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1. Fate and stability of dissolved organic carbon in topsoils and subsoils under beech forests

Author

Kalks, Fabian, Liebmann, Patrick, Wordell-Dietrich, Patrick, Guggenberger, Georg, Kalbitz, Karsten, Mikutta, Robert, Helfrich, Mirjam, Don, Axel, Thünen Institute of Climate-Smart Agriculture, Braunschweig, Germany, Institute of Soil Science, Leibniz University Hannover, Hannover, Germany, Institute of Soil Science and Site Ecology, Technische Universität Dresden, Tharandt, Germany, and Faculty of Natural Sciences III, Martin-Luther-University Halle-Wittenberg, Halle, Germany

Subjects
Dewey Decimal Classification::500 | Naturwissenschaften::550 | Geowissenschaften, Dewey Decimal Classification::500 | Naturwissenschaften::540 | Chemie, 010504 meteorology & atmospheric sciences, spatial analysis, topsoil, soil depth, deep drilling, 01 natural sciences, Forest subsoils, environmental factor, soil horizon, Dissolved organic carbon, subsoil, ddc:550, Fagus, Environmental Chemistry, Incubation experiment, Ecosystem, Deep drilling, soil carbon, 13C, Beech, Subsoil, 0105 earth and related environmental sciences, Earth-Surface Processes, Water Science and Technology, Total organic carbon, Topsoil, biology, ddc:550.78, 04 agricultural and veterinary sciences, deciduous forest, biology.organism_classification, forest soil, carbon sequestration, dissolved organic carbon, Field experiment, Environmental chemistry, ddc:540, Cascade model, 040103 agronomy & agriculture, Litter, 0401 agriculture, forestry, and fisheries, Environmental science
Abstract

Dissolved organic carbon (DOC) from Oa horizons has been proposed to be an important contributor for subsoil organic carbon stocks. We investigated the fate of DOC by directly injecting a DOC solution from 13C labelled litter into three soil depths at beech forest sites. Fate of injected DOC was quantified with deep drilling soil cores down to 2 m depth, 3 and 17 months after the injection. 27 ± 26% of the injected DOC was retained after 3 months and 17 ± 22% after 17 months. Retained DOC was to 70% found in the first 10 cm below the injection depth and on average higher in the topsoil than in the subsoil. After 17 months DOC in the topsoil was largely lost (− 19%) while DOC in the subsoil did not change much (− 4.4%). Data indicated a high stabilisation of injected DOC in the subsoils with no differences between the sites. Potential mineralisation as revealed by incubation experiments however, was not different between DOC injected in topsoil or subsoils underlining the importance of environmental factors in the subsoil for DOC stabilisation compared to topsoil. We conclude that stability of DOC in subsoil is primary driven by its spatial inaccessibility for microorganisms after matrix flow while site specific properties did not significantly affect stabilisation. Instead, a more fine-textured site promotes the vertical transport of DOC due to a higher abundance of preferential flow paths., Deutsche Forschungsgemeinschaft http://dx.doi.org/10.13039/501100001659

Published
2020
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2. The GenTree Leaf Collection: Inter‐ and intraspecific leaf variation in seven forest tree species in Europe

Author

Jérémy Marchon, Alan Gray, Sebastian Richter, Christophe Plomion, René Graf, Francesca Bagnoli, Elisabet Martínez-Sancho, Volker Schneck, Frédéric Bernier, Vladimir L. Semerikov, Henry Bignalet, José Alberto Ramírez-Valiente, Ioannis Ganopoulos, Felix Gugerli, Agathe Hurel, Geir Ostreng, Sandro Morganti, Santiago C. González-Martínez, David López-Quiroga, Luc Puzos, William Brunetto, Raquel Benavides, Damien Bouic, Olivier Ambrosio, Filippos A. Aravanopoulos, Mirko Liesebach, Cristina C. Bastias, Veronique Jorge, Outi Savolainen, Stephen Cavers, Célia Michotey, Bernard Dokhelar, Mehdi Pringarbe, Enja Hollenbach, Camilla Avanzi, Silvio Schueler, José M. García del Barrio, Annie Raffin, Bruno Fady, Anna-Maria Farsakoglou, Olivier Gilg, Pascal Milesi, Sonja T. Kujala, Nicolas Mariotte, Florian Knutzen, Nicolas Cheval, F. J. Auñón, Céline Lalanne, Marc Villar, Catherine Bastien, Katri Kärkkäinen, Nicolas Poinot, Fernando Del Caño, Jan-Philipp Kappner, Florence Jean, Birte Pakull, Tanja Pyhäjärvi, Jørn Henrik Sønstebø, Rémi Dourthe, Ermioni Malliarou, Ivan Scotti, Timo Kumpula, Mariaceleste Labriola, Silvia Matesanz, Bernard Issehuth, Martin Lascoux, Jean Thevenet, Christian Rellstab, Marianne Correard, Ricardo Alía, Johannes Lambertz, Anne Eskild Nilsen, Eva Cremer, Christoph Hartleitner, Darius Danusevičius, Lars Opgenoorth, Fernando Valladares, Arnaud Jouineau, Ana M. Cabanillas‐Saldaña, José Climent, Audrey Albet, Jurata Buchovska, Benjamin Dauphin, Sergio San Segundo, Ilaria Spanu, Antonio Mas, Johan Westin, Eduardo Notivol, Juan J. Robledo-Arnuncio, Andrea Piotti, Evangelos Barbas, Robert Kesälahti, Andreas Fera, Mari Mette Tollefsrud, Helge Meischner, Grégoire Le Provost, Eduardo Ballesteros, Tor Myking, Bárbara Carvalho, Jean-Luc Denou, Katrin Heer, Giovanni G. Vendramin, Evangelia V. Avramidou, Norbert Turion, Patrick Fonti, Delphine Grivet, Department of Biogeography and Global Change, Museo Nacional de Ciencias Naturales [Madrid] (MNCN), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC)-Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), 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)-Université de Montpellier (UM)-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 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), UK Centre for Ecology & Hydrology, Natural Environment Research Council (NERC), Unité expérimentale Forêt Pierroton (UEFP), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Department of Forest Ecology and Genetics, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria = National Institute for Agricultural and Food Research and Technology (INIA), Ecologie des Forêts Méditerranéennes (URFM), Aristotle University of Thessaloniki, Istituto di Bioscienze e BioRisorse [Palermo] (IBBR), National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), Biologie intégrée pour la valorisation de la diversité des Arbres et de la Forêt (BioForA), Office national des forêts (ONF)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Vytautas Magnus University - Vytauto Didziojo Universitetas (VDU), Gobierno de Aragon, Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), Unité Expérimentale Entomologie et Forêt Méditerranéenne (UEFM), Bavarian Office for Forest Seeding and Planting, Partenaires INRAE, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Austrian Research Centre for Forests (BFW), Institute of Plant Breeding and Genetic Resources, Biodiversité, Gènes & Communautés (BioGeCo), Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), LIECO GmbH & Co KG, Philipps Universität Marburg = Philipps University of Marburg, Natural Resources Institute Finland (LUKE), University of Oulu, Department of Ecology and Genetics [Uppsala] (EBC), Uppsala University, Thunen Institute of Forest Ecosystems, Thünen Institute, Área de Biodiversidad y Conservación, Universidad Rey Juan Carlos, Universidad Rey Juan Carlos [Madrid] (URJC), Unité de Recherche Génomique Info (URGI), Norsk institutt for bioøkonomi=Norwegian Institute of Bioeconomy Research (NIBIO), Institute of Plant and Animal Ecology, Ural Branch of Russian Academy of Sciences (UB RAS), Skogforsk - Swedish Forestry Research Institute, Horizon 2020. Grant Numbers: 676876, 4540-143AP, 6, 0032 Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES (Brazil), European Project: 676876,H2020,H2020-SFS-2015-2,GenTree(2016), European Commission, Ministerio de Ciencia, Innovación y Universidades (España), Comunidad de Madrid, State Secretariat for Education, Research and Innovation (Switzerland), Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (Brasil), Museo Nacional de Ciencias Naturales (CSIC), Université Paul-Valéry - Montpellier 3 (UPVM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-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)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Consiglio Nazionale delle Ricerche (CNR), Office National des Forêts (ONF)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centro de Investigacion Y Tecnologia Agroalimentaria de Aragon, Philipps Universität Marburg, Norwegian Institute of Bioeconomy Research (NIBIO), and Centro de Investigacion y Tecnologia Agroalimentaria de Aragon (CITA)

Subjects
0106 biological sciences, Specific leaf area, Population, Phenotypic variation, 010603 evolutionary biology, 01 natural sciences, Ecology and Environment, Leaf functional traits, tree species, Fagus sylvatica, leaf functional traits, Leaf economics spectrum, Leaf size, education, intraspecific variability, Ecology, Evolution, Behavior and Systematics, Global and Planetary Change, education.field_of_study, Ecology, biology, leaf economics spectrum, 010604 marine biology & hydrobiology, Intraspecific variability, Botany, phenotypic variation, Botanik, Interspecific competition, 15. Life on land, biology.organism_classification, Forest genetic resources, Quercus petraea, Sample collection, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, European forests, Tree species
Abstract

[Motivation] Trait variation within species can reveal plastic and/or genetic responses to environmental gradients, and may indicate where local adaptation has occurred. Here, we present a dataset of rangewide variation in leaf traits from seven of the most ecologically and economically important tree species in Europe. Sample collection and trait assessment are embedded in the GenTree project (EU-Horizon 2020), which aims at characterizing the genetic and phenotypic variability of forest tree species to optimize the management and sustainable use of forest genetic resources. Our dataset captures substantial intra- and interspecific leaf phenotypic variability, and provides valuable information for studying the relationship between ecosystem functioning and trait variability of individuals, and the response and resilience of species to environmental changes., [Main types of variable contained] We chose morphological and chemical characters linked to trade-offs between acquisition and conservation of resources and water use, namely specific leaf area, leaf size, carbon and nitrogen content and their ratio, and the isotopic signature of stable isotope 13C and 15N in leaves., [Spatial location and grain] We surveyed between 18 and 22 populations per species, 141 in total, across Europe., [Time period] Leaf sampling took place between 2016 and 2017., [Major taxa and level of measurement] We sampled at least 25 individuals in each population, 3,569 trees in total, and measured traits in 35,755 leaves from seven European tree species, i.e. the conifers Picea abies, Pinus pinaster and Pinus sylvestris, and the broadleaves Betula pendula, Fagus sylvatica, Populus nigra and Quercus petraea., [Software format] The data files are in ASCII text, tab delimited, not compressed., All authors acknowledge support from the European Union’s Horizon 2020 Research and Innovation Programme under grant agreement no. 676876 (Project GenTree). Laboratory work was also supported by other projects: COMEDIAS (CGL2017- 83170-R, Spanish Ministry of Science, Innovation and Universities), REMEDINAL IV (TE-CM S2018/EMT-4338, Project of the Autonomous Community of Madrid, Spain), SPONFOREST (BIODIVERSA-3, PCIN-2016-055), and International Laboratory of Global Change (LINCGlobal 4540-143AP). The Swiss contribution was supported by the Swiss Secretariat for Education, Research and Innovation (SERI) under contract no. 6.0032. BC was funded by a Scholarship from Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES (Brazil).

Published
2021
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3. Development of nuclear SNP markers for Mahogany (Swietenia spp.)

Author

Maristerra R. Lemes, Sheila E. Ward, Malte Mader, Lasse Schindler, Birgit Kersten, Céline Blanc-Jolivet, Maike Paulini, Birte Pakull, Carlos Navarro, Bernd Degen, Omar di Dio, Alexandre Magno Sebbenn, Erwan Guichoux, Stephen Cavers, Thünen Institute of Forest Genetics, Instituto Nacional de Pesquisas da Amazônia (INPA), Universidad Nacional de Costa Rica, Centre for Ecology and Hydrology (CEH), Centre for Ecology and Hydrology, Instituto Florestal de São Paulo, Biodiversité, Gènes & Communautés (BioGeCo), Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), ANR-10-EQPX-0016,XYLOFOREST,Plateforme d'Innovation ' Forêt-Bois-Fibre-Biomasse du Futur '(2010), and ANR-10-LABX-0025,CEBA,CEnter of the study of Biodiversity in Amazonia(2010)

Subjects
WOODS, EXPLOTACIÓN FORESTAL, 0106 biological sciences, Mahogany, Population, Biodiversity, Endangered species, 01 natural sciences, DNA sequencing, 03 medical and health sciences, Swietenia, Genetics, MassARRAY (R) iPLEX (TM), IUCN Red List, education, Genotyping, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Swietenia spp, 0303 health sciences, education.field_of_study, biology, CITES, Agroforestry, ENVIRONMENTAL ASPECTS, 15. Life on land, biology.organism_classification, ASPECTOS AMBIENTALES, Biology and Microbiology, [SDE]Environmental Sciences, MADERAS, FOREST EXPLOITATION, SNPs, 010606 plant biology & botany
Abstract

INISEFOR Swietenia species are the most valuable American tropical timbers and have been heavily overexploited for decades. The three species are listed as either vulnerable or endangered by IUCN and are included on Appendix II of CITES, yet illegal exploitation continues. Here, we used restriction associated DNA sequencing to develop a new set of 120 SNP markers for Swietenia sp., suitable for MassARRAY®iPLEX™ genotyping. These markers can be used for population genetic studies and timber tracking purposes. Las especies de Swietenia son las maderas tropicales estadounidenses más valiosas y han sido muy sobreexplotadas durante décadas. los Tres especies están incluidas como vulnerables o en peligro de extinción por la UICN y están incluidas en el Apéndice II de la CITES, pero son ilegales. la explotación continúa. Aquí, utilizamos la secuenciación de ADN asociada a la restricción para desarrollar un nuevo conjunto de 120 marcadores SNP para Swietenia sp., Adecuada para el genotipado MassARRAY®iPLEX ™. Estos marcadores se pueden utilizar para estudios genéticos de poblaciones. y seguimiento de la madera. As espécies de Swietenia são as madeiras tropicais americanas mais valiosas e têm sido fortemente superexploradas por décadas. As três espécies estão listadas como vulneráveis ​​ou em perigo pela IUCN e estão incluídas no Apêndice II da CITES, mas a exploração ilegal continua. Aqui, usamos o sequenciamento de DNA associado à restrição para desenvolver um novo conjunto de 120 marcadores SNP para Swietenia sp., Adequado para genotipagem MassARRAY®iPLEX ™. Esses marcadores podem ser usados ​​para estudos de genética populacional e fins de rastreamento de madeira. Thünen Institute of Forest Genetics, Germany Instituto Nacional de Pesquisas da Amazônia, Brazil Universidad Nacional, Costa Rica Centre for Ecology & Hydrology, United Kingdom Instituto Florestal de São Paulo, Brazil University of Bordeaux, France Mahogany for the Future Inc., USA Bush Estate, United Kingdom Instituto de Investigación y Servicios Forestales

Published
2020
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4. Nuclear and plastid SNP markers for tracing Cedrela timber in the tropics

Author

Carmen Rosa García-Dávila, Kathelyn Paredes-Villanueva, Malte Mader, Niklas Tysklind, Alexandre Magno Sebbenn, Stephen Cavers, Céline Blanc-Jolivet, Bernd Degen, Henri Caron, Barbara Rocha Venancio Meyer-Sand, Eurídice N. Honorio Coronado, School of Biological Sciences [Bangor], Bangor University, 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), Universidad Autónoma Gabriel René Moreno, Thünen Institute of Forest Genetics, Instituto de Investigaciones de la Amazonía Peruana (IIAP), Instituto Florestal de São Paulo, Universidade Estadual Paulista (Unesp), Université de Guyane, and Centre for Ecology & Hydrology Edinburgh

Subjects
0106 biological sciences, 0301 basic medicine, Cedrela, MassARRAY, MiSeq, Biodiversity, SNP, RADSeq, 010603 evolutionary biology, 01 natural sciences, DNA sequencing, 03 medical and health sciences, [SDV.SA.SF]Life Sciences [q-bio]/Agricultural sciences/Silviculture, forestry, Tracing origin, parasitic diseases, Genetics, Indel, Genotyping, ComputingMilieux_MISCELLANEOUS, Ecology, Evolution, Behavior and Systematics, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], biology, 15. Life on land, biology.organism_classification, Cedrela odorata, 030104 developmental biology, Evolutionary biology, Tropical timber, Illegal logging
Abstract

Made available in DSpace on 2019-10-06T15:52:58Z (GMT). No. of bitstreams: 0 Previous issue date: 2019-01-01 Illegal logging and trade of timber are major worldwide concerns, resulting in biodiversity and economic losses. Tropical tree species in the genus Cedrela, which have historically been heavily exploited, are still often illegally traded and there is an urgent need to develop tools to verify the origin of Cedrela products. A set of 351 SNP loci for Cedrela species from Bolivia, Brazil, Costa Rica, Cuba, Ecuador, French Guiana, Mexico, and Peru was developed using restriction associated DNA sequencing (RADSeq) and low coverage MiSeq genome sequencing, and adapted for MassARRAY genotyping. After screening of 94 individuals covering most of the distribution of Cedrela, a final set of 136 SNP loci which included 92 nuclear SNPs, 22 chloroplast markers (20 SNPs and 2 INDELs), and 22 mitochondrial markers (19 SNPs and 3 INDELs) was selected and tested for potential to verify Cedrela timber origin. Carrera de Ingeniería Forestal Laboratorio de Dendrocronología Facultad de Ciencias Agrícolas Universidad Autónoma Gabriel René Moreno, Km 9 carretera al Norte, El Vallecito Thünen Institute of Forest Genetics, Sieker Landstrasse 2 Instituto de Investigaciones de la Amazonía Peruana (IIAP), Av. José A. Quiñones km 2.5 Instituto Florestal de São Paulo, CP 1322 Faculdade de Engenharia Universidade Estadual Paulista (Unesp) INRA UMR0745 EcoFoG AgroParisTech Cirad CNRS Université des Antilles Université de Guyane, Campus Agronomique, Avenue de France Centre for Ecology & Hydrology Edinburgh, Bush Estate Faculdade de Engenharia Universidade Estadual Paulista (Unesp)

Published
2019
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5. Development of new SNP and INDEL loci for the valuable African timber species Lophira alata

Author

Henri-Noël Bouda, Marie Massot, Germain Yene, Kasso Daïnou, Emmanuel Opuni-Frimpong, Bernd Degen, Céline Blanc-Jolivet, Malte Mader, Thünen Institute of Forest Genetics, Biodiversité, Gènes & Communautés (BioGeCo), Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Biodiversity and Landscape Unit, Gembloux Agro-Bio Tech, Université de Liège, University of Energy and Natural Resources (UENR), Institute of Forest Genetics and Forest Tree Breedings, and Federal Research Centre for Forestry and Forest Products

Subjects
0106 biological sciences, MassARRAY, Biodiversity, Lophira alata, 01 natural sciences, DNA sequencing, 03 medical and health sciences, Genetics, Chimie générale, SNP, Indel, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, 0303 health sciences, biology, 15. Life on land, Azobe, biology.organism_classification, Single nucleotide polymorphism, Overexploitation, Evolutionary biology, Congo brazzaville, [SDE]Environmental Sciences, Illegal logging, Biologie, 010606 plant biology & botany
Abstract

The timber of the species Lophira alata (azobe) is very popular for outdoor constructions, which favours its overexploitation and illegal logging. We sampled individuals from Liberia, Ivory Coast, Ghana, Nigeria, Cameroon, Gabon, Congo Brazzaville and Republic Democratic of Congo to discover new nuclear and plastidial SNP and INDEL loci through restriction associated DNA sequencing (RADSeq) and low coverage MiSeq genome sequencing. From an initial set of 397 loci, a final set of 126 loci was selected for timber tracking purposes., SCOPUS: ar.j, info:eu-repo/semantics/published

Published
2021
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6. Whole‐genome sequencing and genome regions of special interest: Lessons from major histocompatibility complex, sex determination, and plant self‐incompatibility

Author

Niels A. Müller, Xavier Vekemans, Vincent Castric, Helena Westerdahl, Quentin C. B. Cronk, Helen Hipperson, Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo), Université de Lille-Centre National de la Recherche Scientifique (CNRS), Department of Animal and Plant Sciences [Sheffield], University of Sheffield [Sheffield], Thunen Institute of Forest Ecosystems, Thünen Institute, Lund University [Lund], University of British Columbia (UBC), Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo (EEP)), and ANR-18-CE02-0020,TE-MoMa,Mode, tempo et conséquences fonctionnelles de la mobilisation des éléments transposables en relation aux systèmes de reproduction(2018)

Subjects
0106 biological sciences, Locus (genetics), Computational biology, Biology, Major histocompatibility complex, 010603 evolutionary biology, 01 natural sciences, Genome, sex-determining region, Molecular ecology, [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, 03 medical and health sciences, Genetics, Gene, Genotyping, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Whole genome sequencing, 0303 health sciences, Whole Genome Sequencing, Haplotype, High-Throughput Nucleotide Sequencing, Genomics, Sequence Analysis, DNA, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], major histocompatibility complex, whole-genome sequencing, long-read sequencing, biology.protein, self-incompatibility locus
Abstract

International audience; Whole-genome sequencing of non-model organisms is now widely accessible and has allowed a range of questions in the field of molecular ecology to be investigated with greater power. However, some genomic regions that are of high biological interest remain problematic for assembly and data-handling. Three such regions are the major histocompatibility complex (MHC), sex-determining regions (SDRs) and the plant self-incompatibility locus (S-locus). Using these as examples, we illustrate the challenges of both assembling and resequencing these highly polymorphic regions and how bioinformatic and technological developments are enabling new approaches to their study. Mapping short-read sequences against multiple alternative references improves genotyping comprehensiveness at the S-locus thereby contributing to more accurate assessments of allelic frequencies. Long-read sequencing, producing reads of several tens to hundreds of kilobase pairs in length, facilitates the assembly of such regions as single sequences can span the multiple duplicated gene copies of the MHC region, and sequence through repetitive stretches and translocations in SDRs and S-locus haplotypes. These advances are adding value to short-read genome resequencing approaches by allowing, for example, more accurate haplotype phasing across longer regions. Finally, we assessed further technical improvements, such as nanopore adaptive sequencing and bioinformatic tools using pangenomes, which have the potential to further expand our knowledge of a number of genomic regions that remain challenging to study with classical resequencing approaches.

