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41 results on '"Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université de Montpellier (UM)"'

1. Transcriptome profiling of laser-captured crown root primordia reveals new pathways activated during early stages of crown root formation in rice

Author

Jérémy Lavarenne, Mathieu Gonin, Antony Champion, Marie Javelle, Hélène Adam, Jacques Rouster, Geneviève Conejéro, Marc Lartaud, Jean-Luc Verdeil, Laurent Laplaze, Christophe Sallaud, Mikael Lucas, Pascal Gantet, Diversité, adaptation, développement des plantes (UMR DIADE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Limagrain Centre de Recherche – Route d’Ennezat – 63720 Chappes, France, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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), Plateforme d'histocytologie et d'imagerie cellulaire végétale (PHIV), Biochimie et Physiologie Moléculaire des Plantes (BPMP), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-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)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-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)-Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), 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)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), CIFRE fellowship from the Association Nationale de la Recherche Technologique, France (2015/0195), CGIAR, Limagrain, ANR-10-LABX-0001,AGRO,Agricultural Sciences for sustainable Development(2010), ANR-17-CE20-0028,MASTEROOT,Détermination de gènes régulateurs maîtres du développement des racines coronaires pour l'ingénierie de la tolérance au déficit hydrique des céréales.(2017), ANR-10-INBS-0004,France-BioImaging,Développment d'une infrastructure française distribuée coordonnée(2010), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier 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), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro

Subjects
Transcription, Genetic, [SDV]Life Sciences [q-bio], génomique fonctionnelle, Gene Expression, F62 - Physiologie végétale - Croissance et développement, Plant Science, Plant Roots, Biochemistry, F30 - Génétique et amélioration des plantes, Système racinaire, Plant Growth Regulators, Cell Wall, Gene Expression Regulation, Plant, Expression des gènes, Plant Proteins, Plant Anatomy, phytogénétique, Eukaryota, Genomics, Plants, Experimental Organism Systems, Optical Equipment, Medicine, Engineering and Technology, Transcriptome Analysis, Research Article, Science, Arabidopsis Thaliana, Equipment, Oryza sativa, Brassica, Research and Analysis Methods, Model Organisms, stomatognathic system, Plant and Algal Models, DNA-binding proteins, Genetics, Gene Regulation, Grasses, Stade de développement végétal, Lasers, Gene Expression Profiling, Organisms, Biology and Life Sciences, Computational Biology, Proteins, Oryza, Genome Analysis, Regulatory Proteins, Lateral Roots, Animal Studies, Rice, Transcriptome, Transcription Factors
Abstract

International audience; Crown roots constitute the main part of the rice root system. Several key genes involved in crown root initiation and development have been identified by functional genomics approaches. Nevertheless, these approaches are impaired by functional redundancy and mutant lethality. To overcome these limitations, organ targeted transcriptome analysis can help to identify genes involved in crown root formation and early development. In this study, we generated an atlas of genes expressed in developing crown root primordia in comparison with adjacent stem cortical tissue at three different developmental stages before emergence, using laser capture microdissection. We identified 3975 genes differentially expressed in crown root primordia. About 30% of them were expressed at the three developmental stages, whereas 10.5%, 19.5% and 12.8% were specifically expressed at the early, intermediate and late stages, respectively. Sorting them by functional ontology highlighted an active transcriptional switch during the process of crown root primordia formation. Crossanalysis with other rice root development-related datasets revealed genes encoding transcription factors, chromatin remodeling factors, peptide growth factors, and cell wall remodeling enzymes that are likely to play a key role during crown root primordia formation. This atlas constitutes an open primary data resource for further studies on the regulation of crown root initiation and development.

Published
2020

2. Spatio-temporal analysis of strawberry architecture: insights into the control of branching and inflorescence complexity

Author

Marc Labadie, Karine Guy, Marie-Noëlle Demené, Yves Caraglio, Gaetan Heidsieck, Amelia Gaston, Christophe Rothan, Yann Guédon, Christophe Pradal, Béatrice Denoyes, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), Biologie du fruit et pathologie (BFP), Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Invenio, Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université de Montpellier (UM), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Scientific Data Management (ZENITH), Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), and Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)

Subjects
plant architecture, Physiology, OpenAlea, [SDV]Life Sciences [q-bio], branching, multiscale tree graph, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Plant Science, Fragaria × ananassa, hidden hybrid Markov/semi-Markov chain
Abstract

Plant architecture plays a major role in flowering and therefore in crop yield. Attempts to visualize and analyse strawberry plant architecture have been few to date. Here, we developed open-source software combining two- and three-dimensional representations of plant development over time along with statistical methods to explore the variability in spatio-temporal development of plant architecture in cultivated strawberry. We applied this software to six seasonal strawberry varieties whose plants were exhaustively described monthly at the node scale. Results showed that the architectural pattern of the strawberry plant is characterized by a decrease of the module complexity between the zeroth-order module (primary crown) and higher-order modules (lateral branch crowns and extension crowns). Furthermore, for each variety, we could identify traits with a central role in determining yield, such as date of appearance and number of branches. By modeling the spatial organization of axillary meristem fate on the zeroth-order module using a hidden hybrid Markov/semi-Markov mathematical model, we further identified three zones with different probabilities of production of branch crowns, dormant buds, or stolons. This open-source software will be of value to the scientific community and breeders in studying the influence of environmental and genetic cues on strawberry architecture and yield.

Published
2023

3. Why woody plant modularity through time and space must be integrated in fire research?

Author

Marco Antonio Chiminazzo, Tristan Charles-Dominique, Davi Rodrigo Rossatto, Aline Bertolosi Bombo, Alessandra Fidelis, Universidade Estadual Paulista Júlio de Mesquita Filho = São Paulo State University (UNESP), Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université de Montpellier (UM)

Subjects
Miconia albicans, Shrub, Plant architecture, Savanna, [SDE]Environmental Sciences, Grassy biomes, Resprouting, Climate change, Plant Science, Growth form, Fire
Abstract

Different ecosystems evolved and are maintained by fire, with their vegetation hosting species with a wide diversity of persistence strategies allowing them to insulate their body and resprout new branches after fire disturbance. Changes in fire regime are predicted due to climate change, either by promoting more frequent and/or severe fires or by reducing the number fire events due to the limitation of fuel load. Predicting the future of fire-driven ecosystems is a complex task as species’ survival depends on many factors that vary in space and time. Since plants are constantly experiencing new environments as they grow through meristem development, woody plant modularity, modules morpho-physiological aspects and their integration should be considered when investigating species strategies in fire-prone ecosystems: according to their position and their tissue composition, plants’ modules experience fire differently and will contribute differently to other modules and the whole plant survival, with consequences cascading over the overall vegetation structure. Growth modules may hold the key to understanding how fast plants can get protected from fire, ultimately helping us to predict which species will persist across changing fire regimes. We present an empirical example showing how different fire-return intervals translate into distinct pressures on the timing, protection, and location of modules and discuss how these can translate into modifications in the vegetation structure due to climate change.

Published
2023

4. Thresholds for persistent leaf photochemical damage predict plant drought resilience in a tropical rainforest

Author

Claire Fortunel, Clément Stahl, Sabrina Coste, Camille Ziegler, Géraldine Derroire, Sébastien Levionnois, Isabelle Maréchaux, Damien Bonal, Bruno Hérault, Fabien H. Wagner, Lawren Sack, Jérôme Chave, Patrick Heuret, Steven Jansen, Grace John, Christine Scoffoni, Santiago Trueba, Megan K. Bartlett, Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université de Montpellier (UM), Ecologie des forêts de Guyane (UMR ECOFOG), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-AgroParisTech-Université de Guyane (UG)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), SILVA (SILVA), AgroParisTech-Université de Lorraine (UL)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Forêts et Sociétés (UPR Forêts et Sociétés), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Institut National Polytechnique Félix Houphouët-Boigny, University of California (UC), Evolution et Diversité Biologique (EDB), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Universität Ulm - Ulm University [Ulm, Allemagne], University of Florida [Gainesville] (UF), California State University [Los Angeles] (CAL STATE LA), Biodiversité, Gènes & Communautés (BioGeCo), Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and ANR-10-LABX-0025,CEBA,CEnter of the study of Biodiversity in Amazonia(2010)

Subjects
Embolism resistance, Tropical, Drought, Photochemistry, Recovery, Physiology, [SDE]Environmental Sciences, Hydraulics, Plant Science, Rehydration
Abstract

International audience; Water stress can cause declines in plant function that persist after rehydration. Recent work has defined ‘resilience’ traits characterizing leaf resistance to persistent damage from drought, but whether these traits predict resilience in whole-plant function is unknown. It is also unknown whether the coordination between resilience and ‘resistance’ – the ability to maintain function during drought – observed globally occurs within ecosystems. For eight rainforest species, we dehydrated and subsequently rehydrated leaves, and measured water stress thresholds for declines in rehydration capacity and maximum quantum yield of photosystem II (Fv/Fm). We tested correlations with embolism resistance and dry season water potentials (ΨMD), and calculated safety margins for damage (ΨMD – thresholds) and tested correlations with drought resilience in sap flow and growth. Ψ thresholds for persistent declines in Fv/Fm, indicating resilience, were positively correlated with ΨMD and thresholds for leaf vein embolism. Safety margins for persistent declines in Fv/Fm, but not rehydration capacity, were positively correlated with drought resilience in sap flow.Correlations between resistance and resilience suggest that species' differences in performance during drought are perpetuated after drought, potentially accelerating shifts in forest composition. Resilience to photochemical damage emerged as a promising functional trait to characterize whole-plant drought resilience.

Published
2023

5. Plants stand still but hide: Imperfect and heterogeneous detection is the rule when counting plants

Author

Jan Perret, Aurélien Besnard, Anne Charpentier, Guillaume Papuga, Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), Université de Montpellier (UM), Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université de Montpellier (UM)

Subjects
Detectability, Ecology, Observer effect, Plant survey, Field methods, Plant Science, Conservation, Population monitoring, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Ecology, Evolution, Behavior and Systematics, Demography, N-mixture
Abstract

The estimation of population size and its variation across space and time largely relies on counts of individuals, generally carried out within spatial units such as quadrats or sites. Missing individuals during counting (i.e. imperfect detection) results in biased estimates of population size and trends. Imperfect detection has been shown to be the rule in animal studies, and most studies now correct for this bias by estimating detection probability. Yet this correction remains exceptional in plant studies, suggesting that most plant ecologists implicitly assume that all individuals are always detected.To assess if this assumption is valid, we conducted a field experiment to estimate individual detection probability in plant counts conducted in 1×1 m quadrats. We selected 30 herbaceous plant species along a gradient of conspicuousness at 24 sites along a gradient of habitat closure, and asked groups of observers to count individuals in 10 quadrats using three counting methods requiring progressively increasing times to complete (quick count, unlimited count and cell count). In total, 158 participants took part in the experiment, allowing an analysis of the results of 5,024 counts.Over all field sessions, no observer succeeded in detecting all the individuals in the 10 quadrats. The mean detection rate was 0.44 (ranging from 0.11 to 0.82) for the quick count, 0.59 for the unlimited count (range 0.18–0.87) and 0.74 for the cell count (range 0.46-0.94).Detection probability increased with the conspicuousness of the target species and decreased with the density of individuals and habitat closure. The observer’s experience in botany had little effect on detection probability, whereas detection was strongly affected by the time observers spent counting. Yet although the more time-consuming methods increased detection probability, none achieved perfect detection, nor did they reduce the effect on detection probability of the variables we measured.Synthesis. Our results show that detection is imperfect and highly heterogeneous when counting plants. To avoid biased estimates when assessing the size, temporal or spatial trends of plant populations, plant ecologists should use methods that estimate the detection probability of individuals rather than relying on raw counts.

Published
2023

6. Microspines in tropical climbing plants: a small-scale fix for life in an obstacle course

Author

Romain Lehnebach, Cloé Paul-Victor, Elisa Courric, Nick P Rowe, Ecologie des forêts de Guyane (UMR ECOFOG), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-AgroParisTech-Université de Guyane (UG)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Département Environnements et Sociétés (Cirad-ES), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université de Montpellier (UM), ANR-10-LABX-0025,CEBA,CEnter of the study of Biodiversity in Amazonia(2010), and European Project: 82407,GROWBOT

Subjects
Microspines, Searcher stems, Physiology, Attachment, GrowBots, Robotics, Plant Science, Plants, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, Static force, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, Climbing plants, Sliding force, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract

Many climbing plants have microspines on their stems, which facilitate attachment and prevent slipping and falling from host plant supports. Extending via growth through complex environments and anchoring stems to substrates with minimal contact forces are key benefits for climbing plants. Microspines are also highly desirable features for new technologies and applications in soft robotics. Using a novel sled-like device, we investigated static and sliding attachment forces generated by stems in 10 species of tropical climber from French Guiana differing in size and climbing habit. Eight species showed higher static and sliding forces when their stems were pulled in the basal direction against a standard surface than in the apical direction. This anisotropic behaviour suggests that tropical climbers have evolved different ratchet-like mechanisms that allow easy sliding forwards but are resistant to slipping downwards. The presence of a downwards ‘stick-and-slip’ phenomenon, where static attachment is not significantly stronger than maximal sliding attachment, was present in most species apart from three showing relatively weak attachment by microspines. This indicates that diverse microspine attachment strategies exist in climbing plants. This diversity of functional properties offers a range of potential design specifications for climbing strategies on different substrates for artificial climbing artefacts.

Published
2022

7. Novel plant communities after glacial retreat in Colombia: (many) losses and (few) gains

Author

Anthelme, Fabien, Carrasquer, Ines, Ceballos, Jorge Luis, Peyre, Gwendolyn, Ceballos, Jorge, Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université de Montpellier (UM), and Universidad de los Andes [Bogota] (UNIANDES)

Subjects
Tropical alpine, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, Climatic debt, Los Nevados national park, Andes, Plant Science, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Growth forms, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, Biogeographic origins, Post-glacial chronosequence, Ecology, Evolution, Behavior and Systematics
Abstract

International audience; Early plant primary succession in recently deglacierized terrains is a good indicator of the species losses and gains that affect novel alpine plant communities migrating under the pressure of climate warming. In the tropical alpine -páramo- region of the northern Andes, home to the world's greatest alpine phyto-diversity, forced primary succession will condition the conservation of many species. Using a post-glacial chronosequence between the little ice age and present below the Conejeras glacier (Colombia) as a space-for-time substitution approach, we sought to determine how time since deglacierization affects the composition, the biogeographic origin and the growth form distribution of novel tropical alpine plant communities. Using an array of multivariate techniques and the Dirichlet model, we assessed relationships among plant communities and with environmental factors. Communities established in less than 169 years lacked a number of characteristic and endemic species usually found in the national park Los Nevados, such as Calamagrostis effusa, Senecio isabelis and Espeletia hartwegiana. Moreover, these communities have been colonized by non-native species, e.g., Rumex acetosella. Upright shrubs and large tussock grasses, characteristic of the alpine tropics, established slowly because they required highly organic, slow-developing soils. Taxa of tropical biogeographic origin were under-represented early after deglacierization in comparison with temperate taxa. These results suggest the existence of a strong climatic debt for some native species, tropical growth forms and taxa of tropical origin, which may translate into significant taxonomic and functional losses whereas the few observed gains concern the establishment of non-native species.

Published
2022

8. Piperaceae Raddianae : A taxonomic and nomenclatural study of Giuseppe Raddi's Brazilian Piperaceae

Author

Elsie Franklin Guimarães, George Azevedo de Queiroz, Piero G. Delprete, Riccardo M. Baldini, Instituto de Pesquisas Jardim Botanico do Rio de Janeiro (JBRJ), Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université de Montpellier (UM), and Università degli Studi di Firenze = University of Florence (UniFI)

Subjects
Neotropics, Rio de Janeiro, Typification, Plant Science, South America, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, Piper, Ecology, Evolution, Behavior and Systematics, Peperomia
Abstract

International audience; Giuseppe Raddi collected in the state of Rio de Janeiro, Brazil, from November 1817 to June 1818. He published 12 new names in the family Piperaceae in an article that appeared in 1828. Raddi's article has not been cited in specialized literature and these names were never properly studied. In the present study, these names are typified, and their identity is clarified. Five new combinations are here presented, namely Peperomia callitrichoides, P. catesbaeifolia, P. cylindrica, P. gracillima, and P. plantaginifolia. The new name Piper raddianum is published, honoring him and his botanical accomplishments. In addition, the names Piper scutatum, Piper scolopendrifolium, Piper truncatum, Piper fluminense, Steffensia ampla (≡ Piper amplum), Piper variabile, Piper catesbaeafolium, Piper cylindricum, Piper pumilum, Peperomia martiana, and Piper gracillimum are here lectotypified.

