), Universidade Federal do Espirito Santo (UFES), Cenibra, International Paper, Suzano Papel e Celulose, SOERE F-ORE-T network, which is supported annually by Ecofor, Allenvi and the French National Research Infrastructure ANAEE-F, Universidade Estadual Paulista (Unesp), UMR Eco&Sols, University of Montpellier, Coordenação de Pesquisa Florestal, UFES, Universidade de São Paulo = University of São Paulo (USP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Département Performances des systèmes de production et de transformation tropicaux (Cirad-PERSYST), and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)

Subjects
Litière forestière, 0106 biological sciences, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, 01 natural sciences, [SDU.STU.GC]Sciences of the Universe [physics]/Earth Sciences/Geochemistry, Acacia mangium, Tree mixtures, 2. Zero hunger, N 2 fixation, biology, Forestry, Plant litter, Plantation forestière, Eucalyptus, CONSORCIAÇÃO DE CULTURAS, Cycle de l'azote, Tropical plantations, Organic matter, P33 - Chimie et physique du sol, Eucalyptus grandis, Fixation de l'azote, Soil texture, Acacia, Management, Monitoring, Policy and Law, Litterfall, 010603 evolutionary biology, N-2 fixation, Culture en mélange, Eucalypt, Nature and Landscape Conservation, Nutrition, Forest floor, Topsoil, Soil organic matter, P35 - Fertilité du sol, Eucalyptus urophylla, 15. Life on land, biology.organism_classification, K10 - Production forestière, F61 - Physiologie végétale - Nutrition, Agronomy, Environmental science, 010606 plant biology & botany
Abstract

Made available in DSpace on 2019-10-06T15:31:04Z (GMT). No. of bitstreams: 0 Previous issue date: 2019-03-15 Mixing N-fixing trees with eucalypts is an attractive option to improve the long-term soil N status in fast-growing plantations established in tropical soils. A randomized block design was replicated at four sites in Brazil to compare the biogeochemical cycles in mono-specific stands of Eucalyptus (100E) and Acacia mangium (100A) with mixed-species plantations in a proportion of 1:1 (50A50E). Our study aimed to assess the effects of introducing A. mangium trees in Eucalyptus plantations on atmospheric N 2 fixation, N cycling and soil organic matter stocks. Litterfall and soil N mineralization were measured over the last two years of the rotation (4–6 years after planting). Aboveground N accumulation in the trees and C and N stocks in the forest floor and in the top soil were intensively sampled at harvesting age. N 2 fixation rates were estimated using the natural abundance of 15 N as well as by the difference between total N stocks in 100A and 50A50E relative to 100E (accretion method). While the 15 N natural abundance method was unsuitable, the accretion method showed consistently across the four sites that atmospheric N fixation reached about 250 and 400 kg N ha −1 rotation −1 in 50A50E and 100A, respectively. Except at one site with high mortality, N contents within trees at harvesting were approximately 40% higher in 100A than in 100E. Mean N contents in litterfall and N mineralization rates were about 60% higher in 100A than in 100E, with intermediate values in 50A50E. The amounts of N in litterfall were much more dependent on soil N mineralization rates for acacia trees than for eucalypt trees. Soil C and N stocks were dependent on soil texture but not influenced by tree species. N budgets over a 6-year rotation were enhanced by about 65 kg N ha −1 yr −1 in 100A and 40 kg N ha −1 yr −1 in 50A50E relative to monospecific eucalypt plantations. Introducing N-fixing trees in eucalypt plantations might therefore contribute to reducing the need for mineral N fertilization in the long-term. USP ESALQ Forest Science Department UNESP Departamento de Solos e Recursos Ambientais Universidade Estadual Paulista ‘Júlio de Mesquita Filho’ CIRAD UMR Eco&Sols Eco&Sols INRA CIRAD IRD Montpellier SupAgro University of Montpellier USP CENA, Av. Centenário, 303 CENIBRA Coordenação de Pesquisa Florestal, 35196-972 Belo Oriente Department of Forest Science and Wood UFES, 29550-000 Jerônimo Monteiro UNESP Departamento de Solos e Recursos Ambientais Universidade Estadual Paulista ‘Júlio de Mesquita Filho’

Published
2019
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11. Consequences of clear-cutting and drought on fine root dynamics down to 17 m in coppice-managed eucalypt plantations