Published
2021
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7. Climate sensitivity and drought seasonality determine post-drought growth recovery of Quercus petraea and Quercus robur in Europe

Author

Sophia Etzold, Andreas Rigling, Annette Menzel, Arthur Gessler, Andreas Bolte, Roman Zweifel, David I. Forrester, Elisabet Martínez-Sancho, Jordane Gavinet, Arun K. Bose, Patrick Fonti, Flurin Babst, Mathieu Lévesque, Ester González de Andrés, Antonio Gazol, Tanja G. M. Sanders, Burkhard Neuwirth, Tobias Scharnweber, François Lebourgeois, Christof Bigler, Daniel Scherrer, Manuel Nicolas, J. Julio Camarero, Daniel Ziche, Jens Schröder, Isabel Dorado-Liñán, Dirk Nikolaus Karger, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Khulna University, Instituto Pirenaico de Ecologìa = Pyrenean Institute of Ecology [Zaragoza] (IPE - CSIC), Thunen Institute of Forest Ecosystems, Thünen Institute, Department of Environmental Systems Science [ETH Zürich] (D-USYS), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), INIA-CIFOR, Universidad Politécnica de Madrid (UPM), 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), Instituto Aragonés de Ciencias de la Salud [Zaragoza] (IACS), SILVA (SILVA), AgroParisTech-Université de Lorraine (UL)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM), Rheinisch-Westfälische Technische Hochschule Aachen University (RWTH), Office national des forêts (ONF), Universität Greifswald - University of Greifswald, Institute of Terrestrial Ecosystems (ITES), and The study was supported by a Marie Skłodowska-Curie Individual Fellowship (PROJECT ID: 749051-REFOREST) to AKB. A. Gessler acknowledges support by the Swiss National Science Foundation SNF (310030_189109). F.B. acknowledges support by the HOMING programme of the Foundation for Polish Science and European Union (#POIR.04.04.00-00-5F85/18-00). DNK acknowledges funding from Biodiversa with the national funder SNF (20BD21_184131). Part of the sampling was funded within the project DENDROKLIMA by the German Waldklimafond (FKZ 28W-C-4-077-01). We thank colleagues who contributed the ITRDB tree ring database and the CHELSA climate database for generating tree ring width and climate data, respectively. We thank Dr. Thomas Wohlgemuth of the Swiss Federal Research Institute for Forest, Snow and Landscape Research WSL for his valuable comments on an earlier version of the manuscript. We also thank to LANUV Nordrhein-Westfalen, Thüringenforst, LUA Saarland, Landesforsten Rheinland-Pfalz, Landeskompetenzzentrum Forst Eberswalde and Nordwestdeutsche Forstliche Versuchsanstalt for supporting the sampling.

Subjects
Environmental Engineering, 010504 meteorology & atmospheric sciences, [SDE.MCG]Environmental Sciences/Global Changes, Drought tolerance, Legacy effects, Climate change, Forests, 010501 environmental sciences, 01 natural sciences, Trees, Quercus robur, Quercus, Water balance, Warming, Drought, Acclimation, Tree rings, Forest ecology, parasitic diseases, medicine, Environmental Chemistry, Waste Management and Disposal, Ecosystem, 0105 earth and related environmental sciences, biology, Ecology, fungi, food and beverages, Seasonality, biology.organism_classification, medicine.disease, Pollution, Droughts, ddc, Europe, Deciduous, Environmental science, Quercus petraea, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract

Recent studies have identified strong relationships between delayed recovery of tree growth after drought and tree mortality caused by subsequent droughts. These observations raise concerns about forest ecosystem services and post-drought growth recovery given the projected increase in drought frequency and extremes. For quantifying the impact of extreme droughts on tree radial growth, we used a network of tree-ring width data of 1689 trees from 100 sites representing most of the distribution of two drought tolerant, deciduous oak species (Quercus petraea and Quercus robur). We first examined which climatic factors and seasons control growth of the two species and if there is any latitudinal, longitudinal or elevational trend. We then quantified the relative departure from pre-drought growth during droughts, and how fast trees were able to recover the pre-drought growth level. Our results showed that growth was more related to precipitation and climatic water balance (precipitation minus potential evapotranspiration) than to temperature. However, we did not detect any clear latitudinal, longitudinal or elevational trends except a decreasing influence of summer water balance on growth of Q. petraea with latitude. Neither species was able to maintain the pre-drought growth level during droughts. However, both species showed rapid recovery or even growth compensation after summer droughts but displayed slow recovery in response to spring droughts where none of the two species was able to fully recover the pre-drought growth-level over the three post-drought years. Collectively, our results indicate that oaks which are considered resilient to extreme droughts have also shown vulnerability when droughts occurred in spring especially at sites where long-term growth is not significantly correlated with climatic factors. This improved understanding of the role of drought seasonality and climate sensitivity of sites is key to better predict trajectories of post-drought growth recovery in response to the drier climate projected for Europe., Science of The Total Environment, 784, ISSN:0048-9697, ISSN:1879-1026

Published
2021
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8. Growth and resilience responses of Scots pine to extreme droughts across Europe depend on predrought growth conditions

Author

Juan Carlos Linares, Andreas Rigling, Mathieu Lévesque, Matthias Saurer, Annette Menzel, Ana-Maria Hereş, Michel Vennetier, Alessandra Bottero, Luis Matías, Daniel Ziche, Allan Buras, Raúl Sánchez-Salguero, Andrea Hevia, Matthias Haeni, Jordi Martínez-Vilalta, Maxime Cailleret, Arthur Gessler, J. Julio Camarero, Andreas Bolte, Arun K. Bose, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Thunen Institute of Forest Ecosystems, Thünen Institute, Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM), Risques, Ecosystèmes, Vulnérabilité, Environnement, Résilience (RECOVER), Aix Marseille Université (AMU)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Instituto Pirenaico de Ecologia (IPE), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Transilvania University of Brasov, Centre de Ciència i Tecnologia Forestal de Catalunya (CTFC), Institute of Terrestrial Ecosystems (ITES), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Universidad Pablo de Olavide [Sevilla] (UPO), CREAF - Centre for Ecological Research and Applied Forestries, Universidad de Sevilla, Universidad de Sevilla. Departamento de Biología Vegetal y Ecología, European Commission (EC). Fondo Europeo de Desarrollo Regional (FEDER), Ministerio de Ciencia, Innovación y Universidades (MICINN). España, German Waldklimafond, Bavarian State Ministry for Food, Agriculture, and Forestry, Instituto Pirenaico de Ecologìa = Pyrenean Institute of Ecology [Zaragoza] (IPE - CSIC), and Universidad de Sevilla / University of Sevilla

Subjects
0106 biological sciences, 010504 meteorology & atmospheric sciences, acclimation, latitudinal gradient, Pinus sylvestris, predisposition, tree rings, Predisposition, 01 natural sciences, Trees, Germany, Primary Research Article, extreme event, General Environmental Science, Global and Planetary Change, Ecology, biology, 31 Ciencias Agrarias, Droughts, ddc, Europe, climate change, Productivity (ecology), Interactive effects, coniferous tree, [SDE]Environmental Sciences, Eventos extremos, climate effect, drought resistance, Growing season, 010603 evolutionary biology, Acclimatization, Environmental Chemistry, Resilience (network), 0105 earth and related environmental sciences, Resistance (ecology), Global warming, Scots pine, Tree rings, 15. Life on land, Primary Research Articles, biology.organism_classification, 13. Climate action, Spain, physiological response, complexity, Acclimation, global climate
Abstract

Global climate change is expected to further raise the frequency and severity of extreme events, such as droughts. The effects of extreme droughts on trees are difficult to disentangle given the inherent complexity of drought events (frequency, severity, duration, and timing during the growing season). Besides, drought effects might be modulated by trees’ phenotypic variability, which is, in turn, affected by long‐term local selective pressures and management legacies. Here we investigated the magnitude and the temporal changes of tree‐level resilience (i.e., resistance, recovery, and resilience) to extreme droughts. Moreover, we assessed the tree‐, site‐, and drought‐related factors and their interactions driving the tree‐level resilience to extreme droughts. We used a tree‐ring network of the widely distributed Scots pine (Pinus sylvestris) along a 2,800 km latitudinal gradient from southern Spain to northern Germany. We found that the resilience to extreme drought decreased in mid‐elevation and low productivity sites from 1980–1999 to 2000–2011 likely due to more frequent and severe droughts in the later period. Our study showed that the impact of drought on tree‐level resilience was not dependent on its latitudinal location, but rather on the type of sites trees were growing at and on their growth performances (i.e., magnitude and variability of growth) during the predrought period. We found significant interactive effects between drought duration and tree growth prior to drought, suggesting that Scots pine trees with higher magnitude and variability of growth in the long term are more vulnerable to long and severe droughts. Moreover, our results indicate that Scots pine trees that experienced more frequent droughts over the long‐term were less resistant to extreme droughts. We, therefore, conclude that the physiological resilience to extreme droughts might be constrained by their growth prior to drought, and that more frequent and longer drought periods may overstrain their potential for acclimation., We examined tree growth resilience of Scots pine along a 2,800 km latitudinal gradient from southern Spain to north‐eastern Germany using 615 adult trees from 30 different sites. We found that the resilience of Scots pine to extreme drought decreased in mid‐elevation and low productivity sites from 1980–1999 to 2000–2011 due to more frequent and severe droughts in the later period. We showed that the impact of drought on tree‐level resilience was not dependent on its latitudinal location, but rather on the type of sites trees were growing at and on their growth performances during the pre‐drought period.

Published
2020
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9. SNP Markers as a Successful Molecular Tool for Assessing Species Identity and Geographic Origin of Trees in the Economically Important South American Legume Genus Dipteryx

Author

Marie Massot, Valerie Troispoux, Alexandre Magno Sebbenn, Haroldo Cavalcante de Lima, Dennis Del Castillo Torres, Gerardo Flores Llampazo, Gabriel Hidalgo Pizango, Catarina Silva de Carvalho, Malte Mader, Kathelyn Paredes-Villanueva, Barbara R. V. Meyer-Sand, Niklas Tysklind, Bernd Degen, Eurídice N. Honorio Coronado, Céline Blanc-Jolivet, Domingos Cardoso, David Aldana Gomero, Carmen Rosa García-Dávila, Inst Invest Amazonia Peruana IIAP, Thunen Inst Forest Genet, Inst Florestal Sao Paulo, Universidade Estadual Paulista (Unesp), Univ Autonoma Gabriel Rene Moreno, Univ Guyane, Univ Bordeaux, Escola Nacl Bot Trop, Inst Pesquisas Jardim Bot Rio de Janeiro, Universidade Federal da Bahia (UFBA), Instituto de Investigaciones de la Amazonía Peruana (IIAP), Thünen Institute of Forest Genetics, Instituto Florestal de São Paulo, Universidade Estadual Paulista Júlio de Mesquita Filho = São Paulo State University (UNESP), Universidad Autonoma Gabriel René Moreno, School of Biological Sciences [Bangor], Bangor University, 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 des forêts de Guyane (ECOFOG), Ecole Nationale du Génie Rural, des Eaux et des Forêts (ENGREF)-Institut National de la Recherche Agronomique (INRA)-Université des Antilles et de la Guyane (UAG)-Centre National de la Recherche Scientifique (CNRS), Biodiversité, Gènes & Communautés (BioGeCo), Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and Instituto de Pesquisas Jardim Botanico do Rio de Janeiro (JBRJ)

Subjects
0106 biological sciences, Genetic Markers, Genotype, Single-nucleotide polymorphism, 010603 evolutionary biology, 01 natural sciences, Polymorphism, Single Nucleotide, Trees, [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, 03 medical and health sciences, INDEL Mutation, [SDV.SA.SF]Life Sciences [q-bio]/Agricultural sciences/Silviculture, forestry, Snp markers, Genus, Genetics, Cluster Analysis, Indel, genetic assignment, Molecular Biology, Genetics (clinical), Legume, Dipteryx, 030304 developmental biology, 0303 health sciences, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], biology, Geography, Bayes Theorem, 15. Life on land, South America, biology.organism_classification, Evolutionary biology, timber verification, South american, Leguminosae, Identification (biology), Cumaru, Biotechnology
Abstract

Made available in DSpace on 2021-06-25T12:22:16Z (GMT). No. of bitstreams: 0 Previous issue date: 2020-06-01 German Federal Ministry of Food and Agriculture (BMEL) by the LargeScale-project (Forderkennzeichen) Programa Nacional de Innovacion para la Competitividad y Productividad (Innovate Peru) Conseil Regional d'Aquitaine European Union, FEDER Investissements d'avenir Dipteryx timber has been heavily exploited in South America since 2000s due to the increasing international demand for hardwood. Developing tools for the genetic identification of Dipteryx species and their geographical origin can help to promote legal trading of timber. A collection of 800 individual trees, belonging to 6 different Dipteryx species, was genotyped based on 171 molecular markers. After the exclusion of markers out of Hardy Weinberg equilibrium or with no polymorphism or low amplification, 83 nuclear, 29 chloroplast, 13 mitochondrial single nucleotide polymorphisms (SNPs), and 2 chloroplast and 5 mitochondrial INDELS remained. Six genetic groups were identified using Bayesian Structure analyses of the nuclear SNPs, which corresponded to the different Dipteryx species collected in the field. Seventeen highly informative markers were identified as suitable for species identification and obtained self-assignment success rates to species level of 78-96%. An additional set of 15 molecular markers was selected to determine the different genetic clusters found in Dipteryx odorata and Dipteryx ferrea, obtaining self-assignment success rates of 91-100%. The success to assign samples to the correct country of origin using all or only the informative markers improved when using the nearest neighbor approach (69-92%) compared to the Bayesian approach (33-80%). While nuclear and chloroplast SNPs were more suitable for differentiating the different Dipteryx species, mitochondrial SNPs were ideal for determining the genetic clusters of D. odorata and D. ferrea. These 32 selected SNPs will be invaluable genetic tools for the accurate identification of species and country of origin of Dipteryx timber. Inst Invest Amazonia Peruana IIAP, Av Jose A Quinones Km 2-5, Iquitos, Peru Thunen Inst Forest Genet, Sieker Landstr 2, D-22927 Grosshansdorf, Germany Inst Florestal Sao Paulo, CP 1322, BR-01059970 Sao Paulo, SP, Brazil Univ Estadual Paulista, Fac Engn Ilha Solteira, Dept Fitotecnia, Ilha Solteira, SP, Brazil Univ Autonoma Gabriel Rene Moreno, Fac Ciencias Agr, Lab Dendrocronol, Carrera Ingn Forestal, Km 9 Carretera Norte, El Vallecito, Santa Cruz, Bolivia Univ Guyane, Univ Antilles, CNRS, INRA,UMR0745,EcoFoG,AgroParisTech,Cirad, Campus Agron,Ave France,BP97387, Kourou, France Univ Bordeaux, INRAE, BIOGECO, F-33610 Cestas, France Escola Nacl Bot Trop, Rua Pacheco Leao 2040, BR-22460030 Rio De Janeiro, RJ, Brazil Inst Pesquisas Jardim Bot Rio de Janeiro, Rua Pacheco Leao 915, BR-22460030 Rio De Janeiro, RJ, Brazil Univ Fed Bahia, Inst Biol, Rua Barao de Jeremoabo S-N, BR-40170115 Salvador, BA, Brazil Univ Estadual Paulista, Fac Engn Ilha Solteira, Dept Fitotecnia, Ilha Solteira, SP, Brazil German Federal Ministry of Food and Agriculture (BMEL) by the LargeScale-project (Forderkennzeichen): 281-001-01 Programa Nacional de Innovacion para la Competitividad y Productividad (Innovate Peru): 381-PNICP-PIAP-2014 Conseil Regional d'Aquitaine: 20030304002FA Conseil Regional d'Aquitaine: 20040305003FA European Union, FEDER: 2003227 Investissements d'avenir: ANR-10-EQPX-16-01 Investissements d'avenir: CEBA: ANR-10-LABX-25-01

Published
2020
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10. Tree related microhabitats in temperate and Mediterranean European forests: A hierarchical typology for inventory standardization

Author

Alexa K. Michel, Baptiste Regnery, Thibault Lachat, Kris Vandekerkhove, Yoan Paillet, Frank Krumm, Daniel Kraus, Rita Bütler, Laurent Larrieu, Susanne Winter, Dynamiques Forestières dans l'Espace Rural (DYNAFOR), Institut National de la Recherche Agronomique (INRA)-École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Centre Régional de la Propriété Forestière de Midi-Pyrénées (CRPF Midi-Pyrénées), Ecosystèmes forestiers (UR EFNO), Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA), World Wide Fund for Nature, Swiss Federal Research Institute, Chair of Silviculture, University of Freiburg, Haute école des sciences agronomiques, forestières et alimentaires (HAFL), Thunen Institute of Forest Ecosystems, Thünen Institute, Muséum national d'Histoire naturelle (MNHN), Observatoire Régional de l’Environnement Poitou-Charentes (ORE Poitou-Charentes), Research Institute for Nature and Forest (INBO), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Supérieure Agronomique de Toulouse-Institut National Polytechnique (Toulouse) (Toulouse INP), and Research Institute for Nature and Forest

Subjects
0106 biological sciences, Typology, 010504 meteorology & atmospheric sciences, Range (biology), [SDV]Life Sciences [q-bio], Forest management, Wildlife, Biodiversity, General Decision Sciences, Biology, integrative forest management, 010603 evolutionary biology, 01 natural sciences, Temperate climate, forest inventory, Ecology, Evolution, Behavior and Systematics, 0105 earth and related environmental sciences, Forest inventory, Ecology, business.industry, Environmental resource management, 15. Life on land, monitoring, Habitat, wildlife habitat, biodiversity conservation, tree structure, business
Abstract

Tree related Microhabitats (hereafter TreMs) have been widely recognized as important substrates and structures for biodiversity in both commercial and protected forests and are receiving increasing attention in management, conservation and research. How to record TreMs in forest inventories is a question of recent interest since TreMs represent potential indirect indicators for the specialized species that use them as substrates or habitat at least for a part of their life-cycle. However, there is a wide range of differing interpretations as to what exactly constitutes a TreM and what specific features should be surveyed in the field. In an attempt to harmonize future TreM inventories, we propose a definition and a typology of TreM types borne by living and dead standing trees in temperate and Mediterranean forests in Europe. Our aim is to provide users with definitions which make unequivocal TreM determination possible. Our typology is structured around seven basic forms according to morphological characteristics and biodiversity relevance: i) cavities lato sensu, ii) tree injuries and exposed wood, iii) crown deadwood, iv) excrescences, v) fruiting bodies of saproxylic fungi and fungi-like organisms, vi) epiphytic and epixylic structures, and vii) exudates. The typology is then further detailed into 15 groups and 47 types with a hierarchical structure allowing the typology to be used for different purposes. The typology, along with guidelines for standardized recording we propose, is an unprecedented reference tool to make data on TreMs comparable across different regions, forest types and tree species, and should greatly improve the reliability of TreM monitoring. It provides the basis for compiling these data and may help to improve the reliability of reporting and evaluation of the conservation value of forests. Finally, our work emphasizes the need for further research on TreMs to better understand their dynamics and their link with biodiversity in order to more fully integrate TreM monitoring into forest management.