Published
2023

9. Brazilian Flora 2020: Leveraging the power of a collaborative scientific network

Author

Gomes‐da‐silva, Janaína, Filardi, Fabiana L.R., Barbosa, Maria Regina V., Baumgratz, José Fernando A., Bicudo, Carlos E.M., Cavalcanti, Taciana, Coelho, Marcus A.N., Costa, Andrea, Costa, Denise, Dalcin, Eduardo Couto, Labiak, Paulo, Lima, Haroldo, Lohmann, Lúcia, Maia, Leonor, Mansano, Vidal, Menezes, Mariângela, Morim, Marli, Moura, Carlos Wallace N., Lughadha, Eimear Nic, Peralta, Denilson, Prado, Jefferson, Roque, Nádia, Stehmann, João Renato, Sylvestre, Lana, Trierveiler‐pereira, Larissa, Walter, Bruno M.T., Zimbrão, Geraldo, Forzza, Rafaela, Abreu, Fernanda, Abreu, Maria, Abreu, Vanessa H.R., Acuña‐castillo, Rafael, Afonso, Edgar A.L., Agra, Leandro A.N.N., Agra, Maria, Aguiar, Daniel P.P., Aires, Elisa, Almeda, Frank, Almeida, Gracineide S.S., Almeida, Mariana, Almeida, Nicolli B.C., Almeida, Rafael, Almeida, Roberto B.P., Almeida, Thaís, Almeida, Eduardo, Alves, Daniela, Alves, Flávio, Alves, Karina N.L., Alves, Maria B.B., Alves, Rodolfo, Amaral, Maria C.E., Amaral, André L.S., Amélio, Leandro, Amorim, André M.A., Amorim, Bruno, Amorim, Eduardo, Amorim, Vivian, Andrade, Ivanilza, Andrade, Ray, André, Thiago, Andreata, Regina H.P., Andrino, Caroline, Ângulo, María, Anjos, Cassiane, Antar, Guilherme, Antonicelli, Mirian C.A., Antunes, Lorena l.C., Aona, Lidyanne Y.S., Arana, Marcelo, Aranha, João L.M., Araújo, Anderson G.A., Araujo, Andréa, Araújo, Camila, Araujo, Cintia A.T., Araujo, Flávia, Araújo, Mário H.T., Arbo, Maria, Arnou, Emily, Asprino, Renata, Assis, Francine, Assis, Leandro C.S., Assis, Marta, Athayde Filho, Francisco, Athiê‐souza, Sarah, Azevedo, Igor H.F., Bacci, Lucas, Barbosa, Camilo V.O., Barbosa, Juliana, Barbosa‐silva, Rafael, Barcellos, Ian, Barboza, Gloria, Barcelos, Flávia R.B., Barcelos, Laísa, Barreto, Kamilla l., Barros, Fábio, Barros, Thamires l.A., Barros‐barreto, Maria B.B., Bastos, Cid J.P., Bastos, Cláudia, Batista, João A.N., Batista, Marcella M.I., Bautista, Hortencia, Benelli, Adarilda, Berguecio, Nicolás, Bernacci, Luís, Beyer, Maila, Bezerra, Andrea C.C., Bezerra, Luísa M.P.A., Bezerra, Yuri R.L., Bianchetti, Luciano, Bigio, Narcísio, Biral, Leonardo, Bissoli, Vinícius, Bittencourt, Felipe, Bochorny, Thuane, Bohn, Amabily, Bohs, Lynn, Bojacá, Gabriel F.P., Boldorini, Abril, Boldrini, Ilsi, Bolson, Mônica, Bordin, Juçara, Bordon, Natali, Borges, Rafael A.X., Borges, Rodrigo l., Bortoluzzi, Roseli l.C., Bove, Claudia, Bovini, Massimo, Braga, João M.A., Braga, Nayara S.S., Branco, Suema, Brauner, Laiana, Braz, Denise, Bringel, João B.A., Brito, Antonio l.V.T., Brito, Eliete, Bruniera, Carla, Buchoski, Monica, Buck, William, Bueno, Norma, Bueno, Vinicius, Büneker, Henrique, Bünger, Mariana, Buril‐vital, Maria T.A., Burton, George, Cabral, Andressa, Cabral, Elsa l., Cabral, Fernanda, Cabral, Tiara, Caddah, Mayara, Caires, Claudenir, Caires, Taiara, Calazans, Luana S.B., Caldas, Diana K.D., Calió, Maria, Calvo, Joel, Câmara, Paulo E.A.S., Camargo, Rodrigo, Camelo, Mel, Campos‐rocha, Antonio, Cândido, Elisa, Canestraro, Bianca, Canto‐dorow, Thais, Cantuária, Patrick, Cara, Álison l., Cárdenas, Gabriela, Cardoso, Andréia, Cardoso, Domingos B.O.S., Cardoso, Jesiane, Cardoso, Leandro J.T., Cardoso, Pedro, Cardozo, Andrey l., M.D. Cardozo, Nállarett, Carmo, Dimas, Carmo, João A.M., Carneiro, Camila, Carneiro, Cláudia, Carrijo, Tatiana, Caruzo, Maria B.R., Carvalho, Catarina, Carvalho, Dariane A.S., Carvalho, Fernanda, Carvalho, Maria l.S., Carvalho, Jefferson, Carvalho‐silva, Micheline, Castello, Ana C.D., Castro, Márcia, Castro E Silva, Isabella, Catenacci, Fernanda, Cavalcanti, Laise, Cavalheiro, Larissa, Cervi, Armando, Chacon, Roberta, Chagas, Aline, Chagas, Earl C.O., Chautems, Alain, Chauveau, Olivier, Chequín, Renata, Christ, Anderson l., Christ, Jheniffer, Cidrão, Bruno, Clark, Lynn, Coelho, Alexa A.O.P., Coelho, Guilherme, Coelho, Rubens l.G., Colletta, Gabriel, Colli‐silva, Matheus, Conceição, Adilva, Conceição, Tulio, Condack, João P.S., Contro, Fernanda l., Cordeiro, Inês, Cordeiro, Luciana, Cordeiro, Wesley P.F.S., Côrtes, Ana l.A., Costa, Daniel, Costa, Fabiane, Costa, Fernanda S.N., Costa, Francisco C.P., Costa, Géssica A.G., Costa, Isabelle G.C.M., Costa, Itayguara, Costa, Jeferson, Costa, Jorge A.S., Costa, José G.S., Costa, Maria T.R., Costa, Mitchel I.A., Costa, Suzana, Costa, Thiago, Costa, Tiago, Costa E Silva, Maria, Costa‐lima, James l., Cota, Matheus M.T., Couceiro, Yuri S.V., Coutinho, Thales, Couto, Dayvid, Couto, Ricardo, Couvo, Anielly, Cyrillo, Stephany, Dal Molin, Luis, Dalastra, Claudenice, Damasceno, Rafaella G.L., de Lazzari, Lara R.P., Deble, Leonardo, Delfini, Carolina, Delgado Junior, Geadelande, Delgado‐salinas, Alfonso, Della, Aline, Delprete, Piero, Dematteis, Massimiliano, Dettke, Greta, Devecchi, Marcelo, Dewes, Talita, Di Maio, Fernando, Dias, Kauê N.L., Dias, Micheli, Dias, Pedro, Díaz, Yani C.A., Dittrich, Vinícius A.O., Domínguez, Yoannis, Dórea, Marcos, Dorneles, Mariane, Dressler, Stefan, Duarte, Marilia, Duran, Juan D.T., Dutilh, Julie H.A., Dutra, Letícia l., Dutra, Valquíria, Echternacht, Livia, Eggers, Lilian, Erkens, Roy H.J., Eslabão, Marcelo, Espírito Santo, Fábio, Esser, Hans‐joachim, Essi, Liliana, Esteves, Gerleni l., Esteves, Roberto l., Everling, Joel, Ezcurra, Cecilia, Facco, Marlon, Fader, Andrea A.C., Falcão, Marcus J.A., Fantecelle, Laura, Farco, Gabriela, Faria, Allan l.A., Faria, Ana P.G., Faria, Aparecida, Faria, Maria, Faria, Jair, Farias, Sabrina, Farias‐singer, Rosana, Farinaccio, Maria, Fernandes, Ana, Fernandes, Fernando, Fernandes, José, Fernandes, Rozijane, Fernandes, Thiago, Fernandes, Ulisses, Fernandes, Aluisio, Fernando, Emanoel M.P., Ferreira, Carlos D.M., Ferreira, Fabrício, Ferreira, Gabriel, Ferreira, João P.R., Ferreira, Priscila P.A., Ferreira, Silvana, Ferrucci, María, Fiaschi, Pedro, Fidanza, Karina, Filgueiras, Tarciso, Firetti, Fabiana, Fleischmann, Andreas, Florentín, Javier, Florentín, Mariela, Flores, Andréia, Flores, Jerônimo M.M., Flores, Thiago, Fonseca, Luiz H.M., Fontelas, Jean, Fontella‐pereira, Jorge, Forster, Wellington, Fraga, Claudio, Fraga, Fernanda R.M., Fraga, Santiago, França, Flávio, França, Juliana R.K.G., Francisco, Jéssica N.C., Freire‐fierro, Alina, Freitas, Fernanda, Freitas, Joelcio, Freitas, Maria, Fritsch, Peter, Funez, Luís, Furtado, Samyra, Gaem, Paulo, Gaglioti, André l., Gagnon, Edeline, Gama, Beatriz R.A., Garcia, Flávia C.P., Gasper, André l., Gerace, Samuele, Giacomin, Leandro l., Giaretta, Augusto, Gil, André S.B., Gissi, Danilo, Giuffre, Pamela M.W., Giulietti, Ana, Giussani, Liliana, Goebel, Gabriela, Goes, Monique, Góes, Luiz A.A., Goldenberg, Renato, Gomes, Beatriz, Gomes, Fernanda, Gomes, Mario, Gomes‐klein, Vera l., Gonçalez, Victor, Gonçalves, Ana P.S., Gonçalves, Deise J.P., Gonella, Paulo, Gonzaga, Augusto F.N., Gonzaga, Diego, González, Favio, Gonzatti, Felipe, Gouvêa, Yuri, Graham, Shirley A.T., Gregório, Bernarda, Grings, Martin, Groppo, Milton, Grossi, Mariana, Guarçoni, Elidio A.E., Guedes, Felipe, Guedes, Juliana, Guerra, Ethiéne, Guimarães, Elsie, Guimarães, Leonardo R.S., Guimarães, Paulo J.F., Gurgel, Ely S.C., Gutiérrez, Diego, Hall, Climbiê, Harley, Raymond, Hassemer, Gustavo, Hattori, Eric K.O., Hechenleitner, Paulina, Hefler, Sonia, Heiden, Gustavo, Henning, Tilo, Henriques, Diego, Hensold, Nancy, Hinoshita, Lucas K.R., Hirai, Regina, Hirao, Yasmin, Hiriart, Florencia, Hopkins, Michael J.G., Hoyos‐gómez, Saúl, Huamantupa, Isau, Hurbath, Fernanda, Iganci, João R.V., Ilkiu‐borges, Anna l., Imig, Daniela, Inácio, Camila, Indriunas, Alexandre, Jacques, Eliane l., Jacques, Suara S.A., Jaimes, Juliana, Jardim, Jomar, Jesus, Jôane, Jesus, Priscila, Jiménez‐mejías, Pedro, Johnson, David, Jordão, Lucas S.B., Jordão, Valner M.M., Jorge, Taciane, Kaehler, Miriam, Kameyama, Cíntia, Kataoka, Eric, Kessous, Igor, Kilipper, Julia, Kinoshita, Luiza, Klein, Viviane, Klitgaard, Bente, Knapp, Sandra, Koch, Ana, Koch, Ingrid, Kochanovski, Fábio, Kominami, Gabriel F.G., Konno, Tatiana U.P., Koschnitzke, Cristiana, Kotovski, Emília, Kriebel, Ricardo, Külkamp, Josimar, Leal, Brígida, Leal, Eduardo, Leite, Áurea C.F., Leite, Wellerson, Leitman, Paula, Lewis, Gwilym, Lima, Adriana, Lima, Alexandre, Lima, Duane F.S., Lima, Eliene, Lima, Jessica, Lima, Laíce F.G., Lima, Laura C.P., Lima, Letícia, Lima, Lucas, Lima, Luis F.P., Lima, Rita, Lima, Vanessa l., Link‐perez, Melanie, Lirio, Elton, Lobão, Adriana, Loeuille, Benoit F.P., Loiola, Maria I.B., Lombardi, Julio, Longhi‐wagner, Hilda, Lopes, Gabriel S.R., Lopes, Jenifer, Lopes, Letícia, Lopes, Raimundo, Lopes, Rosana, López, Maria, Lorencini, Tiago, Lorenzi, Harri, Lourenço, Ana R.L., Lourenço, Arthur, Louzada, Rafael, Lovo, Juliana, Lozano, Eduardo, Luber, Jaquelini, Lucas, Dióber, Lucas, Eve, Lüdtke, Raquel, Luebert, Federico, Luizi‐ponzo, Andrea, Luna, Bruna, Luna, Naédja K.M., Luz, Cíntia l.S., Machado, Anderson F.P., Machado, Evandro, Machado, Talita, Maciel, Jefferson, Maciel, Sebastião, Magalhães, Rodrigo, Magenta, Mara A.G., Maia, Talita, Mamede, Maria C.H., Marchioretto, Maria, Margalho, Luciano, Marinho, Lucas, Marques, Danilo, Marquete, Ronaldo, Marra, Raquel, Martins, Angela, Martins, Márcio l.L., Martins, Marcos B.S., Martins, Milena, Martins, Renata, Martins, Suzana, Masson, Victória, Matias, Ligia, Matos, Agnes M.M.V., Matos, Andreza, Matos, Fernando, Matozinhos, Carolina, Mattos, Cilene M.J., Mattos, Leticia, Matzenauer, William, Mauad, Anna V.S.R., Maya‐lastra, Carlos, Mayo, Simon, Mazine, Fiorella, Medeiros, Débora, Medeiros, Erika V.S.S., Medeiros, Herison, Medeiros, Maria C.M.P., Meerow, Alan, Meireles, Jose, Meireles, Leonardo, Meirelles, Julia, Melchor‐castro, Briggitthe, Mello, Zelia, Mello‐silva, Renato, Melo, André l., Melo, Caio V.V.D., Melo, Efigenia, Melo, José I.M., Mendes, Jone C.R., Mendes, Maria C.Q., Mendes‐silva, Ingrid, Meneguzzo, Thiago E.C., Menezes, Cristine, Menezes, Felipe G.P., Menini Neto, Luiz, Mentz, Lilian, Mesquita, Antônio l., Messias, Patrícia, Mezzonato‐pires, Ana, Michelangeli, Fabián, Miguel, João, Miguel, Laila, Milward‐de‐azevedo, Michaele, Miotto, Silvia T.S., Miranda, Cecília, Miranda, Vitor F.O., Mitchell, John, Molina, José M.P., Mondin, Cláudio, Monge, Marcelo, Monteiro, Daniele, Monteiro, Fernanda K.S., Monteiro, Raquel, Monteiro, Silvana H.N., Monteiro, Thiago, Monzoli, João V.L., Moore, Paloma G.P., Mora, Martha, Moraes, Marta, Moraes, Mónica, Morales, Juan, Morales, Matías, Moran, Robbin, Moreira, André l.C., Moreira, Andréia D.R., Moreira, Ariane, Moreira, Bianca, Moreira, Giselle l., Moreira, Kassio V.C., Moreira, Pablo F.F., Morokawa, Rosemeri, Moroni, Pablo, Mota, Aline, Mota, Michelle C.A., Mota, Nara F.O., Moura, Beryl E.L., Moura, Ingridy, Moura, Luíza, Moura, Ricardo l., Moura, Tania, Mundim, Júlia, Muniz, Francisca, Muniz, Leticia, Muniz Filho, Eduardo, Mynssen, Claudine, Nakajima, Jimi, Nascimento, Janaina G.A., Nascimento, José, Nascimento, Silvia, Nepomuceno, Francisco A.A., Nervo, Michelle, Nery, Eduardo, Neves, Beatriz, Nóbrega, Giseli, Nogueira, Matheus G.C., Nunes, Annelise, Nunes, Clebiana, Nunes, Teonildes, Oellgaard, Benjamin, O'Leary, Nataly, Oliveira, Adriana l.R., Oliveira, Ana C.S., Oliveira, Andreza G.S., Oliveira, Aron, Oliveira, Bárbara, Oliveira, Caetano, Oliveira, Fernanda M.C., Oliveira, Filipe G.A., Oliveira, Gleison, Oliveira, Gustavo, Oliveira, Hermeson, Oliveira, Iasmin l.C., Oliveira, Joésili C.P., Oliveira, José F.C., Oliveira, Juliana, Oliveira, Juliana R.P.M., Oliveira, Leticia G.R., Oliveira, Lilian F.A., Oliveira, Lorena, Oliveira, Luciana S.D., Oliveira, Marcia C.R., Oliveira, Márcio l.B., Oliveira, Marcos G.M., Oliveira, Marise H.V., Oliveira, Marla I.U., Oliveira, Regina, Oliveira, Renata, Oliveira, Reyjane, Oliveira, Rodrigo C.G., Oliveira, Sylvia, Oliveira, Ykaro, Orlandini, Priscila, Orsolano, Guilherme, Pacífico, Ricardo, Paglia, Isis, Paiva, Gabrielle C.P., Paixão, Liliane, Pastore, José F.B., Pastore, Mayara, Pastori, Tamara, Paucar, Jenny O.A., Paula‐souza, Juliana, Pederneiras, Leandro, Peichoto, Myriam, Peixoto, Ariane l., Pell, Susan, Pellegrini, Marco O.O., Pena, Nelson T.L., Pennington, Richard, Pereira, Amanda P.N., Pereira, Andreza S.S., Pereira, Jovani B.S., Pereira, Maria, Pereira, Paulo E.E., Pereira, Sidney, Pereira‐silva, Rafaela, Perez, Ana P.F., Pessoa, Cleiton, Pessoa, Clenia, Pessoa, Edlley, Pessoa, Maria C.R., Petrongari, Fernanda, Philbrick, Thomas, Pignal, Marc, Pimenta, Karena, Pinto, Rafael, Pioner, Natália, Pirani, José, Pizzardo, Raquel, Plos, Anabela, Ponce, Marta, Pontes, Juliana, Pontes, Ricardo A.S., Pontes, Tiago, Pontes‐pires, Aline, Pott, Vali, Prado, Thainá, Praia, Talita, Prance, Ghillean, Prange, Carolina, Prata, Ana P.N., Prochazka, Luana, Proença, Carolyn E.B., Prudêncio, Renato X.A., Pscheidt, Allan, Quaresma, Aclebia, Quaresma, Aline, Queiroz, George, Queiroz, Luciano, Queiroz, Rubens, Quinet, Alexandre, Ramos, Eliana, Ramos, Geraldo J.P., Rando, Juliana, Rebouças, Natanael, Reginato, Marcelo, Reis, Miguel M.R., Reis, Priscila, Reis‐silva, Genilson, Ribas, Osmar, Ribeiro, André R.O., Ribeiro, Carolina l., Ribeiro, José E.L.S., Ribeiro, Michel, Ribeiro, Pétala, Ribeiro, Rayane T.M., Ribeiro, Ricardo, Ribeiro, Rogério, Riina, Ricarda, Ritter, Mara, Rivadavia, Fernando, Rivera, Vanessa l., Rizzo, Beatriz, Rocha, Antônio E.S., Rocha, Lamarck, Rocha, Maria J.R., Rodrigues, Carine, Rodrigues, Christchellyn, Rodrigues, Izabella M.C., Rodrigues, Marianna, Rodrigues, Rodrigo Sampaio, Rodrigues, Rodrigo Schütz, Rodríguez, Juan F.C., Rodríguez, Pedro, Rollim, Isis, Romanini, Rebeca, Romão, Gerson, Romão, Marcos V.V., Romero, María, Romero, Rosana, Rosa, Bárbara, Rosa, Patrícia, Rosa, Priscila, Rosário, Alessandro, Rossa, Iago, Rossetto, Elson F.S., Rossi, Lucia, Rossini, Josiene, Royer, Carla, Rua, Gabriel, Sá, Cyl F.C., Saavedra, Mariana, Saka, Mariana, Sakuragui, Cassia, Salas, Roberto, Sales, Margareth, Salgado, Vanina, Salimena, Fátima R.G., Salino, Alexandre, Salvador, Rafael, Sampaio, Daniela, Sancho, Gisela, Sano, Paulo, Santana, Jéssica C.O., Santana, Karoline, Santana, Mariana, Santiago, Augusto C.P., Santos, Alessandra, Santos, Amanda P.B., Santos, Ana C.A.S., Santos, Andrea K.A., Santos, Carlos A.G., Santos, Emanuelle l., Santos, Felipe, Santos, Fernanda, Santos, João U.M., Santos, Karin, Santos, Leidiana l., Santos, Matheus, Santos, Otilene, Santos, Rafaela, Santos, Renata G.P., Santos, Thaíla V.A., Santos, Thiago, Santos, Vanessa, Santos‐silva, Fernanda, Santos‐silva, Juliana, São‐mateus, Wallace M.B., Saraiva, Deisy, Sarkinen, Tiina, Sartori, Ângela l.B., Sassone, Agostina, Sauthier, Luana, Scalon, Viviane, Scatigna, André, Schaefer, Juliana, Scheidegger, Najla M.B., Schliewe, Marcos, Schmidt, Eduard D.L., Schneider, Angelo, Schneider, Layla J.C., Schuettpelz, Eric, Schwartsburd, Pedro, Schwarz, Elizabeth, Scudeler, Ana l., Sebastiani, Renata, Secco, Ricardo, Secretti, Elisangela, Segalla, Rosane, Seleme, Elidiene, Semir, João, Senna, Luisa, Setubal, Robberson, Shimizu, Gustavo, Shirasuna, Regina, Silva, Adaíses S.M., Silva, Aline V.M., Silva, Amanda l., Silva, Anádria, Silva, Caroline C.A., Silva, Cassio, Silva, Christian, Silva, Cintia, Silva, Diego, Silva, Dilana, Silva, Fabio, Silva, Fernanda, Silva, Francismeire, Silva, Gabriel, Silva, Gledson, Silva, Guilherme, Silva, Gustavo H.L., Silva, João P.S., Silva, Juliana l., Silva, Juliene F.M., Silva, Leonardo, Silva, Lucas, Silva, Luciana, Silva, Luiza, Silva, Márcio, Silva, Marcio R.P., Silva, Marcos, Silva, Marcus F.O., Silva, Maria l.B., Silva, Maria S.D., Silva, Nilda M.F., Silva, Otávio l.M., Silva, Rafael, Silva, Raphael, Silva, Renata S.A., Silva, Renato, Silva, Ronaldo, Silva, Saura, Silva, Suelma, Silva, Tânia R.S., Silva, Tatiane, Silva, Thaynara, Silva, Wanderson l.S., Silva Filho, Pedro J.S., Silva‐castro, Milene, Silva‐cobra, Gisele, Silva‐gonçalves, Kelly, Silveira, Fernanda, Silveira, João, Silveira, Thamyres, Simão‐bianchini, Rosangela., Simões, Ana, Simões, André, Simon, Marcelo, Siniscalchi, Carolina, Siqueira, Carlos, Smidt, Eric, Smith, Alan, Smith, Nathan, Snak, Cristiane, Soares, Abel E.R., Soares, Arthur, Soares, Edson l.C., Soares, Kelen, Soares, Luanda, Soares, Marcos V.B., Soares, Maria l.C., Soares, Polyana, Soares, Raimundo, Sobrado, Sandra, Sobral, Marcos, Somner, Genise, Sothers, Cynthia, Sousa, Ana A.C., Sousa, Danilo J.L., Sousa, Francisco, Sousa, Gardene, Sousa, Hian C.F., Sousa, Leandro O.F., Sousa, Mayco W.S., Sousa, Valdeci, Souza, Aline, Souza, Bruno, Souza, Elnatan, Souza, Élvia, Souza, Filipe, Souza, Luzia, Souza, Marcelo, Souza, Maria A.D., Souza, Raquel M.B.S., Souza, Vinicius, Souza‐buturi, Fátima, Spina, Andréa, Stadnik, Aline M.S., Staggemeier, Vanessa, Stapf, María N.S., Stefano, Rodrigo, Stern, Stephen, Streher, Nathália, Suchoronczek, Andréia, Sundue, Michael, Takeuchi, Cátia, Tardivo, Rosângela, Taylor, Nigel, Teixeira, Michella D.R., Teles, Aristônio, Temponi, Livia, Thode, Verônica, Thomas, William, Tierno, Lorena, Tissot‐squalli, Mara, Toledo, Cássio A.P., Torke, Benjamin, Torres, Alicia, Torres, Daniela S.C., Torres‐leite, Filipe, Tozzi, Ana M.G.A., Trad, Rafaela, Trevisan, Rafael, Trovó, Marcelo, Tuler, Amélia, Tyrrell, Christopher, Udulutsch, Renata, Uribbe, Fernando, Vahl, Daiane, Valadares, Rodrigo, Valdemarin, Karinne, Valduga, Eduardo, Valente, Emilia, Valls, Jose F.M., van den Berg, Cássio, Vasconcelos, Liziane, Vasconcelos, Thaís N.C., Vasques, Diego, Vaz, Angela M.S.F., Versiane, Ana F.A., Versieux, Leonardo, Via Do Pico, Gisela, Viana, Pedro l., Vianna, Suelen, Vianna Filho, Marcelo D.M., Vidal, Kaio V.A., Vidal, João, Vieira, Fábio C.S., Vieira, Jaqueline, Vieira, João P.S., Vieira, Lucas l.A., Vieira, Tamara A.F., Vieira, Tiago l., Viera‐barreto, Jéssica, Vignoli‐silva, Márcia, Vilas Bôas‐bastos, Silvana, Villarreal, Juan, Vincent, Michael, Vita, Marcela, Vitta, Fabio, Viveros, Raquel, Viviurka, Fernanda, Vogel Ely, Cleusa, Volet, Danilo, Völtz, Rafael, Wallnöfer, Bruno, Wanderley, Maria G.L., Watanabe, Mauricio T.C., Weber, Philipy A.P., Weigend, Maximilian, Welker, Cassiano A.D., Windisch, Paulo, Yoshikawa, Vania, Zamengo, Henrique, Zanatta, Maria R.V., Zannin, Ana, Zappi, Daniela, Zeferino, Laís, Zelenski, Andréia, Zuloaga, Fernando, Zuntini, Alexandre, Maastricht Science Programme, RS: FSE MSP, JANAÍNA GOMES-DA-SILVA, Jardim Botânico do Rio de Janeiro, FABIANA L. R. FILARDI, MARIA REGINA V. BARBOSA, UFPB, JOSÉ FERNANDO A. BAUMGRATZ, CARLOS E. M. BICUDO, TACIANA BARBOSA CAVALCANTI, Cenargen, MARCUS A. N. COELHO, Prefeitura Municipal de Campinas, ANDREA F. COSTA, DENISE P. COSTA, Instituto de Pesquisas Jardim Botanico do Rio de Janeiro, EDUARDO COUTO DALCIN, Rio de Janeiro Botanical Garden Research Institute, PAULO LABIAK, UFPR, HAROLDO C. LIMA, Jardim Botânico do Rio de Janeiro, LÚCIA G. LOHMANN, USP, LEONOR C. MAIA, UFPE, VIDAL F. MANSANO, Jardim Botânico do Rio de Janeiro, MARIÂNGELA MENEZES, UFRJ, MARLI P. MORIM, Instituto de Pesquisas Jardim Botânico do Rio de Janeiro, CARLOS WALLACE N. MOURA, EIMEAR NIC LUGHADHA, DENILSON F. PERALTA, JEFFERSON PRADO, Instituto de Botânica de São Paulo, NÁDIA ROQUE, UFBA, JOÃO RENATO STEHMANN, LANA S. SYLVESTRE, UFRJ, LARISSA TRIERVEILER-PEREIRA, Instituto de Botânica, São Paulo, BRUNO MACHADO TELES WALTER, Cenargen, GERALDO ZIMBRÃO, RAFAELA C. FORZZA, Jardim Botânico do Rio de Janeiro., Instituto de Pesquisas Jardim Botanico do Rio de Janeiro (JBRJ), Universidade Federal da Paraiba (UFPB), Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université de Montpellier (UM), Herbier de Guyane - IRD, and Institut de Recherche pour le Développement (IRD [Guyane])

