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https://hal.inrae.fr/hal-04514679[hal-04514679] Ecological and metabolic implications of the nurse effect of Maihueniopsis camachoi in the Atacama Desert2024-03-21T12:02:10.000+01:002024-03-21T12:02:10.000+01:00Summary Plant–plant positive interactions are key drivers of community structure. Yet, the underlying molecular mechanisms of facilitation processes remain unexplored. We investigated the ‘nursing’ effect of Maihueniopsis camachoi , a cactus that thrives in the Atacama Desert between c . 2800 and 3800 m above sea level. We hypothesised that an important protective factor is thermal amelioration of less cold‐tolerant species with a corresponding impact on molecular phenotypes. To test this hypothesis, we compared plant cover and temperatures within the cactus foliage with open areas and modelled the effect of temperatures on plant distribution. We combined eco‐metabolomics and machine learning to test the molecular consequences of this association. Multiple species benefited from the interaction with M. camachoi . A conspicuous example was the extended distribution of Atriplex imbricata to colder elevations in association with M. camachoi (400 m higher as compared to plants in open areas). Metabolomics identified 93 biochemical markers predicting the interaction status of A. imbricata with 79% accuracy, independently of year. These findings place M. camachoi as a key species in Atacama plant communities, driving local biodiversity with an impact on molecular phenotypes of nursed species. Our results support the stress‐gradient hypothesis and provide pioneer insights into the metabolic consequences of facilitation.https://hal.inrae.fr/hal-04468891[hal-04468891] Genetic control of abiotic stress-related specialized metabolites in sunflower2024-02-20T16:19:28.000+01:002024-02-20T16:19:28.000+01:00Abiotic stresses in plants include all the environmental conditions that significantly reduce yields, like drought and heat. One of the most significant effects they exert at the cellular level is the accumulation of reactive oxygen species, which cause extensive damage. Plants possess two mechanisms to counter these molecules, i.e. detoxifying enzymes and non-enzymatic antioxidants, which include many classes of specialized metabolites. Sunflower, the fourth global oilseed, is considered moderately drought resistant. Abiotic stress tolerance in this crop has been studied using many approaches, but the control of specialized metabolites in this context remains poorly understood. Here, we performed the first genome-wide association study using abiotic stress-related specialized metabolites as molecular phenotypes in sunflower. After analyzing leaf specialized metabolites of 450 hybrids using liquid chromatography-mass spectrometry, we selected a subset of these compounds based on their association with previously known abiotic stress-related quantitative trait loci. Eventually, we characterized these molecules and their associated genes. We putatively annotated 30 compounds which co-localized with abiotic stress-related quantitative trait loci and which were associated to seven most likely candidate genes. A large proportion of these compounds were potential antioxidants, which was in agreement with the role of specialized metabolites in abiotic stresses. The seven associated most likely candidate genes, instead, mainly belonged to cytochromes P450 and glycosyltransferases, two large superfamilies which catalyze greatly diverse reactions and create a wide variety of chemical modifications. This was consistent with the high plasticity of specialized metabolism in plants. This is the first characterization of the genetic control of abiotic stress-related specialized metabolites in sunflower. By providing hints concerning the importance of antioxidant molecules in this biological context, and by highlighting some of the potential molecular mechanisms underlying their biosynthesis, it could pave the way for novel applications in breeding. Although further analyses will be required to better understand this topic, studying how antioxidants contribute to the tolerance to abiotic stresses in sunflower appears as a promising area of research.https://hal.inrae.fr/hal-04461297[hal-04461297] Different wheat loci are associated to heritable free asparagine content in grain grown under different water and nitrogen availability2024-02-16T11:13:28.000+01:002024-02-16T11:13:28.000+01:00The amount of free asparagine in grain of a wheat genotype determines its potential to form harmful acrylamide in derivative food products. Here, we explored the variation in the free asparagine, aspartate, glutamine and glutamate contents of 485 accessions refecting wheat worldwide diversity to defne the genetic architecture governing the accumulation of these amino acids in grain. Accessions were grown under high and low nitrogen availability and in water-defcient and well-watered conditions, and plant and grain phenotypes were measured. Free amino acid contents of grain varied from 0.01 to 1.02 mg g−1 among genotypes in a highly heritable way that did not correlate strongly with grain yield, protein content, specifc weight, thousand-kernel weight or heading date. Mean free asparagine content was 4% higher under high nitrogen and 3% higher in water-defcient conditions. After genotyping the accessions, single-locus and multi-locus genome-wide association study models were used to identify several QTLs for free asparagine content located on nine chromosomes. Each QTL was associated with a single amino acid and growing environment, and none of the QTLs colocalised with genes known to be involved in the corresponding amino acid metabolism. This suggests that free asparagine content is controlled by several loci with minor efects interacting with the environment. We conclude that breeding for reduced asparagine content is feasible, but should be frmly based on multi-environment feld trials. Key message: Diferent wheat QTLs were associated to the free asparagine content of grain grown in four diferent conditions. Environmental efects are a key factor when selecting for low acrylamide-forming potentialhttps://hal.inrae.fr/hal-04433999[hal-04433999] Hyperpolarized NMR metabolomics at natural 13C abundance2024-02-02T11:03:48.000+01:002024-02-02T11:03:48.000+01:00[...]https://hal.inrae.fr/hal-04433980[hal-04433980] Hyperpolarized NMR metabolomics at natural 13C abundance2024-02-02T11:03:47.000+01:002024-02-02T11:03:47.000+01:00[...]https://hal.science/hal-04432708[hal-04432708] Hyperpolarized NMR Metabolomics at Natural 13C Abundance2024-02-01T17:03:34.000+01:002024-02-01T17:03:34.000+01:00[...]https://hal.science/hal-04432581[hal-04432581] Hyperpolarized NMR metabolomics at natural 13C abundance2024-02-01T16:10:06.000+01:002024-02-01T16:10:06.000+01:00[...]https://hal.inrae.fr/hal-04396004[hal-04396004] Using metabolomics and predictive metabolomic to study the physiology of an old rustic oilseed plant.2024-01-15T19:11:32.000+01:002024-01-15T19:11:32.000+01:00In recent years, there has been a growing interest in the stress-tolerant oilseed crop Camelina sativa. However, despite this interest, there has been relatively little research into the plasticity of this species, which has not been subject to significant breeding efforts. To address this knowledge gap, the EU H2020 UNTWIST project (https://www.untwist.eu/) is exploring the diversity of stress response mechanisms in different lines of camelina and using this new understanding to develop predictive models. In this study, we conducted targeted and untargeted metabolomics analyses on 54 camelina lines grown under three different conditions (control, heat, and drought stress). We quantified ten major metabolic traits and used an untargeted LC-MS metabolomics approach to characterise 3,016 metabolic features. The same 54 lines were also evaluated (phenology, physiology and performance parameters) in field trials across Europe (France, England, Italy and Spain). Our findings show that the different camelina lines exhibited a wide range of stress responses, which were not always linked to their genetic background. Using predictive metabolomics, we were able to accurately predict important agronomic and physiological variables, including thousand-kernel-weight and fatty-acid composition, based on data obtained from plants grown in the greenhouse. Our results suggest that metabolites present in early-stage leaves of camelina plants contain information about future performance of the lines. Annotation of the metabolic biomarkers identified in this study will give insights into the biology behind those predictions.https://hal.science/hal-04377185[hal-04377185] A global LC–MS 2 ‐based methodology to identify and quantify anionic phospholipids in plant samples2024-01-07T16:54:19.000+01:002024-01-07T16:54:19.000+01:00Anionic phospholipids (PS, PA, PI, PIPs) are low‐abundant phospholipids with impactful functions in cell signaling, membrane trafficking and cell differentiation processes. They can be quickly metabolized and can transiently accumulate at defined spots within the cell or an organ to respond to physiological or environmental stimuli. As even a small change in their composition profile will produce a significant effect on biological processes, it is crucial to develop a sensitive and optimized analytical method to accurately detect and quantify them. While thin‐layer chromatography (TLC) separation coupled with gas chromatography (GC) detection methods already exist, they do not allow for precise, sensitive, and accurate quantification of all anionic phospholipid species. Here we developed a method based on high‐performance liquid chromatography (HPLC) combined with two‐dimensional mass spectrometry (MS 2 ) by MRM mode to detect and quantify all molecular species and classes of anionic phospholipids in one shot. This method is based on a derivatization step by methylation that greatly enhances the ionization, the separation of each peak, the peak resolution as well as the limit of detection and quantification for each individual molecular species, and more particularly for PA and PS. Our method universally works in various plant samples. Remarkably, we identified that PS is enriched with very long chain fatty acids in the roots but not in aerial organs of Arabidopsis thaliana . Our work thus paves the way for new studies on how the composition of anionic lipids is finely tuned during plant development and environmental responses.https://hal.inrae.fr/hal-04352912[hal-04352912] Ecotoxicité des produits de transformation des pesticides dans les milieux aquatiques2023-12-19T12:15:53.000+01:002023-12-19T12:15:53.000+01:00[...]https://hal.inrae.fr/hal-04346290[hal-04346290] Bioprotection as an alternative to SO<sub>2</sub> in the pre-fermentation phase2023-12-15T09:20:25.000+01:002023-12-15T09:20:25.000+01:00Additives have been used in the food industry for many years, to prevent food spoilage and extend shelf life. These chemical additives are a source of controversy and their use must be reduced in the face of societal demand. In enology, this applies in particular to sulfur dioxide (SO2). There has been recent research on bioprotection as an alternative to sulfite addition in the pre-fermentation phase. This technical article discusses the many advantages of using bioprotection agents.https://hal.inrae.fr/hal-04345671[hal-04345671] Evaluation of the oenological potential of new resistant varieties meeting typical Bordeaux characteristics2023-12-14T19:03:02.000+01:002023-12-14T19:03:02.000+01:00[...]https://hal.science/hal-04344574[hal-04344574] Mise en évidence de stilbènes oligomérisés à potentiel antifongique dans les co-produits de la vigne par une approche de métabolomique non-ciblée2023-12-14T13:16:03.000+01:002023-12-14T13:16:03.000+01:00[...]https://hal.science/hal-04344566[hal-04344566] Les plantes invasives aquatiques : nouvelle source de composes actifs contre les biofilms de Candida albicans - Staphylococcus aureus2023-12-14T13:10:31.000+01:002023-12-14T13:10:31.000+01:00[...]https://hal.science/hal-04344555[hal-04344555] Valorization of invasive plants against the bi-species biofilm Staphylococcus aureus-Candida albicans2023-12-14T13:07:27.000+01:002023-12-14T13:07:27.000+01:00[...]https://hal.science/hal-04344522[hal-04344522] Untargeted metabolomics to identify potential chemical markers responsible for the growth of Brettanomyces bruxellensis in red wines2023-12-14T12:55:51.000+01:002023-12-14T12:55:51.000+01:00[...]https://hal.science/hal-04344500[hal-04344500] Identification des métabolites à activité antioxydante de racines de vigne basée sur un réseau moléculaire2023-12-14T12:49:57.000+01:002023-12-14T12:49:57.000+01:00[...]https://hal.science/hal-04344491[hal-04344491] Mise en évidence de métabolites antifongiques présents dans des co-produits de la vigne par une approche de métabolomique non-ciblée2023-12-14T12:46:37.000+01:002023-12-14T12:46:37.000+01:00[...]https://hal.science/hal-04344441[hal-04344441] Optimization of polyphenols extraction from grapevine canes using natural deep eutectic solvents2023-12-14T12:31:42.000+01:002023-12-14T12:31:42.000+01:00Abstract Mycotoxins are metabolites produced by molds that contaminate food commodities, are harmful to both humans and animals, as well as cause economic losses. Many countries have set regulatory limits and strict thresholds to control the level of mycotoxins in food and