Author

Christophe Jourdan, Jean-Paul Laclau, Agnès Robin, Amandine Germon, Iraê Amaral Guerrini, Bruno Bordron, Lydie Chapuis-Lardy, Yann Nouvellon, Céline Pradier, José Leonardo de Moraes Gonçalves, 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 la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Universidade Estadual Paulista Júlio de Mesquita Filho = São Paulo State University (UNESP), Département Performances des systèmes de production et de transformation tropicaux (Cirad-PERSYST), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Universidade de São Paulo = University of São Paulo (USP), (FAPESP) : 2015/24911-8, (CIRAD), Sao Paulo University, Ecofor, Allenvi, French National Research Infrastructure ANAEE-F, Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA), Universidade de São Paulo (USP), Universidade Estadual Paulista (Unesp), Montpellier SupAgro, UMR Eco&Sols, and LMI IESOL

Subjects
0106 biological sciences, Clearcutting, Eucalyptus grandis, Context (language use), F62 - Physiologie végétale - Croissance et développement, Minirhizotron, Root system, Coppice, Management, Monitoring, Policy and Law, 010603 evolutionary biology, 01 natural sciences, Système racinaire, Coppicing, RAIZ, Coupe rase, Croissance, Subsoil, Nature and Landscape Conservation, 2. Zero hunger, Biomass (ecology), Deep ferralsol profile, Forestry, 15. Life on land, Plantation forestière, Deep root growth, 6. Clean water, K10 - Production forestière, Résistance à la sécheresse, Agronomy, Rhizosphère, 13. Climate action, Throughfall exclusion, Environmental science, Soil horizon, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Brazil, 010606 plant biology & botany, Woody plant
Abstract

Made available in DSpace on 2019-10-06T17:08:56Z (GMT). No. of bitstreams: 0 Previous issue date: 2019-08-01 Centre de Coopération Internationale en Recherche Agronomique pour le Développement Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) Improving our understanding of the spatiotemporal dynamics of fine roots in deep soil layers is of utter importance to manage tropical planted forests in a context of climate change. Our study aimed to assess the effect of clear-cutting and drought on fine-root dynamics down to the water table in Brazilian ferralsol under eucalypt plantations conducted in coppice. Fine roots (i.e. diameter 13 m)and, surprisingly, root mortality remained extremely low whatever the depth and the treatment. Total fine-root biomass in coppice down to 17 m depth was 1266 and 1017 g m−2 in +W and −W, respectively, at 1.5 year after the clear-cut and was 1078 g m−2 in NH 7.5 years after planting. Specific root length and specific root area were about 15% higher in −W than in +W. Proliferation of fine roots at great depths could be an adaptive mechanism for tree survival, enhancing the access to water stored in the subsoil. The root system established before clear-cutting provides access to water stored in very deep layers that probably contribute to mitigate the risk of tree mortality during prolonged drought periods when the eucalypt plantations is conducted in coppice after the clear-cut. UNESP-São Paulo State University School of Agricultural Sciences Eco&Sols Univ Montpellier CIRAD INRA IRD Montpellier SupAgro CIRAD UMR Eco&Sols ESALQ Forest Science Department Escola Superior de Agricultura Luiz de Queiroz Universidade de São Paulo ESALQ Soil Science Department Escola Superior de Agricultura Luiz de Queiroz Universidade de São Paulo IRD UMR Eco&Sols LMI IESOL, BP 1386 UNESP-São Paulo State University School of Agricultural Sciences FAPESP: 2015/24911-8

Published
2019
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12. Adhesion to nanofibers drives cell membrane remodeling through one-dimensional wetting