Subjects
Grandes Datos, Natural history collections, natural history collections, América del Sur, Plant Science, Repositories, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, Colecciones de Historia Natural, Taxonomic impediment, Biodiversidad, Big data, flora, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, big data, taxonomic impedimen, Repositorios, Ecology, Evolution, Behavior and Systematics, biodiversity, Biodiversity, botany, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, Impedimento Taxonómico, South America, collaboration, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, repositories, Brazil
Abstract

The shortage of reliable primary taxonomic data limits the description of biological taxa and the understanding of biodiver sity patterns and processes, complicating biogeographical, ecological, and evolutionary studies. This deficit creates a significant taxo nomic impediment to biodiversity research and conservation planning. The taxonomic impediment and the biodiversity crisis are widely recognized, highlighting the urgent need for reliable taxonomic data. Over the past decade, numerous countries worldwide have devoted considerable effort to Target 1 of the Global Strategy for Plant Conservation (GSPC), which called for the preparation of a working list of all known plant species by 2010 and an online world Flora by 2020. Brazil is a megadiverse country, home to more of the world’s known plant species than any other country. Despite that, Flora Brasiliensis, concluded in 1906, was the last comprehensive treatment of the Brazilian flora. The lack of accurate estimates of the number of species of algae, fungi, and plants occurring in Brazil contributes to the prevailing taxonomic impediment and delays progress towards the GSPC targets. Over the past 12 years, a legion of taxonomists motivated to meet Target 1 of the GSPC, worked together to gather and integrate knowledge on the algal, plant, and fungal diversity of Brazil. Overall, a team of about 980 taxonomists joined efforts in a highly collaborative project that used cybertaxonomy to prepare an updated Flora of Brazil, showing the power of scientific collaboration to reach ambitious goals. This paper presents an overview of the Brazilian Flora 2020 and provides taxonomic and spatial updates on the algae, fungi, and plants found in one of the world’s most biodiverse countries. We further identify collection gaps and summarize future goals that extend be yond 2020. Our results show that Brazil is home to 46,975 native species of algae, fungi, and plants, of which 19,669 are endemic to the country. The data compiled to date suggests that the Atlantic Rainforest might be the most diverse Brazilian domain for all plant groups except gymnosperms, which are most diverse in the Amazon. However, scientific knowledge of Brazilian diversity is still un equally distributed, with the Atlantic Rainforest and the Cerrado being the most intensively sampled and studied biomes in the coun try. In times of “scientific reductionism”, with botanical and mycological sciences suffering pervasive depreciation in recent decades, the first online Flora of Brazil 2020 significantly enhanced the quality and quantity of taxonomic data available for algae, fungi, and plants from Brazil. This project also made all the information freely available online, providing a firm foundation for future research and for the management, conservation, and sustainable use of the Brazilian funga and flora. Fil: Gomes da Silva, Janaina. Jardim Botânico do Rio de Janeiro: Rio de Janeiro, Brasil Fil: Filardi, Fabiana L.R. Jardim Botânico do Rio de Janeiro; Brasil Fil: Barbosa, María Regina de V. Universidade Federal da Paraíba: Joao Pessoa; Brasil Fil: Baumgratz, José Fernando Andrade. Jardim Botânico do Rio de Janeiro; Brasil Fil: de Mattos Bicudo, Carlos Eduardo. Instituto de Botânica. Núcleo de Pesquisa em Ecologia; Brasil Fil: Cavalcanti, Taciana. Empresa Brasileira de Pesquisa Agropecuária Recursos Genéticos e Biotecnologia; Brasil Fil: Coelho, Marcus. Prefeitura Municipal de Campinas; Brasil Fil: Ferreira da Costa, Andrea. Federal University of Rio de Janeiro. Museu Nacional. Department of Botany; Brasil Fil: Costa, Denise. Instituto de Pesquisas Jardim Botanico do Rio de Janeiro; Brasil Fil: Dalcin, Eduardo C. Rio de Janeiro Botanical Garden Research Institute; Brasil Fil: Labiak, Paulo. Universidade Federal do Parana; Brasil Fil: Cavalcante de Lima, Haroldo. Jardim Botânico do Rio de Janeiro; Brasil Fil: Lohmann, Lucia. Universidade de São Paulo; Brasil Fil: Maia, Leonor. Universidade Federal de Pernambuco; Brasil Fil: Mansano, Vidal de Freitas. Instituto de Pesquisas Jardim Botânico do Rio de Janeiro; Brasil. Jardim Botânico do Rio de Janeiro; Brasil Fil: Menezes, Mariângela. Federal University of Rio de Janeiro. Museu Nacional. Department of Botany; Brasil Fil: Morim, Marli. Instituto de Pesquisas Jardim Botânico do Rio de Janeiro; Brasil Fil: Moura, Carlos Wallace do Nascimento. Universidade Estadual de Feira de Santana. Department of Biological Science; Brasil Fil: Lughadha, Eimear NIck. Royal Botanic Gardens; Reino Unido Fil: Peralta, Denilson. Instituto de Pesquisas Ambientais; Brazil Fil: Prado, Jefferson. Instituto de Pesquisas Ambientais; Brasil Fil: Roque, Nádia. Universidade Federal da Bahia; Brasil Fil: Stehmann, Joao. Universidade Federal de Minas Gerais; Brasil Fil: da Silva Sylvestre, Lana. Universidade Federal do Rio de Janeiro; Brasil Fil: Trierveiler-Pereira, Larissa. Universidade Estadual de Maringá. Departamento de Análises Clínicas e Biomedicina; Brasil Fil: Walter, Bruno Machado Teles. EMBRAPA Cenargen Brasília; Brasil Fil: Zimbrão, Geraldo. Universidade Federal do Rio de Janeiro; Brasil Fil: Forzza, Rafaela C. Jardim Botânico do Rio de Janeiro; Brasil Fil: Morales, Matías. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Recursos Biológicos; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad de Morón. Facultad de Agronomía y Ciencias Agroalimentarias; Argentina