feedstuffs. New technologies and strategies have been developed to inhibit toxigenic fungal invasion and to decontaminate mycotoxins. However, many of these strategies do not sufficiently detoxify mycotoxins and leave residual toxic by‐products. This review focuses on the use of phenolic compounds obtained from botanical extracts as promising bioagents to inhibit fungal growth and/or to limit mycotoxin yields. The mechanism of these botanicals, legislation concerning their use, and their safety are also discussed. In addition, recent strategies to overcome stability and solubility constraints of phenolic compounds to be used in food and feed stuffs are also mentioned.https://hal.inrae.fr/hal-04344318[hal-04344318] Unraveling the chemical mechanism of MND formation in red wine during bottle aging : Identification of a new glucosylated hydroxyketone pro-precursor2023-12-14T11:18:44.000+01:002023-12-14T11:18:44.000+01:00[...]https://hal.inrae.fr/hal-04344280[hal-04344280] Uncovering the role of berry maturity stage and grape genotype on wine characteristics: insights from chemical characteristics and volatile compounds analysis2023-12-14T11:11:34.000+01:002023-12-14T11:11:34.000+01:00[...]https://hal.inrae.fr/hal-04344237[hal-04344237] Metabolomic Insights into Wine's Sensory Identity: Unveiling Climate-Driven Changes in Aroma Composition2023-12-14T11:11:33.000+01:002023-12-14T11:11:33.000+01:00[...]https://hal.inrae.fr/hal-04343936[hal-04343936] Impact of temperature and solar radiation on grape composition variability in the Saint-Emilion winegrowing area2023-12-14T10:26:38.000+01:002023-12-14T10:26:38.000+01:00[...]https://hal.inrae.fr/hal-04332027[hal-04332027] Influences de la température et de la lumière sur le métabolome et le lipidome de la microalgue S. costatus2023-12-08T17:09:40.000+01:002023-12-08T17:09:40.000+01:00Les biofilms sont essentiels pour le cycle des nutriments et de l'énergie dans les écosystèmes aquatiques. Ils constituent par ailleurs le premier maillon biologique possiblement impacté par les facteurs de stress environnementaux, tels que la température, la disponibilité des nutriments ou encore l’exposition à des polluants. Les biofilms peuvent être employés pour décrire les relations au sein des chaînes alimentaires aquatiques et sont souvent utilisés comme indicateurs de la qualité des écosystèmes. Ils font l'objet d'une attention croissante car ils constituent notamment une source d'acides gras essentiels pour les maillons trophiques supérieurs . Par ailleurs, l’étude du métabolome et du lipidome de ces communautés gagne en popularité du fait de leur capacité à rendre compte de l’activité microbienne globale de la communauté, ainsi que leur potentiel pour l’identification de marqueurs d’exposition et d’effets face aux changements globaux . Le métabolome, et plus particulièrement la teneur en lipides des microalgues, est fortement influencé par plusieurs facteurs environnementaux, avec un effet primordial des variations de la température du milieu. Au cours de travaux, qui seront exposés, nous avons cultivé l’algue verte Scenedesmus costatus selon des conditions croisées d’intensité lumineuse et de température afin de reproduire les évolutions qui pourraient se produire dans le cadre du changement climatique. Les premières données obtenues mettent en évidence une signature métabolique différente entre les conditions expérimentales. En particulier, nos résultats indiqueraient d’une part un effet plus marqué de la hausse de la température sur la qualité des acides gras, puis d’autre part une modification au niveau des lipides membranaires davantage en lien avec un effet de la lumière. Enfin, ces résultats seront mis en perspective des effets mixtes avec l’exposition à des contaminants, lors d’expérimentations à venir.https://hal.inrae.fr/hal-04332015[hal-04332015] Ecotoxicité des produits de transformation des pesticides dans les milieux aquatiques2023-12-08T17:07:02.000+01:002023-12-08T17:07:02.000+01:00Une fois appliquées sur les cultures, les substances actives de pesticides sont soumises à divers processus biotiques et abiotiques qui gouvernent leur devenir et leur transfert dans les différents compartiments de l’environnement. Les produits de transformation (TP) issus de ces processus sont potentiellement très nombreux, présents à faibles teneurs dans les milieux aquatiques. Leur détection et leur occurrence sont amenées à évoluer compte tenu du développement des stratégies analytiques et de la modification des conditions climatiques. L’écotoxicité des TP est encore peu étudiée, mais diverses études indiquent une écotoxicité potentiellement différente de la substance active mère. Dans ce contexte, le projet TAPIOCA, financé dans le cadre de l’APR Ecophyto II+ « Santé écosystèmes », poursuit trois objectifs : i) mettre au point des méthodes analytiques sensibles pour l’identification de TP de pesticides dans les eaux ; ii) améliorer les connaissances sur les effets d’une sélection de pesticides et de TP associés, sur les communautés microbiennes et les macroinvertébrés aquatiques ; et iii) tester l’apport d’outils de prédiction des propriétés de dissipation et de transferts de TP de pesticides pour mieux cerner leur potentiel de présence dans l’environnement. Ici, nous présentons quelques résultats marquants en lien avec la caractérisation de l’écotoxicité chronique à 3 pesticides (le fongicide tébuconazole, l’insecticide fénoxycarbe et l’herbicide terbuthylazine) et leurs TP. Des expérimentations en microcosmes avec des organismes aquatiques (périphyton, communautés microbiennes d’hyphomycètes ou gammares) ont permis d’évaluer les effets de plusieurs scénarios d’exposition aux pesticides et à des TP associés (produits commercialement disponibles ou obtenus par photodégradation contrôlée de pesticides dits « vieillis ») sur différents descripteurs biologiques. Les premiers résultats montrent globalement une toxicité moindre des TP comparativement aux trois molécules mères sur les organismes étudiés. Néanmoins, la terbuthylazine et son TP terbuthylazine-desethyl présentent une toxicité inattendue pour les fonctions de reproduction des gammares, organismes non-cibles de cet herbicide.https://hal.inrae.fr/hal-04331347[hal-04331347] Comparaison du métabolome de trois microalgues pour étudier les différences de sensibilité des communautés périphytiques2023-12-08T14:20:42.000+01:002023-12-08T14:20:42.000+01:00[...]https://hal.inrae.fr/hal-04331338[hal-04331338] Meta-metabolomics to uncover short vs long term response of periphytic microbiome to a model fungicide2023-12-08T14:14:52.000+01:002023-12-08T14:14:52.000+01:00[...]https://hal.science/hal-02935172[hal-02935172] Improving lipid mapping in Genome Scale Metabolic Networks using ontologies2023-12-08T11:29:15.000+01:002023-12-08T11:29:15.000+01:00Introduction To interpret metabolomic and lipidomic profiles, it is necessary to identify the metabolic reactions that connect the measured molecules. This can be achieved by putting them in the context of genome-scale metabolic network reconstructions. However, mapping experimentally measured molecules onto metabolic networks is challenging due to differences in identifiers and level of annotation between data and metabolic networks, especially for lipids.Objectives To help linking lipids from lipidomics datasets with lipids in metabolic networks, we developed a new matching method based on the ChEBI ontology. The implementation is freely available as a python library and in MetExplore webserver.Methods Our matching method is more flexible than an exact identifier-based correspondence since it allows establishing a link between molecules even if a different level of precision is provided in the dataset and in the metabolic network. For instance, it can associate a generic class of lipids present in the network with the molecular species detailed in the lipidomics dataset. This mapping is based on the computation of a distance between molecules in ChEBI ontology.Results We applied our method to a chemical library (968 lipids) and an experimental dataset (32 modulated lipids) and showed that using ontology-based mapping improves and facilitates the link with genome scale metabolic networks. Beyond network mapping, the results provide ways for improvements in terms of network curation and lipidomics data annotation.Conclusion This new method being generic, it can be applied to any metabolomics data and therefore improve our comprehension of metabolic modulations.https://hal.inrae.fr/hal-04305424[hal-04305424] New alternative ingredients and genetic selection are the next game changers in rainbow trout nutrition: a metabolomics appraisal2023-11-24T16:01:35.000+01:002023-11-24T16:01:35.000+01:00The formulation of sustainable fish feeds based on plant ingredients supplemented by alternative ingredients to plant (insect, micro-algae, yeast) and genetic selection of fish for plant-based diets were tested on rainbow trout in two separate experiments. Plant-based diets and corresponding diets supplemented with an ingredient mix: insect, micro-algae and yeast in Experiment A, and insect and yeast in Experiment B were compared to commercial-like diets. In experiment A, the mixsupplemented diet was successful in compensating the altered growth performance of fish fed their respective plant-based diet compared to those fed the commercial diet, by restoring feed conversion. In experiment B, the selected line demonstrated improved growth performances of fish fed mixsupplemented and plant-based diets compared to the non-selected line. Metabolomics demonstrated a plasma compositional stability in fish fed mix-supplemented and basal plant-based diets comprising an amino acid accumulation and a glucose depletion, compared to those fed commercial diets. The selected line fed mix-supplemented and commercial diets showed changes in inositol, ethanol and methanol compared to the non-selected line, suggesting an involvement of microbiota. Changes in plasma glycine-betaine content in fish fed the mix-supplemented diet suggest the ability of the selected line to adapt to alternative ingredients. Combined with responsible fishing policies, the increasing demand for aquatic products challenges the development of sustainable and efficient fish feed for aquaculture, which currently provides about 50% of the aquatic products consumed 1. Plant ingredients make up at least 90% of the fish feed used for many fish species, including carnivorous ones such as the rainbow trout 2,3. However, sustainable fish feeds free of marine ingredients are not yet sufficiently performant to guarantee a fair economic income to farmers. Fish feeds can be improved by selecting high-quality plant proteins, or by including alternative ingredients of plants ingredients and fish products, that meet the nutritional requirements of fish, increase farming profitability, and support environmental preservation and consumer expectations. A substantial research effort has been conducted to assess the efficacy of a wide range of alternative ingredients to plant-based feedstuffs, from single-cell ingredients to animal by-products.https://hal.science/hal-04234412[hal-04234412] Mixed light photoperiod and biocide pollution affect lipid profiles of periphyton communities in freshwater ecosystems2023-11-17T14:19:20.000+01:002023-11-17T14:19:20.000+01:00Environmental factors, such as light intensity and exposure to contaminants, may significantly influence the lipid composition of algae in periphytic communities. In this study, we investigated the joint effects of dodecylbenzyldimethylammonium chloride (BAC 12), as biocide, and light photoperiods on the polar lipidome of a freshwater biofilm. Exposure to BAC 12 in a microcosm experiment increased the heterotrophic compartment, while phototrophic organisms were severely affected, with corresponding shifts in lipid composition. The overall decrease in polyinsaturated fatty acids suggested a significant impact of the biocide on biofilm microalgae. However, it was difficult to distinguish the influence of light from that of contamination, as there was no observable effect of photoperiod on conventional fatty acid determination. Thus, the molecular species compositions of both glycolipids and phospholipids were explored in additional multivariate analyzes. The results suggested that certain molecular species can serve as more specific markers of light duration at the biofilm scale, independently of the chemical pressure caused by other pollutants.https://hal.science/hal-04266576[hal-04266576] A global LC-MS 2 -based methodology to identify and quantify anionic phospholipids in plant samples2023-10-31T17:02:14.000+01:002023-10-31T17:02:14.000+01:00Anionic phospholipids (PS, PA, PI, PIPs) are low abundant phospholipids with impactful functions in cell signaling, membrane trafficking and cell differentiation processes. They can be quickly metabolized and can transiently accumulate at define spots within the cell or an organ to respond to physiological or environmental stimuli. As even a small change in their composition profile will produce a significant effect on biological processes, it is crucial to develop a sensitive and optimized analytical method to accurately detect and quantify them. While thin layer chromatography (TLC) separation coupled with gas chromatography (GC) detection methods already exist, they do not allow for precise, sensitive and accurate quantification of all anionic phospholipid species. Here we