Author

Charles-Orszag, Arthur, Tsai, Feng-Ching, Bonazzi, Daria, Manriquez, Valeria, Sachse, Martin, Mallet, Adeline, Salles, Audrey, Melican, Keira, Staneva, Ralitza, Bertin, Aurélie, Millien, Corinne, Goussard, Sylvie, Lafaye, Pierre, Shorte, Spencer, Piel, Matthieu, Krijnse-Locker, Jacomine, Brochard-Wyart, Françoise, Bassereau, Patricia, Duménil, Guillaume, Pathogénèse des Infections vasculaires / Pathogenesis of Vascular Infections, Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM), Université Paris Descartes - Paris 5 (UPD5), Laboratoire Physico-Chimie Curie [Institut Curie] (PCC), Institut Curie [Paris]-Institut de Chimie du CNRS (INC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Microscopie ultrastructurale - Ultrapole (CITECH), Institut Pasteur [Paris] (IP), Biologie Cellulaire et Cancer, Institut Curie [Paris]-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Paris-Centre de Recherche Cardiovasculaire (PARCC - UMR-S U970), Hôpital Européen Georges Pompidou [APHP] (HEGP), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), Ingénierie des Anticorps (plate-forme) - Antibody Engineering (Platform), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Institut Pierre-Gilles de Gennes pour la Microfluidique, Institut Curie [Paris], This work was supported by the French ministry for research and higher education (ACO), the Integrative Biology of Emerging Infectious Diseases (IBEID) laboratory of excellence (GD) and the VIP European Research Council starting grant (GD). We gratefully acknowledge the Imagopole—Citech of Institut Pasteur (Paris, France) as well as the France–BioImaging infrastructure network supported by the French National Research Agency (ANR-10–INSB–04, Investments for the Future), and the Région Ile-de-France (program Domaine d’Intérêt Majeur-Malinf) for the use of the Zeiss LSM 780 Elyra PS1 microscope and the Zeiss Auriga scanning electron microscope. The authors greatly acknowledge the Cell and Tissue Imaging (PICT-IBiSA), Institut Curie, member of the French National Research Infrastructure France-BioImaging (ANR10-INBS-04), and the PICT-IBiSA Institut Curie (Paris, France). This work was supported by Institut Curie, Fondation pour la Recherche Médicale (FRM FDT20170437130) and Ecole Doctorale Frontières du Vivant (FdV)–Programme Bettencourt (RS), ERC StG grant STARLIN (DMV), Centre National de la Recherche Scientifique (CNRS), and P. B. and F.B.-W. belong to the CNRS consortium CellTiss, to the Labex CelTisPhyBio (ANR-11-LABX0038) and to Paris Sciences et Lettres (). F.C.T. was funded by the EMBO Long-Term fellowship (ALTF 1527-2014) and Marie Curie actions (H2020-MSCA-IF-2014, project membrane-ezrin-actin)., ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), ANR-11-LABX-0038,CelTisPhyBio,Des cellules aux tissus: au croisement de la Physique et de la Biologie(2011), European Project: 656442,H2020,H2020-MSCA-IF-2014,membrane-ezrin-actin(2016), Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Pasteur [Paris], Institut Pasteur [Paris], Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Hôpital Européen Georges Pompidou [APHP] (HEGP), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO), Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], Physico-Chimie-Curie (PCC), Centre National de la Recherche Scientifique (CNRS)-Institut Curie [Paris]-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Chimie du CNRS (INC), Lafaye, pierre, Integrative Biology of Emerging Infectious Diseases - - IBEID2010 - ANR-10-LABX-0062 - LABX - VALID, Des cellules aux tissus: au croisement de la Physique et de la Biologie - - CelTisPhyBio2011 - ANR-11-LABX-0038 - LABX - VALID, Membrane-ezrin-actin interactions mediated by ezrin binding proteins in reconstituted systems - membrane-ezrin-actin - - H20202016-01-01 - 2018-01-01 - 656442 - VALID, and Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut Curie [Paris]-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Science, Cell Membrane, Nanofibers, Mice, SCID, [SDV.IMM.IMM]Life Sciences [q-bio]/Immunology/Immunotherapy, Neisseria meningitidis, Models, Biological, Bacterial Adhesion, Article, Liposomes, Human Umbilical Vein Endothelial Cells, Wettability, Animals, Humans, lcsh:Q, Cell Surface Extensions, [SDV.IMM.IMM] Life Sciences [q-bio]/Immunology/Immunotherapy, lcsh:Science
Abstract

The shape of cellular membranes is highly regulated by a set of conserved mechanisms that can be manipulated by bacterial pathogens to infect cells. Remodeling of the plasma membrane of endothelial cells by the bacterium Neisseria meningitidis is thought to be essential during the blood phase of meningococcal infection, but the underlying mechanisms are unclear. Here we show that plasma membrane remodeling occurs independently of F-actin, along meningococcal type IV pili fibers, by a physical mechanism that we term ‘one-dimensional’ membrane wetting. We provide a theoretical model that describes the physical basis of one-dimensional wetting and show that this mechanism occurs in model membranes interacting with nanofibers, and in human cells interacting with extracellular matrix meshworks. We propose one-dimensional wetting as a new general principle driving the interaction of cells with their environment at the nanoscale that is diverted by meningococci during infection., Meningococci remodel the plasma membrane of host cells during infection. Here, Charles-Orszag et al. show that plasma membrane remodeling occurs independently of F-actin, along meningococcal type IV pili fibers, by a physical mechanism that they term ‘one-dimensional’ membrane wetting.