Published
2021

10. VegAndes: the vegetation database for the Latin American highlands

Author

Gwendolyn Peyre, Daniel Montesinos, Daniela Giraldo, Antonio Galán de Mera, Barbara Ruthsatz, Federico Luebert, Marcela Ontivero, Nicolas García, Miguel Álvarez, Rosa Isela Meneses, Pablo Lozano, Daniela León, Maximilian Weigend, Fabien Anthelme, Milagro Palma, Carolina Rodriguez, Universidad de los Andes [Bogota] (UNIANDES), Freie Universität Berlin, Universidad San Pablo CEU, Universität Trier, Universidad Central de Chile, Instituto Argentino de Investigaciones de las Zonas Áridas, Consejo Nacional de Investigaciones Científicas y Técnicas [Buenos Aires] (CONICET), Rheinische Friedrich-Wilhelms-Universität Bonn, Institut für Nutzpflanzenwissenschaften und Ressourcenschutz (INRES), Universidad Católica del Norte [Antofagasta], Universidad Estatal Amazonica, University of Tartu, Institut de Recherche pour le Développement (IRD), Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université de Montpellier (UM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), and Universidad de Panamá (UP)

Subjects
www.worldfloraonline.org/) database, phytosociology, Plant Science, TROPICOS (preferential source www.tropicos.org/) World Flora Online (secondary source www.worldfloraonline.org/) database flora highland Mesoamerica phytosociology plot data South America vegetation, World Flora Online (secondary source, Mesoamerica, South America, Agricultural and Biological Sciences (miscellaneous), flora, www.tropicos.org/), vegetation, TROPICOS (preferential source, plot data, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Ecology, Evolution, Behavior and Systematics, database, highland
Abstract

In the era of Big Data, Latin American countries and biomes remain underrepresented. To remediate this issue, promoting repositories for biodiversity data focused on Latin America is a main priority. VegAndes -Dpt the vegetation database for the Latin American highlands (GIVD: SA-00-005), is a novel dataset for georeferenced and standardized information on vascular pants in the region. The database compiles 5,340 vegetation plots sampled above the montane treeline and below the permanent snowline in 11 Latin American countries and spanning over seven decades. VegAndes currently encompasses 5,804 taxon names, corresponding to 3,858 accepted names, as well as 136 syntaxon names. The database is nested within a scientific consortium of Latin American experts on highland vegetation and piloted from the University of the Andes (Colombia). Because the VegAndes data can support multi-scale studies in botany, ecology and biogeography, the database makes an essential contribution to biodiversity research and management perspectives in Latin America. Taxonomic reference: TROPICOS (preferential source, www.tropicos.org/), World Flora Online (secondary source, www.worldfloraonline.org/).

Published
2022

11. Trellis-forming stems of a tropical liana Condylocarpon guianense (Apocynaceae): A plant-made safety net constructed by simple 'start-stop' development

Author

Soffiatti, Patricia, Fort, Emilien, Heinz, Christine, Rowe, Nick P, Universidade Federal do Paraná (UFPR), Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université de Montpellier (UM)

Subjects
Trellis, [SDE]Environmental Sciences, Lianas, Biomechanics, Plant Science, Anatomy, Development, Safety, Mechanical perturbation, Lianoid wood
Abstract

Tropical vines and lianas have evolved mechanisms to avoid mechanical damage during their climbing life histories. We explore the mechanical properties and stem development of a tropical climber that develops trellises in tropical rain forest canopies. We measured the young stems of Condylocarpon guianensis (Apocynaceae) that construct complex trellises via self-supporting shoots, attached stems, and unattached pendulous stems. The results suggest that, in this species, there is a size (stem diameter) and developmental threshold at which plant shoots will make the developmental transition from stiff young shoots to later flexible stem properties. Shoots that do not find a support remain stiff, becoming pendulous and retaining numerous leaves. The formation of a second TYPE II (lianoid) wood is triggered by attachment, guaranteeing increased flexibility of light-structured shoots that transition from self-supporting searchers to inter-connected net-like trellis components. The results suggest that this species shows a “hard-wired” development that limits self-supporting growth among the slender stems that make up a liana trellis. The strategy is linked to a stem-twining climbing mode and promotes a rapid transition to flexible trellis elements in cluttered densely branched tropical forest habitats. These are situations that are prone to mechanical perturbation via wind action, tree falls, and branch movements. The findings suggest that some twining lianas are mechanically fine-tuned to produce trellises in specific habitats. Trellis building is carried out by young shoots that can perform very different functions via subtle development changes to ensure a safe space occupation of the liana canopy.

Published
2022

12. Honoring Sabin Berthelot: Nomenclature and botanical history of Berthelotia DC. (Asteraceae, Inuleae)

Author

Andre A. Naranjo, Rahul R. Pathirickal, Kanchi N. Gandhi, Piero G. Delprete, Riccardo M. Baldini, Arnoldo Santos-Guerra, Lázaro Sánchez-Pinto, Javier Francisco-Ortega, Florida International University [Miami] (FIU), Harvard University Herbaria, Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université de Montpellier (UM), Herbier de Guyane - IRD, Institut de Recherche pour le Développement (IRD [Guyane]), and Università degli Studi di Firenze = University of Florence (UniFI)

Subjects
Ecology, Nomenclature, India, Canary Islands, Plant Science, Asteraceae, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, Sabin Berthelot, Berthelotia, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Mexico, Ecology, Evolution, Behavior and Systematics, Sonora Desert, USA, Phylogeny
Abstract

International audience; The genus Berthelotia DC. (presently a synonym of the accepted name Pluchea Cass.), Asteraceae, Inuleae has been regarded as comprising two species, B. lanceolata DC. and B. sericea (Nutt.) Rydb. It honors the French naturalist Sabin Berthelot (1794-1880) for his contribution to the studies of the flora and fauna of the Canary Islands. Under the leadership of Philip B. Webb (1793-1854), Berthelot co-authored the most important work pertinent to the natural history of this archipelago: Histoire Naturelle des Îles Canaries. The nomenclature of Berthelotia and its associated names are revisited here. The holotype of Polypappus sericeus Nutt. (K000974653) was located, and lectotypes were assigned to B. lanceolata (G00450458) and B. lanceolata var. senegalensis DC. (G00452584). Phylogenetic analyses based on nucleotide sequences of the nrDNA ITS were conducted focusing on members of what is known as the Clade J of the Inuleae. A well-supported clade (100% P.P.) that we have labeled as "Clade I" was uncovered, and it is composed of three species that belong to the Pluchea indica Clade plus P. dioscoridis and P. ovalis; but this lineage did not support a previous hypothesis to include P. lanceolata. The two species of Berthelotia did not form a monophyletic group and seem to be distantly related; furthermore, none of these two taxa is sister to 208 Andre A. Naranjo et al. Tessaria, a South American genus that has been suggested to be a close relative to Berthelotia. Ethnobotanical uses of B. lanceolata and B. sericea are reviewed.

Published
2022

13. An annotated checklist of the tree species of French Guiana, including vernacular nomenclature

Author

Jean-François Molino, Daniel Sabatier, Pierre Grenand, Julien Engel, Dawn Frame, Piero G. Delprete, Marie Fleury, Guillaume Odonne, Damien Davy, Eve J. Lucas, Claire A. Martin, Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université de Montpellier (UM), Herbier de Guyane - IRD, Institut de Recherche pour le Développement (IRD [Guyane]), Patrimoines locaux, Environnement et Globalisation (PALOC), Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU), Laboratoire Ecologie, Evolution, Interactions des Systèmes amazoniens (LEEISA), and Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Guyane (UG)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Malvales, Aquifoliales, Scientific names, Salicaceae, Myrtaceae, Oleaceae, Liliopsida, Metteniusales, Rubiaceae, Plant Science, Arecaceae, Moraceae, Picramniaceae, Magnoliales, Dilleniaceae, Stemonuraceae, Picramniales, Lecythidaceae, Lacistemataceae, Meliaceae, New synonyms, Plantae, Urticaceae, Malvaceae, Lythraceae, Sabiaceae, Euphorbiaceae, Abundance data, trees, Brassicales, Celastraceae, Loganiaceae, Linaceae, Caryophyllales, French Guiana, Lamiales, Ebenaceae, Vernacular names, Santalales, [SDE]Environmental Sciences, Leguminosae, Metteniusaceae, Canellaceae, Olacaceae, new combination, Celastrales, Anacardiaceae, Annonaceae, Capparaceae, Chrysobalanaceae, Proteaceae, Monimiaceae, lectotypifications, Verbenaceae, Rosales, Aptandraceae, Primulaceae, Peraceae, Cordiaceae, Cardiopteridaceae, Quiinaceae, Bixaceae, Caricaceae, Dichapetalaceae, Lectotypifications, Apocynaceae, Apiales, Styracaceae, Cochlospermaceae, Bignoniaceae, Laurales, Hernandiaceae, Melastomataceae, Rhizophoraceae, Ericales, Caryocaraceae, Elaeocarpaceae, Theaceae, Malpighiales, Fabales, Trees, Sapindaceae, vernacular names, Vochysiaceae, Ixonanthaceae, Aquifoliaceae, Symplocaceae, Solanaceae, Lepidobotryaceae, Phyllanthaceae, Fabaceae, Biodiversity, Piperaceae, Ochnaceae, Erythroxylaceae, Piperales, Siparunaceae, Humiriaceae, scientific names, Sapindales, Coulaceae, Burseraceae, Calophyllaceae, New combination, Nyctaginaceae, Malpighiaceae, Achariaceae, Arecales, Opiliaceae, Magnoliopsida, Goupiaceae, Lauraceae, Combretaceae, Acanthaceae, Clusiaceae, Ximeniaceae, abundance data, Rhabdodendraceae, Pentaphylacaceae, Araliaceae, Rosaceae, Rutaceae, Erythropalaceae, Taxonomy, Sapotaceae, Lamiaceae, Solanales, Myrtales, Hypericaceae, Putranjivaceae, Polygonaceae, new synonyms, Proteales, Tracheophyta, Canellales, Cannabaceae, Simaroubaceae, Dilleniales, Oxalidales, Boraginales, Violaceae, Gentianales, Myristicaceae
Abstract

We present a list of tree species of French Guiana, based on data collected from herbarium specimens and tree inventories, and verified against all available taxonomic literature to date. The list contains 1811 taxa representing 87 families and 421 genera, including 143 unnamed species which either may be species not previously recorded in French Guiana, or taxa new to Science. Original demographic data such as global abundance, local maximum frequency and geographic dispersion, are given for the 1293 species present in tree inventories. Our work has led to the recognition of certain taxonomic and nomenclatural novelties, including a new combination in Lecythis Loefl. (Lecythidaceae), several lectotypifications and new synonyms, as well as reinstatement of Sloanea acutiflora Uittien (Elaeocarpaceae), Eugenia sinemariensis Aubl. (Myrtaceae), and four species of Inga (Leguminosae). In addition, we provide the most comprehensive list available to date of corresponding vernacular names (4354 for 1157 species) in nine languages spoken in French Guiana: Palikur, Kali’na, Teko, Wayãpi, Wayana, Nengee tongo (Aluku/Ndjuka/Paramaka), Creole, French, and Brasilian Portuguese. The checklist is complemented by indexes of exsiccata, vernacular names and scientific names. The introductory part is available in French and English., Nous présentons une liste des espèces d’arbres de Guyane française, basée sur des données issues de spécimens d’herbiers et d’inventaires d’arbres. Les noms ont été vérifiés au regard de toute la littérature taxonomique disponible à ce jour. La liste contient 1811 taxons représentant 87 familles et 421 genres, dont 143 espèces non nommées qui peuvent être soit des espèces non répertoriées précédemment en Guyane française, soit des taxons nouveaux pour la Science. Des données démographiques originales telles que l’abondance globale, la fréquence maximale locale et la dispersion géographique, sont données pour les 1293 espèces présentes dans les inventaires d’arbres. Nos travaux ont conduit à la reconnaissance de quelques nouveautés taxonomiques et nomenclaturales, dont une nouvelle combinaison dans le genre Lecythis Loefl. (Lecythidaceae), plusieurs lectotypifications et nouveaux synonymes, ainsi que la réinstallation de Sloanea acutiflora Uittien (Elaeocarpaceae), d’Eugenia sinemariensis Aubl. (Myrtaceae), et de quatre espèces du genre Inga (Leguminosae). En outre, nous fournissons la liste la plus complète disponible à ce jour des noms vernaculaires correspondants (4354 pour 1157 espèces) dans neuf langues parlées en Guyane française : Palikur, Kali’na, Teko, Wayãpi, Wayana, Nengee tongo (Aluku/Ndjuka/Paramaka), Créole, Français, et Portugais du Brésil. Le catalogue est complété par des index des exsiccata, des noms vernaculaires et des noms scientifiques. La partie introductive est proposée en français et en anglais.

Published
2022

14. Domestication Syndrome in Dacryodes edulis (Burseraceae): Comparison of Morphological and Biochemical Traits between Wild and Cultivated Populations

Author

Franca Marcelle Meguem Mboujda, Marie-Louise Avana-Tientcheu, Stéphane Takoudjou Momo, Alix Mboukap Ntongme, Virginie Vaissayre, Laura N. Azandi, Stéphane Dussert, Hilaire Womeni, Jean-Michel Onana, Bonaventure Sonké, Christopher Tankou, Jérôme Duminil, University of Dschang, Diversité, adaptation, développement des plantes (UMR DIADE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM), Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université de Montpellier (UM), University of Yaoundé [Cameroun], Université de Yaoundé I, Université libre de Bruxelles (ULB), and ANR-16-IDEX-0006,MUSE,MUSE(2016)

Subjects
Evolutionary history, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, Ecology, Fruit tree species, African plum tree, Plant Science, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, domestication syndrome, evolutionary history, fruit tree species, non-timber forest products, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, Domestication syndrome, Ecology, Evolution, Behavior and Systematics, Non-timber forest products
Abstract

For millennia, people have harvested fruits from the wild for their alimentation. Gradually, they have started selecting wild individuals presenting traits of interest, protecting and cultivating them. This was the starting point of their domestication. The passage from a wild to a cultivated status is accompanied by a modification of a number of morphological and genetic traits, commonly known as the domestication syndrome. We studied the domestication syndrome in Dacryodes edulis (G.Don) H.J.Lam (known as ‘African plum’ or ‘safoutier/prunier’), a socio-economically important indigenous fruit tree species in West and Central Africa. We compared wild and cultivated individuals for their sex distribution; flower, fruit and seed morphometric characteristics; seed germination temporal dynamic and fruit lipid composition. We found a higher percentage of male and male-hermaphrodite sexual types in wild populations than in cultivated ones; a lower fruit and seed mass in wild individuals; and similar mean time of germination, oil content and fatty acid composition between wild and cultivated individuals. Our results are interpreted in light of the presence of a domestication syndrome in D. edulis.

Published
2022

15. Revision of Carapichea (Rubiaceae-Psychotrieae) in the Guianas, with two new combinations and transfer of three species to Notopleura

Author

Olivier Lachenaud, Piero Delprete, Meise Botanic Garden [Belgium] (Plantentuin), Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université de Montpellier (UM), Herbier de Guyane - IRD, Institut de Recherche pour le Développement (IRD [Guyane]), and ANR-10-LABX-0025,CEBA,CEnter of the study of Biodiversity in Amazonia(2010)

Subjects
Neotropics, Insecta, Arthropoda, Rubiaceae, Carapichea, Plant Science, Uragoga, Magnoliopsida, Acrididea, Animalia, Acridomorpha, Plantae, Suriname, Notopleura, Acrididae, Stachyococcus, Biota, Caelifera, French Guiana, Tracheophyta, Guiana Shield, Eremogryllinae, Orthoptera, Acridoidea, Guyana, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Psychotria, Gentianales
Abstract

Background and aims – The genus Carapichea (Rubiaceae), recently resurrected and separated from Psychotria, currently includes 24 Neotropical species and is morphologically heterogeneous. A revision of the genus in the Guianas is presented here, as part of the authors’ work on the Rubiaceae treatment in the Flora of the Guianas series. Material and methods – This paper is based on a study of herbarium specimens from BBS, BM, BR, BRB, CAY, INPA, K, P, P-JJR, and U; type specimens from other herbaria were consulted online. Some of the species were also studied in the field by the authors. Normal practices of herbarium taxonomy have been applied. Results – Three species previously included in Carapichea (C. altsonii, C. nivea, and C. sandwithiana) show aberrant characters for the genus and are transferred to Notopleura; new combinations are published for the former two (N. altsonii and N. nivea). Eight species of Carapichea, one of them still imperfectly known, are recorded from the Guianas; a ninth species, C. araguariensis, is included in this revision as it is expected to occur in the region. New combinations are published for two species: Carapichea galbaoensis and C. squamelligera, based on Psychotria galbaoensis and P. squamelligera, respectively; the former species was previously included in synonymy of C. guianensis, which is here redefined in a narrower sense. The delimitation of C. ligularis is expanded to include C. pacimonica as a synonym. The first records of C. adinantha in French Guiana – and the Guiana Shield – are documented. The taxonomy of the two remaining species, C. tillettii and C. urniformis, is left unchanged. For every species a complete description is presented, as well as data on distribution, ecology, phenology, local names (when known), and a list of collections studied.