Published
2018
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11. The GenTree Dendroecological Collection, tree-ring and wood density data from seven tree species across Europe

Author

Marlène Lefebvre, Ermioni Malliarou, Silvia Matesanz, Benjamin Dauphin, Marc Villar, Giovanni G. Vendramin, Jean Thevenet, Guillaume Bodineau, Johan Westin, José Alberto Ramírez-Valiente, Katrin Heer, Juan J. Robledo-Arnuncio, Elisabet Martínez-Sancho, Mirko Liesebach, Olivier Gilg, Pascal Milesi, Dominique Veisse, Frédéric Bernier, Eduardo Notivol, Sonja T. Kujala, Cristina C. Bastias, Vincent Lejeune, Bruno Fady, Célia Michotey, Felix Gugerli, Annie Raffin, Claudio Grefen, José M. García del Barrio, Marianne Correard, Florian Knutzen, Norbert Turion, Tanja Pyhäjärvi, Tor Myking, Mariaceleste Labriola, Silvio Schueler, Camilla Avanzi, Bárbara Carvalho, Lenka Slámová, Christophe Plomion, Anna-Maria Farsakoglou, Fernando Valladares, Andrea Piotti, Evangelos Barbas, José Climent, Florence Courdier, Ilaria Spanu, Patrick Fonti, Jean-Paul Charpentier, Birte Pakull, Nicolas Mariotte, Ricardo Alía, Vladimir L. Semerikov, Sandro Morganti, Outi Savolainen, Stephen Cavers, Georg von Arx, Francesca Bagnoli, Arnaud Jouineau, Mari Mette Tollefsrud, Kurt Ramskogler, Catherine Bastien, Filippos A. Aravanopoulos, Katri Kärkkäinen, Grégoire Le-Provost, Christian Rellstab, Darius Danusevičius, Lars Opgenoorth, Martin Lascoux, Santiago C. González-Martínez, Christoph Hartleitner, Agathe Hurel, Raquel Benavides, Mehdi Pringarbe, Alan Gray, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Philipps University, Department of Biogeography and Global Change, Museo Nacional de Ciencias Naturales (CSIC), Bavarian Office for Forest Seeding and Planting, Partenaires INRAE, Centre for Ecology and Hydrology (CEH), Centre for Ecology and Hydrology, Ecologie des Forêts Méditerranéennes (URFM), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria = National Institute for Agricultural and Food Research and Technology (INIA), Aristotle University of Thessaloniki, Institute of the Science of Food Production. CNR., Biologie intégrée pour la valorisation de la diversité des arbres et de la forêt (BioForA), Institut National de la Recherche Agronomique (INRA)-Office National des Forêts (ONF), Unité expérimentale Forêt Pierroton (UEFP), Génétique et Biomasse Forestières Orléans (GBFOR), Institut National de la Recherche Agronomique (INRA), Vytautas Magnus Univ, Biodiversité, Gènes & Communautés (BioGeCo), Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), LIECO GmbH & Co KG, University of Oulu, Uppsala University, Thünen Institute of Forest Genetics, Universidad Rey Juan Carlos [Madrid] (URJC), Norwegian Institute of Bioeconomy Research (NIBIO), Centro de Investigacion y Tecnologia Agroalimentaria de Aragon (CITA), Unité Expérimentale Entomologie et Forêt Méditerranéenne (UEFM), Austrian Research Centre for Forests (BFW), Institute of Plant and Animal Ecology, Ural Branch of Russian Academy of Sciences (UB RAS), and Skogforsk - Swedish Forestry Research Institute

Subjects
Statistics and Probability, 010504 meteorology & atmospheric sciences, Skogsvetenskap, [SDV]Life Sciences [q-bio], Library and Information Sciences, tree-ring and wood density, 01 natural sciences, Black poplar, Ecology and Environment, Education, 03 medical and health sciences, Fagus sylvatica, Recursos genéticos forestales, lcsh:Science, Beech, 030304 developmental biology, 0105 earth and related environmental sciences, 0303 health sciences, biology, Forest Science, Scots pine, Botany, VDP::Landbruks- og Fiskerifag: 900::Landbruksfag: 910::Skogbruk: 915, Forestry, Picea abies, Botanik, 15. Life on land, biology.organism_classification, Bases de datos, Computer Science Applications, Geography, Betula pendula, Pinus pinaster, lcsh:Q, Quercus petraea, Forest ecology, Statistics, Probability and Uncertainty, Europa, Information Systems
Abstract

The dataset presented here was collected by the GenTree project (EU-Horizon 2020), which aims to improve the use of forest genetic resources across Europe by better understanding how trees adapt to their local environment. This dataset of individual tree-core characteristics including ring-width series and whole-core wood density was collected for seven ecologically and economically important European tree species: silver birch (Betula pendula), European beech (Fagus sylvatica), Norway spruce (Picea abies), European black poplar (Populus nigra), maritime pine (Pinus pinaster), Scots pine (Pinus sylvestris), and sessile oak (Quercus petraea). Tree-ring width measurements were obtained from 3600 trees in 142 populations and whole-core wood density was measured for 3098 trees in 125 populations. This dataset covers most of the geographical and climatic range occupied by the selected species. The potential use of it will be highly valuable for assessing ecological and evolutionary responses to environmental conditions as well as for model development and parameterization, to predict adaptability under climate change scenarios. Measurement(s) growth ring • wood density Technology Type(s) measuring table • calculation Factor Type(s) tree species Sample Characteristic - Organism Betula pendula • Fagus sylvatica • Picea abies • Populus nigra • Pinus pinaster • Pinus sylvestris • Quercus petraea Sample Characteristic - Location Europe Published

Published
2020
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12. ENO regulates tomato fruit size through the floral meristem development network

Author

Antonia Fernández-Lozano, Juan Capel, Trinidad Angosto, Begoña García-Sogo, Niels A. Müller, Fernando J. Yuste-Lisbona, Sandra Bretones, Benito Pineda, Ana Ortíz-Atienza, Rafael Lozano, José M. Jiménez-Gómez, Vicente Moreno, Institut Jean-Pierre Bourgin (IJPB), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centro de Investigación en Biotecnología Agroalimentaria, Universidad de Almería (UAL), Department of Plant Breeding and Genetics [Cologne], Max Planck Institute for Plant Breeding Research (MPIPZ), Instituto de Biologia Molecular Y Celular de Plantas, Universitat Politècnica de València (UPV), Genome Research Group, Thünen Institute of Forest Genetics, and Spanish Ministry of Economy and Competitiveness AGL201564991-C3-1-RAGL2015-64991-C3-3-RResearch and Innovation Programme of the European Union Horizon 2020 (Breeding for Resilient, Efficient and Sustainable Organic Vegetable production [BRESOV]) 774244French National Research Agency (ANR)ANR-17-CE20-0024-02French National Research Agency (ANR)ANR-17-ERC2-0013-01

Subjects
0106 biological sciences, 0301 basic medicine, Floral meristem, [SDV]Life Sciences [q-bio], Plant Biology, Locus (genetics), Biology, Gene mutation, 01 natural sciences, 03 medical and health sciences, [SPI]Engineering Sciences [physics], Solanum lycopersicum, Locule, AP2/ERF transcription factor, Transcription factor, Gene, 2. Zero hunger, Genetics, Multidisciplinary, fungi, food and beverages, Promoter, 15. Life on land, Meristem, Biological Sciences, biology.organism_classification, CLAVATA-WUSCHEL regulatory network, GENETICA, 030104 developmental biology, Fruit size, Solanum, 010606 plant biology & botany
Abstract

[EN] A dramatic evolution of fruit size has accompanied the domestication and improvement of fruit-bearing crop species. In tomato (Solanum lycopersicum), naturally occurring cis-regulatory mutations in the genes of the CLAVATA-WUSCHEL signaling pathway have led to a significant increase in fruit size generating enlarged meristems that lead to flowers with extra organs and bigger fruits. In this work, by combining mapping-by-sequencing and CRISPR/ Cas9 genome editing methods, we isolated EXCESSIVE NUMBER OF FLORAL ORGANS (ENO), an AP2/ERF transcription factor which regulates floral meristem activity. Thus, the ENO gene mutation gives rise to plants that yield larger multilocular fruits due to an increased size of the floral meristem. Genetic analyses indicate that eno exhibits synergistic effects with mutations at the LOCULE NUMBER (encoding SlWUS) and FASCIATED (encoding SlCLV3) loci, two central players in the evolution of fruit size in the domestication of cultivated tomatoes. Our findings reveal that an eno mutation causes a substantial expansion of SlWUS expression domains in a flower-specific manner. In vitro binding results show that ENO is able to interact with the GGC-box cis-regulatory element within the SlWUS promoter region, suggesting that ENO directly regulates SlWUS expression domains to maintain floral stem-cell homeostasis. Furthermore, the study of natural allelic variation of the ENO locus proved that a cis-regulatory mutation in the promoter of ENO had been targeted by positive selection during the domestication process, setting up the background for significant increases in fruit locule number and fruit size in modern tomatoes., We thank Dr. R. Fernandez-Munoz (Instituto de Hortofruticultura Subtropical y Mediterranea-Universidad de MalagaConsejo Superior de Investigaciones Cientificas) for providing seeds of wild and cultivated tomato accessions, and Dr. R. Micol-Ponce (Universidad de Almeria) for help with the EMSA experiments. This research was supported by the Spanish Ministry of Economy and Competitiveness (Grants AGL201564991-C3-1-R and AGL2015-64991-C3-3-R) and the Research and Innovation Programme of the European Union Horizon 2020 (Breeding for Resilient, Efficient and Sustainable Organic Vegetable production [BRESOV], Project ID 774244). J.M.J.-G. was funded by Agence Nationale de la Recherche (ANR) Grant tomaTE, ANR-17-CE20-0024-02 and ANR TREMPLIN-European Research Council Grant RITMO, ANR-17-ERC2-0013-01.

Published
2020
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13. Development of new SNPs loci on Quercus robur and Quercus petraea for genetic studies covering the whole species’ distribution range

Author

Erwan Guichoux, Malte Mader, Céline Blanc-Jolivet, Ruslan Yu. Yanbaev, Svetlana Bakhtina, Bernd Degen, Yulai Yanbaev, Thünen Institute of Forest Genetics, Bashkirian Agrarian University, Biodiversité, Gènes & Communautés (BioGeCo), Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and ANR-10-EQPX-0016,XYLOFOREST,Plateforme d'Innovation ' Forêt-Bois-Fibre-Biomasse du Futur '(2010)

Subjects
0106 biological sciences, 0303 health sciences, biology, MassARRAY, Range (biology), Species distribution, Quercus petraea, Single-nucleotide polymorphism, biology.organism_classification, 01 natural sciences, DNA sequencing, Single nucleotide polymorphism, Quercus robur, 03 medical and health sciences, Restriction site, Evolutionary biology, Genotype, [SDE]Environmental Sciences, Genetics, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, 010606 plant biology & botany
Abstract

We used double digest restriction site associated DNA sequencing (ddRAD) to develop new geographically informative nuclear SNP loci in Quercus robur and Quercus petraea. Genotypes derived from sequence data of 95 individuals covering the distribution range of the species were analysed to select geographically informative and polymorphic loci within Russia and Germany. We successfully screened a selected set of 119 loci on a MassARRAY® iPLEX™ platform on 190 individuals from 19 locations in Russia. The newly developed loci will be useful for genetic studies over the whole distribution range of both species.

Published
2020
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14. Impact of chemical pollution on Atlantic eels: Facts, research needs, and implications for management

Author

Peter V. Hodson, Fabien Pierron, Marko Freese, Claude Belpaire, Research Institute for Nature and Forest, Research Institute for Nature and Forest (INBO), UMR 5805 Environnements et Paléoenvironnements Océaniques et Continentaux (EPOC), Observatoire aquitain des sciences de l'univers (OASU), Université Sciences et Technologies - Bordeaux 1-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Sciences et Technologies - Bordeaux 1-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 Thünen Institute of Fisheries Ecology

Subjects
endocrine system, Anguilla rostrata, animal structures, Health, Toxicology and Mutagenesis, [SDE.MCG]Environmental Sciences/Global Changes, 0208 environmental biotechnology, Anthropogenic pressure, 02 engineering and technology, 010501 environmental sciences, 01 natural sciences, Anguillidae, Environmental Chemistry, Sargasso sea, 14. Life underwater, ComputingMilieux_MISCELLANEOUS, 0105 earth and related environmental sciences, biology, Public Health, Environmental and Occupational Health, Chemical pollution, Research needs, biology.organism_classification, Spawn (biology), 020801 environmental engineering, Fishery, Habitat, [SDE]Environmental Sciences, Environmental science, [SDV.TOX.ECO]Life Sciences [q-bio]/Toxicology/Ecotoxicology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract

Multiple eel species of the genus Anguillidae are under anthropogenic pressure. This review presents strong evidence that chemical pollution is a driving force behind the catastrophic decline in recruitment and abundance of both the European (Anguilla anguilla) and the American eel (Anguilla rostrata). In response to this crisis, stock and habitat management policies have blindly focused on increasing the areas available for the recruitment and rearing of yellow eels, and increasing the numbers of silver eels escaping to spawn in the Sargasso Sea. No specific policies or regulations have been adopted to foster recruitment of yellow eels to uncontaminated watersheds, to monitor the quality and condition of silver eels, or to protect silver eels from contaminated environments. Research is needed to identify existing and emerging contaminant problems, to understand their potential impacts on eel reproduction, and to develop indicators of spawner quality and management actions that would increase the likelihood of successful eel reproduction and recruitment.

Published
2019
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15. Nuclear and chloroplastic SNP markers for genetic studies of timber origin for Hymenaea trees

Author

Valerie Troispoux, Marie Massot, Alexandre Magno Sebbenn, Eurídice N. Honorio Coronado, Bernd Degen, Malte Mader, Camila Lucas Chaves, Niklas Tysklind, Barbara R. V. Meyer-Sand, Céline Blanc-Jolivet, Carmen Rosa García-Dávila, Kathelyn Paredes-Villanueva, Universidade de São Paulo (USP), Thunen Inst Forest Genet, Inst Florestal Sao Paulo, Univ Autonoma Gabriel Rene Moreno, IIAP, Univ Guyane, Univ Bordeaux, Universidade Estadual Paulista (Unesp), Thünen Institute of Forest Genetics, Instituto Florestal de São Paulo, Universidade Estadual Paulista Júlio de Mesquita Filho = São Paulo State University (UNESP), Universidad Autonoma Gabriel René Moreno, Instituto de Investigaciones de la Amazonía Peruana (IIAP), Ecologie des forêts de Guyane (UMR ECOFOG), Université des Antilles (UA)-Université de Guyane (UG)-Centre National de la Recherche Scientifique (CNRS)-AgroParisTech-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA), Biodiversité, Gènes & Communautés (BioGeCo), and Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB)

Subjects
0106 biological sciences, 0301 basic medicine, [SDV]Life Sciences [q-bio], Population structure, DNA-fingerprints, MiSeq, Single-nucleotide polymorphism, RADSeq, 010603 evolutionary biology, 01 natural sciences, DNA sequencing, 03 medical and health sciences, Snp markers, Genotype, Geographical origin, Genetics, Hymenaea, SNP, Indel, Ecology, Evolution, Behavior and Systematics, 2. Zero hunger, DNA fingerprints, geographical origin, biology, food and beverages, biology.organism_classification, 030104 developmental biology, SEQUÊNCIA DO DNA
Abstract

Made available in DSpace on 2019-10-04T12:40:45Z (GMT). No. of bitstreams: 0 Previous issue date: 2019-09-01 German Federal Ministry of Food and Agriculture (BMEL) Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) Investissements d'Avenir, Convention attributive d'aide EquipEx Xyloforest European Union, FEDER We developed nuclear and chloroplastic single nucleotide polymorphism (SNP) and INDEL (insertion/deletion) markers using restriction associated DNA sequencing (RADSeq) and low coverage MiSeq genome sequencing to set up a genetic tracking method of the geographical origin of Hymenaea sp. From two initial sets of 358 and 32 loci used to genotype at least 94 individuals, a final set of 75 nSNPs, 50 cpSNPs and 6 INDELs identifying significant population structure was developed. Univ Sao Paulo, Luiz de Queiroz Coll Agr, Dept Forest Sci, Ave Padua Dias,11,POB 9, BR-13418900 Sao Paulo, Brazil Thunen Inst Forest Genet, Sieker Landstr 2, D-22927 Grosshansdorf, Germany Inst Florestal Sao Paulo, CP 1322, BR-01059970 Sao Paulo, SP, Brazil Univ Autonoma Gabriel Rene Moreno, Fac Ciencias Agr, Lab Dendrocronol, Carrera Ingn Forestal, Km 9 Carretera Norte, El Vallecito, Santa Cruz, Bolivia IIAP, LBGM, Ave Jose A Quinones Km 2-5, Iquitos, Peru Univ Guyane, Univ Antilles, CNRS, INRA,UMR0745 EcoFoG,AgroParisTech,Cirad, Campus Agron,Ave France,BP97387, Kourou, France Univ Bordeaux, INRA, BIOGECO, 69 Route Arcachon, F-33610 Cestas, France Univ Estadual Paulista, Dept Fitotecnia, Fac Engn Ilha Solteira, Ilha Solteira, SP, Brazil Univ Estadual Paulista, Dept Fitotecnia, Fac Engn Ilha Solteira, Ilha Solteira, SP, Brazil Investissements d'Avenir, Convention attributive d'aide EquipEx Xyloforest: ANR-10-EQPX-16-01 European Union, FEDER: ANR-10-EQPX-16-01 European Union, FEDER: 2003227 European Union, FEDER: ANR-10-LABX-25-01

Published
2019
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16. A Reference Genome Sequence for the European Silver Fir (Abies alba Mill.): A Community-Generated Genomic Resource

Author

Zeki Kaya, Felix Gugerli, Katalin Csilléry, Jèssica Gómez-Garrido, Katrin Heer, Luca Bianco, Elena Mosca, Birgit Kersten, David B. Neale, Konstantin V. Krutovsky, Christian Rellstab, Mária Höhn, Dušan Gömöry, Lars Opgenoorth, Sabine Brodbeck, Tyler Alioto, Sascha Liepelt, Santiago C. González-Martínez, Fernando Cruz, Giovanni G. Vendramin, Michela Troggio, Matthias Fladung, Berthold Heinze, Barbara Fussi, Christoph Sperisen, Delphine Grivet, Marta Gut, Ole K. Hansen, Kristian K. Ullrich, Bruno Fady, Marjana Westergren, Birgit Ziegenhagen, University of Trento, Centro de Regulación Genómica (CRG), Universitat Pompeu Fabra [Barcelona] (UPF), Centro Ricerca e Innovazione, Fondazione Edmund Mach, Instituto Agrario S. Michele all' Adige, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Department of Evolutionary Biology and Environmental Studies, University of Zurich, Ecologie des Forêts Méditerranéennes (URFM), Institut National de la Recherche Agronomique (INRA), Thünen Institute of Forest Genetics, Bavarian Office for Forestry Seed and Plant Breeding, Partenaires INRAE, Technical University in Zvolen (TUZVO), Biodiversité, Gènes & Communautés (BioGeCo), Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB), 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), University of Copenhagen = Københavns Universitet (KU), Philipps University, Middle East Technical University [Ankara] (METU), Russian Academy of Sciences [Moscow] (RAS), Siberian Federal University (SibFU), Department of Forest Genetics and Forest Tree Breeding, Georg-August-University [Göttingen], Swiss Fed Res Inst WSL, Zurcherstr 111, CH-8903 Birmensdorf, Switzerland, Institute of Bioscience and Bioresources, Slovenian Forestry Institute, PUM, Fac Biol, Karl von Frisch Str 8, D-35032 Marburg, Germany, Federal Research and Training Centre for Forests Natural Hazards and Landscape, Szent István University, Department of Plant Sciences, University of California [Davis] (UC Davis), University of California-University of California, and PT13/0001/0044

Subjects
[SDV.SA]Life Sciences [q-bio]/Agricultural sciences, 0106 biological sciences, chaîne de montagne, Sequence assembly, QH426-470, forêt européenne, génome chloroplastique, 01 natural sciences, Genome, Genome Size, Databases, Genetic, sapin pectine, changement d'affectation des sols, Genetics (clinical), 0303 health sciences, biology, High-Throughput Nucleotide Sequencing, Genomics, Abies alba, annotation, chloroplast genome, conifer genome, genome assembly, Agricultural sciences, évolution du génome, Ploidy, Abies, Genome, Plant, Biotechnology, Nuclear gene, écosystème, Chloroplast, 03 medical and health sciences, Databases, Genetic, Genetics, Genome, Chloroplast, Molecular Biology, Gene, 030304 developmental biology, Whole genome sequencing, Whole Genome Sequencing, Human Genome, Computational Biology, Molecular Sequence Annotation, Plant, 15. Life on land, biology.organism_classification, Genome Report, Evolutionary biology, Settore AGR/03 - ARBORICOLTURA GENERALE E COLTIVAZIONI ARBOREE, Sciences agricoles, 010606 plant biology & botany, Genetic monitoring
Abstract

Silver fir (Abies alba Mill.) is a keystone conifer of European montane forest ecosystems that has experienced large fluctuations in population size during during the Quaternary and, more recently, due to land-use change. To forecast the species’ future distribution and survival, it is important to investigate the genetic basis of adaptation to environmental change, notably to extreme events. For this purpose, we here provide a first draft genome assembly and annotation of the silver fir genome, established through a community-based initiative. DNA obtained from haploid megagametophyte and diploid needle tissue was used to construct and sequence Illumina paired-end and mate-pair libraries, respectively, to high depth. The assembled A. alba genome sequence accounted for over 37 million scaffolds corresponding to 18.16 Gb, with a scaffold N50 of 14,051 bp. Despite the fragmented nature of the assembly, a total of 50,757 full-length genes were functionally annotated in the nuclear genome. The chloroplast genome was also assembled into a single scaffold (120,908 bp) that shows a high collinearity with both the A. koreana and A. sibirica complete chloroplast genomes. This first genome assembly of silver fir is an important genomic resource that is now publicly available in support of a new generation of research. By genome-enabling this important conifer, this resource will open the gate for new research and more precise genetic monitoring of European silver fir forests.