Published
2018
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13. Nitrogen dynamics in a nutrient-poor soil under mixed-species plantations of eucalypts and acacias

Author

Sogni Viviane Tchichelle, Louis Mareschal, Lydie-Stella Koutika, Daniel Epron, Centre de Recherche sur la Durabilité et la Productivité des Plantations Industrielles (CRDPI), Ecologie et Ecophysiologie Forestières [devient SILVA en 2018] (EEF), Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL), Ecologie fonctionnelle et biogéochimie des sols et des agro-écosystèmes (UMR Eco&Sols), Institut National de la Recherche Agronomique (INRA)-Institut de Recherche pour le Développement (IRD)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Intensfix Project ANR-2010-STRA004-03, CIRAD, Ecofor, Allenvi and the french national research infrastructure ANAEE-F, French National Research Agency through the Laboratory of Excellence ARBRE ANR-12-LABXARBRE-01, Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA), and ANR-10-STRA-0004,Intens&Fix,Intensification écologique des écosystèmes de plantations forestières. Modélisation biophysique et évaluation socio-économique de l'association d'espèces fixatrices d'azote(2010)

Subjects
0106 biological sciences, azote particulaire, [SDV]Life Sciences [q-bio], 01 natural sciences, Casuarina equisetifolia, CARBON, Nutrient, acacia, MINERALIZATION, BUDGETS, 2. Zero hunger, CONGO, biology, SOUTHERN CHINA, 04 agricultural and veterinary sciences, Nitrogen, Eucalyptus, Plantation forestière, Arbre fixateur d'azote, eucalyptus, Cycle de l'azote, Fertilizer, culture mixte, Arénosol, Fixation de l'azote, fertilité des sols, Soil Science, Acacia, chemistry.chemical_element, engineering.material, SANDY SOIL, sol pauvre en matière organique, Microbiology, Matière organique du sol, productivité, Fertilité du sol, Culture en mélange, Botany, ORGANIC-MATTER ASSESSMENT, réduction d'intrants, CONSEQUENCES, Soil organic matter, P35 - Fertilité du sol, Mineralization (soil science), 15. Life on land, biology.organism_classification, K10 - Production forestière, mixed cropping, F61 - Physiologie végétale - Nutrition, chemistry, Agronomy, dynamique de l'azote, 040103 agronomy & agriculture, engineering, 0401 agriculture, forestry, and fisheries, Environmental science, Soil fertility, FIXING TREES, FRACTIONS, 010606 plant biology & botany
Abstract

Introducing nitrogen-fixing species (NFS) in eucalypt plantations is a useful practice to compensate nitrogen loss at harvest, reduce fertilizer inputs, improve soil fertility and sustain forest productivity in low input systems.Nitrogen (N) and carbon (C) were evaluated in the active part of soil organic matter (SOM) i.e., the particulate organic matter (POM), which was obtained after soil (0-0.05 m) physical fractionation at the end of a first 7-year rotation (R1Y7) and at year 2 of a second rotation (R2Y2) in pure acacia (100A), pure eucalypt (100E) and mixed-species (50A50E) stands in an experimental plantation established on an Arenosol in the Congolese coastal plains. N concentration (in g kg(-1) of soil) was higher in coarse POM (cPOM, 4000-250 mu m) in 100A and 50A50E compared to 100E at 2YR2, while no difference was found in fine POM (fPOM, 250-50 gm) and in the organo-mineral fraction (OMF, < 50 mu m). N content in cPOM was more than 3 times higher at R2Y2 than at R1Y7. A slight increase was also observed in fPOM, while no difference was observed in OMF between R1Y7 and R2Y2. Lower C:N ratios in the two POM fractions in 100A and, to a lesser extent, in 50A50E compared to 100E suggests an improved soil N status after acacia trees have been introduced in eucalypt plantations.The lack of difference in N content of coarse POM between 100A and 50A50E at R1Y7, despite higher amount of N in the forest floor and N returning to the soil (harvest residues and litterfall) in 100A than in 50A50E, suggests a faster cycling of nitrogen under acacia than under eucalypt.

