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6. Plant metabolomics and breeding

Author

Fernandez, Olivier, primary, Millet, Emilie J., additional, Rincent, Renaud, additional, Prigent, Sylvain, additional, Pétriacq, Pierre, additional, and Gibon, Yves, additional

Published
2021
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9. The dynamics of pattern matching in camouflaging cuttlefish

Author

Woo Theodosia, Liang Xitong, Evans Dominic A., Fernandez Olivier, Kretschmer Friedrich, Reiter Sam, Laurent Gilles, Woo Theodosia, Liang Xitong, Evans Dominic A., Fernandez Olivier, Kretschmer Friedrich, Reiter Sam, and Laurent Gilles

Abstract

Many cephalopods escape detection using camouflage. This behaviour relies on a visual assessment of the surroundings, on an interpretation of visual-texture statistics and on matching these statistics using millions of skin chromatophores that are controlled by motoneurons located in the brain. Analysis of cuttlefish images proposed that camouflage patterns are low dimensional and categorizable into three pattern classes, built from a small repertoire of components. Behavioural experiments also indicated that, although camouflage requires vision, its execution does not require feedback, suggesting that motion within skin-pattern space is stereotyped and lacks the possibility of correction. Here, using quantitative methods, we studied camouflage in the cuttlefish Sepia officinalis as behavioural motion towards background matching in skin-pattern space. An analysis of hundreds of thousands of images over natural and artificial backgrounds revealed that the space of skin patterns is high-dimensional and that pattern matching is not stereotyped-each search meanders through skin-pattern space, decelerating and accelerating repeatedly before stabilizing. Chromatophores could be grouped into pattern components on the basis of their covariation during camouflaging. These components varied in shapes and sizes, and overlay one another. However, their identities varied even across transitions between identical skin-pattern pairs, indicating flexibility of implementation and absence of stereotypy. Components could also be differentiated by their sensitivity to spatial frequency. Finally, we compared camouflage to blanching, a skin-lightening reaction to threatening stimuli. Pattern motion during blanching was direct and fast, consistent with open-loop motion in low-dimensional pattern space, in contrast to that observed during camouflage.

Published
2023

10. Leaf metabolomic data of eight sunflower lines and their sixteen hybrids under water deficit☆

Author

Berton Thierry, Bernillon Stéphane, Fernandez Olivier, Duruflé Harold, Flandin Amélie, Cassan Cédric, Jacob Daniel, Langlade Nicolas B., Gibon Yves, and Moing Annick

Subjects
helianthus, abiotic stress, drought stress, lc-ms, metabolomic profiling, Oils, fats, and waxes, TP670-699
Abstract

This article describes how metabolomic data were produced on sunflower plants subjected to water deficit. Twenty-four sunflower (Helianthus annuus L.) genotypes were selected to represent genetic diversity within cultivated sunflower and included both inbred lines and their hybrids. Drought stress was applied at the vegetative stage to plants cultivated in pots using the high-throughput phenotyping facility Heliaphen. Here, we provide untargeted and targeted metabolomic data of sunflower leaves. These compositional data differentiate both plant water status and different genotype groups. They constitute a valuable resource for the community to study the adaptation of crops to drought and the metabolic bases of heterosis.

Published
2021
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13. Differential carbohydrate-active enzymes and secondary metabolite production by the grapevine trunk pathogen Neofusicoccum parvum Bt-67 grown on host and non-host biomass.

Author

Restrepo-Leal, Julián D., Belair, Marie, Fischer, Jochen, Richet, Nicolas, Fontaine, Florence, Rémond, Caroline, Fernandez, Olivier, and Besaury, Ludovic

Subjects
LIGNOCELLULOSE, XYLANASES, METABOLITES, BIOMASS, PLANT cell walls, GRAPES, GENE expression profiling
Abstract

Neofusicoccum parvum is one of the most aggressive Botryosphaeriaceae species associated with grapevine trunk diseases. This species may secrete enzymes capable of overcoming the plant barriers, leading to wood colonization. In addition to their roles in pathogenicity, there is an interest in taking advantage of N. parvum carbohydrate-active enzymes (CAZymes), related to plant cell wall degradation, for lignocellulose biorefining. Furthermore, N. parvum produces toxic secondary metabolites that may contribute to its virulence. In order to increase knowledge on the mechanisms underlying pathogenicity and virulence, as well as the exploration of its metabolism and CAZymes for lignocellulose biorefining, we evaluated the N. parvum strain Bt-67 capacity in producing lignocellulolytic enzymes and secondary metabolites when grown in vitro with two lignocellulosic biomasses: grapevine canes (GP) and wheat straw (WS). For this purpose, a multiphasic study combining enzymology, transcriptomic, and metabolomic analyses was performed. Enzyme assays showed higher xylanase, xylosidase, arabinofuranosidase, and glucosidase activities when the fungus was grown with WS. Fourier transform infrared (FTIR) spectroscopy confirmed the lignocellulosic biomass degradation caused by the secreted enzymes. Transcriptomics indicated that the N. parvum Bt-67 gene expression profiles in the presence of both biomasses were similar. In total, 134 genes coding CAZymes were up-regulated, where 94 of them were expressed in both biomass growth conditions. Lytic polysaccharide monooxygenases (LPMOs), glucosidases, and endoglucanases were the most represented CAZymes and correlated with the enzymatic activities obtained. The secondary metabolite production, analyzed by high-performance liquid chromatography–ultraviolet/visible spectophotometry–mass spectrometry (HPLC-UV/Vis-MS), was variable depending on the carbon source. The diversity of differentially produced metabolites was higher when N. parvum Bt-67 was grown with GP. Overall, these results provide insight into the influence of lignocellulosic biomass on virulence factor expressions. Moreover, this study opens the possibility of optimizing the enzyme production from N. parvum with potential use for lignocellulose biorefining. [ABSTRACT FROM AUTHOR]