Published
2019
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17. Deciphering the Epigenetic Alphabet Involved in Transgenerational Stress Memory in Crops

Author

Evangelia V. Avramidou, Stéphane Maury, Philippe Gallusci, Efi Sarri, Federico Martinelli, Eleni M. Abraham, Maria Gerakari, Eleni Tani, Na'ama Segal, Chiara Vergata, Mateo Gašparović, Valya Vassileva, Pilar S. Testillano, Glória Pinto, Eirini Kaiserli, Vasileios Fotopoulos, Miroslav Baránek, Hans Hoenicka, Erna Karalija, Dragana Miladinović, Aliki Kapazoglou, Velimir Mladenov, Manuela Nagel, European Cooperation in Science and Technology, Mladenov, Velimir, Fotopoulos, Vasileios, Kaiserli, Eirini, Karalija, Erna, Maury, Stéphane, Baránek, Miroslav, Segal, Na’ama, Testillano, P. S., Vassileva, Valya, Pinto, Glória, Nagel, Manuela, Hoenicka, Hans, Miladinovic, Dragana, Gallusci, Philippe, Vergata, Chiara, Kapazoglou, Aliki, Abraham, Eleni, Tani, Eleni, Sarri, Efi, Avramidou, Evangelia V., Gašparović, Mateo, Martinelli, Federico, Mladenov, Velimir [0000-0002-2182-6579], Fotopoulos, Vasileios [0000-0003-1205-2070], Kaiserli, Eirini [0000-0003-1517-4591], Karalija, Erna [0000-0001-7262-0645], Maury, Stéphane [0000-0003-0481-0847], Baránek, Miroslav [0000-0002-1583-3588], Segal, Na’ama [0000-0002-4133-6411, Testillano, P. S. [0000-0003-4509-7646], Vassileva, Valya [0000-0002-9055-8002], Pinto, Glória [0000-0001-7735-5131], Nagel, Manuela [0000-0003-0396-0333], Hoenicka, Hans [0000-0001-7226-3772], Miladinovic, Dragana [0000-0001-9555-9162], Gallusci, Philippe [0000-0003-1163-8299], Vergata, Chiara [0000-0003-2727-7977], Kapazoglou, Aliki [0000-0002-7584-5994], Abraham, Eleni [0000-0003-4032-5830], Tani, Eleni [0000-0001-6178-0459], Sarri, Efi [0000-0003-4816-2167], Avramidou, Evangelia V. [0000-0002-5932-1189], Gašparović, Mateo [0000-0003-2345-7882], Martinelli, Federico [0000-0002-8502-767X], University of Novi Sad, Cyprus University of Technology, University of Glasgow, University of Sarajevo, UNIVERZITET U SARAJEVU, Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), Université d'Orléans (UO)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Mendel University in Brno (MENDELU), National Center for Mariculture, Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Bulgarian Academy of Sciences (BAS), Universidade de Aveiro, Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben] (IPK-Gatersleben), Thünen Institute of Forest Genetics, Institute of Field and Vegetable Crops [Novi Sad], Ecophysiologie et Génomique Fonctionnelle de la Vigne (UMR EGFV), 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), Università degli Studi di Firenze = University of Florence [Firenze] (UNIFI), Institute for Olive Tree, Subtropical Crops and Viticulture, Hellenic Agricultural Organisation 'DEMETER', Aristotle University of Thessaloniki, Agricultural University of Athens, and University of Zagreb

Subjects
Epigenomics, 0106 biological sciences, 0301 basic medicine, Acclimatization, Inheritance Patterns, Review, 01 natural sciences, Epigenesis, Genetic, Biotic stress, Gene Expression Regulation, Plant, Biology (General), Stress memory, Spectroscopy, 2. Zero hunger, Agricultural Sciences, Epigenetic, food and beverages, General Medicine, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, Adaptation, Physiological, Computer Science Applications, Chemistry, Identification (biology), abiotic stress, biotic stress, epigenetic, methodology, stress memory, transgenerational memory, Crops, Agricultural, QH301-705.5, Biology, Catalysis, Inorganic Chemistry, 03 medical and health sciences, Transgenerational epigenetics, Stress, Physiological, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Epigenetics, Physical and Theoretical Chemistry, QD1-999, Molecular Biology, Abiotic stress, fungi, Organic Chemistry, Methodology, Agriculture Forestry and Fisheries, Transgenerational memory, DNA Methylation, Plant Breeding, 030104 developmental biology, 13. Climate action, Evolutionary biology, Alphabet, Adaptation, 010606 plant biology & botany
Abstract

20 p.-3 fig., Although epigenetic modifications have been intensely investigated over the last decade due to their role in crop adaptation to rapid climate change, it is unclear which epigenetic changes are heritable and therefore transmitted to their progeny. The identification of epigenetic marks that are transmitted to the next generations is of primary importance for their use in breeding and for the development of new cultivars with a broad-spectrum of tolerance/resistance to abiotic and biotic stresses. In this review, we discuss general aspects of plant responses to environmental stresses and provide an overview of recent findings on the role of transgenerational epigenetic modifications in crops. In addition, we take the opportunity to describe the aims of EPI-CATCH, an international COST action consortium composed by researchers from 28 countries. The aim of this COST action launched in 2020 is: (1) to define standardized pipelines and methods used in the study of epigenetic mechanisms in plants, (2) update, share, and exchange findings in epigenetic responses to environmental stresses in plants, (3) develop new concepts and frontiers in plant epigenetics and epigenomics, (4) enhance dissemination, communication, and transfer of knowledge in plant epigenetics and epigenomics, This finalization of the review was funded by COST Action CA19125—EPIgenetic mechanisms of Crop Adaptation to Climate cHange.

Published
2021
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18. Altered energy partitioning across terrestrial ecosystems in the European drought year 2018

Author

Christian Brümmer, Bart Kruijt, Arne Poyda, Bert Gielen, Giovanni Manca, Marilyn Roland, Janina Klatt, Michal Heliasz, Jan Holst, Caroline Vincke, Corinna Rebmann, Meelis Mölder, Natalia Kowalska, Nadia Vendrame, Jinshu Chi, Nina Buchmann, Andreas Ibrom, Jiří Dušek, Stephan Weber, Lenka Foltýnová, Tarek S. El-Madany, Ladislav Šigut, Joachim Ingwersen, Alexander Graf, Mika Korkiakoski, Franziska Koebsch, Frédéric Bornet, Anne De Ligne, Denis Loustau, Eugénie Paul-Limoges, Mats Nilsson, Christophe Chipeaux, Eeva-Stiina Tuittila, Christian Wille, Torsten Sachs, Pascal Kremer, Shiva Ghiasi, Matthias Peichl, Gerald Jurasinski, Harry Vereecken, Matthias Mauder, Mana Gharun, Patrizia Ney, Thomas Grünwald, Hans-Dieter Wizemann, Pia Gottschalk, Marius Schmidt, Vincenzo Magliulo, Edoardo Cremonese, Joël Léonard, Ivan Mammarella, Anne Klosterhalfen, Mirco Migliavacca, Nicola Arriga, Silvano Fares, Milan Fischer, Matthias Cuntz, Andrej Varlagin, Alexander Knohl, Christian Bernhofer, Bernard Longdoz, Ingo Völksch, Frederik Schrader, Günther Heinemann, Sébastien Lafont, Nicolas Brüggemann, Heye Bogena, Bernard Heinesch, Jan Konopka, Matthias Zeeman, Johan Neirynck, Andrea Pitacco, Lukas Siebicke, Lukas Hörtnagl, SILVA (SILVA), AgroParisTech-Université de Lorraine (UL)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), French National Research Agency (ANR)ANR-11-LABX-0002-01ANR-16-SUMF-0001-01Alexander von Humbold Stiftung (MaNiP) Federal Ministry of Education & Research (BMBF)01LN1313AGerman Federal Ministry of Food and Agriculture BMEL (ERA-NET FACCE ERAGAS) German Research Foundation (DFG)BE1721/23PAK 346FOR 1695INST 186/1118-1 FUGGGIP Ecofor SOERE F-ORE-T Finnish Center of Excellence 307331FWOG0H3317NHelmholtz Association HGF (TERENO) VH-NG-821Hainich National Park Horizon 2020 696356ICOS-FINLAND 281255Kempe Foundation SMK-1743Knut & Alice Wallenberg Foundation2015.0047Max-Planck Institute for Biogeochemistry Russian Foundation for Basic Research (RFBR)19-0401234-aSwiss National Science Foundation (SNSF)ICOS-CH Phase 2 20FI20_173691InnoFarm 407340_172433European Commission (SUPER-G) European Commission (RINGO) European Commission (ERA-NET Sumforest) 606803Service Public de Wallonie (DGO6) 1217769SustES CZ. 02.1.01/0.0/0.0/16_019/0000797CzeCOS LM2015061Swedish Research CouncilSwedish Research Council Formas201601289942-2015-49University of Padua CDPA148553, Ludwig-Maximilians University Munich, ∗Agrosphere (IBG-3), Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, Jülich, Germany, Institute of Bio- and Geosciences [Jülich] (IBG), Forschungszentrum Jülich GmbH | Centre de recherche de Juliers, Helmholtz-Gemeinschaft = Helmholtz Association-Helmholtz-Gemeinschaft = Helmholtz Association-Forschungszentrum Jülich GmbH | Centre de recherche de Juliers, Helmholtz-Gemeinschaft = Helmholtz Association-Helmholtz-Gemeinschaft = Helmholtz Association, Department of Biology, University of Antwerp (UA), Institute of Hydrology and Meteorology [Dresden], Technische Universität Dresden = Dresden University of Technology (TU Dresden), Agrosphere, IBG-3, Transfrontalière BioEcoAgro (Transfrontalière 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), Helmholtz-Gemeinschaft = Helmholtz Association, Thünen Institute of Climate-Smart Agriculture, Department of Environmental Systems Science [ETH Zürich] (D-USYS), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Department of Forest Ecology and Management, Swedish University of Agricultural Sciences (SLU), 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), Federal Ministry of Education & Research (BMBF)01LN1313AGerman Federal Ministry of Food and Agriculture BMEL (ERA-NET FACCE ERAGAS) German Research Foundation (DFG)BE1721/23PAK 346FOR 1695INST 186/1118-1 FUGGGIP Ecofor SOERE F-ORE-T Finnish Center of Excellence 307331FWOG0H3317NHelmholtz Association HGF (TERENO) VH-NG-821Hainich National Park Horizon 2020 696356ICOS-FINLAND 281255Kempe Foundation SMK-1743Knut & Alice Wallenberg Foundation2015.0047Max-Planck Institute for Biogeochemistry Russian Foundation for Basic Research (RFBR)19-0401234-aSwiss National Science Foundation (SNSF)ICOS-CH Phase 2 20FI20_173691InnoFarm 407340_172433European Commission (SUPER-G) European Commission (RINGO) European Commission (ERA-NET Sumforest) 606803Service Public de Wallonie (DGO6) 1217769SustES CZ. 02.1.01/0.0/0.0/16_019/0000797CzeCOS LM2015061Swedish Research CouncilSwedish Research Council Formas201601289942-2015-49University of Padua CDPA148553, ANR-16-SUMF-0001,ForRISK,Forest density reduction to minimize the vulnerability of Norway spruce and silver fir to extreme drought – a risk assessment(2016), ANR-11-LABX-0002,ARBRE,Recherches Avancées sur l'Arbre et les Ecosytèmes Forestiers(2011), Ludwig-Maximilians University [Munich] (LMU), 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), and Université catholique de Lille (UCL)-Université catholique de Lille (UCL)

Subjects
Peat, 010504 meteorology & atmospheric sciences, Forests, Atmospheric sciences, 01 natural sciences, Evapotranspiration, water-use efficiency, SDG 15 - Life on Land, Environmental Sciences (social aspects to be 507), Articles, 04 agricultural and veterinary sciences, Grassland, Droughts, Europe, Meteorology and Atmospheric Sciences, [SDE]Environmental Sciences, eddy-covariance, Terrestrial ecosystem, SDG 6 - Clean Water and Sanitation, General Agricultural and Biological Sciences, Farms, net carbon uptake, Climate Change, evapotranspiration, Eddy covariance, heat flux, Sensible heat, General Biochemistry, Genetics and Molecular Biology, ddc:570, Latent heat, eddy covariance, energy balance, Water-use efficiency, Biology, 0105 earth and related environmental sciences, WIMEK, Atmosphere, Global warming, 15. Life on land, 13. Climate action, Wetlands, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, Environmental science, Water Systems and Global Change, Human medicine
Abstract

Drought and heat events, such as the 2018 European drought, interact with the exchange of energy between the land surface and the atmosphere, potentially affecting albedo, sensible and latent heat fluxes, as well as CO 2 exchange. Each of these quantities may aggravate or mitigate the drought, heat, their side effects on productivity, water scarcity and global warming. We used measurements of 56 eddy covariance sites across Europe to examine the response of fluxes to extreme drought prevailing most of the year 2018 and how the response differed across various ecosystem types (forests, grasslands, croplands and peatlands). Each component of the surface radiation and energy balance observed in 2018 was compared to available data per site during a reference period 2004–2017. Based on anomalies in precipitation and reference evapotranspiration, we classified 46 sites as drought affected. These received on average 9% more solar radiation and released 32% more sensible heat to the atmosphere compared to the mean of the reference period. In general, drought decreased net CO 2 uptake by 17.8%, but did not significantly change net evapotranspiration. The response of these fluxes differed characteristically between ecosystems; in particular, the general increase in the evaporative index was strongest in peatlands and weakest in croplands. This article is part of the theme issue ‘Impacts of the 2018 severe drought and heatwave in Europe: from site to continental scale’.

Published
2020
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19. Genetic diversity and differentiation among the species of African mahogany (Khaya spp.) based on a large SNP array

Author

Blandine M. Y. Nacoulma, Doyle McKey, Kudzo Atsu Guelly, Darren Thomas, Bernd Degen, Judy Loo, Jean Joël Loumeto, Lolona Ramamonjisoa, Emmanuel Opuni-Frimpong, Marius R. M. Ekué, Erwan Guichoux, Soulemane Nourou Yorou, Birte Pakull, Ulrich Gaël Bouka Dipelet, Charles Doumenge, Thünen Institute of Forest Genetics, CGIAR, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Université Marien Ngouabi, Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Université Paul-Valéry - Montpellier 3 (UPVM)-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)-Institut de Recherche pour le Développement (IRD [France-Sud]), University of Energy and Natural Resources (UENR), Faculty of Agronomy, University of Parakou, Université Joseph Ki-Zerbo [Ouagadougou] (UJZK), Université de Lomé [Togo], Silo National des Graines Forestières, Antananarivo, Double Helix Tracking Technology, Partenaires INRAE, Biodiversité, Gènes & Communautés (BioGeCo), and Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB)

Subjects
0106 biological sciences, 0301 basic medicine, Identification, timber, [SDV]Life Sciences [q-bio], species identification, Biodiversity, Zoology, forêt tropicale, Biology, 010603 evolutionary biology, 01 natural sciences, Conservation des ressources génétiques, F30 - Génétique et amélioration des plantes, Khaya, 03 medical and health sciences, Variation génétique, K01 - Foresterie - Considérations générales, Genetics, tropical tree, Indel, genetic assignment, Ecology, Evolution, Behavior and Systematics, Genetic diversity, F70 - Taxonomie végétale et phytogéographie, Taxonomie, 15. Life on land, biology.organism_classification, Forensic science, 030104 developmental biology, africa, Genetic marker, Taxonomy (biology), P01 - Conservation de la nature et ressources foncières, Génotype, SNP array
Abstract

International audience; The genus Khaya includes some of the highest-value timber species in natural forests in Africa, which are under heavy exploitation pressure. Genetic identification of Khaya species is important to confirm the taxonomic classification for biodiversity conservation purposes and as a forensic tool aiding law enforcement in the fight against illegal logging. We collected samples from a total of 2222 trees belonging to five or six (depending on classification) different Khaya species (K. ivorensis, K. anthotheca/K. nyasica, K. grandifoliola, K. senegalensis, K. madagascariensis). Representative sampling was conducted over the natural ranges of all sampled Khaya species, in humid tropical forest and savanna zones. We genotyped individuals based on 101 molecular markers (67 nuclear, 11 chloroplast and 22 mitochondrial SNPs, 1 chloroplast indel). Bayesian clustering produced three main genetic groups assigning all K. ivorensis and all K. senegalensis trees, respectively, in two different clusters and all remaining individuals in a third cluster. Genetic self-assignment tests with all 101 SNPs had success rates of 97-100% for all species except for K. nyasica and K. madagascariensis, which could not be clearly distinguished from each other. A success rate for species identification nearly as high was observed using a subset of 15 highly differentiated SNPs. There was only very little evidence for hybridization among species and the vast majority (> 97%) of individuals were assigned to the same species group as identified based on morphological characters.