Published
2022

16. Medicinal Vitex species (Lamiaceae) occupy different niches in Haut-Katanga tropical dry woodlands

Author

Salvatora Nsenga Nkulu, Pierre Meerts, Edouard Ilunga wa Ilunga, Mylor Ngoy Shutcha, David Bauman, Université de Lubumbashi (UNILU), Université libre de Bruxelles (ULB), Meise Botanic Garden [Belgium] (Plantentuin), Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université de Montpellier (UM), and University of Oxford

Subjects
Termite mound, medicinal, tropical dry woodlands, Lamiaceae, miombo, aluminium, conservation, Plant Science, Biota, Lamiales, soil, Vitex, indicator species, Tracheophyta, Magnoliopsida, niche, woody species, [SDE]Environmental Sciences, aluminium conservation indicator species medicinal miombo niche soil termite mound tropical dry woodlands woody species, Plantae
Abstract

Background and aims – Sustainable management of the medicinal plant resources provided by tropical forests is of utmost importance to human populations in developing countries. Trees and shrubs of the genus Vitex (Lamiaceae) are of great medicinal importance in Haut-Katanga (SE D.R. Congo), frequently used to treat tropical diseases. However, the security of supply is threatened, particularly by urban sprawl and mining. A conservation strategy for medicinal plants is urgently needed. In this context, we try to better understand the ecological factors (mostly soil) explaining the distribution of three medicinal species of Vitex (Lamiaceae) (V. fischeri, V. madiensis, and V. mombassae) that co-occur in the tropical dry woodlands in the region of Lubumbashi. Material and methods – In 114 plots (10 m radius), comprising at least one species of Vitex, all woody species with a DBH ≥ 10 cm were inventoried and soil samples were collected. Multivariate Regression Trees (MRT) combined with indicator species index IndVal and Redundancy analysis (RDA) were used to characterise habitats and woody plant communities associated to each Vitex species and to explain the variability of plant community composition. Key results – Four habitats were identified, and the three Vitex species differ significantly in ecological range. Vitex fischeri is a specialist of a most distinctive community on high Mg and low Al soil (termite mounds). Vitex mombassae is indicative of one habitat, corresponding to low altitude (< 1230 m) plots. Vitex madiensis has a broader range, being a generalist of all habitats except termite mounds. Conclusion – These results emphasise the importance of a detailed knowledge of species ecology to design species-specific conservation strategies, even for congeneric species occurring in sympatry in the same landscape.

Published
2022

17. The maximum and the minimum: two new species of Tovomita Aubl. (Clusiaceae) from the Guiana Shield with an unusual number of stamens

Author

Julien Engel, Jean-François Molino, Lucas C. Marinho, Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université de Montpellier (UM), Herbier de Guyane - IRD, Institut de Recherche pour le Développement (IRD [Guyane]), Universidade Federal do Maranhão = Federal University of Maranhão (UFMA), ANR-10-LABX-0025,CEBA,CEnter of the study of Biodiversity in Amazonia(2010), and ANR-11-INBS-0004,E-RECOLNAT,Valorisation de 350 ans de collections d'histoire naturelle : une plateforme numérique(2011)

Subjects
Malpighiales, Biodiversity, Plant Science, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, French Guiana, New species, Guttiferae, Tracheophyta, Magnoliopsida, Guiana Shield, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, Clusiaceae, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Plantae, Clusieae, Taxonomy
Abstract

International audience; Two new species of Tovomita Aubl. (Clusiaceae) from the Guiana Shield are described and illustrated. Tovomita maxima Molino & J.Engel, sp. nov., known from French Guiana, Guyana and Brazil, stands out by its large size (up to 30 m high), large leaves with eucamptodromous venation, calyptrate bracteoles and an unusual variation in the number of stamens (74-145). Tovomita saulensis J.Engel & Molino, sp. nov., probably endemic to central French Guiana, is an understory tree with small leaves with brochidodromous venation and flowers with few stamens (9-15). Illustrations, descriptions, photographs in vivo, a preliminary conservation status, distribution map and comments on the morphology of related species are provided.

Published
2022

18. Additional taxonomic and nomenclatural notes on New Caledonian Eugenia (Myrtaceae)

Author

Neil Snow, John W. Dawson, Jérôme Munzinger, Martin W. Callmander, Pennsylvania State University (Penn State), Penn State System, Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université de Montpellier (UM), and Conservatoire et Jardin Botaniques

Subjects
Nomenclature, Myrtaceae, Myrtales, Plant Science, Biodiversity, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, Eugenia, Tracheophyta, Magnoliopsida, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, New Caledonia, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Plantae, Ecology, Evolution, Behavior and Systematics, Taxonomy
Abstract

International audience; Snow, N., J.W. Dawson†, J. Munzinger & M.W. Callmander (2022). Additional taxonomic and nomenclatural notes on New Caledonian Eugenia (Myrtaceae). Candollea 77: 71–79. In English, English and French abstracts. Ongoing taxonomic studies on Eugenia L. (Myrtaceae) in New Caledonia revealed a number of taxonomic and nomenclatural issues in need of clarification. A new synonymy is proposed: Schizocalyx neocaledonica Brongn. & Gris is reduced to synonymy under Eugenia ovigera Brongn. & Gris. A new name E. pubiflora N. Snow & Callm. is proposed for the illegitimate name E. calycorectoides Guillaumin. Lectotypes are proposed for 15 names: E. bullata Pancher ex Guillaumin, E. daenikeri Guillaumin, E. ericoides Guillaumin, E. horizontalis Pancher ex Brongn. & Gris, E. huerlimannii Guillaumin, E. kaalensis Guillaumin, E. littoralis Pancher ex Brongn. & Gris, E. littoralis var. deplanchei Brongn. & Gris, E. magnifica Brongn. & Gris, E. paludosa Pancher ex Brongn. & Gris, E. stricta Pancher ex Brongn. & Gris, Jambosa canalensis Guillaumin, Myrtus poimbailensis Guillaumin, Schizocalyx neocaledonica Brongn. & Gris, and Xanthomyrtus pergracilis Diels. A neotype is also designated for Eugenia gacognei Montrouz.

Published
2022

19. Coumarin accumulation and trafficking in Arabidopsis thaliana : a complex and dynamic process

Author

Arnaud Hecker, Geneviève Conejero, Nicolas Rouhier, Linnka Lefebvre-Legendre, Frédéric Gaymard, Elodie Sylvestre-Gonon, Marie Barberon, Kevin Robe, Christian Dubos, Fei Gao, Sonia Hem, Esther Izquierdo, Valérie Rofidal, Biochimie et Physiologie Moléculaire des Plantes (BPMP), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-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), Plateforme d'histocytologie et d'imagerie cellulaire végétale (PHIV), 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)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-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)-Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Department of Botany and Plant Biology, University of Geneva, Interactions Arbres-Microorganismes (IAM), Université de Lorraine (UL)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Department of Botany and Plant Biology, ANR-17-CE20-0008,MOBIFER,Dynamique de la sécrétion de coumarines dans le sol, un processus développé par les plantes pour améliorer la nutrition en fer(2017), ANR-10-INBS-0004,France-BioImaging,Développment d'une infrastructure française distribuée coordonnée(2010), and University of Geneva [Switzerland]

Subjects
0106 biological sciences, 0301 basic medicine, Arabidopsis thaliana, Physiology, [SDV]Life Sciences [q-bio], esculin, Arabidopsis, spectral imaging, Plant Science, Root hair, coumarin, Plant Roots, 01 natural sciences, 03 medical and health sciences, chemistry.chemical_compound, iron, PDR9, Coumarins, scopolin, Scopoletin, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, heterocyclic compounds, Rhizosphere, biology, Arabidopsis Proteins, fungi, fraxin, food and beverages, Xylem, Subcellular localization, biology.organism_classification, Cell biology, 030104 developmental biology, chemistry, Fraxetin, Scopolin, 010606 plant biology & botany
Abstract

International audience; Iron (Fe) is a major micronutrient and is required for plant growth and development. Nongrass species have evolved a reduction-based strategy to solubilize and take up Fe. The secretion of Fe-mobilizing coumarins (e.g. fraxetin, esculetin and sideretin) by plant roots plays an important role in this process. Although the biochemical mechanisms leading to their biosynthesis have been well described, very little is known about their cellular and subcellular localization or their mobility within plant tissues. Spectral imaging was used to monitor, in Arabidopsis thaliana, the in planta localization of Fe-mobilizing coumarins and scopolin. Molecular, genetic and biochemical approaches were also used to investigate the dynamics of coumarin accumulation in roots. These approaches showed that root hairs play a major role in scopoletin secretion, whereas fraxetin and esculetin secretion occurs through all epidermis cells. The findings of this study also showed that the transport of coumarins from the cortex to the rhizosphere relies on the PDR9 transporter under Fe-deficient conditions. Additional experiments support the idea that coumarins move throughout the plant body via the xylem sap and that several plant species can take up coumarins present in the surrounding media. Altogether, the data presented here demonstrate that coumarin storage and accumulation in roots is a highly complex and dynamic process.

Published
2020

20. Very High Resolution Species Distribution Modeling Based on Remote Sensing Imagery: How to Capture Fine-Grained and Large-Scale Vegetation Ecology With Convolutional Neural Networks?

Author

Benjamin Deneu, Alexis Joly, Pierre Bonnet, Maximilien Servajean, François Munoz, Scientific Data Management (ZENITH), Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université de Montpellier (UM), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Université Paul-Valéry - Montpellier 3 (UPVM), ADVanced Analytics for data SciencE (ADVANSE), Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), Laboratoire Interdisciplinaire de Physique [Saint Martin d’Hères] (LIPhy ), Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA), and ANR-16-CONV-0004,DIGITAG,Institut Convergences en Agriculture Numérique(2016)

Subjects
[SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, Remote-sensing imagery, Plant functional traits, Species distribution model, Convolutional neural network, Plant Science, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, Ecological interpretation, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, t-SNE, Very fine scale prediction
Abstract

Species Distribution Models (SDMs) are fundamental tools in ecology for predicting the geographic distribution of species based on environmental data. They are also very useful from an application point of view, whether for the implementation of conservation plans for threatened species or for monitoring invasive species. The generalizability and spatial accuracy of an SDM depend very strongly on the type of model used and the environmental data used as explanatory variables. In this article, we study a country-wide species distribution model based on very high resolution (VHR) (1 m) remote sensing images processed by a convolutional neural network. We demonstrate that this model can capture landscape and habitat information at very fine spatial scales while providing overall better predictive performance than conventional models. Moreover, to demonstrate the ecological significance of the model, we propose an original analysis based on the t-distributed Stochastic Neighbor Embedding (t-SNE) dimension reduction technique. It allows visualizing the relation between input data and species traits or environment learned by the model as well as conducting some statistical tests verifying them. We also analyze the spatial mapping of the t-SNE dimensions at both national and local levels, showing the model benefit of automatically learning environmental variation at multiple scales.

Published
2022

21. Patterns of Plumericin Concentration in Leaves of Himatanthus tarapotensis (Apocynaceae) and Its Interactions with Herbivory in the Peruvian Amazon

Author

Carlos A. Amasifuen Guerra, Kirti Patel, Piero G. Delprete, Andréa P. Spina, Juan Grados, Pedro Vásquez-Ocmín, Alice Gadea, Rosario Rojas, Jesús Guzmán, Michel Sauvain, Universidad Peruana Cayetano Heredia (UPCH), Laboratorio Andino-Amazónico de Química de la Vida (LAVI), Universidad Peruana Cayetano Heredia (UPCH)-Institut de Recherche pour le Développement (IRD [Pérou]), Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université de Montpellier (UM), Herbier de Guyane - IRD, Institut de Recherche pour le Développement (IRD [Guyane]), Universidad Nacional Mayor de San Marcos (UNMSM), Pharmacochimie et Biologie pour le Développement (PHARMA-DEV), Institut de Recherche pour le Développement (IRD)-Institut de Chimie de Toulouse (ICT), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), and Université de Toulouse (UT)

Subjects
Ecology, fungi, Plumericin, Plant Science, Precipitation, Soil types, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, plant-herbivore interactions, plumericin, soil types, precipitation, Peru, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Plant-herbivore interactions, Ecology, Evolution, Behavior and Systematics, purl.org/pe-repo/ocde/ford#4.01.01 [https]
Abstract

18 páginas We explored the concentration patterns of the bioactive metabolite plumericin produced by Himatanthus tarapotensis (Apocynaceae) under different edaphic conditions and variations in rainfall intensity, as well as its potential role in the chemical defense against insect herbivores. Values of plumericin concentration from leaves were obtained by High-Performance Liquid Chromatography, and evaluated as a function of differences in soil types, variation of precipitation, and variation of the abundance of insect herbivores, using first a Repeated Measures Correlation (rmcorr) and then a Generalized Linear Mixed Model (GLMM) analysis. Plumericin concentration is highly variable among plants, but with a significantly higher concentration in plants growing on clay soil compared to that of the white-sand soil habitat (p < 0.001). Plumericin concentration is not affected by precipitation. The caterpillar of Isognathus leachii (Lepidoptera: Sphingidae) is the most conspicuous herbivore of H. tarapotensis, and its presence is continuous but not related to plumericin concentration, probably because of its capacity to elude the chemical defense of this plant. Nevertheless, our multivariate model revealed that plumericin concentration is related to the abundance of Hymenoptera (Formicidae), and this relationship is significantly influenced by the soil parameters of carbon percentage, clay percentage, and phosphorous percentage (p < 0.001). Plumericin is a mediating agent in the interaction between H. tarapotensis and its natural environment. Variation in plumericin concentration would be induced by the abundance of Hymenoptera (Formicidae), probably as a chemical response against these insects, and by differences in soil nutrient availability. 1. Introduction. 2. Results. 3. Discussion. 4. Materials and methods. References.

Published
2022

22. Responses of Soil Microbial Metabolic Activity and Community Structure to Different Degraded and Restored Grassland Gradients of the Tibetan Plateau

Author

Dangjun, Wang, Huakun, Zhou, Juan, Zuo, Peng, Chen, Yandi, She, Buqing, Yao, Shikui, Dong, Jianshuang, Wu, Fan, Li, Denis Mburu, Njoroge, Guoxi, Shi, Xufeng, Mao, Li, Ma, Zhonghua, Zhang, Zhun, Mao, WUHAN BOTANICAL GARDEN (WBG), Chinese Academy of Sciences [Beijing] (CAS), Northwest Plateau Institute of Biology, University of Chinese Academy of Sciences [Beijing] (UCAS), Beijing Forestry University, Chinese Academy of Agricultural Sciences (CAAS), Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China, Tianshui Normal University, Qinghai Normal University, Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université de Montpellier (UM), Second Tibetan Plateau Scientific Expedition and Research Program (2019QZKK0302) to HZ and BY, The Qinghai Natural Science Foundation Innovation team Project (2021-ZJ-902) to HZ, LM, YS, BY, XM, GS, and ZZ, Chinese Academy of Sciences and Qinghai Provincial People’s Government (LHZX-2020-08) to HZ, LM, ZZ, and YS, Joint Research Project of Three-River-Resource National Park National Natural Science Foundation of China (U21A20186) to HZ, and National Natural Science Foundation of China (31860146) to GS.