Published
2017
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14. Boron Dissolved and Particulate Atmospheric Inputs to a Forest Ecosystem (Northeastern France)

Author

Damien Lemarchand, Marie-Pierre Turpault, Gil Kirchen, Paul-Olivier Redon, Philippe Roux, Unité de recherche Biogéochimie des Ecosystèmes Forestiers (BEF), Institut National de la Recherche Agronomique (INRA), Université de Strasbourg (UNISTRA), Agence Nationale pour la Gestion des Déchets Radioactifs (ANDRA), Region Lorraine, ANDRA (French national radioactive waste management agency), Ecofor, Allenvi, and french national research infrastructure ANAEE-F

Subjects
010504 meteorology & atmospheric sciences, EROSION, NUTRIENT INPUTS, [SDV]Life Sciences [q-bio], TRACER, chemistry.chemical_element, input, bore, Isotopes of boron, Forests, 010502 geochemistry & geophysics, 01 natural sciences, Forest ecology, Environmental Chemistry, ISOTOPIC COMPOSITION, DEPOSITION, Boron, Ecosystem, EMISSIONS, 0105 earth and related environmental sciences, écosystème forestier, ASIAN CONTINENT, FRACTIONATION, atmospheric deposition, Mean value, General Chemistry, Atmospheric dust, 15. Life on land, Particulates, forest ecosystem, est de la france, chemistry, 13. Climate action, apport atmosphérique, Environmental chemistry, PRECIPITATION, STRENGBACH, intrant, Environmental science, France, boron, Environmental Monitoring
Abstract

Boron concentrations and isotopic compositions of atmospheric dust and dissolved depositions were monitored over a two-year period (2012-2013) in the forest ecosystem of Montiers (Northeastern France).This time series allows the determination of the boron atmospheric inputs to this forest ecosystem and contributes to refine our understanding of the sources and processes that control the boron atmospheric cycle. Mean annual dust and dissolved boron atmospheric depositions are comparable in size (13 g.ha(-1).yr(-1) and 16 g.ha(-1).yr(-1), respectively), which however show significant intra- and interannual variations.Boron isotopes in dust differ from dissolved inputs, with an annual mean value of +1 and +18 for, respectively. The notable high boron contents (190-390 mu g.g(1)) of the dust samples are interpreted as resulting from localized spreading of boron-rich fertilizers, thus indicating a significant local impact of regional agricultural activities. Boron isotopes in dissolved depositions show a clear seasonal trend.The absence of correlation with marine cyclic solutes contradicts a control of atmospheric boron by dissolution of seasalts. Instead, the boron data from this study are consistent with a Rayleigh-like evolution of the atmospheric gaseous boron reservoir with possible but limited anthropogenic and/or biogenic contributions.

Published
2017
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15. Denoising and compensation of the missing wedge in cryo electron tomography

Author

Moebel, Emmanuel, Kervrann, Charles, Space-timE RePresentation, Imaging and cellular dynamics of molecular COmplexes (SERPICO), Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Fondation Fourmentin-Guilbert, Région Bretagne, French National Research Infrastructure France-BioImaging (ANR-10-INSB-04), European Microscopy Society, and Kervrann, Charles

Subjects
[SDV] Life Sciences [q-bio], [INFO.INFO-TI] Computer Science [cs]/Image Processing [eess.IV], fourier transform, [INFO.INFO-TI]Computer Science [cs]/Image Processing [eess.IV], [SDV]Life Sciences [q-bio], cryo electron tomography, inpainting, denoising, missing wedge, [SPI.SIGNAL]Engineering Sciences [physics]/Signal and Image processing, [SPI.SIGNAL] Engineering Sciences [physics]/Signal and Image processing
Abstract