Published
2019
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20. Nuclear and plastidial SNP and INDEL markers for genetic tracking studies of Jacaranda copaia

Author

Céline Blanc-Jolivet, Alexandre Magno Sebbenn, Carmen Rosa García-Dávila, Valerie Troispoux, Kathelyn Paredes-Villanueva, Bernd Degen, Malte Mader, Niklas Tysklind, Barbara R. V. Meyer-Sand, Eurídice N. Honorio Coronado, Adline Delcamp, Instituto Florestal de São Paulo, Thünen Institute of Forest Genetics, Universidade Estadual Paulista Júlio de Mesquita Filho = São Paulo State University (UNESP), Universidad Autonoma Gabriel René Moreno, Instituto de Investigaciones de la Amazonía Peruana (IIAP), Ecologie des forêts de Guyane (UMR ECOFOG), Université des Antilles (UA)-Université de Guyane (UG)-Centre National de la Recherche Scientifique (CNRS)-AgroParisTech-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA), Biodiversité, Gènes & Communautés (BioGeCo), Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB), Inst Florestal Sao Paulo, Thunen Inst Forest Genet, Universidade Estadual Paulista (Unesp), Univ Autonoma Gabriel Rene Moreno, IIAP, Univ Guyane, and Univ Bordeaux

Subjects
0106 biological sciences, 0301 basic medicine, food.ingredient, Jacaranda copaia, MassARRAY, [SDV]Life Sciences [q-bio], DNA-fingerprints, MiSeq, Population genetics, Single-nucleotide polymorphism, Biology, RADSeq, 010603 evolutionary biology, 01 natural sciences, DNA sequencing, 03 medical and health sciences, massARRAY, food, Geographical origin, Genotype, parasitic diseases, Genetics, SNP, Indel, Ecology, Evolution, Behavior and Systematics, 2. Zero hunger, DNA fingerprints, geographical origin, 15. Life on land, Genetic differentiation, 030104 developmental biology, tropical timber, Tropical timber
Abstract

Made available in DSpace on 2019-10-04T12:40:46Z (GMT). No. of bitstreams: 0 Previous issue date: 2019-09-01 German Federal Ministry of Food and Agriculture Conseil Regional d'Aquitaine European Union FEDER Investissements d'avenir Nuclear and plastidial single nucleotide polymorphism (SNP) and INDEL markers were developed using restriction associated DNA sequencing (RADSeq) and low coverage MiSeq genome sequencing for population genetics and timber tracking purposes in the Neotropical timber species Jacaranda copaia. We used 407 nuclear SNPs, 29 chloroplast, and 31 mitochondrial loci to genotype 92 individuals from Brazil, Bolivia, French Guiana, and Peru. Based on high amplification rates and genetic differentiation among populations, 113 nuclear SNPs, 11 chloroplast, and 4 mitochondrial loci were selected, and their use validated for genetic tracking of timber origin. Inst Florestal Sao Paulo, CP 1322, BR-01059970 Sao Paulo, SP, Brazil Thunen Inst Forest Genet, Sieker Landstr 2, D-22927 Grosshansdorf, Germany Univ Estadual Paulista, Fac Engn Ilha Solteira, Dept Fitotecnia, Ilha Solteira, SP, Brazil Univ Autonoma Gabriel Rene Moreno, Fac Ciencias Agr, Lab Dendrocronol, Carrera Ingn Forestal, Km 9 Carretera Norte, El Vallecito, Santa Cruz, Bolivia IIAP, Ave Jose A Quinones Km 2-5, Iquitos, Peru Univ Guyane, Univ Antilles, CNRS, INRA,UMR0745 EcoFoG,AgroParisTech,Cirad, Campus Agron,Ave France,BP97387, Kourou, France Univ Bordeaux, INRA, BIOGECO, F-33610 Cestas, France Univ Estadual Paulista, Fac Engn Ilha Solteira, Dept Fitotecnia, Ilha Solteira, SP, Brazil Conseil Regional d'Aquitaine: 20030304002FA Conseil Regional d'Aquitaine: 20040305003FA FEDER: 2003227 Investissements d'avenir: ANR-10-EQPX-16-01 Investissements d'avenir: CEBA: ANR-10-LABX-25-01 : 001-2016-SERFOR-DGGSPFFS-DGSPF

Published
2019
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21. Development of nuclear and plastid SNP and INDEL markers for population genetic studies and timber traceability of Carapa species

Author

Céline Blanc-Jolivet, Alexandre Magno Sebbenn, Henri Caron, Carmen Rosa García-Dávila, Kathelyn Paredes-Villanueva, Malte Mader, Eurídice N. Honorio Coronado, Niklas Tysklind, Erwan Guichoux, Valerie Troispoux, Bernd Degen, Barbara R. V. Meyer-Sand, Ecologie des forêts de Guyane (UMR ECOFOG), Université des Antilles (UA)-Université de Guyane (UG)-Centre National de la Recherche Scientifique (CNRS)-AgroParisTech-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA), Thünen Institute of Forest Genetics, Universidade Estadual Paulista Júlio de Mesquita Filho = São Paulo State University (UNESP), Universidad Autonoma Gabriel René Moreno, Instituto de Investigaciones de la Amazonía Peruana (IIAP), Instituto Florestal de São Paulo, Biodiversité, Gènes & Communautés (BioGeCo), Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB), Université de Guyane, Universidade Estadual Paulista (Unesp), Universidad Autónoma Gabriel René Moreno, and University Bordeaux

Subjects
0106 biological sciences, 0301 basic medicine, Carapa guianensis, MassARRAY, [SDV]Life Sciences [q-bio], Population, DNA-fingerprints, MiSeq, Carapa surinamensis, Single-nucleotide polymorphism, Biology, RADSeq, 010603 evolutionary biology, 01 natural sciences, Genome, DNA sequencing, 03 medical and health sciences, massARRAY, Geographical origin, parasitic diseases, Genetics, Indel, education, Genotyping, Ecology, Evolution, Behavior and Systematics, education.field_of_study, geographical origin, food and beverages, 15. Life on land, 030104 developmental biology, DNA profiling, Genetic marker, tropical timber, Tropical timber
Abstract

Made available in DSpace on 2019-10-06T15:45:24Z (GMT). No. of bitstreams: 0 Previous issue date: 2019-09-15 Bundesministerium für Ernährung und Landwirtschaft Conseil Régional Aquitaine Agence Nationale de la Recherche Low coverage MiSeq genome sequencing and restriction associated DNA sequencing (RADseq) were used to identify nuclear and plastid SNP and INDEL genetic markers in Carapa guianensis. 261 genetic markers including 237 nuclear SNPs, 22 plastid SNPs, and 2 plastid INDELs are described based on 96 genotyped individuals from French Guiana, Brazil, Peru, and Bolivia. The best 117 SNPs for identifying population structure and performing individual assignment are assembled into four multiplexes for MassARRAY genotyping. INRA UMR0745 EcoFoG AgroParisTech Cirad CNRS Université des Antilles Université de Guyane, Campus Agronomique, Avenue de France Thünen Institute of Forest Genetics, Sieker Landstrasse 2 School of Natural Sciences and Engineering São Paulo State University (UNESP) Carrera de Ingeniería Forestal Laboratorio de Dendrocronología Facultad de Ciencias Agrícolas Universidad Autónoma Gabriel René Moreno, Km 9 carretera al Norte, El Vallecito Instituto de Investigaciones de la Amazonía Peruana (IIAP), Av. José A. Quiñones km 2.5 Instituto Florestal de São Paulo, CP 1322 BIOGECO INRA University Bordeaux School of Natural Sciences and Engineering São Paulo State University (UNESP) Conseil Régional Aquitaine: 20030304002FA Conseil Régional Aquitaine: 20040305003FA Agence Nationale de la Recherche: ANR-10-EQPX-16-01 Agence Nationale de la Recherche: ANR-10-LABX-25-01

Published
2019
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22. Development of nuclear and plastid SNP markers for genetic studies of Dipteryx tree species in Amazonia

Author

Céline Blanc-Jolivet, Alexandre Magno Sebbenn, Marie Massot, Malte Mader, Niklas Tysklind, Eurídice N. Honorio Coronado, Bernd Degen, Kathelyn Paredes-Villanueva, Carmen Rosa García-Dávila, Valerie Troispoux, Barbara R. V. Meyer-Sand, Instituto de Investigaciones de la Amazonía Peruana (IIAP), Thünen Institute of Forest Genetics, Instituto Florestal de São Paulo, Faculdad de Ciencias Agricolas - Laboratorio de Dendrocronologia - Carrera de Ingenieria Forestal, Universidad Autonoma Gabriel René Moreno, Ecologie des forêts de Guyane (UMR ECOFOG), Université des Antilles (UA)-Université de Guyane (UG)-Centre National de la Recherche Scientifique (CNRS)-AgroParisTech-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA), Instituto de Investigaciones de la Amazonía Peruana, 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), IIAP, Thunen Inst Forest Genet, Inst Florestal Sao Paulo, Universidade Estadual Paulista (Unesp), Univ Autonoma Gabriel Rene Moreno, Univ Guyane, and INRA

Subjects
0106 biological sciences, 0301 basic medicine, MassaARRAY, MassARRAY, [SDV]Life Sciences [q-bio], Population genetics, SNP, Single-nucleotide polymorphism, 010603 evolutionary biology, 01 natural sciences, DNA sequencing, 03 medical and health sciences, Genetics, Timber species, Plastid, Indel, Ecology, Evolution, Behavior and Systematics, 2. Zero hunger, biology, Amazon rainforest, food and beverages, 15. Life on land, biology.organism_classification, Dipteryx, 030104 developmental biology, cumaru, timber species, Cumaru
Abstract

Made available in DSpace on 2019-10-04T12:40:45Z (GMT). No. of bitstreams: 0 Previous issue date: 2019-09-01 German Federal Ministry of Food and Agriculture (BMEL) Programa Nacional de Innovacion para la Competitividad y Productividad Conseil Regional d'Aquitaine European Union, FEDER We developed nuclear and plastid single nucleotide polymorphism (SNP) and insertion/deletion (INDEL) markers for Dipteryx species using a combination of restriction associated DNA sequencing (RADSeq) and low coverage MiSeq genome sequencing. Of the total 315 loci genotyped using a MassARRAY platform, 292 loci were variable and polymorphic among the 73 sampled individuals from French Guiana, Brasil, Peru, and Bolivia. A final set of 56 nuclear SNPs, 26 chloroplast SNPs, 2 chloroplast INDELs, and 32 mitochondrial SNPs identifying significant population structure was developed. This set of loci will be useful for studies on population genetics of Dipteryx species in Amazonia. IIAP, Ave Jose A Quinones Km 2-5, Iquitos, Peru Thunen Inst Forest Genet, Sieker Landstr 2, D-22927 Grosshansdorf, Germany Inst Florestal Sao Paulo, CP 1322, BR-01059970 Sao Paulo, SP, Brazil Univ Estadual Paulista, Fac Engn Ilha Solteira, Dept Fitotecnia, Ilha Solteira, SP, Brazil Univ Autonoma Gabriel Rene Moreno, Fac Ciencias Agr, Lab Dendrocronol, Carrera Ingn Forestal, Km 9 Carretera Norte, El Vallecito, Santa Cruz, Bolivia Univ Guyane, Univ Antilles, CNRS, INRA,UMR0745 EcoFoG,AgroParisTech,Cirad, Campus Agron,Ave France,BP97387, Kourou, France INRA, Plateforme Genome Transcriptome Bordeaux, Site Pierroton Batiment Artiga,69 Route Arcachon, F-33610 Cestas, France Univ Estadual Paulista, Fac Engn Ilha Solteira, Dept Fitotecnia, Ilha Solteira, SP, Brazil Programa Nacional de Innovacion para la Competitividad y Productividad: 381-PNICP-PIAP-2014 Conseil Regional d'Aquitaine: 20030304002FA Conseil Regional d'Aquitaine: 20040305003FA European Union, FEDER: 2003227 European Union, FEDER: ANR-10-EQPX-16-01 European Union, FEDER: ANR-10-LABX-25-01

Published
2019
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23. Towards long-term standardised carbon and greenhouse gas observations for monitoring Europe's terrestrial ecosystems: a review

Author

Tiphaine Tallec, Arnaud Carrara, Ralf Kiese, Juha-Pekka Tuovinen, Mika Aurela, Olaf Kolle, Bernard Heinesch, Sébastien Gogo, Annalea Lohila, Maarten Op de Beeck, Nina Buchmann, Nicola Arriga, Hans Peter Schmid, Jukka Pumpanen, Ladislav Šigut, Meelis Mölder, Lilian Joly, Lukas Hörtnagl, Giorgio Matteucci, Leonardo Montagnani, Anders Lindroth, Hanna Silvennoinen, Robert Clement, Eric Ceschia, George Burba, Matthias Peichl, Bruce Osborne, Ana López-Ballesteros, B. Longdoz, Thomas Grünwald, Domenico Vitale, Rainer Steinbrecher, Andrea Pitacco, Lukas Siebicke, Mikaell Ottosson Löfvenius, Peter Waldner, Pasi Kolari, Marion Schrumpf, Alexander Graf, Tuomas Laurila, Oliver Sonnentag, Gianluca Filippa, Daniel Berveiller, Jouni Heiskanen, Michael P. Jones, Marc Aubinet, Sébastien C. Biraud, Mathias Herbst, Philip Meier, Mirco Migliavacca, Marian Pavelka, Per Weslien, Roland Fuß, Bert Gielen, Kamel Soudani, Mari Pihlatie, Radek Pokorný, Manuel Acosta, Simone Mereu, Mats Nilsson, Achim Grelle, Caroline Vincke, Guillaume Simioni, Patrick M. Crill, Leif Klemedtsson, Christine Moureaux, Natascha Kljun, Stefan Metzger, Christian Brümmer, Lutz Merbold, Katja Klumpp, Matthias Mauder, Christine Herschlein, Claudy Jolivet, Simone Sabbatini, Patrice Soulé, Mireille Barbaste, Céline Ratié, Edoardo Cremonese, Patrik Vestin, Nicolas Saby, Patrick Gross, Penélope Serrano Ortiz, Hakima Boukir, Giacomo Nicolini, Stefan Fleck, Sune Linder, Pavel Sedlák, Sami Haapanala, Gaëlle Vincent, David R. Nelson, Werner L. Kutsch, Edward Ayres, Lisa Wingate, Nuria Altimir, Anne De Ligne, Andreas Ibrom, Marilyn Roland, Eeva-Stiina Tuittila, Timothy Brown, Corinna Rebmann, Eiko Nemitz, Sara Maraňón Jiménez, Koen Hufkens, Andrew S. Kowalski, Ivan Mammarella, Timo Vesala, Sigrid Dengel, Eva Darenova, Markus Hehn, Anne Thimonier, Mark S. Zahniser, Matthew Saunders, John Grace, Georg Wohlfahrt, A. Cescatti, Ute Skiba, Dominique Arrouays, Petra D'Odorico, Olli Peltola, Daniela Franz, Tanguy Manise, Gerardo Fratini, Thunen Institute of Climate-Smart Agriculture, Czech Academy of Sciences [Prague] (CAS), Institute for Atmosphere and Earth System Research/ Physics, Partenaires INRAE, Centre de Ciència i Tecnologia Forestal de Catalunya (CTFC), University of Antwerp (UA), InfoSol (InfoSol), Institut National de la Recherche Agronomique (INRA), Université de Liège, Finnish Meteorological Institute (FMI), National Ecological Observatory Network, Science Office (NEON), Trinity College Dublin, Unité de service et de recherches en analyses végétales et environnementales (USRAVE), 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), Australian National University (ANU), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), LI-COR Biosciences, University of Nebraska [Lincoln], University of Nebraska System, Centro de Estudios Ambientales del Mediterraneo, European Commission, Centre d'études spatiales de la biosphère (CESBIO), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Midi-Pyrénées (OMP), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS), University of Edinburgh, Environmental Protection Agency of Aosta Valley, Stockholm University, Thunen Institute of Forest Ecosystems, Thünen Institute, Interactions Sol Plante Atmosphère (UMR ISPA), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Supérieure des Sciences Agronomiques de Bordeaux-Aquitaine (Bordeaux Sciences Agro), Unité Mixte de Recherche sur l'Ecosystème Prairial - UMR (UREP), Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Ecologie des Forêts Méditerranéennes (URFM), University of Nebraska–Lincoln, Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Midi-Pyrénées (OMP), and Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)

Subjects
Oobservational network, 010504 meteorology & atmospheric sciences, ICOS, GHG exchange, carbon cycle, [SDV]Life Sciences [q-bio], ICOS, GHG exchange, carbon cycle, standardised monitoring, observational network, climate change, Climate change, Eddy covariance, 01 natural sciences, Atmospheric Sciences, Carbon cycle, standardised monitoring, 11. Sustainability, Forest ecology, Sampling design, ddc:550, SDG 13 - Climate Action, Ecosystem, Biology, standardized protocols, 0105 earth and related environmental sciences, SDG 15 - Life on Land, business.industry, Environmental resource management, Agronomy & Agriculture, 04 agricultural and veterinary sciences, Vegetation, 15. Life on land, Earth sciences, climate change, 13. Climate action, Greenhouse gas, [SDE]Environmental Sciences, 040103 agronomy & agriculture, observational network, 0401 agriculture, forestry, and fisheries, ddc:640, Terrestrial ecosystem, business
Abstract

Research infrastructures play a key role in launching a new generation of integrated long-term, geographically distributed observation programmes designed to monitor climate change, better understand its impacts on global ecosystems, and evaluate possible mitigation and adaptation strategies. The pan-European Integrated Carbon Observation System combines carbon and greenhouse gas (GHG; CO2, CH4, N2O, H2O) observations within the atmosphere, terrestrial ecosystems and oceans. High-precision measurements are obtained using standardised methodologies, are centrally processed and openly available in a traceable and verifiable fashion in combination with detailed metadata. The Integrated Carbon Observation System ecosystem station network aims to sample climate and land-cover variability across Europe. In addition to GHG flux measurements, a large set of complementary data (including management practices, vegetation and soil characteristics) is collected to support the interpretation, spatial upscaling and modelling of observed ecosystem carbon and GHG dynamics. The applied sampling design was developed and formulated in protocols by the scientific community, representing a trade-off between an ideal dataset and practical feasibility. The use of open-access, high-quality and multi-level data products by different user communities is crucial for the Integrated Carbon Observation System in order to achieve its scientific potential and societal value.