Published
2023
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17. Differential carbohydrate-active enzymes and secondary metabolite production by the grapevine trunk pathogen Neofusicoccum parvumBt-67 grown on host and non-host biomass

Author

Restrepo-Leal, Julián D., Belair, Marie, Fischer, Jochen, Richet, Nicolas, Fontaine, Florence, Rémond, Caroline, Fernandez, Olivier, and Besaury, Ludovic

Abstract

ABSTRACTNeofusicoccum parvumis one of the most aggressive Botryosphaeriaceae species associated with grapevine trunk diseases. This species may secrete enzymes capable of overcoming the plant barriers, leading to wood colonization. In addition to their roles in pathogenicity, there is an interest in taking advantage of N. parvumcarbohydrate-active enzymes (CAZymes), related to plant cell wall degradation, for lignocellulose biorefining. Furthermore, N. parvumproduces toxic secondary metabolites that may contribute to its virulence. In order to increase knowledge on the mechanisms underlying pathogenicity and virulence, as well as the exploration of its metabolism and CAZymes for lignocellulose biorefining, we evaluated the N. parvumstrain Bt-67 capacity in producing lignocellulolytic enzymes and secondary metabolites when grown in vitro with two lignocellulosic biomasses: grapevine canes (GP) and wheat straw (WS). For this purpose, a multiphasic study combining enzymology, transcriptomic, and metabolomic analyses was performed. Enzyme assays showed higher xylanase, xylosidase, arabinofuranosidase, and glucosidase activities when the fungus was grown with WS. Fourier transform infrared (FTIR) spectroscopy confirmed the lignocellulosic biomass degradation caused by the secreted enzymes. Transcriptomics indicated that the N. parvumBt-67 gene expression profiles in the presence of both biomasses were similar. In total, 134 genes coding CAZymes were up-regulated, where 94 of them were expressed in both biomass growth conditions. Lytic polysaccharide monooxygenases (LPMOs), glucosidases, and endoglucanases were the most represented CAZymes and correlated with the enzymatic activities obtained. The secondary metabolite production, analyzed by high-performance liquid chromatography–ultraviolet/visible spectophotometry–mass spectrometry (HPLC-UV/Vis-MS), was variable depending on the carbon source. The diversity of differentially produced metabolites was higher when N. parvumBt-67 was grown with GP. Overall, these results provide insight into the influence of lignocellulosic biomass on virulence factor expressions. Moreover, this study opens the possibility of optimizing the enzyme production from N. parvumwith potential use for lignocellulose biorefining.

Published
2023
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20. Combining phenotypic, metabolome and proteome data to study maize response to a mild nitrogen deficit

Author

Urrutia, Maria, Blein-Nicolas, Melisande, Fernandez, Olivier, Bernillon, Stéphane, Maucourt, Mickael, Deborde, Catherine, Balliau, Thierry, Bénard, Camille, Prigent, Sylvain, Quilleré, Isabelle, Jacob, Daniel, Gibon, Yves, Zivy, Michel, Giauffret, Catherine, Hirel, Bertrand, Moing, Annick, and Blein-Nicolas, Mélisande

Subjects
[SDV] Life Sciences [q-bio], [SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], [SDV.BV.AP] Life Sciences [q-bio]/Vegetal Biology/Plant breeding
Abstract

To decipher the biochemical bases of nitrogen (N) utilization and metabolism of silage maize inrelation to growth and productivity, an untargeted metabolomic (proton NMR- and LC-QTOF-MSbased) and proteomic approach was conducted on leaves of 29 hybrids cultivated in the field underoptimal and reduced N fertilization. The corresponding biochemical data were analyzed eitherindividually (PCA, ANOVA), or integrated with that of eco-physiological, developmental and yield-related traits (multi-block sparse PLS-DA). Such integrated analysis was conducted to interpret theunderlying physiology concerning the plant response to a mild N deficit often occurring underagronomic conditions. The genetic diversity of the core panel of 29 European dent hybrids crossed toa flint tester was exploited to highlight common N-responsive metabolites and proteins in order toidentify putative biological markers that could be used to pilot and rationalize N fertilization. Theresponses of metabolites, proteins, and yield-related traits to the reduced N treatment were alsoexploited to identify biochemical markers representative of a maize ideotype exhibiting betteragronomic performances when N fertilization is limited. These markers could be used to select high-yielding commercial maize hybrids used for silage production requiring less N fertilizer inputs.