developed a method based on high performance liquid chromatography (HPLC) combined with two-dimensional mass spectrometry (MS 2 ) by MRM mode to detect and quantify all molecular species and classes of anionic phospholipids in one-shot. This method is based on a derivatization step by methylation that greatly enhances the ionization, the separation of each peaks, the peak resolution as well as the limit of detection and quantification for each individual molecular species, and more particularly for PA and PS. Our method universally works in various plant samples. Remarkably, we identified that PS is enriched with very long chain fatty acids in the roots but not in aerial organs of Arabidopsis thaliana . Our work thus paves the way to new studies on how the composition of anionic lipids is finely tuned during plant development and environmental responses. Significance Statement While anionic phospholipids have key functions in plant cellular processes, their low concentration in biological samples and their low stability during the analysis complicate their quantification. Here, we present the first one-shot analytical method for the profiling and quantification of all anionic phospholipid classes and species from plant tissues with unprecedented sensitivity. This method open the way to future studies requiring a fine quantification of anionic phospholipids to understand their role in plant cell processes.https://hal.inrae.fr/hal-04256711[hal-04256711] Maggot : Designed to foster good data management, with « data sharing » in mind.2023-10-25T11:10:32.000+02:002023-10-25T11:10:32.000+02:00Sharing descriptive metadata is the first essential step towards the so-called “Open Data” approach. With this in mind, the Maggot tool was specially designed to allow users to easily add descriptive metadata to datasets produced within a collective (research unit, platform, multi-partner project, etc.), thus promoting the sharing of metadata within this same collective and beyond.https://hal.science/hal-04249822[hal-04249822] Genome editing of a rice CDP-DAG synthase confers multipathogen resistance2023-10-19T15:42:27.000+02:002023-10-19T15:42:27.000+02:00[...]https://hal.inrae.fr/hal-04213772[hal-04213772] Effects of Lagarosiphon major extracts on the metabolome and photosynthesis of Microcystis aeruginosa2023-09-21T15:32:47.000+02:002023-09-21T15:32:47.000+02:00Over the last decades, Aquitaine lakes have been exposed to growing biomasses of invasive macrophytes, in particular Lagarosiphon major, and to frequent blooms of the cyanobacteria Microcystis aeruginosa. Our aim was to explore the potential role of L. major in the regulation of such blooms, through allelopathic interactions. Experiments consisted of exponential growth phase cells incubated for 96 h in L. major extracts at increasing concentrations. Our approach was based on untargeted metabolomics and photosynthetic activity measurements. We demonstrated the anticyanobacterial properties of L. major extracts. In particular, we reported that L. major extracts inhibited M. aeruginosa photosynthesis, and affected the production of various metabolite classes and pathways mainly involved in the secondary metabolism of the cyanobacteria. We further provided clear evidence about the existence of metabolite classes in L. major that may be involved in allelopathic interactions with M. aeruginosa, such as caffeic acid.https://hal.inrae.fr/hal-04207231[hal-04207231] Genetic architecture of leaf specialized metabolites natural variation within sessile oak populations2023-09-14T14:34:01.000+02:002023-09-14T14:34:01.000+02:00Specialized or secondary metabolites (SMs) play a key role in plant resistance against abiotic stresses and defences against bioaggressors. For example, in sessile oaks Quercus petraea, phenolics contribute to reduce herbivore damage and improve drought resistance. In the context of global climate change the extensive diversity of compounds and variation of biosynthesis within species may play a key role to mitigate the increased frequency of stressful events such as drought, heat waves or emergent pathogens. Here, we study the genetic basis of leaf SMs natural variation in nine European provenances of sessile oaks and investigate signature of selections along the genome. We sampled mature leaves from high and low branches on 225 sessile oak trees located in a common garden and used untargeted metabolomics to characterise the variation of 219 leaf specialized metabolites. In addition, we used whole genome low-depth sequencing to genotype all individuals for 1.4M genetic markers. We then performed genome-wide association analyses, identified candidate genes underlying the variation of leaf SMs and compared signatures of selection at these genes to the rest of the genome. We found that leaf SMs displayed extensive within-provenance variation, but very little differentiation between provenances. For ∼10% of the metabolites we detected, most of this variation could be explained by a single genetic marker. Our results suggest that genetic variation of most leaf SMs is unlikely to be locally adaptive, and that varying selective pressures may act locally to maintain diversity at loci associated with leaf SM variation.https://hal.science/hal-04188505[hal-04188505] Scaling-up metabolomics: Current state and perspectives2023-09-12T15:51:11.000+02:002023-09-12T15:51:11.000+02:00Metabolomics is now a mature phenotyping tool that provides substantial results within various scientific communities. Its application at large-scale, i.e. on large populations and/or samples, has shown its power for research activities from plant science to human epidemiology and medicine, but it still needs key methodological developments for its routine application. Here, we review the current state of large-scale metabolomics applications, providing recent examples of large cohort studies in human and plant/environment research, and present the remaining scientific challenges of both fields. Then, we address the key common methodological issues, from analytics to data science, to fulfil these objectives and go towards a more comprehensive and interoperable large-scale metabolomics, making it a new key actor in the frame of the One-Health future research.https://hal.inrae.fr/hal-04198979[hal-04198979] Circulating Human Metabolites Resulting from TOTUM-070 Absorption (a Plant-Based, Polyphenol-Rich Ingredient) Improve Lipid Metabolism in Human Hepatocytes: Lessons from an Original Ex Vivo Clinical Trial2023-09-07T16:27:12.000+02:002023-09-07T16:27:12.000+02:00TOTUM-070 is a patented polyphenol-rich blend of five different plant extracts showing separately a latent effect on lipid metabolism and potential synergistic properties. In this study, we investigated the health benefit of such a formula. Using a preclinical model of high fat diet, TOTUM-070 (3 g/kg of body weight) limited the HFD-induced hyperlipemia with a reduction in triglyceride (−32% after 6 weeks; −20.3% after 12 weeks) and non-HDL cholesterol levels (−21% after 6 weeks; −38.4% after 12 weeks). To further investigate such a benefit and its underlying mechanisms in humans, we designed an ex vivo clinical approach to collect the circulating bioactives resulting from TOTUM-070 ingestion and to determine their biological activities on human hepatocytes. Human serum was obtained from healthy subjects before and after intake of TOTUM-070 (4995 mg). The presence of circulating metabolites was assessed by UPLC-MS/MS. Serum containing metabolites was further incubated with hepatocytes cultured in a lipotoxic environment (palmitate, 250 µM). RNA sequencing analyses show that lipid metabolism was one of the most impacted processes. Using histologic, proteomic, and enzymatic assays, the effects of human TOTUM-070 bioactives on hepatocyte metabolism were characterized by (1) the inhibition of lipid storage, including both (2) triglycerides (−41%, p < 0.001) and (3) cholesterol (−50%, p < 0.001) intracellular content, (4) a reduced de novo cholesterol synthesis (HMG-CoA reductase activity −44%, p < 0.001), and (5) a lowered fatty acid synthase protein level (p < 0.001). Altogether, these data support the beneficial impact of TOTUM-070 on lipid metabolism and provide new biochemical insights in human mechanisms occurring in liver cells.https://hal.inrae.fr/hal-04190430[hal-04190430] Revealing the lipidome and proteome of Arabidopsis thaliana plasma membrane2023-08-29T17:23:58.000+02:002023-08-29T17:23:58.000+02:00Abstract The plant plasma membrane (PM) plays a key role in nutrition, cell homeostasis, perception of environmental signals, and set-up of appropriate adaptive responses. An exhaustive and quantitative description of the whole set of lipids and proteins constituting the PM is thus necessary to understand how its individual components, the way they are organized and interact together, allow to fulfill such essential physiological functions. Here we provide by state-of-the-art approaches the first combined reference of the plant PM lipidome and proteome from Arabidopsis thaliana suspension cell culture. We identified a core set of 2,165 proteins (406 of which had not been shown associated to PM previously), which is by far the largest set of available data concerning the plant PM proteome. Using the same samples, we combined lipidomic approaches, allowing the identification and quantification of an unprecedented repertoire of 405 molecular species of lipids. We showed that the different classes of lipids (sterols, phospholipids, and sphingolipids) were present in similar proportions in the plant PM. Within each lipid class, the precise amount of each lipid family and the relative proportion of each molecular species were then determined, allowing us to establish the complete lipidome of Arabidopsis PM, and highlighting specific characteristics of the different molecular species of lipids (for instance fatty acyl chain length and saturation according to the polar head). Results obtained are consistent with plant PM being an ordered mosaic of domains and point to a finely tuned adjustment of the molecular characteristics of lipids and proteins. More than a hundred proteins related to lipid metabolism, transport or signaling have been identified and put in perspective of the lipids with which they are associated. All these results provide an overall view of both the organization and the functioning of the PM.https://hal.inrae.fr/hal-04186121[hal-04186121] Correction: Impact of membrane lipid polyunsaturation on dopamine D2 receptor ligand binding and signaling2023-08-23T16:37:20.000+02:002023-08-23T16:37:20.000+02:00No abstract availablehttps://hal.inrae.fr/hal-04185814[hal-04185814] Comparative constraint‐based modelling of fruit development across species highlights nitrogen metabolism in the growth‐defence trade‐off2023-08-23T11:15:23.000+02:002023-08-23T11:15:23.000+02:00Although primary metabolism is well conserved across species, it is useful to explore the specificity of its network to assess the extent to which some pathways may contribute to particular outcomes. Constraintbased metabolic modelling is an established framework for predicting metabolic fluxes and phenotypes and helps to explore how the plant metabolic network delivers specific outcomes from temporal series. After describing the main physiological traits during fruit development, we confirmed the correlations between fruit relative growth rate (RGR), protein content and time to maturity. Then a constraint-based method is applied to a panel of eight fruit species with a knowledge-based metabolic model of heterotrophic cells describing a generic metabolic network of primary metabolism. The metabolic fluxes are estimated by constraining the model using a large set of metabolites and compounds quantified throughout fruit development. Multivariate analyses showed a clear common pattern of flux distribution during fruit development with differences between fast-and slow-growing fruits. Only the latter fruits mobilise the tricarboxylic acid cycle in addition to glycolysis, leading to a higher rate of respiration. More surprisingly, to balance nitrogen, the model suggests, on the one hand, nitrogen uptake by nitrate reductase to support a high RGR at early stages of cucumber and, on the other hand, the accumulation of alkaloids during ripening of pepper and eggplant. Finally, building virtual fruits by combining 12 biomass compounds shows that the growthdefence trade-off is supported mainly by cell wall synthesis for fast-growing fruits and by total polyphenols accumulation for slow-growing fruits.https://hal.inrae.fr/hal-04185467[hal-04185467] Nitrogen-mediated metabolic patterns of susceptibility to Botrytis cinerea infection in tomato (Solanum lycopersicum) stems2023-08-22T18:48:44.000+02:002023-08-22T18:48:44.000+02:00[...]https://hal.inrae.fr/hal-04185066[hal-04185066] Metabolic fluxes estimated by constraint-based modelling highlight specific response of susceptible tomato (Solanum lycopersicum) stems infected by Botrytis cinerea under gradual nitrogen nutrition2023-08-22T13:01:47.000+02:002023-08-22T13:01:47.000+02:00[...]https://hal.inrae.fr/hal-04183193[hal-04183193] Multi-omics quantitative data of tomato fruit unveils regulation modes of least variable metabolites2023-08-18T17:09:37.000+02:002023-08-18T17:09:37.000+02:00Background The composition of ripe fruits depends on various metabolites which content evolves greatly throughout fruit development and may be