Published
2018
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24. Isolating organic carbon fractions with varying turnover rates in temperate agricultural soils – A comprehensive method comparison

Author

Marco Griepentrog, Dinesh K. Benbi, Paola Gioacchini, Axel Don, Michelle L. Haddix, Christopher Poeplau, Sabina Yeasmin, Pere Rovira, Stephanie Grand, Rolf Nieder, Martin Wiesmeier, Bas van Wesemael, Yakov Kuzyakov, Michael Kaiser, Jennifer L. Soong, Sylvain Trigalet, Edward G. Gregorich, Anna Kühnel, Delphine Derrien, Johan Six, M. Francesca Cotrufo, Claire Chenu, I. V. Yevdokimov, Lynne M. Macdonald, Anna Gunina, Marie-Liesse Vermeire, Thünen Institute of Climate-Smart Agriculture, Department of Environmental Systems Science [ETH Zürich] (D-USYS), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology in Zürich [Zürich] (ETH Zürich), University of Kassel, University of Nebraska [Lincoln], University of Nebraska System, Punjab Agricultural University, Ecologie fonctionnelle et écotoxicologie des agroécosystèmes (ECOSYS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Université Paris-Saclay, Natural Resource Ecology Laboratory [Fort Collins] (NREL), Colorado State University [Fort Collins] (CSU), Unité de recherche Biogéochimie des Ecosystèmes Forestiers (BEF), Institut National de la Recherche Agronomique (INRA), University of Bologna, Université de Lausanne (UNIL), Agriculture and Agri-Food Canada (AAFC), Agriculture and Agri-Food [Ottawa] (AAFC), Biogeoscience [D-ERDW], Department of Earth Sciences [ETH Zürich] (D-ERDW), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology in Zürich [Zürich] (ETH Zürich)-Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology in Zürich [Zürich] (ETH Zürich), Laboratory of Applied Physical Chemistry - ISOFYS (Gent, Belgium), Universiteit Gent [Ghent], Georg-August-University [Göttingen], Bangor University, Technical University of Munich (TUM), CSIRO Agriculture and Food (CSIRO), University of Antwerp (UA), Centre Georges Lemaître for Earth and Climate Research [Louvain] (TECLIM), Earth and Life Institute [Louvain-La-Neuve] (ELI), Université Catholique de Louvain (UCL)-Université Catholique de Louvain (UCL), Université Catholique de Louvain (UCL), Forest Sciences Centre of Catalonia (CTFC), Bavarian State Research Center for Agriculture, TUM School of Life Sciences Weihenstephan, The University of Sydney, Institute of Physicochemical and Biological Problems in Soil Science, RAS, Technische Universität Braunschweig [Braunschweig], Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Department of Earth Sciences [Swiss Federal Institute of Technology - ETH Zürich] (D-ERDW), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich)- Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Universiteit Gent = Ghent University [Belgium] (UGENT), Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM), Université Catholique de Louvain = Catholic University of Louvain (UCL)-Université Catholique de Louvain = Catholic University of Louvain (UCL), Université Catholique de Louvain = Catholic University of Louvain (UCL), Centre de Ciència i Tecnologia Forestal de Catalunya (CTFC), Technische Universität Braunschweig = Technical University of Braunschweig [Braunschweig], UCL - SST/ELI/ELIC - Earth & Climate, and UCL - SST/ELI/ELIE - Environmental Sciences

Subjects
Carbon sequestration, 010504 meteorology & atmospheric sciences, [SDV]Life Sciences [q-bio], Soil Science, Fractionation, Carbon stabilization, 01 natural sciences, Microbiology, Organic matter, Biology, 0105 earth and related environmental sciences, Stable isotopes, 2. Zero hunger, Total organic carbon, chemistry.chemical_classification, Soil organic matter, Agricultural and Veterinary Sciences, Chemistry, Soil chemistry, Agronomy & Agriculture, 04 agricultural and veterinary sciences, Soil carbon, 15. Life on land, Biological Sciences, Environmental chemistry, Soil water, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, Environmental Sciences
Abstract

Fractionation of soil organic carbon (SOC) is crucial for mechanistic understanding and modeling of soil organic matter decomposition and stabilization processes. It is often aimed at separating the bulk SOC into fractions with varying turnover rates, but a comprehensive comparison of methods to achieve this is lacking. In this study, a total of 20 different SOC fractionation methods were tested by participating laboratories for their suitability to isolate fractions with varying turnover rates, using agricultural soils from three experimental sites with vegetation change from C3 to C4 22-36 years ago. Enrichment of C4-derived carbon was traced and used as a proxy for turnover rates in the fractions. Methods that apply a combination of physical (density, size) and chemical (oxidation, extraction) fractionation were identified as most effective in separating SOC into fractions with distinct turnover rates. Coarse light SOC separated by density fractionation was the most C4-carbon enriched fraction, while oxidation-resistant SOC left after extraction with NaOCl was the least C4-carbon enriched fraction. Surprisingly, even after 36 years of C4 crop cultivation in a temperate climate, no method was able to isolate a fraction with more than 76% turnover, which challenges the link to the most active plant-derived carbon pools in models. Particles with density > 2.8 g cm(-3) showed similar C4-carbon enrichment as oxidation resistant SOC, highlighting the importance of sesquioxides for SOC stabilization. The importance of clay and silt sized particles (< 50 mu m) for SOC stabilization was also confirmed. Particle size fractionation significantly outperformed aggregate size fractionation, due to the fact that larger aggregates contain smaller aggregates and organic matter particles of various sizes with different turnover rates. An evaluation scheme comprising different criteria was used to identify the most suitable methods for isolating fractions with distinct turnover rates, and potential benefits and trade-offs associated with a specific choice. Our findings can be of great help to select the appropriate method(s) for fractionation of agricultural soils.

Published
2018
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25. Mutations in EID1 and LNK2 caused light-conditional clock deceleration during tomato domestication

Author

José M. Jiménez-Gómez, Lei Zhang, Maarten Koornneef, Niels A. Müller, Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research (MPIPZ), Institute of Forest Genetics, Johann Heinrich von Thünen Institute, Laboratory of Genetics, Wageningen University and Research [Wageningen] (WUR), Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Université Paris Saclay (COmUE), Max Planck Society, International Max Planck Research School PhD fellowship, German Research Foundation under the German-Israeli Project Cooperation program (Deutsche Forschungsgemeinschaft, Deutsch-Israelische Projektkooperation) [FE552/12-1], Agence Nationale de la Recherche (ANR) Tremplin-ERC program [ANR-17-ERC2-0013-01], and LabEx Saclay Plant Sciences [ANR-10-LABX-0040-SPS]

Subjects
0301 basic medicine, Light, [SDV]Life Sciences [q-bio], Period (gene), Circadian clock, Arabidopsis, Biology, Tomato, Domestication, Light signaling, 03 medical and health sciences, Solanum lycopersicum, Phytochrome B, Circadian Clocks, Commentaries, [SDV.IDA]Life Sciences [q-bio]/Food engineering, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Groep Koornneef, [SPI.GPROC]Engineering Sciences [physics]/Chemical and Process Engineering, Circadian rhythms, Circadian rhythm, 2. Zero hunger, Multidisciplinary, Phytochrome, Arabidopsis Proteins, fungi, food and beverages, Central America, Biological Sciences, Europe, CLOCK, Fixation (population genetics), 030104 developmental biology, Evolutionary biology, Mutation, Trans-Activators, Adaptation
Abstract

International audience; Circadian period and phase of cultivated tomato (Solanum lycopersicum) were changed during domestication, likely adapting the species to its new agricultural environments. Whereas the delayed circadian phase is mainly caused by allelic variation of EID1, the genetic basis of the long circadian period has remained elusive. Here we show that a partial deletion of the clock gene LNK2 is responsible for the period lengthening in cultivated tomatoes. We use resequencing data to phylogenetically classify hundreds of tomato accessions and investigate the evolution of the eid1 and lnk2 mutations along successive domestication steps. We reveal signatures of selection across the genomic region of LNK2 and different patterns of fixation of the mutant alleles. Strikingly, LNK2 and EID1 are both involved in light input to the circadian clock, indicating that domestication specifically targeted this input pathway. In line with this, we show that the clock deceleration in the cultivated tomato is light-dependent and requires the phytochrome B1 photoreceptor. Such conditional variation in circadian rhythms may be key for latitudinal adaptation in a variety of species, including crop plants and livestock.

Published
2018
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26. Interpreting canopy development and physiology using a European phenology camera network at flux sites

Author

Bernard Longdoz, Cristina Gimeno, Christophe Moisy, Christine Moureaux, Andres Plaza-Aguilar, A. Ibrom, Matthew Wilkinson, Tanguy Manise, Pasi Kolari, Katja Klumpp, Eero Nikinmaa, Thomas Grünwald, Charles George, Dario Papale, Richard Joffre, Barbara Köstner, Lukas Hörtnagl, Lisa Wingate, Georg Wohlfahrt, Birgit Gielen, Werner Eugster, Albert Porcar-Castell, Hella Ellen Ahrends, Jean-Marc Ourcival, Marta Galvagno, Werner L. Kutsch, Bernard Heinesch, Michael Sprintsin, Tatsuro Nakaji, Olaf Kolle, Margareta Hellström, Bernard Genty, Anders Lindroth, Dominique Guyon, James I. L. Morison, Gianluca Filippa, John Grace, Edoardo Cremonese, Jérôme Ogée, Jin-Hong Guan, Albin Hammerle, Janne Levula, Toshie Mizunuma, Alexander Knohl, Dan Yakir, Manuela Balzarolo, Mirco Migliavacca, Interactions Sol Plante Atmosphère (UMR ISPA), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Supérieure des Sciences Agronomiques de Bordeaux-Aquitaine (Bordeaux Sciences Agro), Aosta Valley Regional Environmental Protection Agency (ARPA), University of Edinburgh, Max-Planck-Institut für Biogeochemie (MPI-BGC), Alice Holt Lodge, Forest Research [Great Britain], Gembloux Agro-Bio Tech [Gembloux], Université de Liège, European Academy of Bozen-Bolzano (EURAC), Universität Innsbruck [Innsbruck], Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Centro de Estudios Ambientales del Mediterraneo, University of Helsinki, Hokkaido University [Sapporo, Japan], Georg-August-University [Göttingen], Johann Heinrich von Thünen Institute, Federal Research Institute for Rural Areas, Forestry and Fisheries, Institute of Sea Fisheries, Risø National Laboratory for Sustainable Energy (Risø DTU), Technical University of Denmark [Lyngby] (DTU), Universiteit Antwerpen [Antwerpen], Università degli studi della Tuscia [Viterbo], Département Ecologie des Forêts, Prairies et milieux Aquatiques (DEPT EFPA), Institut National de la Recherche Agronomique (INRA), Technische Universität Dresden = Dresden University of Technology (TU Dresden), Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Université Paul-Valéry - Montpellier 3 (UPVM)-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)-Institut de Recherche pour le Développement (IRD [France-Sud]), Lund University [Lund], Centre for Ecology and Hydrology (CEH), Natural Environment Research Council (NERC), Ecologie et Ecophysiologie Forestières [devient SILVA en 2018] (EEF), Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL), Biologie végétale et microbiologie environnementale - UMR7265 (BVME), Institut de Biosciences et Biotechnologies d'Aix-Marseille (ex-IBEB) (BIAM), 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)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-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)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Weizmann Institute of Science [Rehovot, Israël], Universität zu Köln, Department of Plant Sciences (Cambridge, UK), University of Cambridge [UK] (CAM), Interactions Sol Plante Atmosphère (ISPA), Forest Research, Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology in Zürich [Zürich] (ETH Zürich), Hokkaido University, Georg-August-Universität Göttingen, Technische Universität Dresden (TUD), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université Paul-Valéry - Montpellier 3 (UM3), Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-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)-Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-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), Weizmann Institute of Science, Helsingin yliopisto = Helsingfors universitet = University of Helsinki, Georg-August-University = Georg-August-Universität Göttingen, Danmarks Tekniske Universitet = Technical University of Denmark (DTU), Universiteit Antwerpen = University of Antwerpen [Antwerpen], Université Paul-Valéry - Montpellier 3 (UPVM)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Universität zu Köln = University of Cologne, Department of Forest Sciences, Department of Physics, Eero Nikinmaa / Principal Investigator, Viikki Plant Science Centre (ViPS), Ecosystem processes (INAR Forest Sciences), Micrometeorology and biogeochemical cycles, and Forest Ecology and Management

Subjects
0106 biological sciences, Canopy, DECIDUOUS BROADLEAF FOREST, NET CARBON UPTAKE, 010504 meteorology & atmospheric sciences, [SDV]Life Sciences [q-bio], lcsh:Life, 01 natural sciences, regression analysis, digital image, SDG 13 - Climate Action, spatiotemporal analysis, SDG 15 - Life on Land, 4112 Forestry, concentration (composition), Ecology, Phenology, Physics, lcsh:QE1-996.5, Temperate forest, deciduous forest, Vegetation, parameterization, Europe, Chemistry, Deciduous, TEMPERATE FOREST, 1181 Ecology, evolutionary biology, canopy development, Growing season, photoperiod, phenology, 114 Physical sciences, 010603 evolutionary biology, Ecology and Environment, ECOSYSTEM RESPIRATION, pigment, lcsh:QH540-549.5, Segmented regression, SCOTS PINE, Biology, 1172 Environmental sciences, Ecology, Evolution, Behavior and Systematics, 0105 earth and related environmental sciences, Earth-Surface Processes, videography, LEAF CHLOROPHYLL, carbon dioxide, temperature, 15. Life on land, Evergreen, carbon sequestration, lcsh:Geology, lcsh:QH501-531, GREENHOUSE-GAS BALANCE, 13. Climate action, DIGITAL REPEAT PHOTOGRAPHY, CHLOROPHYLL CONTENT, Environmental science, nutrient availability, lcsh:Ecology, SOIL-TEMPERATURE, Physical geography, soil moisture
Abstract

Plant phenological development is orchestrated through subtle changes in photoperiod, temperature, soil moisture and nutrient availability. Presently, the exact timing of plant development stages and their response to climate and management practices are crudely represented in land surface models. As visual observations of phenology are laborious, there is a need to supplement long-term observations with automated techniques such as those provided by digital repeat photography at high temporal and spatial resolution. We present the first synthesis from a growing observational network of digital cameras installed on towers across Europe above deciduous and evergreen forests, grasslands and croplands, where vegetation and atmosphere CO2 fluxes are measured continuously. Using colour indices from digital images and using piecewise regression analysis of time series, we explored whether key changes in canopy phenology could be detected automatically across different land use types in the network. The piecewise regression approach could capture the start and end of the growing season, in addition to identifying striking changes in colour signals caused by flowering and management practices such as mowing. Exploring the dates of green-up and senescence of deciduous forests extracted by the piecewise regression approach against dates estimated from visual observations, we found that these phenological events could be detected adequately (RMSE < 8 and 11 days for leaf out and leaf fall, respectively). We also investigated whether the seasonal patterns of red, green and blue colour fractions derived from digital images could be modelled mechanistically using the PROSAIL model parameterised with information of seasonal changes in canopy leaf area and leaf chlorophyll and carotenoid concentrations. From a model sensitivity analysis we found that variations in colour fractions, and in particular the late spring `green hump' observed repeatedly in deciduous broadleaf canopies across the network, are essentially dominated by changes in the respective pigment concentrations. Using the model we were able to explain why this spring maximum in green signal is often observed out of phase with the maximum period of canopy photosynthesis in ecosystems across Europe. Coupling such quasi-continuous digital records of canopy colours with co-located CO2 flux measurements will improve our understanding of how changes in growing season length are likely to shape the capacity of European ecosystems to sequester CO2 in the future.

Published
2015
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27. Development of nuclear SNP markers for the timber tracking of the African tree species Sapelli, Entandrophragma cylindricum

Author

Erwan Guichoux, Nils Bourland, Bernd Degen, Adline Delcamp, Birgit Kersten, Jean-Louis Doucet, Céline Blanc-Jolivet, Thünen Institute of Forest Genetics, Royal Museum of Central Africa, Center for International Forestry Research (CIFOR), Consultative Group on International Agricultural Research [CGIAR] (CGIAR), Resources & Synergies Development Pte Ltd, Partenaires INRAE, Biodiversité, Gènes & Communautés (BioGeCo), Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB), and Nature+

Subjects
0106 biological sciences, 0301 basic medicine, Genetics, [SDV]Life Sciences [q-bio], Single-nucleotide polymorphism, Putative snps, Biology, biology.organism_classification, 010603 evolutionary biology, 01 natural sciences, DNA sequencing, 03 medical and health sciences, 030104 developmental biology, Genetic marker, Entandrophragma, Snp markers, Tree species, Ecology, Evolution, Behavior and Systematics
Abstract

International audience; We describe the development of new nuclear SNP markers for the genetic timber tracking of the geographical origin of Sapelli, Entandrophragma cylindricum (Meliaceae). Restriction associated DNA sequencing (RADseq) of two reference individuals yielded 1131 putative SNPs. Among those, 131 were selected to design four MassARRAY multiplexes and screened at 178 individuals. Seventy-two loci were selected for further use in genetic tracking.

Published
2018
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28. Development of nuclear SNP markers for genetic tracking of Iroko, Milicia excelsa and Milicia regia

Author

Céline Blanc-Jolivet, Adline Delcamp, Olivier J. Hardy, Erwan Guichoux, Kasso Daïnou, Birgit Kersten, Bernd Degen, Johann Heinrich von Thünen Institute, Nature+, Université Nationale d’Agriculture de Porto Novo, Faculté des Sciences, Evolutionary Biology and Ecology, Université Libre de Bruxelles [Bruxelles] (ULB), Biodiversité, Gènes et Communautés, Institut National de la Recherche Agronomique (INRA), Université libre de Bruxelles (ULB), Biodiversité, Gènes & Communautés (BioGeCo), and Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB)

Subjects
0301 basic medicine, Genetics, bois, timber tracking, polymorphisme des nucléotides simples, Milicia regia, biology, timber, [SDV]Life Sciences [q-bio], Milicia excelsa, marqueur génétique, Single-nucleotide polymorphism, 15. Life on land, RAD sequencing, biology.organism_classification, DNA sequencing, mass ARRAY, Single nucleotide polymorphism, milicia, 03 medical and health sciences, 030104 developmental biology, Natural range, Snp markers, Ecology, Evolution, Behavior and Systematics
Abstract

Restriction associated DNA sequencing was conducted on two genetically independent individuals of Iroko, Milicia excelsa, for the discovery of nuclear SNPs. Ninety-four samples, well-distributed over the natural range and including timber DNA, were screened at 138 loci on a MassARRAY iPLEX system. Amplification success was high and 77 loci were selected to design a set of markers for genetic timber tracking purposes.

Published
2017
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29. Does upwelling intensity determine larval fish habitats in upwelling ecosystems ? The case of Senegal and Mauritania

Author

Maik Tiedemann, Julian Döring, Christian Möllmann, Heino O. Fock, Patrice Brehmer, Thünen Institute, Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD), Institut Sénégalais de Recherches Agricoles [Dakar] (ISRA), Leibniz Centre for Tropical Marine Research (ZMT), Center for Earth System Research and Sustainability (CEN), Universität Hamburg (UHH), European Project: 603521,EC:FP7:ENV,FP7-ENV-2013-two-stage,PREFACE(2013), Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO), and Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0106 biological sciences, sardine sardina-pilchardus, Sardinella aurita, 010504 meteorology & atmospheric sciences, Effects of global warming on oceans, Canary current large marine ecosystem, Aquatic Science, Biology, Oceanography, 01 natural sciences, recruitment success, generalized additive models, Round sardinella, 14. Life underwater, Sardinella, satellite-observations, Sardina pilchardus, 0105 earth and related environmental sciences, geography, geography.geographical_feature_category, spanish sardine, upwelling index, optimal environmental window, Northwest Africa, Ecology, Continental shelf, 010604 marine biology & hydrobiology, ACL, Sardine, small pelagic fish, Pelagic zone, Ichthyoplankton, biology.organism_classification, fish larvae, eastern boundary, Upwelling, west-africa, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, sea-surface, anchovy engraulis-encrasicolus, Canary Current Large Marine Ecosystem
Abstract

WOS:000412425500005; International audience; European sardine (Sardina pilchardus) and round sardinella (Sardinella aurita) comprise two-thirds of total landings of small pelagic fishes in the Canary Current Eastern Boundary Ecosystem (CCEBE). Their spawning habitat is the continental shelf where upwelling is responsible for high productivity. While upwelling intensity is predicted to change through ocean warming, the effects of upwelling intensity on larval fish habitat expansion is not well understood. Larval habitat characteristics of both species were investigated during different upwelling intensity regimes. Three surveys were carried out to sample fish larvae during cold (permanent upwelling) and warm (low upwelling) seasons along the southern coastal upwelling area of the CCEBE (13 degrees-22.5 degrees N). Sardina pilchardus larvae were observed in areas of strong upwelling during both seasons. Larval habitat expansion was restricted from 22.5 degrees N to 17.5 degrees N during cold seasons and to 22.5 degrees N during the warm season. Sardinella aurita larvae were observed from 13 degrees N to 15 degrees N during cold seasons and 16-21 degrees N in the warm season under low upwelling conditions. Generalized additive models predicted upwelling intensity driven larval fish abundance patterns. Observations and modeling revealed species-specific spawning times and locations, that resulted in a niche partitioning allowing species' co-existence. Alterations in upwelling intensity may have drastic effects on the spawning behavior, larval survival, and probably recruitment success of a species. The results enable insights into the spawning behavior of major small pelagic fish species in the CCEBE. Understanding biological responses to physical variability are essential in managing marine resources under changing climate conditions.