Published
2022

21. Assessment of a New Copper-Based Formulation to Control Esca Disease in Field and Study of Its Impact on the Vine Microbiome, Vine Physiology and Enological Parameters of the Juice

Author

Mondello, Vincenzo, primary, Lemaître-Guillier, Christelle, additional, Trotel-Aziz, Patricia, additional, Gougeon, Régis, additional, Acedo, Alberto, additional, Schmitt-Kopplin, Philippe, additional, Adrian, Marielle, additional, Pinto, Cátia, additional, Fernandez, Olivier, additional, and Fontaine, Florence, additional

Published
2022
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24. Presence/absence variations and SNPs equally contribute to the variations of protein and metabolite abundance

Author

Djabali, Yacine, Blein, Mélisande, Moing, Annick, Duarte, Jorge, Berton, Thierry, Bernillon, Stéphane, Prigent, Sylvain, Fernandez, Olivier, Pétriacq, Pierre, Mabire, Clément, Madur, Delphine, Cabrera-Bosquet, Llorenç, Welcker, Claude, Tardieu, Francois, Gibon, Yves, Zivy, Michel, Charcosset, Alain, Nicolas, Stephane, Génétique Quantitative et Evolution - Le Moulon (Génétique Végétale) (GQE-Le Moulon), AgroParisTech-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Plateforme Metabolome Bordeaux, INRAE, 2018, MetaboHUB, Centre INRAE Nouvelle Aquitaine Bordeaux, doi: 10.15454/1.5572412770331912E12 (PMB), Institut National de la Recherche Agronomique (INRA), Groupe Limagrain, Biologie du fruit et pathologie (BFP), Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire des Interactions Plantes Microbes Environnement (LIPME), Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre National de la Recherche Scientifique (CNRS)-AgroParisTech-Université Paris-Sud - Paris 11 (UP11)-Institut National de la Recherche Agronomique (INRA), Écophysiologie des Plantes sous Stress environnementaux (LEPSE), 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), and ANR-10-BTBR-0001,AMAIZING,Développer de nouvelles variétés de maïs pour une agriculture durable: une approche intégrée de la génomique à la sélection(2010)

Subjects
[SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, [SDV.BV.AP]Life Sciences [q-bio]/Vegetal Biology/Plant breeding, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], food and beverages
Abstract

International audience; Understanding the mechanisms of adaptation to the environment in cultivated plants is a promising way to meet the challenge of maintaining food security in the context of global warming. In the case of maize, high-throughput sequencing has revealed that structural variations represent a large part of the genome and could have huge phenotypic effects. Among these, Presence Absence Variants (PAVs) may be involved in adaptation of maize to its environment, but their contribution to the genetic determinism of traits and genotype by environment interactions remains largely unknown. To address this issue, we performed a genome-wide association study between two types of polymorphisms, SNPs and Insetions/Deletions (InDels), and molecular traits obtained from proteomics and metabolomics analyses. The genetic panel used for this study was composed of 254 dent inbred lines genotyped with 978,134 SNPs and 72,041 InDels. The latter encompassed from 37 to 129,700 pb, including thousands of PAVs that are not present in the B73 reference genome. Proteins and metabolites were quantified by mass spectrometry in leaf samples from F1 hybrids obtained by crossing the inbred lines with one flint tester line. Hybrid plants were grown under two watering conditions (well-watered and water deficit) in greenhouse. In total, we detected 61,225 QTLs associated with proteome or metabolome variations. Among these, 4,766 QTLs were exclusively detected by InDels. To take into account the difference of marker density between InDels and SNPs, we used a re-sampling approach which showed that there is no difference for effect size distribution of QTLs between InDels and SNPs and for the number of QTLs detected by InDels or SNPs. Additionally, the QTLs detected by the two types of polymorphism were equally distributed in the two watering conditions. Our results suggest that InDels and SNPs equally contributed to molecular trait variation and response to drought stress.

Published
2021

29. Using metabolomic data to predict Maize yield

Author

Prigent, Sylvain, Fernandez, Olivier, Bernillon, Stéphane, Pétriacq, Pierre, Moing, Annick, Berton, Thierry, Cabrera-Bosquet, Llorenç, Millet, Émilie, Welcker, Claude, Tardieu, François, Gibon, Yves, Biologie du fruit et pathologie (BFP), Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Plateforme Metabolome MetaboHUB INRA Nouvelle Aquitaine, Institut National de la Recherche Agronomique (INRA), Écophysiologie des Plantes sous Stress environnementaux (LEPSE), 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), and Gauthier, Muriel

Subjects
[SDV] Life Sciences [q-bio], Métabolome, Plante céréalière, Métabolisme, [SDV]Life Sciences [q-bio], Métabolite, Maïs, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SDV.BV] Life Sciences [q-bio]/Vegetal Biology, rendement, ComputingMilieux_MISCELLANEOUS, Métabolomique
Abstract

International audience

Published
2019

30. The holobiont, a biological lever to manage some declines of grapevine

Author

Trouvelot, Sophie, Fontaine, Florence, Mahé, Héloise, Bettenfeld, Pauline, van Schaik, Evert, Adrian, Marielle, Dal, François, Fernandez, Olivier, Grosjean, Claire, Larignon, Philippe, MOUILLE, Grégory, Martin, Fabrice, ZEKRI, Olivier, Mondy, Samuel, Wipf, Daniel, Courty, Pierre-Emmanuel, ProdInra, Migration, Agroécologie [Dijon], Université de Bourgogne (UB)-Institut National de la Recherche Agronomique (INRA)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, SFR Condorcet, Université de Reims Champagne-Ardenne (URCA)-Université de Picardie Jules Verne (UPJV)-Centre National de la Recherche Scientifique (CNRS), Institut Français de la Vigne et du Vin (IFV), Interactions Sol Plante Atmosphère (UMR ISPA), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Supérieure des Sciences Agronomiques de Bordeaux-Aquitaine (Bordeaux Sciences Agro), Chambre d’Agriculture de Bourgogne Franche-Comté, Pépinières Mercier Frères, and Partenaires INRAE