influenced by the environment. The corresponding metabolism regulations have been widely described in tomato during fruit growth and ripening. However, the regulation of other metabolites that do not show large changes in content have scarcely been studied. Results We analysed the metabolites of tomato fruits collected on different trusses during fruit development, using complementary analytical strategies. We identified the 22 least variable metabolites, based on their coefficients of variation. We first verified that they had a limited functional link with the least variable proteins and transcripts. We then posited that metabolite contents could be stabilized through complex regulations and combined their data with the quantitative proteome or transcriptome data, using sparse partial-least-square analyses. This showed shared regulations between several metabolites, which interestingly remained linked to early fruit development. We also examined regulations in specific metabolites using correlations with individual proteins and transcripts, which revealed that a stable metabolite does not always correlate with proteins and transcripts of its known related pathways. Conclusions The regulation of the least variable metabolites was then interpreted regarding their roles as hubs in metabolic pathways or as signalling molecules.https://hal.inrae.fr/hal-04155487v2[hal-04155487] NMR metabolite quantification of a synthetic urine sample: an inter-laboratory comparison of processing workflows2023-08-16T15:03:38.000+02:002023-08-16T15:03:38.000+02:00Introduction Absolute quantification of individual metabolites in complex biological samples is crucial in targeted metabolomic profiling. Objectives An inter-laboratory test was performed to evaluate the impact of the NMR software, peak-area determination method (integration vs. deconvolution) and operator on quantification trueness and precision. Methods A synthetic urine containing 32 compounds was prepared. One site prepared the urine and calibration samples, and performed NMR acquisition. NMR spectra were acquired with two pulse sequences including water suppression used in routine analyses. The pre-processed spectra were sent to the other sites where each operator quantified the metabolites using internal referencing or external calibration, and his/her favourite in-house, open-access or commercial NMR tool. Results For 1D NMR measurements with solvent presaturation during the recovery delay (zgpr), 20 metabolites were successfully quantified by all processing strategies. Some metabolites could not be quantified by some methods. For internal referencing with TSP, only one half of the metabolites were quantified with a trueness below 5%. With peak integration and external calibration, about 90% of the metabolites were quantified with a trueness below 5%. The NMRProcFlow integration module allowed the quantification of several additional metabolites. The number of quantified metabolites and quantification trueness improved for some metabolites with deconvolution tools. Trueness and precision were not significantly different between zgpr- and NOESYpr-based spectra for about 70% of the variables. Conclusion External calibration performed better than TSP internal referencing. Inter-laboratory tests are useful when choosing to better rationalize the choice of quantification tools for NMR-based metabolomic profiling and confirm the value of spectra deconvolution tools.https://hal.inrae.fr/hal-04181587[hal-04181587] Integrated multi-omic analysis of fruit maturity identifies biomarkers with drastic abundance shifts spanning the harvest period in ‘Royal Gala’ apple2023-08-16T12:20:44.000+02:002023-08-16T12:20:44.000+02:00Accurate assessment of apple fruit maturity at harvest is required since fruit harvested too early or too late are susceptible to physiological disorders or excessive softening during subsequent storage. Biological markers of early fruit maturity allow forecasting of optimal harvest time, contributing significant industry value through more accurate management of harvest logistics. This study investigated the changes in cortex of apple (Malus x domestica ‘Royal Gala’) fruit at four harvests: very early (H1), early (H2), commercial (H3) and late (H4), using a combination of transcriptomics, metabolomics, hormone abundances and enzyme activity profiles. Harvest times were discriminated based on several sets of variates, showing that metabolism was very active within this short time period. Good discrimination between H1 and H2 and between H2 and H3 was observed in the declining abundance of a range of photosystem transcripts and the increasing abundance of early ripening markers. Degradation of the photosynthetic apparatus was correlated with ethylene production. Multi-omics analysis using mixOmics identified groups of variates whose abundance declined or increased during the harvest period, and strong correlations between components of different pathways were evident. We identify a suite of biomarkers, including Chl a/b binding protein of LHCII, Xyloglucan glycosyltransferase 5, PG1, ACO1, internal ethylene concentration and starch pattern index, for orchardists to accurately predict harvest time several weeks in advance, thus providing time to mobilise the necessary logistical resources.https://hal.inrae.fr/hal-04178513[hal-04178513] Enzyme‐based kinetic modelling of ASC–GSH cycle during tomato fruit development reveals the importance of reducing power and ROS availability2023-08-08T12:32:42.000+02:002023-08-08T12:32:42.000+02:00Summary The ascorbate–glutathione (ASC–GSH) cycle is at the heart of redox metabolism, linking the major redox buffers with central metabolism through the processing of reactive oxygen species (ROS) and pyridine nucleotide metabolism. Tomato fruit development is underpinned by changes in redox buffer contents and their associated enzyme capacities, but interactions between them remain unclear. Based on quantitative data obtained for the core redox metabolism, we built an enzyme‐based kinetic model to calculate redox metabolite concentrations with their corresponding fluxes and control coefficients. Dynamic and associated regulations of the ASC–GSH cycle throughout the whole fruit development were analysed and pointed to a sequential metabolic control of redox fluxes by ASC synthesis, NAD(P)H and ROS availability depending on the developmental phase. Furthermore, we highlighted that monodehydroascorbate reductase and the availability of reducing power were found to be the main regulators of the redox state of ASC and GSH during fruit growth under optimal conditions. Our kinetic modelling approach indicated that tomato fruit development displayed growth phase‐dependent redox metabolism linked with central metabolism via pyridine nucleotides and H 2 O 2 availability, while providing a new tool to the scientific community to investigate redox metabolism in fruits.https://hal.inrae.fr/hal-04177128[hal-04177128] Staphylococcus epidermidis isolates from atopic or healthy skin have opposite effect on skin cells: potential implication of the AHR pathway modulation2023-08-04T11:13:16.000+02:002023-08-04T11:13:16.000+02:00Introduction S taphylococcus epidermidis is a commensal bacterium ubiquitously present on human skin. This species is considered as a key member of the healthy skin microbiota, involved in the defense against pathogens, modulating the immune system, and involved in wound repair. Simultaneously, S. epidermidis is the second cause of nosocomial infections and an overgrowth of S. epidermidis has been described in skin disorders such as atopic dermatitis. Diverse isolates of S. epidermidis co-exist on the skin. Elucidating the genetic and phenotypic specificities of these species in skin health and disease is key to better understand their role in various skin conditions. Additionally, the exact mechanisms by which commensals interact with host cells is partially understood. We hypothesized that S. epidermidis isolates identified from different skin origins could play distinct roles on skin differentiation and that these effects could be mediated by the aryl hydrocarbon receptor (AhR) pathway. Methods For this purpose, a library of 12 strains originated from healthy skin (non-hyperseborrheic (NH) and hyperseborrheic (H) skin types) and disease skin (atopic (AD) skin type) was characterized at the genomic and phenotypic levels. Results and discussion Here we showed that strains from atopic lesional skin alter the epidermis structure of a 3D reconstructed skin model whereas strains from NH healthy skin do not. All strains from NH healthy skin induced AhR/OVOL1 path and produced high quantities of indole metabolites in co-culture with NHEK; especially indole-3-aldehyde (IAld) and indole-3-lactic acid (ILA); while AD strains did not induce AhR/OVOL1 path but its inhibitor STAT6 and produced the lowest levels of indoles as compared to the other strains. As a consequence, strains from AD skin altered the differentiation markers FLG and DSG1. The results presented here, on a library of 12 strains, showed that S. epidermidis originated from NH healthy skin and atopic skin have opposite effects on the epidermal cohesion and structure and that these differences could be linked to their capacity to produce metabolites, which in turn could activate AHR pathway. Our results on a specific library of strains provide new insights into how S. epidermidis may interact with the skin to promote health or disease.https://hal.inrae.fr/hal-04176065[hal-04176065] GABA shunt pathway is stimulated in response to early defoliation-induced carbohydrate limitation in Mandarin fruits2023-08-02T16:57:34.000+02:002023-08-02T16:57:34.000+02:00The regulation of sugar and organic acid metabolism during fruit development has a major effect on high-quality fruit production. The reduction of leaf area is a common feature in plant growth, induced by abiotic and biotic stresses and disturbing source/sink ratio, thus impacting fruit quality. Here, we induced carbohydrate limitation by partial leaf defoliation at the beginning of the second stage of mandarin development (before the citrate peak). Resulting changes were monitored in the short-term (48 h and 1 week) and long-term (7 weeks) after the defoliation. Short-term response to early defoliation implied metabolic settings to re-feed TCA for sustaining respiration rate. These features involved (i) vacuolar sucrose degradation (high acid invertase activity and mRNA expression level) and enhanced glycolytic flux (high ATP-phosphofructokinase activity), (ii) malic and citric acid utilization (increased phosphoenolpyr-uvate kinase and NADP-Isocitrate dehydrogenase) associated with vacuolar citric acid release (high mRNA expression of the transporter CsCit1) and (iii) stimulation of GABA shunt pathway (low GABA content and increased mRNA expression of succinate semialdehyde dehydrogenase). A steady-state proline level was found in ED fruits although an increase in P5CS mRNA expression level. These results contribute to a better knowledge of the molecular basis of the relationship between defoliation and sugar and organic acid metabolism in mandarin fruit.https://hal.inrae.fr/hal-04173364[hal-04173364] Dissipation of pesticides by stream biofilms is influenced by hydrological histories2023-07-28T19:56:46.000+02:002023-07-28T19:56:46.000+02:00Abstract To evaluate the effects of hydrological variability on pesticide dissipation capacity by stream biofilms, we conducted a microcosm study. We exposed biofilms to short and frequent droughts (daily frequency), long and less frequent droughts (weekly frequency) and permanently immersed controls, prior to test their capacities to dissipate a cocktail of pesticides composed of tebuconazole, terbuthylazine, imidacloprid, glyphosate and its metabolite aminomethylphosphonic acid. A range of structural and functional descriptors of biofilms (algal and bacterial biomass, extracellular polymeric matrix (EPS) concentration, microbial respiration, phosphorus uptake and community-level physiological profiles) were measured to assess drought effects. In addition, various parameters were measured to characterise the dynamics of pesticide dissipation by biofilms in the different hydrological treatments (% dissipation, peak asymmetry, bioconcentration factor, among others). Results showed higher pesticide dissipation rates in biofilms exposed to short and frequent droughts, despite of their lower biomass and EPS concentration, compared to biofilms in immersed controls or exposed to long and less frequent droughts. High accumulation of hydrophobic pesticides (tebuconazole and terbuthylazine) was measured in biofilms despite the short exposure time (few minutes) in our open-flow microcosm approach. This research demonstrated the stream biofilms capacity to adsorb hydrophobic pesticides even in stressed drought environments.https://hal.inrae.fr/hal-04173358[hal-04173358] Mixed Light and Biocide Pollution Affects Lipid Profiles of Periphyton Communities in Freshwater Ecosystems2023-07-28T19:56:45.000+02:002023-07-28T19:56:45.000+02:00[...]https://hal.inrae.fr/hal-04173352[hal-04173352] Impacts of urban stressors on freshwater biofilms2023-07-28T19:56:44.000+02:002023-07-28T19:56:44.000+02:00Abstract In urban areas, aquatic ecosystems and their communities are exposed to numerous stressors of various natures (chemical and physical), which impacts are often poorly documented. In epidemic context such