Published
2017
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30. Assessing environmental impacts of genetically modified plants on non-target organisms: The relevance of in planta studies

Author

Marco Nuti, Jeremy Sweet, Antoine Messéan, Jozsef Kiss, Christoph C. Tebbe, Salvatore Arpaia, Joop J. A. van Loon, Joe N. Perry, A. Nicholas E. Birch, DTE-BBC, Research Centre Trisaia, Italian National Agency for New Tecnologies Energy and Sustainable Economic Development (ENEA), The James Hutton Institute, Plant Protection Institute [Budapest] (ATK NOVI), Centre for Agricultural Research [Budapest] (ATK), Hungarian Academy of Sciences (MTA)-Hungarian Academy of Sciences (MTA), Laboratory of Entomology, Wageningen University and Research [Wageningen] (WUR), Unité Impacts Ecologiques des Innovations en Production Végétale (ECO-INNOV), Institut National de la Recherche Agronomique (INRA), Universita degli studi di Pisa, University of Greenwich, Sweet Environmental Consultants, Thünen Institute of Biodiversity, European Project: 289706, Wageningen University and Research Centre [Wageningen] (WUR), Arpaia, S., Birch, A. N. E., Kiss, J., van Loon, J. J. A., Messean, A., Nuti, M., Perry, J. N., Sweet, J. B., Tebbe, C. C., and University of Pisa - Università di Pisa

Subjects
0301 basic medicine, Environmental Engineering, [SDV]Life Sciences [q-bio], Bacillus thuringiensis, Genetically modified crops, Biology, Environment, Risk Assessment, 03 medical and health sciences, Non target, Ecological relationship, Environmental Chemistry, Relevance (law), media_common.cataloged_instance, Ecosystem services, European Union, Laboratory of Entomology, European union, Waste Management and Disposal, Insect resistance, media_common, Environmental risk assessment, 2. Zero hunger, Ecology, business.industry, fungi, food and beverages, 15. Life on land, Laboratorium voor Entomologie, Plants, Genetically Modified, Pollution, Biotechnology, 030104 developmental biology, Risk management, Sustainable management, Non-target organisms, Insect-plant interactions, EPS, business, Environmental Monitoring
Abstract

In legal frameworks worldwide, genetically modified plants (GMPs) are subjected to pre-market environmental risk assessment (ERA) with the aim of identifying potential effects on the environment. In the European Union, the EFSA Guidance Docuinent introduces the rationale that GMPs, as well as their newly produced metabolites, represent the potential stressor to be evaluated during ERA. As a consequence, during several phases of ERA for cultivation purposes, it is considered necessary to use whole plants or plant parts in experimental protocols. The importance of in planta studies as a strategy to address impacts of GMPs tin non-target organislns is demonstrated, to evaluate both effects due to the intended modification in plant phenotype (e.g. expression of Cry proteins) and effects due to unintended modifications in plant phenotype resultihg from the transformation process (e.g. due to somaclonal variations or pleiotropic effects). In planta tests are also necessary for GMPs in which newly expressed metabolites cannot easily be studied in vitro. This paper reviews the scientific literature supporting the choice of in planta studies as a fundamental tool in ERA of GMPs in cultivation dossiers; the evidence indicates they can realistically mimic the ecological relationships occurring in their receiving environments and provide important insights into the biology and sustainable management of GMPs.

Published
2017
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31. Variation in xylem vulnerability to embolism in European beech from geographically marginal populations

Author

Hervé Cochard, Marta Benito-Garzón, José M. Torres-Ruiz, Jordi Martínez-Vilalta, Anders Ræbild, Sylvain Delzon, M. de Luis, Marzena Suchocka, Claudia Cocozza, Andreas Bolte, Srdjan Stojnic, Roberto Tognetti, Branislav Cvjetković, Institute of Lowland Forestry and Environment, University of Novi Sad, Landscape University Department, Warsaw University of Life Sciences (SGGW), Biodiversité, Gènes et Communautés, Institut National de la Recherche Agronomique (INRA), Laboratoire de Physique et Physiologie Intégratives de l’Arbre en environnement Fluctuant - Clermont Auvergne (PIAF), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne (UCA), Thunen Institute of Forest Ecosystems, Thünen Institute, Instituto per la Protezione Sostenibile delle Plante (IPSP), Faculty of Forestry, Czech University of Agriculture, IUCA, University of Zaragoza - Universidad de Zaragoza [Zaragoza], Centre de Recerca Ecològica i Aplicacions Forestals (CREAF), Department of Geosciences and Natural Resource Management [Copenhagen] (IGN), Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Dipartemento of Biocienze e Territorio, Università degli Studi del Molise, Biodiversité, Gènes & Communautés (BioGeCo), Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB), Laboratoire de Physique et Physiologie Intégratives de l’Arbre en environnement Fluctuant (PIAF), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Institut National de la Recherche Agronomique (INRA), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), and Università degli Studi del Molise = University of Molise (UNIMOL)

Subjects
European beech, climatic niche, marginal population, phenotypic variation, xylem embolism resistance, 0106 biological sciences, Physiology, Range (biology), Climate Change, Species distribution, Climate change, Plant Science, xylem, 010603 evolutionary biology, 01 natural sciences, Fagus, medicine, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Beech, biology, Resistance (ecology), Plant Dispersal, Ecology, xylème, fungi, Water, Xylem, 15. Life on land, medicine.disease, biology.organism_classification, Droughts, hêtre, Europe, Phenotype, Forest dieback, Embolism, embolisme, 13. Climate action, variation phénotypique, 010606 plant biology & botany
Abstract

Climate change is expected to increase the frequency and intensity of droughts and heatwaves in Europe, leading to effects on forest growth and major forest dieback events due to hydraulic failure caused by xylem embolism. Inter-specific variability in embolism resistance has been studied in detail, but little is known about intra-specific variability, particularly in marginal populations. We evaluated 15 European beech populations, mostly from geographically marginal sites of the species distribution range, focusing particularly on populations from the dry southern margin. We found small, but significant differences in resistance to embolism between populations, with xylem pressures causing 50% loss of hydraulic conductivity ranging from −2.84 to −3.55 MPa. Significant phenotypic clines of increasing embolism resistance with increasing temperature and aridity were observed: the southernmost beech populations growing in a warmer drier climate and with lower habitat suitability have higher resistance to embolism than those from Northern Europe growing more favourable conditions. Previous studies have shown that there is little or no difference in embolism resistance between core populations, but our findings show that marginal populations have developed ways of protecting their xylem based on either evolution or plasticity.

Published
2017
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32. Performance of process-based models for simulation of grain N in crop rotations across Europe

Author

Gaëtan Louarn, Kiril Manevski, Isik Öztürk, Dominique Ripoche-Wachter, Iñaki García de Cortázar-Atauri, Xiaogang Yin, Remy Manderscheid, Nicolas Beaudoin, Mirek Trnka, Behzad Sharif, Sanmohan Baby, Lianhai Wu, Chris Kollas, Tobias Conradt, Thomas Gaiser, Holger Hoffmann, Jørgen E. Olesen, Bruno Mary, Taru Palosuo, Kurt Christian Kersebaum, Marie Launay, P. Hlavinka, Luisa Giglio, Claas Nendel, Wilfried Mirschel, Monia Charfeddine, Françoise Ruget, Domenico Ventrella, Reimund P. Rötter, Julie Constantin, Andreas Pacholski, Frank Ewert, Munir P. Hoffmann, Hans Joachim Weigel, Agroressources et Impacts environnementaux (AgroImpact), Institut National de la Recherche Agronomique (INRA), Department of Agroecology, Aarhus University [Aarhus], Institute of Landscape Systems Analysis, Leibniz-Zentrum für Agrarlandschaftsforschung = Leibniz Centre for Agricultural Landscape Research (ZALF), Institut de Recherche pour le Développement (IRD [Nouvelle-Calédonie]), Rheinische Friedrich-Wilhelms-Universität Bonn, Rothamsted Research, Tropical Plant Prodution and Agricultural Systems Modelling (TROPAGS), Georg-August-University [Göttingen], Unità di ricerca per i sistemi colturali degli ambienti caldo-aridi (CREA-SCA), Consiglio per la Ricerca in Agricoltura e l’analisi dell’economia agraria (CREA), AGroécologie, Innovations, teRritoires (AGIR), Institut National de la Recherche Agronomique (INRA)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Agroclim (AGROCLIM), Global Change Research Institute, Czech Academy of Sciences [Prague] (CAS), Institute of Agrosystems and Bioclimatology, Mendel University in Brno, Mendel University in Brno (MENDELU), Unité de Recherche Pluridisciplinaire Prairies et Plantes Fourragères (P3F), Thünen Institute of Biodiversity, Graduate School/Inkubator, Leuphana University of Lüneburg, Environnement Méditerranéen et Modélisation des Agro-Hydrosystèmes (EMMAH), Avignon Université (AU)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), MACSUR project (2812ERA147) CARBIOCIAL research project (01LL0902 ) MACSUR project (031A103B), NORFASYS (decision nos. 268277 and 292944) MACSUR project (2851ERA01), Program I (NPU I LO1415) National Agency for Agricultural Research project no. QJ1310123., Unité d'Agronomie de Laon-Reims-Mons (AGRO-LRM), Georg-August-Universität Göttingen, UMR : AGroécologie, Innovations, TeRritoires, Ecole Nationale Supérieure Agronomique de Toulouse, UE Agroclim (UE AGROCLIM), Czech Academy of Sciences [Prague] (ASCR), and Mendel University in Brno

Subjects
Secale, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, Irrigation, model evaluation, 010504 meteorology & atmospheric sciences, Grain N content, klim, 01 natural sciences, Sustainability Science, Crop, Sativum, crop rotation, model initialization, Cover crop, 0105 earth and related environmental sciences, Mathematics, 2. Zero hunger, Crop mode, biology, crop model, 04 agricultural and veterinary sciences, Crop rotation, biology.organism_classification, calibration, Agronomy, Ecosystems Research, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, Continuous simulation, Animal Science and Zoology, Hordeum vulgare, Agronomy and Crop Science, grain N content
Abstract

The accurate estimation of crop grain nitrogen (N; N in grain yield) is crucial for optimizing agricultural N management, especially in crop rotations. In the present study, 12 process-based models were applied to simulate the grain N of i) seven crops in rotations, ii) across various pedo-climatic and agro-management conditions in Europe, iii) under both continuous simulation and single year simulation, and for iv) two calibration levels, namely minimal and detailed calibration. Generally, the results showed that the accuracy of the simulations in predicting grain N increased under detailed calibration. The models performed better in predicting the grain N of winter wheat (Triticum aestivum L.), winter barley (Hordeum vulgare L.) and spring barley (Hordeum vulgare L.) compared to spring oat (Avena sativa L.), winter rye (Secale cereale L.), pea (Pisum sativum L.) and winter oilseed rape (Brassica napus L.). These differences are linked to the intensity of parameterization with better parameterized crops showing lower prediction errors. The model performance was influenced by N fertilization and irrigation treatments, and a majority of the predictions were more accurate under low N and rainfed treatments. Moreover, the multi-model mean provided better predictions of grain N compared to any individual model. In regard to the Individual models, DAISY, FASSET, HERMES, MONICA and STICS are suitable for predicting grain N of the main crops in typical European crop rotations, which all performed well in both continuous simulation and single year simulation. Our results show that both the model initialization and the cover crop effects in crop rotations should be considered in order to achieve good performance of continuous simulation. Furthermore, the choice of either continuous simulation or single year simulation should be guided by the simulation objectives (e.g. grain yield, grain N content or N dynamics), the crop sequence (inclusion of legumes) and treatments (rate and type of N fertilizer) included in crop rotations and the model formalism.

Published
2017
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33. Remotely-sensed detection of effects of extreme droughts on gross primary production

Author

André Granier, Serge Rambal, Bernard Longdoz, Iolanda Filella, Josep Peñuelas, Alexander Knohl, Manuela Balzarolo, Chao Zhang, Jan Verbesselt, Aleixandre Verger, Zoltán Nagy, M. Mund, Sara Vicca, Achim Zeileis, Mathias Herbst, Krisztina Pintér, Plant and Vegetation Ecology (PLECO), University of Antwerp (UA), Centre de Recerca Ecològica i Aplicacions Forestals (CREAF), Universitat Autònoma de Barcelona (UAB), Ecologie et Ecophysiologie Forestières [devient SILVA en 2018] (EEF), Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL), Thünen Institute of Climate Smart Agriculture, Georg-August-University [Göttingen], Silviculture & Forest Ecol Temperate Zones, MTA SZIE Plant Ecol Res Grp, Szent István University, Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Université Paul-Valéry - Montpellier 3 (UPVM)-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)-Institut de Recherche pour le Développement (IRD [France-Sud]), Dept Biol, Universidade Federal de Lavras (UFLA), Lab Geoinformat Sci & Remote Sensing, Wageningen University and Research [Wageningen] (WUR), Fac Econ & Stat, Dept Stat, University of Innsbruck, Methusalem program of the Flemish Government, Spanish Ministry of Science and Innovation, European Union, Spanish Government, CGL2013-48074-P Catalan Government grant, SGR2014-274, European Research Council grant ERC-SyG-610028, Universitat Autònoma de Barcelona [Barcelona] (UAB), Georg-August-Universität Göttingen, Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université Paul-Valéry - Montpellier 3 (UM3), Wageningen University and Research Centre [Wageningen] (WUR), Georg-August-University = Georg-August-Universität Göttingen, Université Paul-Valéry - Montpellier 3 (UPVM)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Universidade Federal de Lavras = Federal University of Lavras (UFLA), Leopold Franzens Universität Innsbruck - University of Innsbruck, and Université Paul-Valéry - Montpellier 3 (UM3)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)

Subjects
0106 biological sciences, 010504 meteorology & atmospheric sciences, [SDV]Life Sciences [q-bio], drought, Forests, Photochemical Reflectance Index, Atmospheric sciences, 01 natural sciences, Grassland, MANIPULATION EXPERIMENTS, Laboratory of Geo-information Science and Remote Sensing, temperate climate, CLIMATE EXTREMES, broadleaved forests, Photosynthesis, quercus ilex, sécheresse, Multidisciplinary, geography.geographical_feature_category, biology, Ecology, télédétection par satellite, prairie, Vegetation, PE&RC, Droughts, Deciduous, forêt feuillue, mediterranean climate, France, MEDITERRANEAN FOREST, MODIS VEGETATION INDEXES, climat semi-aride, fagus sylvatica, climat tempéré, Article, indicateur de stress, Fagus sylvatica, PHOTOCHEMICAL REFLECTANCE INDEX, european beech, climat méditerranéen, Life Science, TERRESTRIAL PRIMARY PRODUCTION, Laboratorium voor Geo-informatiekunde en Remote Sensing, Biology, Beech, SPECTRAL REFLECTANCE, 0105 earth and related environmental sciences, geography, LIGHT-USE EFFICIENCY, NET ECOSYSTEM EXCHANGE, DECIDUOUS FOREST, production primaire brute, Primary production, Enhanced vegetation index, 15. Life on land, biology.organism_classification, 13. Climate action, Remote Sensing Technology, Environmental science, grassland, 010606 plant biology & botany, gross primary production, Remotely-sensed detection
Abstract

Severe droughts strongly impact photosynthesis (GPP), and satellite imagery has yet to demonstrate its ability to detect drought effects. Especially changes in vegetation functioning when vegetation state remains unaltered (no browning or defoliation) pose a challenge to satellite-derived indicators. We evaluated the performance of different satellite indicators to detect strong drought effects on GPP in a beech forest in France (Hesse), where vegetation state remained largely unaffected while GPP decreased substantially. We compared the results with three additional sites: a Mediterranean holm oak forest (Puéchabon), a temperate beech forest (Hainich), and a semi-arid grassland (Bugacpuszta). In Hesse, a three-year reduction in GPP following drought was detected only by the Enhanced Vegetation Index (EVI). The Photochemical Reflectance Index (PRI) also detected this drought effect, but only after normalization for absorbed light. In Puéchabon normalized PRI outperformed the other indicators, while the short-term drought effect in Hainich was not detected by any tested indicator. In contrast, most indicators, but not PRI, captured the drought effects in Bugacpuszta. Hence, PRI improved detection of drought effects on GPP in forests and we propose that PRI normalized for absorbed light is considered in future algorithms to estimate GPP from space.

Published
2016
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34. Back to the Future of Soil Metagenomics

Author

J. Colin Murrell, Geertje van Keulen, Alexander Sczyrba, Hilary M. Lappin-Scott, Philippe Lemanceau, Jan Tind Sørensen, Ines Mandic-Mulec, Timothy M Vogel, John J. Parnell, Dominique Brunel, Joseph Nesme, Edward Topp, Michael Wagner, Christa Schleper, Yong-Guan Zhu, Christoph C. Tebbe, Mark J. Bailey, Tong Zhang, Juan L. Ramos, Sara Sjöling, Wafa Achouak, Petr Baldrian, Michael Schloter, Angela Sessitsch, Xiaojun Zhang, George Tsiamis, Victor Satler Pylro, Antonio Lagares, Åsa Frostegård, Jan Dirk van Elsas, Denis Le Paslier, Thierry Heulin, Alfred Pühler, Fergal O'Gara, Liping Zhao, Spiros N. Agathos, David D. Myrold, Edouard Jurkevitch, Kristiina Kruus, Renaud Nalin, Josh D. Neufeld, Luiz Fernando Wurdig Roesch, Pascal Simonet, Søren J. Sørensen, Franco Widmer, Paolo Nannipieri, George A. Kowalchuk, Janet K. Jansson, Ampère, Département Bioingénierie (BioIng), 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), Institut de Biosciences et Biotechnologies d'Aix-Marseille (ex-IBEB) (BIAM), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-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), Laboratoire d'Ecologie Microbienne de la Rhizosphère et d'Environnements Extrêmes (LEMIRE), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), UCL - Unité de Génie Biologique (UCL), Université Catholique de Louvain = Catholic University of Louvain (UCL), Maclean Building, Benson Lane, Centre for Ecology and Hydrology, Institute of Microbiology of the CAS, Etude du Polymorphisme des Génomes Végétaux (EPGV), Institut National de la Recherche Agronomique (INRA), Dept. of Chemistry Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Pacific Northwest National Laboratory (PNNL), Technical Research Centre of Finland, VTT Technical Research Centre of Finland (VTT), Netherlands Institute of Ecology - NIOO-KNAW (NETHERLANDS), Universidad Nacional de la Plata [Argentine] (UNLP), Swansea University, Microbiologie du Sol et de l'Environnement (MSE), Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), University of Ljubljana, School of Environmental Sciences [Norwich], University of East Anglia [Norwich] (UEA), Oregon State University (OSU), LIBRAGEN S.A., Libragen, Dipartimento Scienza del Suolo e Nutrizione della Pianta, Università degli Studi di Firenze = University of Florence (UniFI), University of Waterloo [Waterloo], School of Biomedical Science, Curtin University [Perth], Planning and Transport Research Centre (PATREC)-Planning and Transport Research Centre (PATREC), School of Geosciences, University of Aberdeen, Institut für Medizinische Mikrobiologie - Institute of Medical Microbiology, Justus-Liebig-Universität Gießen = Justus Liebig University (JLU), Fiocruz Minas - René Rachou Research Center / Instituto René Rachou [Belo Horizonte, Brésil], Fundação Oswaldo Cruz / Oswaldo Cruz Foundation (FIOCRUZ), Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Grupo de Modelado y Realidad Virtual [Madrid] (GMRV), Universidad Rey Juan Carlos [Madrid] (URJC), Department for Terrestrial Ecogenetics, Helmholtz Zentrum München = German Research Center for Environmental Health, Archaea Biology and Ecogenomics Group, University of Vienna [Vienna], Center for Biotechnology (CeBiTec), Universität Bielefeld = Bielefeld University, Austrian Institute of Technology [Vienna] (AIT), School of Natural Sciences and Environmental Studies, Södertörn University (Sweden), Section of Microbiology [Copenhagen], Department of Biology [Copenhagen], Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH)-Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), Thünen Institute of Biodiversity, Agriculture and Agri-Food (AAFC), Department of Environmental and Natural Resources Management, University of Patras, GELIFES, Department of Microbial Ecology, University of Groningen, Institute for Sustainability Sciences, Agroscope, University of Kassel, Rensselaer Polytechnic Institute (RPI), Laboratory of Molecular Microbial Ecology and Ecogenomics, Department of Biological Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University [Shanghai], Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences (CAS), UCL - SST/ELI/ELIM - Applied Microbiology, 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)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Università degli Studi di Firenze = University of Florence [Firenze] (UNIFI), Justus-Liebig-Universität Gießen (JLU), Fundação Oswaldo Cruz (FIOCRUZ), German Research Center for Environmental Health, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Agriculture and Agri-Food [Ottawa] (AAFC), University of Patras [Patras], Van Elsas lab, Simonet, Pascal, Ministère de l’Enseignement supérieur et de la Recherche (France), Ampère, Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-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), Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-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)-Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Université Catholique de Louvain (UCL), Faculté d’Agriculture, de l’Alimentation et de l’Environnement, Université Hébraïque de Jérusalem, Università degli Studi di Firenze [Firenze], René Rachou Research Centre, Institut National des Sciences Appliquées (INSA)-Université de Lyon-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), and Institut National des Sciences Appliquées (INSA)-Université de Lyon-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)