Subjects
[SDV] Life Sciences [q-bio], [SDE] Environmental Sciences, [SDV]Life Sciences [q-bio], [SDE]Environmental Sciences, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SDV.BV] Life Sciences [q-bio]/Vegetal Biology
Abstract

International audience; The concept of a multicellular organism to describe complex organisms composed of groups of analogous cells called tissues and organs with specific functions, shows currently some limitations. An organism such as a plant does not live alone, but closely associated with different microbial communities making up its microbiomes. The microbiomes, specific to a tissue, interact with the plant and modulate some of its functions, including physiology and immunity. The host and the associated microbiomes define a holobiont, whose function is influenced by the spatio-temporal dynamics of their interactions. Thus, a dysfunction of the grapevine holobiont (linked for example to inappropriate technical itineraries or to climate change) could lead to the development of diseases or physiological disorders, similarly to the alteration of gut microbiota observed in numerous human diseases as type 2 diabetes, obesity and irritable bowel syndrome. The analysis of microbial communities associated with a plant such as grapevine has until recently been limited by the fact that most microorganisms cannot be cultured in vitro. New methods (named -omics) based on the analysis of genome, metabolome and proteome allow to define the taxonomic and functional characteristics of the different microbiomes associated with a plant, in particular organisms (i.e. bacteria, fungi) that are not cultivable. In the Holoviti project, we aim to characterize the role of microbiomes in grapevine homeostasis by describing and comparing the holobiont of i) healthy grapevines and ii) grapevines affected by three declines (Esca / BDA, fanleaf and linked to 161-49C rootstock). One of our objectives is to identify taxonomic and functional bio-indicators (linked to either microbes or the plant) of the host sanitary status. One prospect could be handle the microbial component of the holobiont to improve some ecosystemic services, such as the control of pathogens or the fight against abiotic stresses.

Published
2019

31. Trial with an innovative product based on a biocompatible drug delivery system on GTDs incidence, disease development and vine physiology

Author

Mondello, Vincenzo, Fernandez, Olivier, Trotel-Aziz, Patricia, Christophe, Clément, FLORENCE, FONTAINE, Résistance Induite et Bioprotection des Plantes - EA 4707 (RIBP), Université de Reims Champagne-Ardenne (URCA)-SFR Condorcet, and Université de Reims Champagne-Ardenne (URCA)-Université de Picardie Jules Verne (UPJV)-Centre National de la Recherche Scientifique (CNRS)-Université de Reims Champagne-Ardenne (URCA)-Université de Picardie Jules Verne (UPJV)-Centre National de la Recherche Scientifique (CNRS)

Subjects
[SDV]Life Sciences [q-bio], ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2019

32. Grapevine and fungal trunk pathogens interactions and the global impacts of climatic events

Author

Songy, Aurelie, Pinto, Catia, Trotel-Aziz, Patricia, Fernandez, Olivier, Clément, Christophe, FLORENCE, FONTAINE, Résistance Induite et Bioprotection des Plantes - EA 4707 (RIBP), Université de Reims Champagne-Ardenne (URCA)-SFR Condorcet, and Université de Reims Champagne-Ardenne (URCA)-Université de Picardie Jules Verne (UPJV)-Centre National de la Recherche Scientifique (CNRS)-Université de Reims Champagne-Ardenne (URCA)-Université de Picardie Jules Verne (UPJV)-Centre National de la Recherche Scientifique (CNRS)

Subjects
[SDV]Life Sciences [q-bio], ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2018

33. Chapter Seven: Plant metabolomics and breeding.

Author

Fernandez, Olivier, Millet, Emilie J., Rincent, Renaud, Prigent, Sylvain, Pétriacq, Pierre, and Gibon, Yves

Subjects
*PLANT performance, *MASS spectrometry, *PREDICTION models, *METABOLIC regulation, *LEAF physiology, *BIOMASS, *PLANT breeding
Abstract

Metabolomics has become essential in the field of phenotyping, providing information halfway between genomes and phenotypes that can be used to predict complex traits. Thus in plants, studies have shown that metabolomics can be used to predict complex traits such as leaf biomass or yield. From a fundamental point of view, these advances can be used to identify new mechanisms involved in plant performance, for example, through identifying and deciphering QTLs involved in the control of the underlying metabolic pathways. From a breeding perspective, "phenomic selection" protocols combining phenotyping under optimal and/or stressing conditions, and metabolomics can be used to construct models that are able to predict traits of interest. Such developments will only be relevant if high throughput and reasonable costs can be achieved, if possible not far from those of genomic selection. The combination of robotics and nontargeted mass spectrometry already allows to process thousands of samples whereas the current capabilities of bioinformatics make it possible to develop predictive models from thousands variables. [ABSTRACT FROM AUTHOR]