as the COVID 19 pandemic, the use of biocides such as the dodecylbenzyldimethylammonium chloride (BAC 12) increased, resulting in an expectable increase in their concentrations in urban aquatic ecosystems. This compound is known to be toxic to most aquatic organisms. Besides, artificial light at night (ALAN) is increasing globally, especially in urban areas. ALAN may have a negative impact on photosynthetic cycles of periphytic biofilms, which in turn may result in changes in their metabolic functioning. Moreover, studies suggest that exposure to artificial light could increase the biocidal effect of BAC 12 on biofilms. The present study investigates the individual and combined effects of BAC 12 and/or ALAN on the functioning and structure of photosynthetic biofilms. We exposed biofilms to a nominal concentration of 30 mg.L-1 of BAC 12 and/or ALAN for 10 days. BAC 12 had a negative impact on biofilm functioning by decreasing the amount and the quality of photosynthetic pigments, resulting in a >90% decrease in photosynthetic efficiency after 2 days of exposure. We also noted a strong decrease in glycolipids that resulted in a shift in lipid profiles. We found no significant effect of ALAN on the endpoints assessed and no interaction between the two stress factors. Graphical abstracthttps://hal.inrae.fr/hal-04173350[hal-04173350] Urban stressors impact lipid profiles in freshwater periphytic communities2023-07-28T19:56:43.000+02:002023-07-28T19:56:43.000+02:00The composition of lipids in algae are significantly influenced by environmental factors, including light intensity. Exposure to organic and inorganic contaminants can also disrupt the synthesis of fatty acids, changing the lipid composition of microalgae in periphytic communities. In this study, we looked at how a biocide such as dodecylbenzyldimethylammonium chloride (BAC 12) and two photoperiod durations can affect a biofilm's polar lipidome in a microcosm experiment. The heterotrophic compartment appeared to be raised by exposure to BAC 12 at the expense of phototrophic organisms. Additionally, the overall decline in polyinsaturated fatty acids indicated that the biofilm's phototrophic organisms were all severely impacted. However, it may be difficult to differentiate the effects of contamination from those of light, since there was no observable effect of photoperiods on the conventional fatty acid determination. The molecular species composition of both glycolipids and phospholipids was investigated in additional multivariate analyses. It was suggested that some molecular species may serve as more specific markers of light duration at the biofilm scale. Lastly, we recommend applying a similar lipidomic approach with monospecific cultures of microalgal strains in future research to support these findings, as the methodology used in this study would be applicable to other biofilm-derived microorganisms.https://hal.science/hal-04173305[hal-04173305] Periphytic and sediment microbiomes in aquatic ecotoxicology: current challenges and perspectives2023-07-28T17:55:10.000+02:002023-07-28T17:55:10.000+02:00One major challenge of ecotoxicology is to better understand the causal links between exposure to chemical mixtures and the impairment of ecosystem functions and services in a multi-stress context. To this aim, aquatic microbial communities are increasingly used because of their high taxonomic and functional diversity and their key role in multiple ecosystem processes. Hence, the last decades have seen the implementation of in situ and laboratory experiments associated to the development of various descriptors at the physiological/functional and structural levels to unravel the response of these assemblages to various chemical stresses (i.e. macropollutants, organic and inorganic micropollutants, and to further improve biomonitoring of freshwater ecosystem chemical and ecological qualities. Despite increasing knowledge, a strong research effort is still needed to gain understanding of acclimation/adaptation/tolerance mechanisms to better assess and even predict the taxonomic and functional resilience of these communities facing chemical stresses in the global change context and further develop specific biological markers of water quality impairment. Current challenges include (i) a better understanding of the links of biological responses throughout temporal scale (from early responses to chronic) and biological organization (from molecular to individual, population and community responses), (ii) an assessment of the role of phenotypic plasticity and functional redundancy in community resilience to chemical stresses under global change. Such an assessment would be facilitated by the definition of baseline variability, which needs the identification of the environmental factors that drive the spatial and temporal heterogeneity in microbial communities, at both structural and functional levels. During the last two decades, research units from INRAE (former Cemagref, Irstea) have widely contributed to the field of microbial ecotoxicology focusing on periphytic and sediment microbial communities to address both fundamental and practical research questions along the exposure-fate-effects continuum. These researches overall support a better understanding of the role of aquatic microbial communities in the fate of organic and inorganic chemicals (toxicokinetic) and their response to chemical exposure at structural and functional levels (toxicodynamic). These researches also strongly support the improvement of biomonitoring of the chemical and ecological quality of contaminated aquatic ecosystems. For both purpose, numerous structural (e.g. teratogenesis, distribution of tolerant vs sensitive species) and functional (e.g. tolerance and biodegradation capacities) have been developed and implemented under controlled conditions and in the field. The development and implementation of innovative omics approaches are currently tested as potential early and sensitive markers of exposure and effects at the community level (e.g. metabolomics, lipidomics). Current advantages and limitations of these approaches will be illustrated and discussed based on recent and ongoing projects.https://hal.science/hal-04173298[hal-04173298] Identification et écotoxicité des produits de transformation des pesticides dans les milieux aquatiques2023-07-28T17:55:09.000+02:002023-07-28T17:55:09.000+02:00Une fois appliquées pour protéger les cultures, les substances actives de pesticides sont soumises à divers processus biotiques et abiotiques qui gouvernent leur devenir et leur transfert dans les différents compartiments de l’environnement (sol, eau, air). Les pesticides peuvent s’y dégrader en produits de transformation (TP), et les processus de dégradation et de transfert des TP sont variables dans le temps et l’espace, en fonction de la période d’application de la molécule mère, de ses caractéristiques et des conditions physico-chimiques du milieu. Les TP, bien que peu recherchés, sont potentiellement très nombreux [1], et présents à faibles teneurs dans les milieux aquatiques. L’écotoxicité des TP est encore peu étudiée, mais diverses études indiquent qu’ils peuvent avoir un potentiel écotoxique différent de la substance active mère [2]. A ce jour, bien que l’importance des TP du point de vue toxicologique, écotoxicologique ou environnemental soit régulièrement mise en avant, seuls quelques TP sont bien identifiés [1]. Il apparait donc un besoin d’améliorer les connaissances sur les processus de formation de ces TP, leur devenir, voire leurs effets dans l’environnement et les prendre en compte dans des modèles, notamment ceux utilisés dans des approches réglementaires [3]. Dans ce contexte, le projet TAPIOCA, co-financé par l’Office Français de la Biodiversité (OFB) dans le cadre de l’APR Ecophyto II+ « Santé écosystèmes », poursuit trois objectifs complémentaires : i) mettre au point des méthodes analytiques sensibles pour la recherche et l’identification de TP de pesticides dans les milieux aquatiques afin de mieux caractériser leur occurrence ; ii) améliorer les connaissances sur les effets d’une sélection de pesticides et de TP associés, sur les communautés microbiennes et les macroinvertébrés aquatiques ; et iii) tester l’apport d’outils de prédiction des propriétés de dissipation et de transferts hydriques de TP de pesticides pour mieux cerner leur potentiel de présence dans les milieux naturels (sol, nappe superficielle, cours d’eau) en petits bassins agricoles. Nous présentons ici quelques résultats marquants du projet, associant des approches analytiques, écotoxicologiques et de modélisation, pour améliorer la caractérisation des niveaux d’exposition chronique aux TP de pesticides sélectionnés (le fongicide tébuconazole, l’insecticide fénoxycarbe et l’herbicide terbuthylazine), et des effets biologiques associés pour différents organismes aquatiques non-cibles (communautés microbiennes, macroinvertébrés). Des listes étendues de TP potentiellement formés dans l’environnement ont été construites à partir de la bibliographie et de logiciels de prédiction (ex. pour le tébuconazole avec 291 TP uniques, [4]). Des analyses « suspectées » par chromatographie couplée à la spectrométrie de masse haute résolution (LC-HRMS) ont été mises en œuvre, en s’appuyant sur ces listes, pour identifier des TP présents dans des échantillons prélevés in situ. L’apport de la chromatographie bidimensionnelle 2D-LC-HRMS a également été évalué pour améliorer l’identification des TP dans les matrices environnementales. Des expérimentations en microcosmes avec des organismes aquatiques (périphyton, communautés microbiennes d’hyphomycètes ou gammares) ont permis d’évaluer les effets de plusieurs scénarios d’exposition aux pesticides et TP associés sur différents descripteurs biologiques. Les premiers résultats montrent globalement une toxicité moindre des TP comparativement aux trois molécules mères sur les organismes étudiés. Le croisement des résultats issus des différentes échelles d’études (laboratoire, terrain) et des approches expérimentales et de modélisation apporte des informations précieuses pour améliorer les niveaux de connaissances sur la présence et les effets écotoxiques des produits de transformation de contaminants organiques encore très méconnus. Références : [1] Anagnostopoulou K., Nannou C., Evgenidou E., Lambropoulou D. (2022). Overarching issues on relevant pesticide transformation products in the aquatic environment: A review. doi.org/10.1016/j.scitotenv.2021.152863 [2] Chibwe L., Titaley I.A., Hoh E., Simonich S.L.M. (2017). Integrated Framework for Identifying Toxic Transformation Products in Complex Environmental Mixtures. doi/10.1021/acs.estlett.6b00455 [3] Gassmann, M. (2021). Modelling the fate of pesticide transformation products from plot to catchment scale — State of knowledge and future challenges. doi: 10.3389/fenvs.2021.717738 [4] Rocco K., Margoum C., Richard L., Coquery M. (2022). Enhanced database creation with in silico workflows for suspect screening of unknown tebuconazole transformation products in environmental samples by UHPLC-HRMS. doi.org/10.1016/j.jhazmat.2022.129706https://twitter.com/MaryamKhalili62/status/1684942278798848000🌿🍇🤳 Exploring nature's secrets! 🌞🔬 Sampling grapevine berries for metabolomic analysis all on my own during this Summer Holiday. 🍇📊 Exciting to unrave...2023-07-28T17:01:58.000+02:002023-07-28T17:01:58.000+02:00🌿🍇🤳 Exploring nature's secrets! 🌞🔬 Sampling grapevine berries for metabolomic analysis all on my own during this Summer Holiday. 🍇📊 Exciting to unravel the hidden compounds in these delicious fruits! @UMREGFV @GPR_BPS @BdxMetabolome pic.twitter.com/JCxCTH3Ia4
🌿🍇🤳 Exploring nature's secrets! 🌞🔬 Sampling grapevine berries for metabolomic analysis all on my own during this Summer Holiday. 🍇📊 Exciting to unravel the hidden compounds in these delicious fruits! @UMREGFV @GPR_BPS @BdxMetabolome pic.twitter.com/JCxCTH3Ia4
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Maryam Khalili (@MaryamKhalili62)https://hal.science/hal-04172925[hal-04172925] Combined effect of time, temperature and light intensity on the metabolome of the model green microalgae (Scenedesmus costatus) in the global change context2023-07-28T12:52:25.000+02:002023-07-28T12:52:25.000+02:00In the context of the global change, aquatic environments are subject to temperature and luminosity increases. Green algae at the base of the trophic chain and through their key role in aquatic ecosystems of primary production and are very relevant for investigating the impact of temperature increase. This study concerns the characterization of the potential effect of a temperature difference of 18 and 23°C and a light intensity of 72 and 189 µmol.m-2.s-1 on a green algae using an untargeted metabolomics approach based on high resolution mass spectrometry. To do this, the strain Scenedesmus costatus common to French rivers was exposed during 7 days. Sampling took place on D0, D4 and D7.https://twitter.com/BdxMetabolome/status/1684821458613071872We analysed the metabolome of tomato fruits and focused on the most homeostatic metabolites. Several of them were hubs in metabolic pathways or had ...2023-07-28T09:01:52.000+02:002023-07-28T09:01:52.000+02:00We analysed the metabolome of tomato fruits and focused on the most homeostatic metabolites. Several of them were hubs in metabolic pathways or had a signalling role, and seemed regulated by complex changes in proteins and transcripts.