Subjects
0301 basic medicine, Microbiology (medical), Opinion, 030106 microbiology, lcsh:QR1-502, ta220, Biology, microbial ecology, Microbiology, lcsh:Microbiology, 03 medical and health sciences, Microbial ecology, RARE, Soil ecology, ta219, metagenomic, GeneralLiterature_REFERENCE(e.g.,dictionaries,encyclopedias,glossaries), Ciencias Exactas, 2. Zero hunger, Resistance (ecology), Ecology, Phylum, ta1183, [SPI.NRJ]Engineering Sciences [physics]/Electric power, Edaphic, DNA, 15. Life on land, soil microbiology, soil ecology, Biology and Microbiology, 030104 developmental biology, Agriculture and Soil Science, Microbial population biology, 13. Climate action, Metagenomics, BACTERIA, ComputingMethodologies_DOCUMENTANDTEXTPROCESSING, terrestrial microbiology, Soil microbiology, MICROBIAL DIVERSITY
Abstract

Direct extraction and characterization of microbial community DNA through PCR amplicon surveys and metagenomics has revolutionized the study of environmental microbiology and microbial ecology. In particular, metagenomic analysis of nucleic acids provides direct access to the genomes of the “uncultivated majority.” Accelerated by advances in sequencing technology, microbiologists have discovered more novel phyla, classes, genera, and genes from microorganisms in the first decade and a half of the twenty-first century than since these “many very little living animalcules” were first discovered by van Leeuwenhoek. The unsurpassed diversity of soils promises continued exploration of a range of industrial, agricultural, and environmental functions. The ability to explore soil microbial communities with increasing capacity offers the highest promise for answering many outstanding who, what, where, when, why, and with whom questions such as: Which microorganisms are linked to which soil habitats? How do microbial abundances change with changing edaphic conditions? How do microbial assemblages interact and influence one another synergistically or antagonistically? What is the full extent of soil microbial diversity, both functionally and phylogenetically? What are the dynamics of microbial communities in space and time? How sensitive are microbial communities to a changing climate? What is the role of horizontal gene transfer in the stability of microbial communities? Do highly diverse microbial communities confer resistance and resilience in soils?, La lista completa de autores que integran el documento puede consultarse en el archivo., Facultad de Ciencias Exactas

Published
2016
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35. Species-specific and generic biomass equations for seedlings and saplings of European tree species

Author

Christian Wirth, Catherine Collet, Bastian Hirschfelder, Damien Provendier, Jörg Ewald, Jate Sathornkich, Heike Kawaletz, Gerald Kändler, Peter Annighöfer, Peter Schall, Philippe Balandier, Josephine Haase, Na Lin, Christian Kuehne, N. Bartsch, Sandra Cristina Müller, Jörg Wollmerstädt, Aitor Ameztegui, Anja Kahl, Michael Scherer-Lorenzen, André Marquier, Tsegay Gebereyesus, Andreas Bolte, Nico Frischbier, Christian Ammer, Carolin Seele, Jens Schröder, Tobias Hamm, Philippe Malagoli, Johannes Weidig, André Lacointe, Susanne Promberger, Heinz Röhle, M. Mund, Heino Wolf, Magnus Löf, Lluís Coll, Franka Huth, Department of Silviculture and Forest Ecology of the Temperate Zones, Georg-August-University [Göttingen], Forest Sciences Centre of Catalonia, Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA), Thunen Institute of Forest Ecosystems, Thünen Institute, Forest Sciences Center of Catalonia, Laboratoire d'Etudes des Ressources Forêt-Bois (LERFoB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, University of Applied Science of Weihenstephan, Forestry research and Competence Centre, University of Zurich, Technische Universität Dresden (TUD), Forest Research Institute Baden-Wuerttemberg (FVA), Universität Leipzig [Leipzig], DBU Naturerbe GmbH, University of Maine, Laboratoire de Physique et Physiologie Intégratives de l'Arbre Fruitier et Forestier (PIAF), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Chinese Academy of Forestry, Swedish University of Agricultural Sciences (SLU), University of Freiburg, Bavarian State Institute of Forestry, Plante and Cité, Kasetsart University, Faculty of Forest and Environment, Eberswalde University for Sustainable Development (HNE), Forestry and Forest Products Research Institute (FFPRI), Federal Agency for Nature Conservation of the Federal Ministry for the Environment Nature Conservation and Nuclear Safety (FKZ 3511 84 0200), Centre de Ciència i Tecnologia Forestal de Catalunya (CTFC), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Technische Universität Dresden = Dresden University of Technology (TU Dresden), Georg-August-University = Georg-August-Universität Göttingen, Ecosystèmes forestiers (UR EFNO), Universität Zürich [Zürich] = University of Zurich (UZH), Universität Leipzig, and Kasetsart University (KU)

Subjects
0106 biological sciences, Forest regeneration, european tree species, 010504 meteorology & atmospheric sciences, Global climate, Tree allometry, Plant Science, Biology, 01 natural sciences, Carbon cycle, Tree biomass, Afforestation, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, biomass equation, 0105 earth and related environmental sciences, Ecology, Reforestation, Forestry, 15. Life on land, Plant ecology, Allometric equations, 13. Climate action, Tree species, 010606 plant biology & botany
Abstract

Biomass equations are a helpful tool to estimate the tree and stand biomass production and standing stock. Such estimations are of great interest for science but also of great importance for global reports on the carbon cycle and the global climate system. Even though there are various collections and generic meta-analyses available with biomass equations for mature trees, reports on biomass equations for juvenile trees (seedlings and saplings) are mainly missing. Against the background of an increasing amount of reforestation and afforestation projects and forests in young successional stages, such equations are required. In this study we have collected data from various studies on the aboveground woody biomass of 19 common tree species growing in Europe. The aim of this paper was to calculate species-specific biomass equations for the aboveground woody biomass of single trees in dependence of root-collar-diameter (RCD), height (H) and the combination of the two (RCD2 H). Next to calculating species-specific biomass equations for the species available in the dataset, we also calculated generic biomass equations for all broadleaved species and all conifer species. The biomass equations should be a contribution to the pool of published biomass equations, whereas the novelty is here that the equations were exclusively derived for young trees. We thank the national research project “Ecosystem Services of Natural Forests at Forestry and Climate Policy (FKZ 3511 84 0200),” from the Federal Agency for Nature Conservation (BfN) of the Federal Ministry for the Environment Nature Conservation and Nuclear Safety (BMU) for funding this project.

Published
2016
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36. How is water-use efficiency of terrestrial ecosystems distributed and changing on Earth?

Author

Albert Olioso, Thomas Kolb, Xibao Xu, Juhua Luo, Christof Ammann, Kim Pilegaard, Xuguang Tang, Li Yao, Hengpeng Li, Werner L. Kutsch, Barbara Köstner, Zoltán Nagy, Ankur R. Desai, Department of Physics, Nanjing Institute of Geography and Limnology (Niglas), Chinese Academy of Sciences [Beijing] (CAS), Department of Atmospheric and Oceanic Sciences [Madison], University of Wisconsin-Madison, MTA-SZIE Plant Ecology Research Group, Szent István University, Northern Arizona University [Flagstaff], Environnement Méditerranéen et Modélisation des Agro-Hydrosystèmes (EMMAH), Avignon Université (AU)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), School of Geographical Science [Changchun], Northeast Normal University, Institute for Climate-Smart Agriculture, Johann Heinrich von Thünen-Institute, ICOS Headoffice, Department of Physics, Department of Chemical and Biochemical Engineering (IVC-SEP), Technical University of Denmark [Lyngby] (DTU), Institute of Hydrology and Meteorology [Dresden], Technische Universität Dresden = Dresden University of Technology (TU Dresden), Climate and Air PollutionGroup, Agroscope, This study was jointly supported by the National Natural Science Foundation of China (41030745, 41401221, 41271500), the Key Research Program of the Chinese Academy of Sciences (KZZD-EW-10-04), and the Natural Science Foundation of Jiangsu Province, China (BK20141058), School of Geographical Science, and Technische Universität Dresden (TUD)

Subjects
planète, Earth, Planet, Climate, GLOBAL-SCALE, ecosystem evapotranspiration, évapotranspiration, Atmospheric sciences, ecosystem productivity, CARBON-DIOXIDE, FORESTS, Evapotranspiration, terrestrial ecosystem, carbon 7440-44-0, changement global, global climate pattern, SDG 13 - Climate Action, water-use efficiency, Water cycle, Milieux et Changements globaux, EXCHANGE, SDG 15 - Life on Land, Multidisciplinary, EVAPOTRANSPIRATION, Ecology, long-term flux tower observation applied and field techniques, satellite-based remote sensing data, Trend analysis, Terrestrial ecosystem, CO2, efficience d'utilisation de l'eau, utilisation de l'eau, cycle du carbone, FLUXES, utilisation du sol, cycle de l'eau, [SDE.MCG]Environmental Sciences/Global Changes, education, UNITED-STATES, Subtropics, Biology, donnée satellite, 114 Physical sciences, Article, Latitude, environmental biology - General and methods [07502, Ecology], Water Supply, ressource en eau, AMERIFLUX DATA, Humans, Ecosystem, carbon-water interaction, Primates Mammalia Vertebrata Chordata Animalia (Animals, Chordates, Humans, Mammals, Primates, Vertebrates) - Hominidae [86215] human common, Terrestrial Ecology, 1172 Environmental sciences, écosystème terrestre, latitude effect, Northern Hemisphere, Water, 15. Life on land, Carbon, MODIS, 13. Climate action, Ecology, Environmental Sciences, MULTIDISCIPLINARY
Abstract

A better understanding of ecosystem water-use efficiency (WUE) will help us improve ecosystem management for mitigation as well as adaption to global hydrological change. Here, long-term flux tower observations of productivity and evapotranspiration allow us to detect a consistent latitudinal trend in WUE, rising from the subtropics to the northern high-latitudes. The trend peaks at approximately 51 degrees N, and then declines toward higher latitudes. These ground-based observations are consistent with global-scale estimates of WUE. Global analysis of WUE reveals existence of strong regional variations that correspond to global climate patterns. The latitudinal trends of global WUE for Earth's major plant functional types reveal two peaks in the Northern Hemisphere not detected by ground-based measurements. One peak is located at 20 degrees similar to 30 degrees N and the other extends a little farther north than 51 degrees N. Finally, long-term spatiotemporal trend analysis using satellite-based remote sensing data reveals that land-cover and land-use change in recent years has led to a decline in global WUE. Our study provides a new framework for global research on the interactions between carbon and water cycles as well as responses to natural and human impacts.

Published
2014
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37. Understory dynamics after disturbance accelerate succession from spruce to beech-dominated forest—the Siggaboda case study

Author

Lutz Hilbrig, Britt Maria Grundmann, Andreas Roloff, Andreas Bolte, Johann Heinrich von Thünen-Institute (TI), and Institute of Forest Botany and Forest Zoology

Subjects
Ecology, biology, [SDV]Life Sciences [q-bio], Forest management, Climate change, Forestry, Picea abies, Ecological succession, Understory, 15. Life on land, biology.organism_classification, Disturbance (ecology), Fagus sylvatica, 13. Climate action, Environmental science, Beech
Abstract

International audience; & Context It is assumed that climate change will favour European beech (Fagus sylvatica L.) to Norway spruce (Picea abies [L.] Karst.) at its northern range margins due to climate change and induced disturbance events. & Aims An old-growth mixed forest of spruce and beech, situated near the northern beech margin, was studied to reveal effects of disturbances and response processes on natural forest dynamics, focussing on the understory. & Methods We carried out analyses on understory dynamics of beech and spruce in relation to overstory release. This was done based on a sequence of stand and tree vitality inventories after a series of abiotic and biotic disturbances. & Results It became apparent that beech (understory) has a larger adaptive capacity to disturbance impacts and oversto-ry release (68 % standing volume loss) than spruce. Understory dynamics can play a key role for forest succes-sion from spruce to beech-dominated forests. Disturbances display an acceleration effect on forest succession in the face of climate change. & Conclusion Beech is poised strategically to replace spruce as the dominant tree species at the study area. Due to an increasing productivity and a lower risk of stand failure, beech may raise into the focus of forestry in southern Sweden.

Published
2014
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38. PCR survey of 50 introns in animals: Cross-amplification of homologous EPIC loci in eight non-bilaterian, protostome and deuterostome phyla

Author

Reinhold Hanel, Sylvain Mousset, Didier Aurelle, Ralf Bastrop, Andreja Ramsak, Sylvie Lapegue, Thomas Remerie, Anne Chenuil, Sophie Arnaud-Haond, Pierre Chevaldonné, Karin Gérard, Christopher Lejeusne, Edith Guilloton, Sophie Derycke, Frédérique Viard, Jean-Pierre Féral, Laboratorio Ecología Molecular, 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), Laboratoire Environnement Profond (LEP), Etudes des Ecosystèmes Profonds (EEP), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), University of Rostock, Universiteit Gent = Ghent University (UGENT), Thünen-Institute of Fisheries Ecology, Laboratoire de Génétique et Pathologie des Mollusques Marins (LGPMM), Santé, Génétique et Microbiologie des Mollusques (SGMM), Estación Biológica de Doñana (EBD), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Sexe et évolution, Département PEGASE [LBBE] (PEGASE), 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), National Institute of Biology [Ljubljana] (NIB), DIVersité et COnnectivité dans le paysage marin côtier (DIVCO), Adaptation et diversité en milieu marin (AD2M), Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut méditerranéen de biodiversité et d'écologie marine et continentale ( IMBE ), Université d'Avignon et des Pays de Vaucluse ( UAPV ) -Aix Marseille Université ( AMU ) -Institut de recherche pour le développement [IRD] : UMR237-Centre National de la Recherche Scientifique ( CNRS ), IFREMER- Département Etude des Ecosystèmes Profonds ( DEEP/LEP ), Institut Français de Recherche pour l'Exploitation de la Mer ( IFREMER ), University of Rostock [Germany], Ghent University [Belgium] ( UGENT ), Laboratoire de Génétique et Pathologie des Mollusques Marins - Ifremer ( SG2M-LGPMM ), Doñana biological station - CSIC (SPAIN), Laboratoire de Biométrie et Biologie Evolutive ( LBBE ), Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique ( Inria ) -Centre National de la Recherche Scientifique ( CNRS ), National Institute of Biology, DIVersité et COnnectivité dans le paysage marin côtier ( DIVCO ), Adaptation et diversité en milieu marin ( ADMM ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Centre National de la Recherche Scientifique ( CNRS ) -Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Centre National de la Recherche Scientifique ( CNRS ), Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UMR237-Aix Marseille Université (AMU)-Avignon Université (AU), IFREMER- Département Etude des Ecosystèmes Profonds (DEEP/LEP), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Universiteit Gent = Ghent University [Belgium] (UGENT), and Laboratoire de Génétique et Pathologie des Mollusques Marins - Ifremer (SG2M-LGPMM)

Subjects
0106 biological sciences, Eunicidae, Nematoda [Nematodes], Intron, Population genetics, Alternative barcoding, Ophiocten, Polymerase Chain Reaction, Rimicaris, 01 natural sciences, Mya [gapers], Aurelia, Alvinocaris, Non-model species, Phylogeny, Eunicella, Genetics, 0303 health sciences, Echinodermata [Echinoderms], biology, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Mesopodopsis, Porifera [Sponges], 3. Good health, [ SDV.BID.EVO ] Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Acanthaster, Annelida [segmented worms], Litoditis, Protostome, Universal primers, Nucleic Acid Amplification Techniques, Mollusca [Molluscs], Platynereis, Genetic Markers, Genome evolution, Urochordata [Sea squirts], Lophelia, Hediste, Aquatic Science, 010603 evolutionary biology, 03 medical and health sciences, Arthropoda [Arthropods], Rhizostoma, Animals, Hemimysis, Crepidula fornicata, Genetic marker, DNA Primers, 030304 developmental biology, Phylum, Intron, Non-model species, biology.organism_classification, Invertebrates, Introns, [cnidarians], Aplysina, Pelagia, Phylogeography, Evolutionary biology, Ophioderma
Abstract

Exon Primed Intron Crossing (EPIC) markers provide molecular tools that are susceptible to be variable within species while remaining amplifiable by PCR using potentially universal primers. In this study we tested the possibility of obtaining PCR products from 50 EPIC markers on 23 species belonging to seven different phyla (Porifera, Cnidaria, Arthropoda, Nematoda, Mollusca, Annelida, Echinodermata) using 70 new primer pairs. A previous study had identified and tested those loci in a dozen species, including another phylum, Urochordata (Chenuil et al., 2010). Results were contrasted among species. The best results were achieved with the oyster (Mollusca) where 28 loci provided amplicons susceptible to contain an intron according to their size. This was however not the case with the other mollusk Crepidula fornicata, which seems to have undergone a reduction in intron number or intron size. In the Porifera, 13 loci appeared susceptible to contain an intron, a surprisingly high number for this phylum considering its phylogenetic distance with genomic data used to design the primers. For two cnidarian species, numerous loci (24) were obtained. Ecdysozoan phyla (arthropods and nematodes) proved less successful than others as expected considering reports of their rapid rate of genome evolution and the worst results were obtained for several arthropods. Some general patterns among phyla arose, and we discuss how the results of this EPIC survey may give new insights into genome evolution of the study species. This work confirms that this set of EPIC loci provides an easy-to-use toolbox to identify genetic markers potentially useful for population genetics, phylogeography or phylogenetic studies for a large panel of metazoan species. We then argue that obtaining diploid sequence genotypes for these loci became simple and affordable owing to Next-Generation Sequencing development. Species surveyed in this study belong to several genera ( Acanthaster, Alvinocaris, Aplysina, Aurelia, Crepidula, Eunicella, Hediste, Hemimysis, Litoditis, Lophelia, Mesopodopsis, Mya, Ophiocten, Ophioderma, Ostrea, Pelagia, Platynereis, Rhizostoma, Rimicaris), two of them, belonging to the family Vesicomydae and Eunicidae, could not be determined at the genus level. © 2013 Elsevier B.V.

Published
2013
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39. Mechanisms and spread of bacterial resistance to antimicrobial agents

Author

Marilyn C. Roberts, Axel Cloeckaert, Stefan Schwarz, Federal Agriculture Research Center (FAL), Thünen Institute, Infectiologie Animale et Santé Publique (UR IASP), Institut National de la Recherche Agronomique (INRA), University of Washington [Seattle], Frank M. Aarestrup, and ProdInra, Migration

Subjects
0303 health sciences, biology, 030306 microbiology, medicine.drug_class, [SDV]Life Sciences [q-bio], Antibiotics, Drug resistance, biology.organism_classification, Antimicrobial, 3. Good health, Microbiology, Multiple drug resistance, [SDV] Life Sciences [q-bio], 03 medical and health sciences, Antibiotic resistance, Plasmid, medicine, Efflux, Bacteria, 030304 developmental biology
Abstract

Chapitre 6; International audience; Nowadays, antimicrobial agents are among the most frequently used therapeutics in human and veterinary medicine. Resistance to antimicrobial agents can be subdivided into two basic types of resistance, intrinsic resistance and acquired resistance. Resistance to ß-lactam antibiotics is mainly due to inactivation by ß-lactamases and decreased ability to bind to penicillin-binding proteins (PBPs) in both gram-positive and gram-negative bacteria, but may also be based on decreased uptake of ß-lactams due to permeability barriers or increased efflux via multidrug transporter systems. Different types of multidrug transporters mediating resistance to tetracycline in addition to resistance to a number of structurally unrelated compounds are described, for instance, in Escherichia coli, Salmonella, and P. aeruginosa. Plasmids, genomic islands, transposons, gene cassettes, and integrons are spread vertically during the division of the host cell, but can also be transferred horizontally between bacteria of the same or different species and genera via transduction, conjugation and mobilization, or transformation. The development of antimicrobial resistance—by either mutations, generation of new resistance genes, or acquisition of resistance genes already present in other bacteria—is a complex process that involves different mechanisms. Due to the usage of all types of antimicrobial substances for selection of resistant bacteria, prudent use of the antimicrobial agents is strongly recommended in both human and veterinary medicine, as well as in food animal production, to retain the efficacy of antimicrobial agents for the control of bacterial infections in animals.

Published
2006
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