Published
2021
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34. Cyclic lipopeptides from Bacillus subtilis activate distinct patterns of defence responses in grapevine

Author

Farace, Giovanni, Fernandez, Olivier, Jacquens, Lucile, Coutte, François, Krier, François, Jacques, Philippe, Clément, Christophe, Barka, Essaid Ait, Jacquard, Cédric, Dorey, Stéphan, Résistance Induite et Bioprotection des Plantes - EA 4707 (RIBP), Université de Reims Champagne-Ardenne (URCA)-SFR Condorcet, and Université de Reims Champagne-Ardenne (URCA)-Université de Picardie Jules Verne (UPJV)-Centre National de la Recherche Scientifique (CNRS)-Université de Reims Champagne-Ardenne (URCA)-Université de Picardie Jules Verne (UPJV)-Centre National de la Recherche Scientifique (CNRS)

Subjects
[SDV]Life Sciences [q-bio], ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2015

35. Characterization of the role of flagellin in the innate immunity triggered by the endophytic pgpr burkholderia phytofirmans in arabidopsis and grapevine

Author

Fernandez, Olivier, Trdá, Lucie, Boutrot, Freddy, Héloir, Marie-Claire, Kelloniemi, Jani-Petri, Daire, Xavier, Adrian, Marielle, Clément, Christophe, Zipfel, Cyril, Poinssot, Benoît, Dorey, Stephan, Résistance Induite et Bioprotection des Plantes - EA 4707 (RIBP), Université de Reims Champagne-Ardenne (URCA)-SFR Condorcet, Université de Reims Champagne-Ardenne (URCA)-Université de Picardie Jules Verne (UPJV)-Centre National de la Recherche Scientifique (CNRS)-Université de Reims Champagne-Ardenne (URCA)-Université de Picardie Jules Verne (UPJV)-Centre National de la Recherche Scientifique (CNRS), Agroécologie [Dijon], Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, The Sainsbury Laboratory [Norwich] (TSL), and ProdInra, Migration

Subjects
[SDV] Life Sciences [q-bio], [SDE] Environmental Sciences, plant microbe interaction, Arabidopsis thaliana, Vitis vinifera, Plant Growth Rhizobacteria (PGPR), [SDV]Life Sciences [q-bio], [SDE]Environmental Sciences, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SDV.BV] Life Sciences [q-bio]/Vegetal Biology, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2014

36. Identification and characterization of the grapevine flagellin receptor vvfls2

Author

Trdá, Lucie, Fernandez, Olivier, Boutrot, Freddy, Héloir, Marie-Claire, Kelloniemi, Jani-Petri, Daire, Xavier, Adrian, Marielle, Clément, Christophe, Zipfel, Cyril, Dorey, Stephan, Poinssot, Benoît, ProdInra, Migration, Résistance Induite et Bioprotection des Plantes - EA 4707 (RIBP), Université de Reims Champagne-Ardenne (URCA)-SFR Condorcet, Université de Reims Champagne-Ardenne (URCA)-Université de Picardie Jules Verne (UPJV)-Centre National de la Recherche Scientifique (CNRS)-Université de Reims Champagne-Ardenne (URCA)-Université de Picardie Jules Verne (UPJV)-Centre National de la Recherche Scientifique (CNRS), The Sainsbury Laboratory [Norwich] (TSL), Agroécologie [Dijon], and Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement

Subjects
microbe associated molecular pattern (MAMP), [SDV] Life Sciences [q-bio], [SDE] Environmental Sciences, plant microbe interaction, [SDV]Life Sciences [q-bio], Vitis vinifera, [SDE]Environmental Sciences, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SDV.BV] Life Sciences [q-bio]/Vegetal Biology, ComputingMilieux_MISCELLANEOUS, pattern recognition receptor (PRR)
Abstract

International audience

Published
2014

37. Les matières organiques en France : état de l'art et prospectives : résumés

Author

Garnier, Patricia, Fernandez, Olivier, Cambier, Christophe, Chenu, Claire, Recous, Sylvie, Environnement et Grandes Cultures (EGC), Institut National de la Recherche Agronomique (INRA)-Institut National Agronomique Paris-Grignon (INA P-G), Biogéochimie et écologie des milieux continentaux (Bioemco), Centre National de la Recherche Scientifique (CNRS)-AgroParisTech-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Recherche Agronomique (INRA)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL), École normale supérieure - Paris (ENS-PSL), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Université Pierre et Marie Curie - Paris 6 (UPMC)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS)

Subjects
DECOMPOSITION, SOL, POROSITE, STRUCTURE DU SOL, MATIERE ORGANIQUE, RESIDU VEGETAL, [SDV.SA.SDS]Life Sciences [q-bio]/Agricultural sciences/Soil study, MODELISATION
Published
2006

39. The grapevine flagellin receptor VvFLS2 differentially recognizes flagellin‐derived epitopes from the endophytic growth‐promoting bacterium Burkholderia phytofirmans and plant pathogenic bacteria

Author

Trdá, Lucie, primary, Fernandez, Olivier, additional, Boutrot, Freddy, additional, Héloir, Marie‐Claire, additional, Kelloniemi, Jani, additional, Daire, Xavier, additional, Adrian, Marielle, additional, Clément, Christophe, additional, Zipfel, Cyril, additional, Dorey, Stéphan, additional, and Poinssot, Benoit, additional

Published
2013
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44. The grapevine flagellin receptor Vv FLS2 differentially recognizes flagellin-derived epitopes from the endophytic growth-promoting bacterium Burkholderia phytofirmans and plant pathogenic bacteria.