doi.org/10.1186/s12870…
We analysed the metabolome of tomato fruits and focused on the most homeostatic metabolites. Several of them were hubs in metabolic pathways or had a signalling role, and seemed regulated by complex changes in proteins and transcripts.
doi.org/10.1186/s12870…
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Bordeaux Metabolome (@BdxMetabolome)https://twitter.com/PetriacqP/status/1683440534629543937The Rio connection strikes again 🤘 during Bordeaux Summer School 2023 on redox and foodomics with @univbordeaux and @marilarraz !
@BdxMetabolome @INR...2023-07-24T13:34:34.000+02:002023-07-24T13:34:34.000+02:00The Rio connection strikes again 🤘 during Bordeaux Summer School 2023 on redox and foodomics with @univbordeaux and @marilarraz !
@BdxMetabolome @INRAE_NA_BDX @bdxPlantMetabo @Metabohub pic.twitter.com/IwN2JMhtxI
The Rio connection strikes again 🤘 during Bordeaux Summer School 2023 on redox and foodomics with @univbordeaux and @marilarraz !
@BdxMetabolome @INRAE_NA_BDX @bdxPlantMetabo @Metabohub pic.twitter.com/IwN2JMhtxI
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Dr Pierre Pétriacq (@PetriacqP)https://hal.inrae.fr/hal-04167438[hal-04167438] Soil metabolomics: A powerful tool for predicting and specifying pesticide sorption2023-07-20T18:49:32.000+02:002023-07-20T18:49:32.000+02:00Sorption regulates the dispersion of pesticides from cropped areas to surrounding water bodies as well as their persistence. Assessing the risk of water contamination and evaluating the efficiency of mitigation measures, requires fine-resolution sorption data and a good knowledge of its drivers. This study aimed to assess the potential of a new approach combining chemometric and soil metabolomics to estimate the adsorption and desorption coefficients of a range of pesticides. It also aims to identify and characterise key components of soil organic matter (SOM) driving the sorption of these pesticides. We constituted a dataset of 43 soils from Tunisia, France and Guadeloupe (West Indies), covering extensive ranges of texture, organic carbon and pH. We performed untargeted soil metabolomics by liquid chromatography coupled with high-resolution mass spectrometry (UPLC-HRMS). We measured the adsorption and desorption coefficients of three pesticides namely glyphosate, 2,4-D and difenoconazole for these soils. We developed Partial Least Square Regression (PLSR) models for the prediction of the sorption coefficients from the RT-m/z matrix and conducted further ANOVA analyses to identify, annotate and characterise the most significant constituents of SOM in the PLSR models. The curated metabolomics matrix yielded 1213 metabolic markers. The prediction performance of the PLSR models was generally high for the adsorption coefficients Kdads (0.3 < R2 < 0.8) and for the desorption coefficients Kfdes (0.6 < R2 < 0.8) but low for ndes (0.03 < R2 < 0.3). The most significant features in the predictive models were annotated with a confidence level of 2 or 3. The molecular descriptors of these putative compounds suggest that the pool of SOM compounds driving glyphosate sorption is reduced compared to 2,4-D and difenoconazole, and these compounds are generally more polar. This approach can provide estimates of the adsorption and desorption coefficients of pesticides, including polar pesticide, for contrasted pedoclimates.https://twitter.com/Laim_Ziz/status/1681299084508790785EMN Committee applications are open now! forms.gle/9Cm75rT2hVzBa7… Contribute to Metabolomics Society as Early-career researcher! #MetSoc2023 #MetSoc2...2023-07-18T15:45:13.000+02:002023-07-18T15:45:13.000+02:00EMN Committee applications are open now! forms.gle/9Cm75rT2hVzBa7… Contribute to Metabolomics Society as Early-career researcher! #MetSoc2023 #MetSoc2024 @EMN_MetSoc @MetabolomicsSoc @BdxMetabolome @IMN_2020 @TMIC_Canada @metabolomicaceu @SocietyNordic @swiss_society @LampsNetwork twitter.com/emn_metsoc/sta…
EMN Committee applications are open now! forms.gle/9Cm75rT2hVzBa7… Contribute to Metabolomics Society as Early-career researcher! #MetSoc2023 #MetSoc2024 @EMN_MetSoc @MetabolomicsSoc @BdxMetabolome @IMN_2020 @TMIC_Canada @metabolomicaceu @SocietyNordic @swiss_society @LampsNetwork twitter.com/emn_metsoc/sta…
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RT: Bordeaux Metabolome (@BdxMetabolome)https://hal.inrae.fr/hal-04155487[hal-04155487] NMR metabolite quantification of a synthetic urine sample: an inter-laboratory comparison of processing workflows2023-07-07T16:01:41.000+02:002023-07-07T16:01:41.000+02:00Introduction Absolute quantification of individual metabolites in complex biological samples is crucial in targeted metabolomic profiling. Objectives An inter-laboratory test was performed to evaluate the impact of the NMR software, peak-area determination method (integration vs. deconvolution) and operator on quantification trueness and precision. Methods A synthetic urine containing 32 compounds was prepared. One site prepared the urine and calibration samples, and performed NMR acquisition. NMR spectra were acquired with two pulse sequences including water suppression used in routine analyses. The pre-processed spectra were sent to the other sites where each operator quantified the metabolites using internal referencing or external calibration, and his/her favourite in-house, open-access or commercial NMR tool. Results For 1D NMR measurements with solvent presaturation during the recovery delay (zgpr), 20 metabolites were successfully quantified by all processing strategies. Some metabolites could not be quantified by some methods. For internal referencing with TSP, only one half of the metabolites were quantified with a trueness below 5%. With peak integration and external calibration, about 90% of the metabolites were quantified with a trueness below 5%. The NMRProcFlow integration module allowed the quantification of several additional metabolites. The number of quantified metabolites and quantification trueness improved for some metabolites with deconvolution tools. Trueness and precision were not significantly different between zgpr- and NOESYpr-based spectra for about 70% of the variables. Conclusion External calibration performed better than TSP internal referencing. Inter-laboratory tests are useful when choosing to better rationalize the choice of quantification tools for NMR-based metabolomic profiling and confirm the value of spectra deconvolution tools.https://twitter.com/BdxMetabolome/status/1676583375455281152It's dissection time for the @UNTWIST_H2020 project. Camelina fruits are now separated between seeds and siliques and ready for further analysis! pic....2023-07-05T15:26:40.000+02:002023-07-05T15:26:40.000+02:00It's dissection time for the @UNTWIST_H2020 project. Camelina fruits are now separated between seeds and siliques and ready for further analysis! pic.twitter.com/cDgBIimUuk
It's dissection time for the @UNTWIST_H2020 project. Camelina fruits are now separated between seeds and siliques and ready for further analysis! pic.twitter.com/cDgBIimUuk
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RT: Bordeaux Metabolome (@BdxMetabolome)https://hal.inrae.fr/hal-04144753[hal-04144753] Extensive variation of leaf specialized metabolite production in sessile oak ( Quercus petraea ) populations is to a large extent genetically determined but not locally adaptive2023-06-28T18:13:26.000+02:002023-06-28T18:13:26.000+02:00Specialized or secondary metabolites (SMs) play a key role in plant resistance against abiotic stresses and defences against bioaggressors. For example, in sessile oaks Quercus petraea , phenolics contribute to reduce herbivore damage and improve drought resistance. Here, we explored the natural variation of SMs in nine European provenances of sessile oaks and aimed to detect its underlying genetic bases. We sampled mature leaves from high and low branches on 225 sessile oak trees located in a common garden and used untargeted metabolomics to characterise the variation of 219 specialized metabolites. In addition, we used whole genome low-depth sequencing to genotype individuals for 1.4M genetic markers. We then performed genome-wide association analyses to identify the genetic bases underlying the variation of leaf SMs. We found that leaf SMs displayed extensive within-provenance variation, but very little differentiation between provenances. For ∼10% of the metabolites we detected, most of this variation could be explained by a single genetic marker. Our results suggest that genetic variation for most leaf SMs is unlikely to be locally adaptive, and that selective pressures may act locally to maintain diversity at loci associated with leaf SM variation within oak populations.https://hal.inrae.fr/hal-04144594[hal-04144594] Genome-wide association study of leaf specialized metabolites in sessile oak (Quercus petraea) provenances.2023-06-28T16:44:39.000+02:002023-06-28T16:44:39.000+02:00European white oaks are long-lived species and are one of the most important foundation species in European temperate forests. In the context of global climate change, droughts, heat waves and emerging biotic enemies such as insects and pathogens are putting populations and ecosystems at risk. Specialized metabolites play a key role in tree defenses against natural enemies and protection against abiotic stresses such as UV exposure and drought. Here, we used high-throughput MS-based metabolomics to explore the natural variation of over 100 leaf specialized metabolites in 25 sessile oaks from nine provenances, all growing in a common garden in France. Among the metabolites analyzed, which included mostly hydrolysable tannins and flavonoïds, very few displayed differentiation among provenances, of which 22 displayed clear bimodal distributions with phenotypic classes present at balanced frequencies in all provenances. To investigate the genetic bases of leaf specialized metabolites, we performed whole-genome low coverage (~10X) sequencing of all individuals phenotyped in order to perform genome-wide association mapping. We identified over 1.6 million genome-wide SNPs, which revealed little genetic differentiation among provenances. Linkage disequilibrium (r2) decayed below 0.2 over 2 kb, suggesting that our genome-wide SNPs were sufficient to capture most genetic variation. We performed a genome-wide association analysis for the leaf specialized metabolites, identified candidate genes and checked for signatures of selection along the genome. Our results suggest that (i) oak provenances display extensive variation for leaf specialized metabolites, (ii) this variation is to a great extent genetically determined, and (iii) variation of individual metabolites is governed by few major loci.https://hal.inrae.fr/hal-04064687[hal-04064687] The receptor kinase FERONIA regulates phosphatidylserine localization at the cell surface to modulate ROP signaling2023-04-11T16:35:45.000+02:002023-04-11T16:35:45.000+02:00Cells maintain a constant dialog between the extracellular matrix and their plasma membrane to fine tune signal transduction processes. We found that the receptor kinase FERONIA (FER), which is a proposed cell wall sensor, modulates phosphatidylserine plasma membrane accumulation and nano-organization, a key regulator of Rho GTPase signaling in Arabidopsis. We demonstrate that FER is required for both Rho-of-Plant 6 (ROP6) nano-partitioning at the membrane and downstream production of reactive oxygen species upon hyperosmotic stimulus. Genetic and pharmacological rescue experiments indicate that phosphatidylserine is required for a subset of, but not all, FER functions. Furthermore, application of FER ligand shows that its signaling controls both phosphatidylserine membrane localization and nanodomains formation, which, in turn, tunes ROP6 signaling. Together, we propose that a cell wall–sensing pathway controls via the regulation of membrane phospholipid content, the nano-organization of the plasma membrane, which is an essential cell acclimation to environmental perturbations.https://hal.science/hal-03990193[hal-03990193] Characterization of the metabolomic response of freshwater biofilms to urban wastewater effluents2023-02-15T12:23:08.000+01:002023-02-15T12:23:08.000+01:00Urban wastewater treatment plants (WWTPs) release large amounts of pollutants (e.g. chemicals, microbes) into aquatic environments that may impact