Subjects
[SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, degradation gradient, soil properties, artificial grassland establishment, food and beverages, natural sciences, Plant Science, alpine grassland, microbial community, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, complex mixtures
Abstract

International audience; Climate change and land-use disturbances are supposed to have severely affected the degraded alpine grasslands on the Tibetan Plateau. Artificial grassland establishment has been implemented as a restoration tool against grassland degradation. However, the impact of such degradation and restoration processes on soil microbial communities and soil quality is not clearly understood. Here, we aim to investigate how the dynamics of microbial community and soil quality of alpine grasslands respond to a gradient of degradation and that of restoration, respectively. We conducted a randomised experiment with four degradation stages (light, moderate, heavy, and extreme degradation) and three restoration stages (artificial restoration for 1, 5, and 10 years). We analysed the abundance and diversity of soil bacteria and fungi, and measured soil nutrients, enzymatic activity and microbial biomass. The concentration of soil nitrogen (TN), soil organic matter (OM) in heavy degraded grassland decreased significantly by 37.4 and 45.08% compared with that in light degraded grassland. TN and OM in 10-years restored grassland also increased significantly by 33.10 and 30.42% compared to that in 1-year restored grassland. Four soil enzymatic activity indicators related to microbial biomass decreased with degradation gradient and increased with recovery time (i.e., restoration gradient). Both bacterial and fungal community structure was significantly different among grassland degradation or restoration successional stages. The LEfSe analysis revealed that 29 fungal clades and 9 bacterial clades were susceptible to degraded succession, while16 fungal clades and 5 bacterial clades were susceptible to restoration succession. We conclude that soil quality (TN, OM, and enzymatic activity) deteriorated significantly in heavy degraded alpine grassland. Soil microbial community structure of alpine is profoundly impacted by both degradation and restoration processes, fungal communities are more sensitive to grassland succession than bacterial communities. Artificial grasslands can be used as an effective method of restoring degraded grassland, but the soil functions of artificial grassland, even after 10 years of recovery, cannot be restored to the original state of alpine grassland.

Published
2022

23. Deep Species Distribution Modeling From Sentinel-2 Image Time-Series: A Global Scale Analysis on the Orchid Family

Author

Joaquim Estopinan, Maximilien Servajean, Pierre Bonnet, François Munoz, Alexis Joly, Scientific Data Management (ZENITH), Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), ADVanced Analytics for data SciencE (ADVANSE), Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université de Montpellier (UM), Laboratoire Interdisciplinaire de Physique [Saint Martin d’Hères] (LIPhy ), Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA), and CACTUS Fund - INRIA

Subjects
[SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, Deep learning, Convolutional neural networks, Plant Science, Remote sensing, Sentinel-2, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Macroecology, Image time-series, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, Data science, Species distribution modeling
Abstract

Species distribution models (SDMs) are widely used numerical tools that rely on correlations between geolocated presences (and possibly absences) and environmental predictors to model the ecological preferences of species. Recently, SDMs exploiting deep learning and remote sensing images have emerged and have demonstrated high predictive performance. In particular, it has been shown that one of the key advantages of these models (called deep-SDMs) is their ability to capture the spatial structure of the landscape, unlike prior models. In this paper, we examine whether the temporal dimension of remote sensing images can also be exploited by deep-SDMs. Indeed, satellites such as Sentinel-2 are now providing data with a high temporal revisit, and it is likely that the resulting time-series of images contain relevant information about the seasonal variations of the environment and vegetation. To confirm this hypothesis, we built a substantial and original dataset (calledDeepOrchidSeries) aimed at modeling the distribution of orchids on a global scale based on Sentinel-2 image time series. It includes around 1 million occurrences of orchids worldwide, each being paired with a 12-month-long time series of high-resolution images (640 x 640 m RGB+IR patches centered on the geolocated observations). This ambitious dataset enabled us to train several deep-SDMs based on convolutional neural networks (CNNs) whose input was extended to include the temporal dimension. To quantify the contribution of the temporal dimension, we designed a novel interpretability methodology based on temporal permutation tests, temporal sampling, and temporal averaging. We show that the predictive performance of the model is greatly increased by the seasonality information contained in the temporal series. In particular, occurrence-poor species and diversity-rich regions are the ones that benefit the most from this improvement, revealing the importance of habitat's temporal dynamics to characterize species distribution.

Published
2022

24. Can Artificial Intelligence Help in the Study of Vegetative Growth Patterns from Herbarium Collections? An Evaluation of the Tropical Flora of the French Guiana Forest

Author

Hervé Goëau, Titouan Lorieul, Patrick Heuret, Alexis Joly, Pierre Bonnet, Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université de Montpellier (UM), Scientific Data Management (ZENITH), Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), ANR-10-LABX-0025,CEBA,CEnter of the study of Biodiversity in Amazonia(2010), and ANR-11-INBS-0004,E-RECOLNAT,Valorisation de 350 ans de collections d'histoire naturelle : une plateforme numérique(2011)

Subjects
Ecology, Deep learning, Plant Science, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, Neural network, Natural history collection, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, Machine learning, Visual analysis, Vegetative phenology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, vegetative phenology, plant growth, herbarium specimens, natural history collection, deep learning, machine learning, neural network, visual analysis, Ecology, Evolution, Behavior and Systematics, Plant growth, Herbarium specimens
Abstract

International audience; A better knowledge of tree vegetative growth phenology and its relationship to environmental variables is crucial to understanding forest growth dynamics and how climate change may affect it. Less studied than reproductive structures, vegetative growth phenology focuses primarily on the analysis of growing shoots, from buds to leaf fall. In temperate regions, low winter temperatures impose a cessation of vegetative growth shoots and lead to a well-known annual growth cycle pattern for most species. The humid tropics, on the other hand, have less seasonality and contain many more tree species, leading to a diversity of patterns that is still poorly known and understood. The work in this study aims to advance knowledge in this area, focusing specifically on herbarium scans, as herbariums offer the promise of tracking phenology over long periods of time. However, such a study requires a large number of shoots to be able to draw statistically relevant conclusions. We propose to investigate the extent to which the use of deep learning can help detect and type-classify these relatively rare vegetative structures in herbarium collections. Our results demonstrate the relevance of using herbarium data in vegetative phenology research as well as the potential of deep learning approaches for growing shoot detection.

Published
2022
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25. Environmental variation drives the decoupling of leaf and root traits within species along an elevation gradient

Author

Weemstra, Monique, Roumet, Catherine, Cruz-Maldonado, Nereyda, Anthelme, Fabien, Stokes, Alexia, Freschet, Grégoire, Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université de Montpellier (UM), Station d'Ecologie Théorique et Expérimentale (SETE), Centre National de la Recherche Scientifique (CNRS)-Fédération de Recherche Agrobiosciences, Interactions et Biodiversité (FR AIB), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), ANR-10-LABX-0041,TULIP,Towards a Unified theory of biotic Interactions: the roLe of environmental(2010), and ANR-16-CE03-0009,ECOPICS,Services écosystémiques souterrains produits par les communautés végétales le long de gradients altitudinaux en France et au Mexique(2016)

Subjects
leaf traits, Climate, fungi, food and beverages, Plant Science, Original Articles, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, Environment, Plants, Plant Roots, Plant Leaves, Soil, root traits, Phenotype, intraspecific trait variation, trait correlations, elevation gradient, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, trait covariation
Abstract

Background and Aims Plant performance is enhanced by balancing above- and below-ground resource uptake through the intraspecific adjustment of leaf and root traits. It is assumed that these organ adjustments are at least partly coordinated, so that analogous leaf and root traits broadly covary. Understanding the extent of such intraspecific leaf–root trait covariation would strongly contribute to our understanding of how plants match above- and below-ground resource use strategies as their environment changes, but comprehensive studies are lacking. Methods We measured analogous leaf and root traits from 11 species, as well as climate, soil and vegetation properties along a 1000-m elevation gradient in the French Alps. We determined how traits varied along the gradient, to what extent this variation was determined by the way different traits respond to environmental cues acting at different spatial scales (i.e. within and between elevations), and whether trait pairs covaried within species. Key Results Leaf and root trait patterns strongly diverged: across the 11 species along the gradient, intraspecific leaf trait patterns were largely consistent, whereas root trait patterns were highly idiosyncratic. We also observed that, when compared with leaves, intraspecific variation was greater in root traits, due to the strong effects of the local environment (i.e. at the same elevation), while landscape-level effects (i.e. at different elevations) were minor. Overall, intraspecific trait correlations between analogous leaf and root traits were nearly absent. Conclusions Our study suggests that environmental gradients at the landscape level, as well as local heterogeneity in soil properties, are the drivers of a strong decoupling between analogous leaf and root traits within species. This decoupling of plant resource acquisition strategies highlights how plants can exhibit diverse whole-plant acclimation strategies to modify above- and below-ground resource uptake, improving their resilience to environmental change.

Published
2022

26. New records of Asteraceae for the non-native flora of Tunisia and north Africa with some nomenclatural remarks

Author

Ridha El Mokni, Duilio Iamonico, Errol Véla, Filip Verloove, Gianniantonio Domina, Université de Monastir - University of Monastir (UM), University of Pisa - Università di Pisa, Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université de Montpellier (UM), Meise Botanic Garden [Belgium] (Plantentuin), Università degli studi di Palermo - University of Palermo, El Mokni R., Iamonico D., Vela E., Verloove F., and Domina G.

Subjects
Asteroideae, Compositae, Ecology, Settore BIO/02 - Botanica Sistematica, Plant Science, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, alien flora, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, naturalization, Alien flora, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, Settore BIO/03 - Botanica Ambientale E Applicata, typification, Typification, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Ecology, Evolution, Behavior and Systematics, Cichorioideae, Naturalization
Abstract

International audience; Sixteen new Asteraceae are added to the non-indigenous flora of Tunisia. Six of them (Dimorphotheca ecklonis, Gaillardia pulchella, Gazania linearis var. linearis, Guizotia abyssinica, Rudbeckia triloba and Tithonia diversifolia) are also new for the flora of North Africa. Chrysanthemum morifolium is here first reported for the Mediterranean Basin. Seven genera (Argyranthemum, Bidens, Dimorphotheca, Gaillardia, Guizotia, Rudbeckia and Tithonia) are recorded for the first time for the vascular flora of Tunisia. Most of these species escaped from gardens and pots and became casual along roadsides and/or disturbed areas after cypsela dispersion (except for Chrysanthemum morifolium). Some species, even though appearing to be well established locally and are potentially invasive at a worldwide level, still do not behave so in Tunisia. In addition to the floristic notes, the typification of the names Dimorphotheca ecklonis, Gorteria linearis and Mirasolia diversifolia are discussed.

Published
2022

27. The ECAT dataset: expert-validated distribution data of endemic and sub-endemic trees of Central Africa (Dem. Rep. Congo, Rwanda, Burundi)

Author

Wesley Tack, Henry Engledow, Nuno Veríssimo Pereira, Christian Amani, Steven P. Bachman, Patricia Barberá, Henk J. Beentje, Gaël U. D. Bouka, Martin Cheek, Ariane Cosiaux, Gilles Dauby, Petra De Block, Corneille E. N. Ewango, Eberhard Fischer, Roy E. Gereau, Serene Hargreaves, Yvette Harvey-Brown, Davy U. Ikabanga, Edouard Ilunga wa Ilunga, James Kalema, Peris Kamau, Olivier Lachenaud, Quentin Luke, Ithe Mwanga Mwanga, Sydney T. Ndolo Ebika, Jacques Nkengurutse, Aimable Nsanzurwimo, Salvator Ntore, Sophie L. Richards, Reddy Shutsha Ehata, Murielle Simo-Droissart, Tariq Stévart, Marc S. M. Sosef, Meise Botanic Garden [Belgium] (Plantentuin), Université officielle de Bukavu, Royal Botanic Gardens [Kew], Missouri Botanical Garden, International Union for Conservation of Nature (IUCN), University of Yaoundé [Cameroun], Université de Montpellier (UM), Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université de Montpellier (UM), Université libre de Bruxelles (ULB), and Université de Yaoundé I

Subjects
flowering plants, endemics, geographic range, conservation, threatened, Plant Science, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, IUCN Red List, data capture, flora, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, Africa, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Ecology, Evolution, Behavior and Systematics, data cleaning, herbarium
Abstract

International audience; In this data paper, we present a specimen-based occurrence dataset compiled in the framework of the Conservation of Endemic Central African Trees (ECAT) project with the aim of producing global conservation assessments for the IUCN Red List. The project targets all tree species endemic or sub-endemic to the Central African region comprising the Democratic Republic of the Congo (DR Congo), Rwanda, and Burundi. The dataset contains 6361 plant collection records with occurrences of 8910 specimens from 337 taxa belonging to 153 genera in 52 families. Many of these tree taxa have restricted geographic ranges and are only known from a small number of herbarium specimens. As assessments for such taxa can be compromised by inadequate data, we transcribed and geo-referenced specimen label information to obtain a more accurate and complete locality dataset. All specimen data were manually cleaned and verified by botanical experts, resulting in improved data quality and consistency.

Published
2022

28. Stronger wind, smaller tree: Testing tree growth plasticity through a modelling approach

Author

Haoyu Wang, Jing Hua, Mengzhen Kang, Xiujuan Wang, Xing-Rong Fan, Thierry Fourcaud, Philippe de Reffye, Chinese Academy of Sciences [Beijing] (CAS), Chongqing Technology and Business University (CTBU), Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université de Montpellier (UM), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Major S&T project (Innovation 2030) of China (2021ZD0113704), and CAS-NSTDA Joint Research Program (GJHZ2076)

Subjects
Facteur lié au site, functional-structural plant model, Réponse de la plante, F62 - Physiologie végétale - Croissance et développement, modèle de croissance forestière, facteurs abiotiques, Plant Science, F50 - Anatomie et morphologie des plantes, mechanical model, tree breakage, Modélisation, [SDE]Environmental Sciences, K01 - Foresterie - Considérations générales, Plasticité phénotypique, thigmomorphogenesis, Adaptation, optimization, critical wind speed
Abstract

Plants exhibit plasticity in response to various external conditions, characterized by changes in physiological and morphological features. Although being non-negligible, compared to the other environmental factors, the effect of wind on plant growth is less extensively studied, either experimentally or computationally. This study aims to propose a modeling approach that can simulate the impact of wind on plant growth, which brings a biomechanical feedback to growth and biomass distribution into a functional–structural plant model (FSPM). Tree reaction to the wind is simulated based on the hypothesis that plants tend to fit in the environment best. This is interpreted as an optimization problem of finding the best growth-regulation sink parameter giving the maximal plant fitness (usually seed weight, but expressed as plant biomass and size). To test this hypothesis in silico, a functional–structural plant model, which simulates both the primary and secondary growth of stems, is coupled with a biomechanical model which computes forces, moments of forces, and breakage location in stems caused by both wind and self-weight increment during plant growth. The Non-dominated Sorting Genetic Algorithm II (NSGA-II) is adopted to maximize the multi-objective function (stem biomass and tree height) by determining the key parameter value controlling the biomass allocation to the secondary growth. The digital trees show considerable phenotypic plasticity under different wind speeds, whose behavior, as an emergent property, is in accordance with experimental results from works of literature: the height and leaf area of individual trees decreased with wind speed, and the diameter at the breast height (DBH) increased at low-speed wind but declined at higher-speed wind. Stronger wind results in a smaller tree. Such response of trees to the wind is realistically simulated, giving a deeper understanding of tree behavior. The result shows that the challenging task of modeling plant plasticity may be solved by optimizing the plant fitness function. Adding a biomechanical model enriches FSPMs and opens a wider application of plant models.

Published
2022

29. Contrasting nickel and manganese accumulation and localization in New Caledonian Cunoniaceae

Author

Antony van der Ent, Yohan Pillon, Bruno Fogliani, Vidiro Gei, Tanguy Jaffré, Peter D. Erskine, Guillaume Echevarria, Kathryn M. Spiers, Adrian L. D. Paul, Sandrine Isnard, University of Queensland [Brisbane], Laboratoire Sols et Environnement (LSE), Université de Lorraine (UL)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire des symbioses tropicales et méditerranéennes (UMR LSTM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), Institut de sciences exactes et appliquées (ISEA), Université de la Nouvelle-Calédonie (UNC), Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université de Montpellier (UM), Deutsches Elektronen-Synchrotron [Hamburg] (DESY), CAUL, Australian Research Council, Pacific Fund Project, and European Project: 730872,CALIPSOplus

Subjects
Ultramafic soils, Elemental mapping, Manganese, XRF, Hyperaccumulator, Soil Science, Plant Science, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, ddc:580, New Caledonia, Nickel, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Cunoniaceae
Abstract

Plant and soil 475(1-2), 515 - 534 (2022). doi:10.1007/s11104-022-05388-3, PurposeThe Cunoniaceae are a major component of the New Caledonian flora with 91 endemic species that are highly unusual in that multiple metals are hyperaccumulated in different species. This makes it an ideal model system for studying the nature of the hyperaccumulation phenomenon.MethodsX-ray fluorescence spectroscopy (XRF) scanning of all herbarium collections of the Cunoniaceae was undertaken at the Herbarium of New Caledonia to reveal incidences of nickel (Ni) and manganese (Mn) accumulation. Following on, the Mn hyperaccumulating P. reticulata and the Ni hyperaccumulating P. xaragurensis were selected for detailed follow-up investigations using synchrotron-based X-ray fluorescence microscopy (XFM).ResultsThe systematic XRF screening of herbarium specimens showed that numerous species have high foliar Mn and Ni with species either accumulating Ni or Mn, but not both elements simultaneously. Soil ‘extractable’ Mn and Ni concentrations associated with Pancheria reticulata and P. xaragurensis greatly varies between the species. The XFM data shows that P. reticulata has a distinctive distribution pattern with Mn concentrated in large hypodermal cells. This contrasts with P. xaragurensis where Ni was mainly localized in and around the epidermis, and hypodermal cells were not observed., Published by Springer Science + Business Media B.V, Dordrecht [u.a.]