Author

Trdá, Lucie, Fernandez, Olivier, Boutrot, Freddy, Héloir, Marie‐Claire, Kelloniemi, Jani, Daire, Xavier, Adrian, Marielle, Clément, Christophe, Zipfel, Cyril, Dorey, Stéphan, and Poinssot, Benoit

Subjects
*FLAGELLIN, *VITIS vinifera, *EPITOPES, *BURKHOLDERIA, *PATHOGENIC bacteria, *PLANT growth-promoting rhizobacteria, *ARABIDOPSIS thaliana
Abstract

The role of flagellin perception in the context of plant beneficial bacteria still remains unclear. Here, we characterized the flagellin sensing system flg22- FLAGELLIN SENSING 2 ( FLS2) in grapevine, and analyzed the flagellin perception in the interaction with the endophytic plant growth-promoting rhizobacterium ( PGPR) Burkholderia phytofirmans., The functionality of the grapevine FLS2 receptor, Vv FLS2, was demonstrated by complementation assays in the Arabidopsis thaliana fls2 mutant, which restored flg22-induced H2 O2 production and growth inhibition. Using synthetic flg22 peptides from different bacterial origins, we compared recognition specificities between Vv FLS2 and At FLS2., In grapevine, flg22-triggered immune responses are conserved and led to partial resistance against Botrytis cinerea. Unlike flg22 peptides derived from Pseudomonas aeruginosa or Xanthomonas campestris, flg22 peptide derived from B. phytofirmans triggered only a small oxidative burst, weak and transient defense gene induction and no growth inhibition in grapevine. Although, in Arabidopsis, all the flg22 epitopes exhibited similar biological activities, the expression of Vv FLS2 into the fls2 background conferred differential flg22 responses characteristic for grapevine., These results demonstrate that Vv FLS2 differentially recognizes flg22 from different bacteria, and suggest that flagellin from the beneficial PGPR B. phytofirmans has evolved to evade this grapevine immune recognition system. [ABSTRACT FROM AUTHOR]

Published
2014
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45. Aroma in white winemaking.

Author

Fauveau, Céline, Fernandez, Olivier, Lefol, Blandine, and Bajard-Sparrow, Céline

Abstract

Each winemaker has his/her own recipe including the use of aromatic varieties, pre-fermentation maceration, drastic clarification, selected yeast strains, low temperature of fermentation. In all cases priority is given to aroma! Grape aromas are volatile compounds recognised by specific receptors in the human nose. The perception thresholds (minimal concentration that must be reached) vary amongst individuals and with the different compounds. There are three main families of aromas: the varietal aromas, the fermentative aromas derived from yeast metabolism and wine ageing aromas. The first two are discussed in this article. [ABSTRACT FROM AUTHOR]

Published
2009

46. Metabolomic characterization of sunflower leaf allows discriminating genotype groups or stress levels with a minimal set of metabolic markers

Author

Daniel J. Jacob, Pierre Maury, Maria Urrutia, Annick Moing, Olivier Fernandez, Thierry Berton, Nicolas B. Langlade, Catherine Deborde, Stéphane Bernillon, Mickaël Maucourt, Yves Gibon, Harold Duruflé, Centre recherche en CardioVasculaire et Nutrition (C2VN), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Biologie du fruit et pathologie (BFP), Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1, Centre de Bioinformatique de Bordeaux (CBIB), CGFB, UMR : AGroécologie, Innovations, TeRritoires, Ecole Nationale Supérieure Agronomique de Toulouse, Laboratoire de Recherche en Sciences Végétales (LRSV), Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Interactions cellulaires et moléculaires (ICM), Centre National de la Recherche Scientifique (CNRS)-IFR140-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Laboratoire des interactions plantes micro-organismes (LIPM), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), ANR-10-BTBR-0001, Agence Nationale de la Recherche, Centre recherche en CardioVasculaire et Nutrition = Center for CardioVascular and Nutrition research (C2VN), Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1 (UB), AGroécologie, Innovations, teRritoires (AGIR), Institut National de la Recherche Agronomique (INRA)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), ANR-10-BTBR-0001,AMAIZING,Développer de nouvelles variétés de maïs pour une agriculture durable: une approche intégrée de la génomique à la sélection(2010), Prémilleux, Annick, Biotech - Bioressources - Développer de nouvelles variétés de maïs pour une agriculture durable: une approche intégrée de la génomique à la sélection - - AMAIZING2010 - ANR-10-BTBR-0001 - BTBR - VALID, Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS), Université de Toulouse (UT)-Université de Toulouse (UT), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), and Fernandez, Olivier