exposed organisms. Among these organisms, aquatic biofilms, as a complex assemblage of microorganisms with a short life cycle (e.g. microalgae, bacteria) and by their key role in aquatic ecosystems (e.g. primary production), are relevant and increasingly used to investigate the impact of chemical contamination at the community level. Despite increasing knowledge on the impact of chemical stress on these communities, the underlying (molecular/biochemical) mechanisms remain poorly described while usual descriptors provide a partial picture of the phenotype. To tackle this issue, untargeted metabolomics approach is relevant through the simultaneous characterization of chemical exposure and the global response of the whole biofilm. In this context, this study focuses on the characterization of the potential impact of urban WWTPs on aquatic periphytic microbial communities by implementing an untargeted metabolomic approach. To do so, biofilm colonization/exposure was carried out during 4 weeks at upstream and downstream sites from three WWTPs along the main tributary of Arcachon Bay (Belin Béliet: upstream, Salles: intermediate; Mios: downstream). First, multivariate analyses (PCA and HCA) showed discrepancies in the metabolomics profile between the three WWTPs and between upstream and downstream site of each WWTP. This difference is more marked at the downstream site (Mios), likely because of increasing disturbances along the tributary (e.g detection of pesticides only on the downstream site). Moreover, the strong discrimination between upstream and downstream sites at Mios suggested that this WWTP is a source of pollutants. At this site, further univariate analysis combined to pathways analysis allowed preliminary annotation (i.e. based only on MS1) that highlighted a potential impact on the respiration and photosynthesis pathways. Overall, this study confirms the relevance of untargeted metabolomics to highlight potential impact of urban discharges on aquatic microbial communities.https://hal.science/hal-03990184[hal-03990184] Metabolomic insight in the responses of stream biofilms to the herbicide diuron2023-02-15T12:20:16.000+01:002023-02-15T12:20:16.000+01:00Regarding the increasing aquatic pollution, there is a need to establish the causality link between the exposure to chemicals and the effect(s) at the ecosystem level. To tackle this challenge, metabolomic allows the simultaneous characterization of all exposures and induced effects on cellular biomolecules (i.e. molecular phenotype). Also, periphytic biofilms are increasingly used because of their relevance to investigate the impact of multiple environmental stressors at the community level (function and structure). This study aims to investigate the metabolomics response of periphytic communities to a model herbicide in parallel of more usual functional (photosynthesis) and structural descriptors. To this end, stream biofilms colonized at a reference site were exposed to the diuron - a model compound for photosynthesis inhibition- at the laboratory under different controlled conditions. The metabolomics responses were assessed through an untargeted approach by using an UPLC-ToF system The results revealed the down regulation of two plant-specific fatty acids, the docosapentaenoic acid and the eicosapentaenoic acid in parallel of the inhibition of the photosynthetic activity. These are two omega-3 fatty acids that play a major in the sustainability of the trophic chain and so eco-systemic services since they are difficult to produce by higher trophic level (i.e. high metabolic cost). Overall, this study highlighted the relevance of untargeted metabolomic approach to improve knowledge about biochemica alteration associated to impairement of ecological function towards the discovery of ecosystem biomarkers.https://hal.science/hal-03990145[hal-03990145] Metabolomics insight in the response and tolerance of periphytic biofilms to wastewater effluent2023-02-15T12:17:35.000+01:002023-02-15T12:17:35.000+01:00Recent evidences highlighted the effect of urban effluent on the structure/functions of dowstream periphytic communities associated to increased tolerance to chemical stress. Nevertheless, the molecular mechanisms of these responses remain poorly understood while usual descriptors provide a partial picture of the phenotype of the communities. In this context, this study aims to gain knowledge about the molecular/biochemical responses of periphyton under urban stress through the implementation of untargeted metabolomics approach. To do so, following exposure in indoor channels connected to an urban effluent, the metabolomic responses of the biofilms were characterized in parallel of structural and functional responses. First, no marked effects were noted on the photosynthesis, respiration, primary/secondary production, as well as on biomass whereas exposure to the raw effluent led to tolerance acquisition to further chemical stress. Then, the metabolomic profiles showed discrepancies between all the conditions demonstrating a clear effect of the effluent on the molecular phenotype of the biofilms. Moreover, the clear separation between raw and ultrafiltrated conditions highlighted the potential contribution of the microbes from the effluent in the response. Such pattern paralleled with the shift in microbial diversity. The influence of the microbes was further confirmed through HCA showing that control and ultrafiltrated conditions were clustered together. Further trend analysis revealed up/down regulation on several pathways. Finally, statistical comparison between the metabolomic profiles of raw vs ultrafiltrated conditions highlighted that only 11% down- and 13% up-regulated signals contributed to the tolerance of the biofilm. Overall, this study shows that the metabolomic response is more sensitive than usual descriptors through its ability to discriminate all the experimental conditions. Moreover, it shows that urban microbes contribute to these various molecular/biochemical responses. Further investigations are ongoing to confirm the identity of the candidate metabolites and pathways and discriminate their link to urban microbes vs chemicals.https://hal.science/hal-03990045[hal-03990045] Toxicokinetic of a pesticides cocktail pulse on stream biofilms with different hydrological histories2023-02-15T11:54:35.000+01:002023-02-15T11:54:35.000+01:00Session: Microbial roles in contaminant fate and bioremediation The potential adverse effects of pesticides on stream ecosystems subjected to extreme hydrological events has been poorly explored. Therefore, there is an urgent need to increase our knowledge to propose suitable pesticide mitigation strategies in the context of global change scenarios affecting stream ecosystems. In this study, a microcosm experiment was performed to assess the dissipation kinetics of a pulse of pesticide mixture (glyphosate, aminomethylphosphonic acid (AMPA), tebuconazole, terbuthylazine and imidacloprid) by stream biofilms with a different hydrological history. The effects of two types of drought events caused by hydropeaking (short and more frequent droughts) and agricultural practices (long and less frequent droughts) on aquatic biofilm structure-function were evaluated and compared with an immersed control, before and after the pesticide cocktail pulse. Different biomass and functional parameters were analyzed in biofilms to determine the combined impact of droughts and pesticides, whereas the dissipation kinetics of each pesticide molecule of the cocktail was evaluated in the water as well as in the biofilm. Algal biomass measured as chlorophylla concentration was significantly lower under drought conditions compared to the control and these differences were more remarkable after the application of the pesticides cocktail. Microbial respiration per unit of microbial (algal and bacterial) carbon was higher in biofilms subjected to droughts, which tended to accumulate lower extracellular polymeric substances (EPS) comparing to the immersed control. Droughts also modified the organic matter decomposition fingerprint of stream biofilms, independently from pesticides cocktail exposure. The diffusion of glyphosate and AMPA into biofilms was lower than that of tebuconazole, terbuthylazine and imidacloprid and this was explained by the differences in molecules’ hydrophobicity. However, long droughts tended to further decrease the diffusion of pesticides per unit of biofilm EPS in comparison the short droughts and control treatments.https://hal.science/hal-03990007[hal-03990007] Metabolomic responses of freshwater periphytic microbiome to combined stress of artificial light at night (ALAN) and benzalkonium chloride2023-02-15T11:41:04.000+01:002023-02-15T11:41:04.000+01:00Urban activities can be a threat for ecosystem sustainability. For instance, there are numerous findings about the adverse effects of anthropogenic chemicals released from urban treatment plants on freshwater periphytic communities, which play key role in ecosystems function and associated services. Despite this increasing evidence, there a still a paucity of knowledge on the effect of chemicals combined to other anthropogenic stress. Among them, of particular concern is the Artificial Light At Night (ALAN). Thus, through ten days exposure of freshwater periphyton in controlled conditions, we have recently highlighted the combined effect of ALAN and benzalkonium chloride (i.e. main component of alcohol-based hand sanitizers) on photosynthetic function, diatoms morphology and pigment composition whereas the associated molecular/biochemical mechanisms/responses remained unknown. In this context, the present study aims to fill this gap of knowledge by providing metabolomic insights on this combined effect. To this end, following the same experiment the metabolome and the lipidome were characterized. In particular, high-resolution mass spectrometry based-untargeted metabolomics was implemented in order to provide a comprehensive picture of the microbial activities (i.e. molecular phenotype) and identify biochemical pathways involved in the physiological and morphological impairments. In addition, targeted analysis of key class of lipids (phospholipids, glycerolipids, fatty acids) was performed to highlight potential effect on energy storage and chloroplast/thylakoid membranes. Preliminary results show clear effect of both individual factors and their combination through the discovery of specific metabolome fingerprints and associated pathways that change over exposure time. Complementary analyses are still ongoing. The results highlight as well a shift in the composition of targeted lipid classes following exposure to (e.g. unsaturation rates of polar lipids). Overall, this study confirms the relevance of metabolomics/lipidomics approaches to provide mechanistic understanding of the response of environmental microbiomes to multiple stress, further supporting the discovery of biomarkers of ecosystem function impairment along the adverse outcomes pathway framework.https://hal.science/hal-03975152[hal-03975152] Sphingolipids are involved in insect egg-induced cell death in Arabidopsis2023-02-06T14:33:16.000+01:002023-02-06T14:33:16.000+01:00In Brassicaceae, hypersensitive-like programmed cell death (HR-like) is a central component of direct defenses triggered against eggs of the large white butterfly (Pieris brassicae). The signaling pathway leading to HR-like in Arabidopsis (Arabidopsis thaliana) is mainly dependent on salicylic acid (SA) accumulation, but downstream components are unclear. Here, we found that treatment with P. brassicae egg extract (EE) triggered changes in expression of sphingolipid metabolism genes in Arabidopsis and black mustard (Brassica nigra). Disruption of ceramide (Cer) synthase activity led to a significant decrease of EE-induced HR-like whereas SA signaling and reactive oxygen species levels were unchanged, suggesting that Cer are downstream activators of HR-like. Sphingolipid quantifications showed that Cer with C16:0 side chains accumulated in both plant species and this response was largely unchanged in the SA-induction deficient2 (sid2-1) mutant. Finally, we provide genetic evidence that the modification of fatty acyl chains of sphingolipids modulates HR-like. Altogether, these results show that sphingolipids play a key and specific role during