Published
2022

30. When architectural plasticity fails to counter the light competition imposed by planting design: an in silico approach using a functional–structural model of oil palm

Author

Raphaël P A Perez, Rémi Vezy, Loïc Brancheriau, Frédéric Boudon, François Grand, Merlin Ramel, Doni Artanto Raharjo, Jean-Pierre Caliman, Jean Dauzat, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université de Montpellier (UM), BioWooEB (UPR BioWooEB), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM), Département Performances des systèmes de production et de transformation tropicaux (Cirad-PERSYST), Smart Research Institute [Indonésie] (SMARTRI), SMART agribusiness and food [Jakarta] (SMART), Agrosystèmes Biodiversifiés (UMR ABSys), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre International de Hautes Etudes Agronomiques Méditerranéennes - Institut Agronomique Méditerranéen de Montpellier (CIHEAM-IAMM), Centre International de Hautes Études Agronomiques Méditerranéennes (CIHEAM)-Centre International de Hautes Études Agronomiques Méditerranéennes (CIHEAM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)

Subjects
plant architecture, LiDAR, F40 - Écologie végétale, Plant Science, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, F50 - Anatomie et morphologie des plantes, phenotypic plasticity, Biochemistry, Genetics and Molecular Biology (miscellaneous), planting design, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, Elaeis guineensis, FSPM, Morphologie végétale, U10 - Informatique, mathématiques et statistiques, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, Physiologie végétale, Modélisation, Anatomie végétale, Modeling and Simulation, Plasticité phénotypique, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Agronomy and Crop Science
Abstract

Functional–structural plant modelling approaches (FSPM) explore the relationships between the 3D structure and the physiological functioning of plants in relation to environmental conditions. In this study, we present a methodological approach that integrated architectural responses to planting design in an oil palm FSPM, and test the impact of planting design and architectural plasticity on physiological responses such as light interception and carbon assimilation. LiDAR-derived and direct measurements were performed on five planting designs to assess the phenotypic plasticity of architectural traits, and allowed evaluating the variations of the main parameters of an existing 3D plant model. Accordingly, we proposed a neighbourhood index (NI) as a simple explanatory variable of architectural plasticity, and used NI-based allometries to simulate architectural variations in 3D virtual plants. Light interception and carbon assimilation were then simulated on virtual plots reproducing the five studied designs. We found that the main traits affected by plant proximity were leaf dimensions, leaf weight and leaf erectness, whereas other structural traits like the frequency of leaflets along the rachis or biomechanical properties of leaves remained unchanged. Our simulation study highlighted model compliance to reproduce architectural plasticity and illustrated how architectural plasticity improved light interception via leaf area expansion, but how the competition for light imposed by the design can counterbalance this benefit in terms of carbon assimilation at stand scale. We conclude on the importance of planting patterns for plants with low architectural plasticity such as oil palm, and how in silico experiments can help in designing innovative planting patterns.

Published
2022

31. Tyloses in fossil plants: New data from a Mississippian tree, with a review of previous records

Author

Anne-Laure Decombeix, Carla J. Harper, Jean Galtier, Brigitte Meyer-Berthaud, Michael Krings, Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université de Montpellier (UM), Trinity College Dublin, and Ludwig-Maximilians-Universität München (LMU)

Subjects
Carboniferous, anatomy, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, Xylem, Embolism, Plant–pathogen interactions, Paleobotany, Plant Science, Plant, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy
Abstract

International audience; Tyloses are protoplasmic swellings of parenchyma cells into the lumen of adjacent conducting cells. They develop as part of the heartwood formation process, or in response to embolism or pathogen infection. Here, we report the oldest fossil evidence to date of tylosis formation that occurs in permineralized wood of the (pro)gymnosperm Dameria hueberi from the Tournaisian (lower Mississippian, ca. 350 Ma) of Australia. Different developmental stages of tylosis formation are recognizable that range from small bubble-like protrusions to dense tyloses entirely filling the lumen of the conducting cells. The trigger for the development of tyloses in D. hueberi remains unknown. A survey of the fossil record of tyloses shows their occurrence in most groups of vascular plants since the Carboniferous. Future research in this field will screen even older (Devonian) fossils for evidence of tyloses and aim to understand the roles these structures have had in plant?pathogen interactions and plant hydraulic properties in the past.

Published
2022

32. Radial variations in wood functional traits in a rain forest from eastern Amazonia

Author

Juan M. Posada, Romain Lehnebach, Bruno Clair, Jacques Beauchêne, Andrés González-Melo, Katherine Rivera, Sébastien Levionnois, Universidad del Rosario [Bogota], Ecologie des forêts de Guyane (UMR ECOFOG), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-AgroParisTech-Université de Guyane (UG)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Département Environnements et Sociétés (Cirad-ES), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Universiteit Gent = Ghent University [Belgium] (UGENT), Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-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), Universidad Distrital Francisco Jose de Caldas [Bogota], Bois (BOIS), Laboratoire de Mécanique et Génie Civil (LMGC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Universiteit Gent = Ghent University (UGENT), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université de Montpellier (UM), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), and The authors acknowledge financial support from Colciencias (Colombian Agency for Science and Technology) and the University of Guyane.

Subjects
0106 biological sciences, Tropical trees, Physiology, Plant Science, 01 natural sciences, F50 - Anatomie et morphologie des plantes, Structure du bois, Hydraulic conductivity, K01 - Foresterie - Considérations générales, Forêt tropicale humide, Wood functional traits, Biomass (ecology), Ecology, Amazon rainforest, Forestry, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, Physiologie végétale, visual_art, Accroissement du diamètre, visual_art.visual_art_medium, Bark, Pith, Diamètre, Tree functioning, Tree species, Propriété du bois, Rainforest, Biology, Anatomie du bois, 010603 evolutionary biology, Radial variation, Écologie forestière, Wood anatomy, Morphologie végétale, 15. Life on land, Tropical forest, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, 010606 plant biology & botany
Abstract

International audience; Trees can modify their wood structure in response to changes in mechanical, hydraulic and storage demands during their life-cycles. Thus, examining radial variations in wood traits is important to expand our knowledge of tree functioning and species ecological strategies. Yet, several aspects of radial changes in wood functional traits are still poorly understood, especially in angiosperm trees from tropical humid forests. Here, we examined radial shifts in wood traits in trunks of tropical forest species and explored their potential ecological implications. We first examined radial variations in wood specific gravity (WSG). Then, we asked what anatomical traits drove radial variations in WSG, and whether WSG, vessel fraction and specific hydraulic conductivity vary independently from each other along the radius gradients. We measured WSG and eight wood anatomical traits, at different radial positions along the trunks, in 19 tree species with contrasting shade-tolerance from a lowland tropical forest in eastern Amazonia. Most species had significant radials shifts in WSG. Positive radial gradients in WSG (i.e., increments from pith to bark) were common among shade-intolerant species and were explained by different combinations of fiber and parenchyma traits, while negative radial shifts in WSG (e.g., decreases towards the bark) were present in shade-tolerants, but were generally weakly related to anatomical traits. We also found that, in general, WSG was unrelated to vessel fraction and specific hydraulic conductivity in any radial position. This study illustrates the contrasting radial variations in wood functional traits that occur in tree species from a humid lowland tropical forest. In particular, our results provide valuable insights into the anatomical traits driving WSG variations during tree development. These insights are important to expand our knowledge on tree ecological strategies by providing evidence on how wood allocation varies as trees grow, which in turn can be useful in studying trait-demography associations, and in estimating tree above-ground biomass.

Published
2022

33. Going Viral: Virus-Based Biological Control Agents for Plant Protection

Author

Wagemans, Jeroen, Holtappels, Dominique, Vainio, Eeva, Rabiey, Mojgan, Marzachì, Cristina, Herrero, Salvador, Ravanbakhsh, Mohammadhossein, Tebbe, Christoph C., Ogliastro, Mylène, Ayllón, María A., Turina, Massimo, Sub Ecology and Biodiversity, Ecology and Biodiversity, Sub Ecology and Biodiversity, Ecology and Biodiversity, Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), Natural Resources Institute Finland (LUKE), University of Birmingham [Birmingham], CNR Istituto per la Protezione Sostenibile delle Piante [Torino, Italia] (IPSP), National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), Estructura de Recerca Interdisciplinar en Biotecnologia I Biomedicina (ERI-BIOTECMED, Department of Genetics Faculty of Biological Sciences, Universidad de Valencia, Utrecht University [Utrecht], Thünen Institute of Biodiversity, Diversité, Génomes & Interactions Microorganismes - Insectes [Montpellier] (DGIMI), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université de Montpellier (UM), Universidad Politécnica de Madrid (UPM), and European Project: 773567,VIROPLANT

Subjects
Insecta, Bacteria, nanotechnology, Fungi, [SDV.BC.BC]Life Sciences [q-bio]/Cellular Biology/Subcellular Processes [q-bio.SC], virus, Plant Science, Plants, entomovirus, [SDV.BA.ZI]Life Sciences [q-bio]/Animal biology/Invertebrate Zoology, Biological Control Agents, bacteriophage, mycovirus, Viruses, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Animals, biocontrol, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Ecosystem, Plant Diseases
Abstract

International audience; The most economically important biotic stresses in crop production are caused by fungi, oomycetes, insects, viruses, and bacteria. Often chemical control is still the most commonly used method to manage them. However, the development of resistance in the different pathogens/pests, the putative damage on the natural ecosystem, and the toxic residues in the field and thus contamination of the environment have stimulated the search for safer alternatives such as the use of biological control agents (BCAs). Among BCAs, viruses, a major driver for controlling host populations and evolution, are somewhat underused, mostly because of regulatory hurdles that make the cost of registration of such host-specific BCAs not affordable in comparison with the limited potential market. Here, we provide a comprehensive overview of the state of the art of virus-based BCAs against fungi, bacteria, viruses, and insects, with a specific focus on new approaches that rely on not only the direct biocidal virus component but also the complex ecological interactions between viruses and their hosts that do not necessarily result in direct damage to the host. Expected final online publication date for the Annual Review of Phytopathology, Volume 60 is August 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Published
2022

34. Assemblages of anoxygenic phototrophic bacteria in tank bromeliads exhibit a host‐specific signature

Author

Anne‐hélène Le Jeune, Régis Céréghino, Christian Jeanthon, François Enault, Corinne Bardot, Anne-Catherine Lehours, Vincent Darbot, Antoine Vergne, Jean-François Carrias, Eric Giraud, Bruno Corbara, Isabelle Mary, Céline Leroy, Laboratoire Microorganismes : Génome et Environnement (LMGE), Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne (UCA), Laboratoire Ecologie Fonctionnelle et Environnement (ECOLAB), Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-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)-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées, Ecologie des forêts de Guyane (UMR ECOFOG), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-AgroParisTech-Université de Guyane (UG)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-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), Adaptation et diversité en milieu marin (AD2M), Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Laboratoire des symbioses tropicales et méditerranéennes (UMR LSTM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-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), Laboratoire Ecologie Fonctionnelle et Environnement (LEFE), Université de Toulouse (UT)-Université de Toulouse (UT)-Observatoire Midi-Pyrénées (OMP), 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)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-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 Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-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), ANR-10-LABX-0025,CEBA,CEnter of the study of Biodiversity in Amazonia(2010), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-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)-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (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)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)

Subjects
Assembly rules, [SDV]Life Sciences [q-bio], Plant Science, 03 medical and health sciences, Nitrogen fixation, Dominance (ecology), Plant–bacteria interactions, Ecology, Evolution, Behavior and Systematics, Phylogenetic analyses, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0303 health sciences, Ecology, biology, Phototroph, 030306 microbiology, Illumina sequencing, 15. Life on land, biology.organism_classification, Anoxygenic photosynthesis, Rhodobacterales, Burkholderiales, [SDE]Environmental Sciences, Biological dispersal, Evolutionary ecology
Abstract

International audience; Anoxygenic phototrophic bacteria (APB) are a very significant metabolic functional group in the phytotelmata of tank-forming Bromeliaceae plants. Considering the close relationships existing between the bromeliad and its tank microbiota, the dominance of APB raises the question of their role in the ecology and evolution of these plants. Here, using pufM gene sequencing for taxonomic profiling, we investigated the structure of APB communities in the tanks of five bromeliad species exhibiting different habitat characteristics (i.e. physicochemical factors associated with the host), and occurring in different localities of French Guiana. We found that APB assemblages were specific to plant species and were less dependent on location or on bromeliad habitat characteristics. This convergence suggests that the identity of the bromeliad species per se is more important than habitat filtering or dispersal to control specific assembly rules for APB. The pufM OTUs were affiliated with five orders of Alpha- and Beta-proteobacteria (Rhodobacterales, Sphingomonadales, Rhizobiales, Burkholderiales and Rhodospirillales), and we assume that they may be major components of the core microbiota of plant-held waters. Our findings also revealed that up to 79% of the sequences were affiliated with APB clades possessing nitrogen-fixing genes suggesting that this metabolic capability is widespread within the APB community inhabiting tank bromeliads. We hypothesized that bromeliads may benefit nutritionally from associations with free-living APB capable to fix atmospheric nitrogen. Synthesis. Understanding the dominance of APB in tank bromeliads and determining whether a potential interplay exists between these partners is an intriguing aspect of possible mutualistic and coevolving interactions between the two existing forms of chlorophototrophy (i.e. bacteriochlorophyll-based anoxygenic and chlorophyll-based oxygenic phototrophy). In the present study, we found that bromeliad species was the main factor that explained variance in APB community composition. These findings suggest that APB and tank bromeliads may have a close, mutualistic relationship and we hypothesize according to our genomic analyses that APB may promote the bromeliad growth by provisioning essential nutrients like nitrogen.

Published
2021

35. Modelling the functional dependency between root and shoot compartments to predict the impact of the environment on the architecture of the whole plant. Methodology for model fitting on simulated data using Deep Learning techniques

Author

Jean-François Barczi, Yves Caraglio, Philippe Borianne, Abel Louis Masson, Eric Nicolini, AgroParisTech, Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-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), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université de Montpellier (UM)

Subjects
0106 biological sciences, Root (linguistics), Plant Science, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, 01 natural sciences, apprentissage machine, Mathematics, Facteur du milieu, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, Modeling and Simulation, Simulated data, Shoot, Calibration, Biological system, F40 - Écologie végétale, Whole plant, F60 - Physiologie et biochimie végétale, DeepLearning, Model fitting, 010603 evolutionary biology, Biochemistry, Genetics and Molecular Biology (miscellaneous), [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, Architecture, Croissance, Modélisation environnementale, Changement climatique, FSPM, Root/Shoot, business.industry, Deep learning, 15. Life on land, Modélisation, 13. Climate action, Pousse, Artificial intelligence, U30 - Méthodes de recherche, Plante de culture, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, business, Functional dependency, Agronomy and Crop Science, Racine, 010606 plant biology & botany
Abstract

Tree structural and biomass growth studies mainly focus on the shoot compartment. Tree roots usually have to be taken apart due to the difficulties involved in measuring and observing this compartment, particularly root growth. In the context of climate change, the study of tree structural plasticity has become crucial and both shoot and root systems need to be considered simultaneously as they play a joint role in adapting traits to climate change (water availability for roots and light or carbon availability for shoots). We developed a botanically accurate whole-plant model and its simulator (RoCoCau) with a linkable external module (TOY) to represent shoot and root compartment dependencies and hence tree structural plasticity in different air and soil environments. This paper describes a new deep neural network calibration trained on simulated data sets computed from a set of more than 360 000 random TOY parameter values and random climate values. These data sets were used for training and for validation. For this purpose, we chose VoxNet, a convolutional neural network designed to classify 3D objects represented as a voxelized scene. We recommend further improvements for VoxNet inputs, outputs and training. We were able to teach the network to predict the value of environment data well (mean error < 2 %), and to predict the value of TOY parameters for plants under water stress conditions (mean error < 5 % for all parameters), and for any environmental growing conditions (mean error < 20 %).