Subjects
Genotype, Endocrinology, Diabetes and Metabolism, Water stress, [SDV]Life Sciences [q-bio], Clinical Biochemistry, education, Computational biology, Biology, 01 natural sciences, Biochemistry, Stress level, Fight-or-flight response, Maintainer–restorer lines, Metabolic markers, Metabolomics, Sunflower, 03 medical and health sciences, Gene Expression Regulation, Plant, Stress, Physiological, Metabolic Marker, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0303 health sciences, Vegetal Biology, fungi, 010401 analytical chemistry, Cytoplasmic male sterility, food and beverages, 0104 chemical sciences, Droughts, Plant Leaves, [SDV] Life Sciences [q-bio], [SDV.AEN] Life Sciences [q-bio]/Food and Nutrition, Helianthus, Original Article, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, Biologie végétale, Biomarkers
Abstract

Plant and crop metabolomic analyses may be used to study metabolism across genetic and environmental diversity. Complementary analytical strategies are useful for investigating metabolic changes and searching for biomarkers of response or performance., The experimental material consisted in eight sunflower lines with two line status, four restorers (R, used as males) and four maintainers (B, corresponding to females) routinely used for sunflower hybrid varietal production, respectively to complement or maintain the cytoplasmic male sterility PET1. These lines were either irrigated at full soil capacity (WW) or submitted to drought stress (DS). Our aim was to combine targeted and non-targeted metabolomics to characterize sunflower leaf composition in order to investigate the effect of line status genotypes and environmental conditions and to find the best and smallest set of biomarkers for line status and stress response using a custom-made process of variables selection., H-NMR, MS-based profiles and targeted analyses of major metabolites. Based on statistical analyses, a limited number of markers were able to separate WW and DS samples in a more discriminant manner than previously published physiological data. Another metabolic marker set was able to discriminate line status., This study underlines the potential of metabolic markers for discriminating genotype groups and environmental conditions. Their potential use for prediction is discussed.

Published
2019

47. Entre underground et gentrification : Bert Papenfuß, dernière icône des cercles littéraires non officiels de Berlin-Est ?

Author

Goepper, Sibylle, Institut d'Etudes Transtextuelles et Transculturelles (IETT), Université Jean Moulin - Lyon 3 (UJML), Université de Lyon-Université de Lyon, Cécilia Fernandez, Olivier Hanse (dir.), and Goepper, Sibylle

Subjects
[SHS.LITT] Humanities and Social Sciences/Literature, Berlin, [SHS.LITT]Humanities and Social Sciences/Literature, Bert Papenfuss, [SHS] Humanities and Social Sciences, Contre-culture, Poésie, Underground, Prenzlauer Berg, [SHS]Humanities and Social Sciences
Abstract

Die Studie widmet sich den verschiedenen Tätigkeiten des Untergrund-Dichters Bert Papenfuß (1956) von der Mitte der 1970er Jahre im Ostteil der DDR-Hauptstadt bis heute im vereinigten Berlin. Es soll gezeigt werden, wie er von einer abweichenden Subkultur in eine politisierte Gegen-Kultur überging. Zunächst wird das Verhältnis untersucht, das die «Prenzlauer-Berg-Szene», zu deren Leitfiguren Papenfuß gehörte, zum Begriff der Gegen-Kultur unterhielt. In der Folge der Stasi-Skandale der 1990er Jahre wurde die Unabhängigkeit der inoffiziellen künstlerischen Kreise grundsätzlich in Frage gestellt. Trotz ihrer ambivalenten Position zeichneten sie sich jedoch durch Merkmale aus, die viele Ähnlichkeiten mit zahlreichen historischen Gegen-Kulturen aufwiesen. Nach dem Verschwinden der DDR änderte sich der Produktionsrahmen von Papenfuß grundlegend. Dennoch griff er weiter auf die in der DDR entwickelten Arbeitsmethoden zurück: Selbstverlag im Druckhaus GALREV, Vernetzung der Produktionsmittel für die Herausgabe der Zeitschriften Sklaven und Gegner. Die Wende brachte neue Möglichkeiten mit sich, so dass sich Papenfuß’ Werk auch in verschie¬dene Richtungen entfaltete. Parallel zur größeren Öffentlichkeit des von ihm vertretenen Untergrunds, z.B. dank der Leitung des Kaffee Burgers in Berlin Mitte, ist eine politische Radikalisierung in den lyrischen und essayistischen Texten zu beobachten. Durch die Wiederbelebung des Anarchisten Silvio Gesell oder des Freigeld-Experiments von Wörgl, erscheinen Papenfuß‘ heutige Tätigkeiten eindeutiger als Ausdruck einer Gegen-Kultur als in der Zeit der DDR. Durch die Gentrifizierung der Hauptstadt hat sich allerdings der Handlungsspielraum stark reduziert. Dies erklärt, dass der Literatur wieder eine zentrale Stellung zukommt. So rückte u.a. die Figur des Seeräubers Klaus Störtebeker in den Mittelpunkt des Zyklus Rumbalotte Continua. Gleichzeitig öffnete Papenfuß eine gleichnamige «Schankwirt¬schaft» mit einem Piratenschiff als Aushängeschild. Nach wie vor sei die ausgesprochene Absicht, sich von der mainstream Kultur abzugrenzen., Cette étude est consacrée aux différentes activités du poète underground Bert Papenfuß né en 1956 dans l’ancienne RDA. En retraçant son parcours du milieu des années 1970 à Berlin-Est à nos jours dans la capitale réunifiée, elle entreprend de montrer comment, au fil du temps, Papenfuß est passé d’une sous-culture déviante à une contre-culture politisée. Une première partie s’interroge sur le rapport entretenu pas la «scène» du Prenzlauer Berg – dont Papenfuß était un des leaders – à la notion de contre-culture. Les scandales qui ont éclaté dans les années 1990, lorsqu’a été découverte la collaboration avec la Stasi de certains artistes, ont considérablement altéré l’image d’indépendance des cercles non officiels. Pourtant, malgré l’ambi¬guïté de leur position, ces derniers présentaient des similitudes avec de nom¬breuses contre-cultures historiques. La disparation de la RDA a radicalement modifié le cadre de production de Papenfuß. Dans la décennie 1990, il a malgré tout eu recours aux méthodes de travail développées en RDA: auto-édition avec la maison d’édition GALREV, mutualisation des moyens pour l’édition des revues Sklaven et Gegner. Le «tournant» a ouvert de nouveaux horizons si bien que l’œuvre de Papenfuß s’est considérablement diversifiée. Parallèlement à la visibilité croissante de l’underground qu’il incarne, grâce par exemple à l’animation du Kaffee Burger dans le quartier de Mitte, on observe une radicalisation politique des essais et de la poésie. La référence à l’anarchiste Silvio Gesell ou la reprise de l’expérience de la monnaie accélérée de Wörgl placent, plus clairement que du temps de la RDA, les activités de Papenfuß du côté de la contre-culture. Le phénomène de gentri¬fi¬cation que connaît Berlin a cependant grandement réduit les marges de manœuvre. Dans ce contexte, la littérature redevient un lieu privilégié pour formuler un discours contre-culturel. Après avoir mis au centre du cycle Rumbalotte Continua la figure du pirate Klaus Störtebeker, Papenfuß a ouvert un nouveau bar, placé sous le signe du bateau de pirates. Comme par le passé, il s’agit pour lui de se distinguer de la culture mainstream.