International audience; In this study, we have addressed two important issues in cryo electron tomography images: the lowsignal-to-noise ratio and the presence of a missing wedge (MW) of information in the spectral domain. Indeed,according to the Fourier slice theorem, limited angle tomography results into an incomplete sampling of theFourier domain. Therefore, the Fourier domain is separated into two regions: the known spectrum (KS) and theunknown spectrum, the latter having the shape of a missing wedge (see Figure). The proposed method tacklesboth issues jointly, by iteratively applying a denoising algorithm in order to fill up the MW, and proceeds asfollows:[1] Excitation step: Add noise into the MW[2] Denoising step: Apply a patch-based denoising algorithm[3] Repeat steps 1 and 2, by keeping KS constant through the iterationsThe excitation step is used to randomly initialize the coefficients of the MW, whereas the denoising step acts as aspatial regularization. The employed denoising algorithm, which exploits the self-similarity of the image, filtersout coefficient values which are dissimilar to KS, thereby keeping similar ones. By iterating these steps, we areable to diffuse the information contained in KS into the MW.An application example on experimental data can be seen on the Figure, which shows the data in both spectraland spatial domain. The data contains a spherical gold particle, deformed by MW induced artifacts: elongation ofthe object, side- and ray-artifacts. From the residue image it can be seen that noise and MW artifacts have beenreduced, while preserving the details of the image. Experiments are being performed to verify if particledetection and alignment are enhanced by using the method as a pre-processing step.

Published
2016

16. A non-parametric procedure for co-localization studies in fluorescence microscopy

Author

Pécot, Thierry, Lavancier, Frédéric, Kervrann, Charles, Space-timE RePresentation, Imaging and cellular dynamics of molecular COmplexes (SERPICO), Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Département de Mathématiques et Informatique - Université de Nantes, Université de Nantes (UN), and French National Research Infrastructure France-BioImaging (ANR-10-INSB-04)

Subjects
[MATH.MATH-ST]Mathematics [math]/Statistics [math.ST], [INFO.INFO-TI]Computer Science [cs]/Image Processing [eess.IV], microscopy, fluorescence, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, co-localisation, image segmentation, random sets, point processes, spatial statistics
Abstract

International audience; Spatial proximity between proteins is a potential evidence of their interaction. Modern light microscopy associated with fluorescence molecule tagging allow to acquire images with two or more distinct proteins at the same time to characterize the joint spatial repartition and the spatial overlap between them. This analysis is commonly called a « co-localization » study. We propose a non-parametric testing procedure for co-localization based on the overlapping areas defined by the segmented proteins. This procedure is more powerful than existing methods to detect co-localization. In addition, this testing procedure is robust to protein shapes and sizes.

Published
2016

17. A Guided Tour of Selected Image Processing and Analysis Methods for Fluorescence and Electron Microscopy

Author

Carlos Oscar S. Sorzano, Michael Unser, Scott T. Acton, Jean-Christophe Olivo-Marin, Charles Kervrann, Space-timE RePresentation, Imaging and cellular dynamics of molecular COmplexes (SERPICO), Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Centro Nacional de Biotecnología [Madrid] (CNB-CSIC), Biocomputing Unit [Madrid], University of Virginia [Charlottesville], Analyse d'Images Quantitative (AIQ), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Biomedical Imaging Group [Lausanne], Ecole Polytechnique Fédérale de Lausanne (EPFL), Agence Nationale de la Recherche (French National Research Infrastructure France-BioImaging (ANR-10-INBS-04) and ANR-10-LABEX-62-IBEID), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), University of Virginia, and Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0301 basic medicine, [PHYS.PHYS.PHYS-BIO-PH]Physics [physics]/Physics [physics]/Biological Physics [physics.bio-ph], detection, Nanotechnology, Image processing, law.invention, 03 medical and health sciences, [INFO.INFO-TS]Computer Science [cs]/Signal and Image Processing, law, image analysis, intra-cellular traffic analysis, Microscopy, Fluorescence microscope, denoising, [INFO.INFO-IM]Computer Science [cs]/Medical Imaging, Electrical and Electronic Engineering, Analysis method, neuron shape analysis, Fluorescence microscopy, electron microscopy, motion analysis, segmentation, Fluorescence, 3. Good health, image processing, 030104 developmental biology, Science research, Signal Processing, cell motility analysis, Electron microscope
Abstract

International audience; Microscopy imaging, including fluorescence microscopy and electron microscopy, has taken a prominent role in life science research and medicine due to its ability to investigate the 3D interior of live cells and organisms. A long-term research in bio-imaging at the sub-cellular and cellular scales consists then in inferring the relationships between the dynamics of macromolecules and their functions. In this area, image processing and analysis methods are now essential to understand the dynamic organization of groups of interacting molecules inside molecular machineries and to address issues in fundamental biology driven by advances in molecular biology, optics and technology. In this paper, we present recent advances in fluorescence and electron microscopy and we focus on dedicated image processing and analysis methods required to quantify phenotypes for a limited number but typical studies in cell imaging.