Published
2021

36. Exploring complementarities between modelling approaches that enable upscaling from plant community functioning to ecosystem services as a way to support agroecological transition

Author

Noémie Gaudio, Gaëtan Louarn, Romain Barillot, Clémentine Meunier, Rémi Vezy, Marie Launay, AGroécologie, Innovations, teRritoires (AGIR), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Unité de Recherche Pluridisciplinaire Prairies et Plantes Fourragères (P3F), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-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), Agroclim (AGROCLIM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université de Montpellier (UM), Département Systèmes Biologiques (Cirad-BIOS), and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)

Subjects
0106 biological sciences, individual-based models, crop mixtures, [SDV.SA.AGRO]Life Sciences [q-bio]/Agricultural sciences/Agronomy, 04 agricultural and veterinary sciences, Plant Science, 15. Life on land, 01 natural sciences, Biochemistry, Genetics and Molecular Biology (miscellaneous), [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, process-based models, crop models, pest regulation, Modeling and Simulation, [SDE]Environmental Sciences, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, Agronomy and Crop Science, 010606 plant biology & botany, modelling synergies
Abstract

Promoting plant diversity through crop mixtures is a mainstay of the agroecological transition. Modelling this transition requires considering both plant–plant interactions and plants’ interactions with abiotic and biotic environments. Modelling crop mixtures enables designing ways to use plant diversity to provide ecosystem services, as long as they include crop management as input. A single modelling approach is not sufficient, however, and complementarities between models may be critical to consider the multiple processes and system components involved at different and relevant spatial and temporal scales. In this article, we present different modelling solutions implemented in a variety of examples to upscale models from local interactions to ecosystem services. We highlight that modelling solutions (i.e. coupling, metamodelling, inverse or hybrid modelling) are built according to modelling objectives (e.g. understand the relative contributions of primary ecological processes to crop mixtures, quantify impacts of the environment and agricultural practices, assess the resulting ecosystem services) rather than to the scales of integration. Many outcomes of multispecies agroecosystems remain to be explored, both experimentally and through the heuristic use of modelling. Combining models to address plant diversity and predict ecosystem services at different scales remains rare but is critical to support the spatial and temporal prediction of the many systems that could be designed.

Published
2021

37. The Arabidopsis NRT1.1 transceptor coordinately controls auxin biosynthesis and transport to regulate root branching in response to nitrate

Author

Eva Benková, Alain Gojon, Carine Alcon, Amel Maghiaoui, Candela Cuesta, Lien Bach, Gabriel Krouk, Francine Perrine-Walker, Eleonore Bouguyon, Philippe Nacry, Biochimie et Physiologie Moléculaire des Plantes (BPMP), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-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), Université de La Réunion - UFR Santé (UR UFRS), Université de La Réunion (UR), Institute of Science and Technology [Austria] (IST Austria), School of Life and Environmental Sciences A08 [Australia) (University of Sydney), The University of Sydney, Plateforme d'histocytologie et d'imagerie cellulaire végétale (PHIV), 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)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-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)-Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and ANR-16-CE20-0022,NitraSense,Intégration des réponses physiologiques et développementales de la plante au nitrate: rôle de la signalisation dépendante de NRT1.1 (NPF6.3/CHL1) dans l'efficience d'utilisation de l'azote(2016)

Subjects
0106 biological sciences, Auxin influx, Cell signaling, Physiology, [SDV]Life Sciences [q-bio], lateral root primordia, Plant Science, 01 natural sciences, 03 medical and health sciences, chemistry.chemical_compound, Nitrate, transceptor, Auxin, nitrate, Arabidopsis, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Primordium, development, 030304 developmental biology, chemistry.chemical_classification, 0303 health sciences, biology, Lateral root, fungi, food and beverages, biology.organism_classification, Cell biology, chemistry, Stele, NRT1.1, 010606 plant biology & botany, auxin signaling
Abstract

International audience; In agricultural systems, nitrate is the main source of nitrogen available for plants. Besides its role as a nutrient, nitrate has been shown to act as a signal molecule for plant growth, development and stress responses. In Arabidopsis, the NRT1.1 nitrate transceptor represses lateral root (LR) development at low nitrate availability by promoting auxin basipetal transport out of the LR primordia (LRPs). In addition, our present study shows that NRT1.1 acts as a negative regulator of the TAR2 auxin biosynthetic gene expression in the root stele. This is expected to repress local auxin biosynthesis and thus to reduce acropetal auxin supply to the LRPs. Moreover, NRT1.1 also negatively affects expression of the LAX3 auxin influx carrier, thus preventing cell wall remodeling required for overlying tissues separation during LRP emergence. Both NRT1.1-mediated repression of TAR2 and LAX3 are suppressed at high nitrate availability, resulting in the nitrate induction of TAR2 and LAX3 expression that is required for optimal stimulation of LR development by nitrate. Altogether, our results indicate that the NRT1.1 transceptor coordinately controls several crucial auxin-associated processes required for LRP development, and as a consequence that NRT1.1 plays a much more integrated role than previously anticipated in regulating the nitrate response of root system architecture.

Published
2020

38. Flavonoids and Phenolic Compounds From the Parasitic Gymnosperm Parasitaxus usta Endemic to New Caledonia

Author

Tsukasa Iwashina, Hiroshi Tobe, Takahisa Nakane, Takayuki Mizuno, Tanguy Jaffré, National Museum of Nature and Science, Kyoto Botanical Garden, Showa Pharmaceutical University [Tokyo, Japan], Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université de Montpellier (UM), Institut de Recherche pour le Développement (IRD [Nouvelle-Calédonie]), and Herbier de Nouvelle-Calédonie (Herbier NOU)

Subjects
Flavonoids, Podocarpaceae, Pharmacology, Parasitaxus usta, Plant Science, General Medicine, Nouvelle-Calédonie, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, Phenolic compounds, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, New Caledonia, Complementary and alternative medicine, Drug Discovery, Parasitic gymnosperm, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract

Parasitaxus usta (Podocarpaceae) is the only parasitic gymnosperm and endemic to New Caledonia. In this survey, 11 flavonoids and 6 phenolic compounds were isolated from the aerial parts. As for flavonoids, six flavones, apigenin 7- O-glucoside (1), luteolin (2), luteolin 7- O-glucoside (3), chrysoeriol (4), chrysoeriol 7- O-glucoside (5) and tricetin 3′- O-glucoside (6), one C-glycosylflavone, orientin (7), one flavonol, quercetin 3- O-glucoside (8), one anthocyanin, cyanidin 3- O-glucoside (9), and two biflavones, isoginkgetin (10) and agathisflavone (11) were identified by UV, liquid chromatograph–mass spectra (LC-MS), acid hydrolysis, NMR and/or HPLC comparisons with authentic samples. On the other hand, six phenolic compounds were identified as 5- O- E- p-coumaroyl quinic acid (12), 5- O- Z- p-coumaroyl quinic acid (13), 5- O- E- p-coumaroyl quinic acid methyl ester (14), 5- O- Z- p-coumaroyl quinic acid methyl ester (15), E-caffeic acid methyl ester 3- O-β-glucopyranoside (16), and Z-caffeic acid methyl ester 3- O-β-glucopyranoside (17) by UV, LC-MS and NMR. Chemical components of P usta were reported in this survey for the first time. Their chemical characters were chemotaxonomically compared with those of other Podocarpaceae species.

Published
2022

39. Characterization of the grapevine Shaker K+ channel VvK3.1 supports its function in massive potassium fluxes necessary for berry potassium loading and pulvinus-actuated leaf movements

Author

Rémy Gibrat, Sabine Zimmermann, Manuel Nieves-Cordones, Bertrand Moreau, Isabelle Chérel, Isabelle Gaillard, Nadine Paris, Mamy-Jean de Dieu Andrianteranagna, Teresa Cuéllar, Martin Boeglin, Jean-Luc Verdeil, Biochimie et Physiologie Moléculaire des Plantes (BPMP), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Plateforme d'histocytologie et d'imagerie cellulaire végétale (PHIV), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-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)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-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)-Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université de Montpellier (UM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), and Plateforme RIO Imaging (PHIV MRI)

Subjects
0106 biological sciences, 0301 basic medicine, Stress dû à la sécheresse, Physiology, F60 - Physiologie et biochimie végétale, Potassium, chemistry.chemical_element, teneur en potassium, Plant Science, Berry, 01 natural sciences, Petiole (botany), phloem, F30 - Génétique et amélioration des plantes, baie de raisin, 03 medical and health sciences, grape berry K+ loading, phloème, Expression des gènes, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Pulvinus, Shaker, shaker potassium channel, Chemistry, paraheliotropic movements, phytogénétique, Hybridation, food and beverages, Ripening, Apoplast, Physiologie végétale, grapevine, 030104 developmental biology, Vitis vinifera, Biophysics, Phloem, canaux potassiques shaker, vigne, 010606 plant biology & botany
Abstract

In grapevine, climate changes lead to increased berry potassium (K+ ) contents that result in must with low acidity. Consequently, wines are becoming 'flat' to the taste, with poor organoleptic properties and low potential aging, resulting in significant economic loss. Precise investigation into the molecular determinants controlling berry K+ accumulation during its development are only now emerging. Here, we report functional characterization by electrophysiology of a new grapevine Shaker-type K+ channel, VvK3.1. The analysis of VvK3.1 expression patterns was performed by qPCR and in situ hybridization. We found that VvK3.1 belongs to the AKT2 channel phylogenetic branch and is a weakly rectifying channel, mediating both inward and outward K+ currents. We showed that VvK3.1 is highly expressed in the phloem and in a unique structure located at the two ends of the petiole, identified as a pulvinus. From the onset of fruit ripening, all data support the role of the VvK3.1 channel in the massive K+ fluxes from the phloem cell cytosol to the berry apoplast during berry K+ loading. Moreover, the high amount of VvK3.1 transcripts detected in the pulvinus strongly suggests a role for this Shaker in the swelling and shrinking of motor cells involved in paraheliotropic leaf movements.

Published
2019

40. Into the functional ecology of ectomycorrhizal communities: environmental filtering of enzymatic activities

Author

Selosse Marc-André, Munoz François, Criquet Stéven, Courty Pierre-Emmanuel, Richard Franck, Duchemin Myriam, Plassard Claude, Taudière Adrien, Garbaye Jean, Buée Marc, Ziarelli Fabio, Department of Biology, University of Fribourg, Switzerland, Zurich-Basel Plant Science Center, Department of Environmental Sciences, Botany, University of Basel, Institut Français de Pondichéry (IFP), Ministère de l'Europe et des Affaires étrangères (MEAE)-Centre National de la Recherche Scientifique (CNRS), Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Biologie Intégrative des Populations, École pratique des hautes études (EPHE)-Centre National de la Recherche Scientifique (CNRS), Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), 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), 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), Aix-Marseille Université - Faculté des Sciences (AMU SCI), Aix Marseille Université (AMU), Interactions Arbres-Microorganismes (IAM), Université de Lorraine (UL)-Institut National de la Recherche Agronomique (INRA), Ecologie fonctionnelle et biogéochimie des sols et des agro-écosystèmes (UMR Eco&Sols), Institut National de la Recherche Agronomique (INRA)-Institut de Recherche pour le Développement (IRD)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Université de Fribourg = University of Fribourg (UNIFR), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université de Montpellier (UM), Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-Université Pierre et Marie Curie - Paris 6 (UPMC)-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), 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), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL), FUNDIV project (ANR606-BDIV-06), Swiss National Science Foundation (PZ00P3_136651), ANR-06-BDIV-0006,FUNDIV,Conserving and exploiting the functionnal diversity of ectomycorhizal fungi in forest ecosystems(2006), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD [France-Sud]), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), 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]), Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UMR237-Aix Marseille Université (AMU)-Avignon Université (AU), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)

Subjects
0106 biological sciences, interaction sol plante, taxonomie, Ecology (disciplines), Functional response, Plant Science, Biology, niche écologique, Ectomycorrhizal fungal communities, 010603 evolutionary biology, 01 natural sciences, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, Ectomycorrhizal fungi (ECM), Functional diversity, Community assembly, RLQ analysis, Environmental filtering, Niche differentiation, Forest ecology, Ecosystem, [SDV.MP.MYC]Life Sciences [q-bio]/Microbiology and Parasitology/Mycology, Ecology, Evolution, Behavior and Systematics, écosystème forestier, Enymatic activities, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, Functional ecology, diversité fonctionnelle, Ecology, activité enzymatique, champignon ectomycorhizien, Interspecific competition, 15. Life on land, Trait, 010606 plant biology & botany
Abstract

International audience; Characterizing the ecological processes driving the assembly and functional composition of ectomycorrhizal (ECM) fungal communities is an area of active research. Here, we applied a trait-based framework to address whether and how environmental filtering and niche differentiation influence the diversity of ECM fungal enzymatic activities in two oak-dominated forest ecosystems. We hypothesized that fungal enzymatic activities and ECM community assembly are influenced by the availability of targeted resources in the surrounding soil. We pinpointed a major influence of environmental filtering on ECM fungal taxonomic and functional composition. Contrasted taxonomic composition among forest ecosystems was linked to broad interspecific trait variation and entailed contrasted functional responses at community level. However, intraspecific trait variation contributed to community response within ecosystems. We characterized a strong relationship between enzymatic activities and targeted resource availability in surrounding soil, suggesting a functional role of the enzymes for the acquisition of these resources. Conversely, we did not find a significant influence of niche differentiation in ECM community assembly. Synthesis. Heterogeneous distribution of soil resources drives a community-level functional response and determines the functional and taxonomic mosaic of ECM communities in forest ecosystems.

Published
2016

41. Advances in genotyping microsatellite markers through sequencing and consequences of scoring methods for Ceratonia siliqua (Leguminosae)

Author

Viruel, Juan, Haguenauer, Anne, Juin, Marianick, Mirleau, Fatma, Bouteiller, Delphine, Boudagher‐Kharrat, Magda, Ouahmane, Lahcen, La Malfa, Stefano, Medail, Frederic, Sanguin, Hervé, Nieto Feliner, Gonzalo, Baumel, Alex, Agence Nationale de la Recherche (France), 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), Neurologie et thérapeutique expérimentale, Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR70-Université Pierre et Marie Curie - Paris 6 (UPMC), Université Cadi Ayyad [Marrakech] (UCA), Università degli studi di Catania [Catania], Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-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), ANR-14-CE02-0016,DYNAMIC,Décryptage des réseaux symbiotiques au sein des agro-écosystèmes méditerranéens à caroubier(2014), Laboratoire des symbioses tropicales et méditerranéennes (UMR LSTM), 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)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD), French National Research Agency [ANR-14-CE02-0016], DYNAMIC [ANR-14-CE02-0016], Marie Skodowska-Curie Individual Fellowship [704464-YAMNOMICS-MSCA-IF-EF-ST], Université Pierre et Marie Curie - Paris 6 (UPMC)-IFR70-Institut National de la Santé et de la Recherche Médicale (INSERM), Università degli studi di Catania = University of Catania (Unict), and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université Montpellier 1 (UM1)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)

Subjects
Application Article, [SDV.GEN]Life Sciences [q-bio]/Genetics, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], Ecology, MicNeSs, Evolution, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], food and beverages, homoplasy, Plant Science, genetic diversity, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, Simple sequence repeat (SSR), next-generation sequenc-ing, Genetic diversity, F30 - Génétique et amélioration des plantes, Carob tree, Behavior and Systematics, simple sequence repeat (SSR), carob tree, next-generation sequencing, Ecology, Evolution, Behavior and Systematics, Application Articles, Homoplasy, Next‐generation sequencing
Abstract

Premise of the Study: Simple sequence repeat (SSR) or microsatellite markers have been used in a broad range of studies mostly scoring alleles on the basis of amplicon size as a proxy for the number of repeat units of an SSR motif. However, additional sources of variation within the SSR or in the flanking regions have largely remained undetected. Methods: In this study, we implemented a next-generation sequencing–based genotyping approach in a newly characterized set of 18 nuclear SSR markers for the carob tree, Ceratonia siliqua. Our aim was to evaluate the effect of three different methods of scoring molecular variation present within microsatellite markers on the genetic diversity and structure results. Results: The analysis of the sequences of 77 multilocus genotypes from four populations revealed SSR variation and additional sources of polymorphism in 87% of the loci analyzed (42 single-nucleotide polymorphisms and five insertion/deletion polymorphisms), as well as divergent paralog copies in two loci. Ignoring sequence variation under standard amplicon size genotyping resulted in incorrect identification of 69% of the alleles, with important effects on the genetic diversity and structure estimates. Discussion: Next-generation sequencing allows the detection and scoring of SSRs, single-nucleotide polymorphisms, and insertion/deletion polymorphisms to increase the resolution of population genetic studies., This research is part of the DYNAMIC project funded by the French National Research Agency (ANR‐14‐CE02‐0016). J.V. benefited from a postdoctoral fellowship funded by DYNAMIC (ANR‐14‐CE02‐0016) and a Marie Skłodowska‐Curie Individual Fellowship (704464‐YAMNOMICS‐MSCA‐IF‐EF‐ST).

Published
2018

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