Published
2014

48. Untargeted Analysis of Semipolar Compounds by LC-MS and Targeted Analysis of Fatty Acids by GC-MS/GC-FID: From Plant Cultivation to Extract Preparation.

Author

Bénard C, Acket S, Rossez Y, Fernandez O, Berton T, Gibon Y, and Cabasson C

Subjects
Chromatography, Liquid methods, Fatty Acids analysis, Gas Chromatography-Mass Spectrometry methods, Mass Spectrometry methods, Plant Extracts analysis
Abstract

The way plants are grown and samples are harvested, prepared, and extracted has a profound impact on the output of a metabolomics experiment. In this chapter, we detail the experimental procedures from plant cultivation to extract preparation, in order to avoid difficulties that could result in contamination or undesired changes of the analytes. Two plant organs are mentioned as examples: tomato fruits (Solanum lycopersicum) and flax seeds (Linum usitatissimum). Extractions designed for the untargeted analysis of semipolar compounds by liquid chromatography-mass spectrometry (LC-MS) and targeted analysis of fatty acids by gas chromatography-mass spectrometry (GC-MS) or gas chromatography with flame ionization detector (GC-FID) are described.

Published
2018
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49. Cyclic lipopeptides from Bacillus subtilis activate distinct patterns of defence responses in grapevine.

Author

Farace G, Fernandez O, Jacquens L, Coutte F, Krier F, Jacques P, Clément C, Barka EA, Jacquard C, and Dorey S

Subjects
Botrytis metabolism, Fatty Acids pharmacology, Lipopeptides pharmacology, Peptides, Cyclic pharmacology, Bacillus subtilis metabolism, Oligopeptides pharmacology, Vitis drug effects, Vitis metabolism
Abstract

Non-self-recognition of microorganisms partly relies on the perception of microbe-associated molecular patterns (MAMPs) and leads to the activation of an innate immune response. Bacillus subtilis produces three main families of cyclic lipopeptides (LPs), namely surfactins, iturins and fengycins. Although LPs are involved in induced systemic resistance (ISR) activation, little is known about defence responses induced by these molecules and their involvement in local resistance to fungi. Here, we showed that purified surfactin, mycosubtilin (iturin family) and plipastatin (fengycin family) are perceived by grapevine plant cells. Although surfactin and mycosubtilin stimulated grapevine innate immune responses, they differentially activated early signalling pathways and defence gene expression. By contrast, plipastatin perception by grapevine cells only resulted in early signalling activation. Gene expression analysis suggested that mycosubtilin activated salicylic acid (SA) and jasmonic acid (JA) signalling pathways, whereas surfactin mainly induced an SA-regulated response. Although mycosubtilin and plipastatin displayed direct antifungal activity, only surfactin and mycosubtilin treatments resulted in a local long-lasting enhanced tolerance to the necrotrophic fungus Botrytis cinerea in grapevine leaves. Moreover, challenge with specific strains overproducing surfactin and mycosubtilin led to a slightly enhanced stimulation of the defence response compared with the LP-non-producing strain of B. subtilis. Altogether, our results provide the first comprehensive view of the involvement of LPs from B. subtilis in grapevine plant defence and local resistance against the necrotrophic pathogen Bo. cinerea. Moreover, this work is the first to highlight the ability of mycosubtilin to trigger an immune response in plants., (© 2014 BSPP AND JOHN WILEY & SONS LTD.)

Published
2015
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