Published
2016
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18. Differences in nitrogen cycling and soil mineralisation between a eucalypt plantation and a mixed eucalypt and Acacia mangium plantation on a sandy tropical soil

Author

Louis Mareschal, Sogni Viviane Tchichelle, Fidèle Mialoundama, Lydie-Stella Koutika, Jean-Michel Harmand, Jean-Pierre Bouillet, Daniel Epron, Ecologie et Ecophysiologie Forestières [devient SILVA en 2018] (EEF), Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL), Centre de Recherche sur la Durabilité et la Productivité des Plantations Industrielles (Dispositif en Partenariat) (CRDPI), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-UR Génétique Amélioration Diversité, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Université Marien Ngouabi, Faculté des Sciences et Techniques, Ecologie fonctionnelle et biogéochimie des sols et des agro-écosystèmes (UMR Eco&Sols), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA), Intensfix Project ANR-2010-STRA-004-03, EU, Ecofor, Allenvi, French national research infrastructure ANAEE-F, CIRAD AI1, French National Research Agency through the Laboratory of Excellence ARBRE ANR-12-LABXARBRE-01, ANR-10-STRA-0004,Intens&Fix,Intensification écologique des écosystèmes de plantations forestières. Modélisation biophysique et évaluation socio-économique de l'association d'espèces fixatrices d'azote(2010), ANR-11-LABX-0002,ARBRE,Recherches Avancées sur l'Arbre et les Ecosytèmes Forestiers(2011), ANR-11-INBS-0001,ANAEE-FR,ANAEE-Services(2011), and Institut National de la Recherche Agronomique (INRA)-Institut de Recherche pour le Développement (IRD)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)

Subjects
0106 biological sciences, Litière forestière, [SDV]Life Sciences [q-bio], 01 natural sciences, CARBON, Acacia mangium, 2. Zero hunger, TREE GROWTH, CONGO, biology, PRODUCTIVITY, Forestry, Soil classification, 04 agricultural and veterinary sciences, Plant litter, Plantation forestière, Arbre fixateur d'azote, ORGANIC-MATTER, Cycle de l'azote, SOLO ARENOSO, Ammonium, Arénosol, NITRATE, P33 - Chimie et physique du sol, Eucalyptus grandis, Fixation de l'azote, PROTON FLUXES, Acacia, SPECIES PLANTATIONS, LITTER DECOMPOSITION, Culture en mélange, Fertilité du sol, ammonium, arenosol, Congo, ecological intensification, forest plantation, mixed species, N2 fixation, nitrate, 14. Life underwater, Croissance, Forest floor, AVAILABILITY, P35 - Fertilité du sol, 15. Life on land, Eucalyptus urophylla, biology.organism_classification, K10 - Production forestière, F61 - Physiologie végétale - Nutrition, Soil water, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, Environmental science, Monoculture, Soil fertility, 010606 plant biology & botany, Minéralisation de l'azote
Abstract

Sustainable wood production requires appropriate management of commercial forest plantations. Establishment of industrial eucalypt plantations on poor sandy soils leads to a high loss of nutrients including nitrogen (N) after wood harvesting. An ecological intensification of eucalypt plantations was tested with the replacement of half of the Eucalyptus urophylla × E. grandis by Acacia mangium in the eucalypt monoculture to sustain soil fertility through enhancement of the N biological cycle. A randomised block design was set up on ferralitic arenosol in the Congolese coastal plains to assess differences in soil N mineralisation, N fluxes in litterfall, and N stocks in forest floor litter and soil between pure acacia (100A), pure eucalypt (100E) and mixed-species treatments (50A50E). Soil N mineralisation was enhanced under acacia, reaching on average 0.17 and 0.15 mg kg−1 soil d−1 in 100A and 50A50E, respectively, compared with 0.09 mg kg−1 soil d−1 in 100E. Higher amounts of N returning to the soil through harvest residues and litterfall were observed under acacia than under eucalypt. However, N stock in mineral soil was not increased in 100A and exhibited a limited increase only in the top soil layer of 50A50E. Our results suggest a much faster N turnover under acacia than under eucalypt. Although A. mangium is an exotic N2-fixing tree in central Africa, it appears to be well adapted to the climatic and edaphic conditions of the Congo, showing an efficient growth strategy. Eucalypt trees could benefit from the increase in soil N availability in mixed-species stands.Keywords: ammonium, arenosol, Congo, ecological intensification, forest plantation, mixed species, N2 fixation, nitrate

Published
2016
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