insect egg-triggered HR-like.https://hal.science/hal-03938561[hal-03938561] Impact of membrane lipid polyunsaturation on dopamine D2 receptor ligand binding and signaling2023-01-13T18:32:29.000+01:002023-01-13T18:32:29.000+01:00Increasing evidence supports a relationship between lipid metabolism and mental health. In particular, the biostatus of polyunsaturated fatty acids (PUFAs) correlates with some symptoms of psychiatric disorders, as well as the efficacy of pharmacological treatments. Recent findings highlight a direct association between brain PUFA levels and dopamine transmission, a major neuromodulatory system implicated in the etiology of psychiatric symptoms. However, the mechanisms underlying this relationship are still unknown. Here we demonstrate that membrane enrichment in the n-3 PUFA docosahexaenoic acid (DHA), potentiates ligand binding to the dopamine D2 receptor (D2R), suggesting that DHA acts as an allosteric modulator of this receptor. Molecular dynamics simulations confirm that DHA has a high preference for interaction with the D2R and show that membrane unsaturation selectively enhances the conformational dynamics of the receptor around its second intracellular loop. We find that membrane unsaturation spares G protein activity but potentiates the recruitment of β-arrestin in cells. Furthermore, in vivo n-3 PUFA deficiency blunts the behavioral effects of two D2R ligands, quinpirole and aripiprazole. These results highlight the importance of membrane unsaturation for D2R activity and provide a putative mechanism for the ability of PUFAs to enhance antipsychotic efficacy.https://hal.inrae.fr/hal-03915351[hal-03915351] Coumarin biosynthesis genes are required after foliar pathogen infection for the creation of a microbial soil-borne legacy that primes plants for SA-dependent defenses2022-12-29T15:06:31.000+01:002022-12-29T15:06:31.000+01:00Plants deposit photosynthetically-fixed carbon in the rhizosphere, the thin soil layer directly around the root, thereby creating a hospitable environment for microbes. To manage the inhabitants of this nutrient-rich environment, plant roots exude and dynamically adjust microbe-attracting and -repelling compounds to stimulate specific members of the microbiome. Previously, we demonstrated that foliar infection of Arabidopsis thaliana by the biotrophic downy mildew pathogen Hyaloperonospora arabidopsidis ( Hpa ) leads to a disease-induced modification of the rhizosphere microbiome. Soil conditioned with Hpa -infected plants provided enhanced protection against foliar downy mildew infection in a subsequent population of plants, a phenomenon dubbed the soil-borne legacy (SBL). Here, we show that for the creation of the SBL, plant-produced coumarins play a prominent role as coumarin-deficient myb72 and f6’h1 mutants were defective in creating a Hpa -induced SBL. Root exudation profiles changed significantly in Col-0 upon foliar Hpa infection, and this was accompanied by a compositional shift in the root microbiome that was significantly different from microbial shifts occurring on roots of Hpa -infected coumarin-deficient mutants. Our data further show that the Hpa -induced SBL primes Col-0 plants growing in SBL-conditioned soil for salicylic acid (SA)-dependent defenses. The SA-signaling mutants sid2 and npr1 were unresponsive to the Hpa -induced SBL, suggesting that the protective effect of the Hpa -induced shift in the root microbiome results from an induced systemic resistance that requires SA-signaling in the plant.https://hal.inrae.fr/hal-03914288[hal-03914288] Genotype determines Arbutus unedo L. physiological and metabolomic responses to drought and recovery2022-12-28T12:43:48.000+01:002022-12-28T12:43:48.000+01:00Strawberry tree (Arbutus unedo) is a small resilient species with a circum-Mediterranean distribution, high ecological relevance in southern European forests and with several economical applications. As most orchards are usually installed on marginal lands where plants usually face severe drought, selecting plants that can better cope with water restriction is critical, and a better understanding of the tolerance mechanisms is required. Strawberry tree plants under drought follow a typical isohydric strategy, by limiting transpiration through stomata closure. However, the contribution of genotype and its bio-geographic origin on plant performance needs clarification, as well as the involvement of a specific metabolic reactions associated with the mechanical response. To test this hypothesis, several eco-physiological and biochemical parameters were assessed on different genotypes, and the metabolic profiles studied, including important stress-related phytohormones, on plants under different water regimes (plants watered to 70% and 18% field capacity) and a recovery assay. A contrasting drought tolerance was found in plants from different genotypes, associated with physiological and metabolic responses. Metabolomics revealed more than 500 metabolic features were differentially accumulated, including abscisic and salicylic acids, for the genotype with better performance under drought (A4). This genotype also recovered faster when the imposed stress was interrupted, thus indicating the relevance of metabolic adaptation under water deficit conditions. By correlating carbon assimilation with identified metabolites, some proved to be satisfactory predictors of plant performance under drought and might be used for marker assisted breeding. Therefore, our study proves the importance of genotype as a major selection criterion of resistant plants to drought and provides empirical knowledge of the metabolic response involved. We also hypothesized the involvement of phenolics on response mechanisms under drought, which is worth to be explored to shed light on the metabolic pathways involved in plant response to water stress.https://hal.inrae.fr/hal-03855200[hal-03855200] Impaired cell growth under ammonium stress explained by modeling the energy cost of vacuole expansion in tomato leaves2022-12-27T17:48:09.000+01:002022-12-27T17:48:09.000+01:00[...]https://hal.science/hal-03879922[hal-03879922] Peptide filtering differently affects the performances of XIC-based quantifcation methods2022-11-30T18:23:15.000+01:002022-11-30T18:23:15.000+01:00[...]https://hal.science/hal-03879730[hal-03879730] Presence/absence variations and SNPs equally contribute to the variations of protein and metabolite abundance2022-11-30T17:04:40.000+01:002022-11-30T17:04:40.000+01:00Understanding 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, which include insertion/deletion of large DNA sequences) 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 InDels, and molecular traits obtained from proteomics and metabolomics analyses to detect quantitative trait loci (QTLs). 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 was no difference between InDels and SNPs regarding the number and effect of the QTLs detected . Additionally, the QTLs detected by the two types of polymorphism were equally distributed in the two watering conditions. These preliminary results show that InDels are worse considering to detect new genetic regions of interest. They also suggest that InDels and SNPs equally contribute to molecular trait variation and response to drought stress.https://hal.science/hal-03878405[hal-03878405] Combining phenotypic, metabolome and proteome data to study maize response to a mild nitrogen deficit2022-11-29T19:03:19.000+01:002022-11-29T19:03:19.000+01:00To decipher the biochemical bases of nitrogen (N) utilization and metabolism of silage maize in relation to growth and productivity, an untargeted metabolomic (proton NMR- and LC-QTOF-MS based) and proteomic approach was conducted on leaves of 29 hybrids cultivated in the field under optimal and reduced N fertilization. The corresponding biochemical data were analyzed either individually (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 the underlying physiology concerning the plant response to a mild N deficit often occurring under agronomic conditions. The genetic diversity of the core panel of 29 European dent hybrids crossed to a flint tester was exploited to highlight common N-responsive metabolites and proteins in order to identify putative biological markers that could be used to pilot and rationalize N fertilization. The responses of metabolites, proteins, and yield-related traits to the reduced N treatment were also exploited to identify biochemical markers representative of a maize ideotype exhibiting better agronomic 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.https://hal.inrae.fr/hal-03864023[hal-03864023] Natural fluctuation of metabolome and photosynthetic yield sensitivity of a periphytic biofilm exposed to a model herbicide2022-11-21T17:02:07.000+01:002022-11-21T17:02:07.000+01:00The present study aims to characterize the changes of sensitivity of freshwater periphyton over months through the combined measurement of the photosynthetic yield (ΦPSII) and the metabolomics response based on high-resolution mass spectrometry (HRMS).https://hal.science/hal-03366412[hal-03366412] Biosynthesis and Functions of Very-Long-Chain Fatty Acids in the Responses of Plants to Abiotic and Biotic Stresses2022-11-21T11:59:09.000+01:002022-11-21T11:59:09.000+01:00Very-long-chain fatty acids (i.e., fatty acids with more than 18 carbon atoms; VLCFA) are important molecules that play crucial physiological and structural roles in plants. VLCFA are specifically present in several membrane lipids and essential for membrane homeostasis. Their specific accumulation in the sphingolipids of the plasma membrane outer leaflet is of primordial importance for its correct functioning in intercellular communication. VLCFA are found in phospholipids, notably in phosphatidylserine and phosphatidylethanolamine, where they could play a role in membrane domain organization and interleaflet coupling. In epidermal cells, VLCFA are precursors of the cuticular waxes of the plant cuticle, which are of primary importance for many interactions of the plant with its surrounding environment. VLCFA are also major components of the root suberin barrier, which has been shown to be fundamental for nutrient homeostasis and plant adaptation to adverse conditions. Finally, some plants store VLCFA in the triacylglycerols of their seeds so that they later play a pivotal role in seed germination. In this review, taking advantage of the many studies conducted using Arabidopsis thaliana as a model, we present our current knowledge on the biosynthesis and regulation of VLCFA in plants, and on the various functions that VLCFA and their derivatives play in the interactions of plants with their abiotic and biotic environment.https://hal.science/hal-03818861[hal-03818861] A combination of plasma membrane sterol biosynthesis and autophagy is required for shade-induced hypocotyl elongation2022-10-18T12:40:35.000+02:002022-10-18T12:40:35.000+02:00Plant growth ultimately depends on fixed carbon, thus the available light for photosynthesis. Due to canopy light absorption properties, vegetative shade combines low blue (LB) light and a low red to far-red ratio (LRFR). In shade-avoiding plants, these two conditions independently trigger growth adaptations to enhance light access. However, how these conditions, differing in light quality and quantity, similarly promote hypocotyl growth remains unknown. Using RNA sequencing we show that these two features of shade trigger different transcriptional reprogramming. LB induces starvation responses, suggesting a switch to a catabolic state. Accordingly, LB promotes autophagy. In contrast, LRFR induced anabolism including expression of sterol biosynthesis genes in hypocotyls in a manner dependent on PHYTOCHROME-INTERACTING FACTORs (PIFs). Genetic analyses show that the combination of sterol biosynthesis and autophagy is essential for hypocotyl growth promotion in vegetative shade. We propose that vegetative shade enhances hypocotyl growth by combining autophagy-mediated recycling and promotion of specific lipid biosynthetic processes.https://hal.inrae.fr/hal-03800373[hal-03800373] Décryptage métabolomique de la relation exposition-effet dans la réponse écosystémique des biofilms périphytiques dulçaquicoles à la pression chimique2022-10-06T18:21:37.000+02:002022-10-06T18:21:37.000+02:00[...]https://hal.inrae.fr/hal-03800021[hal-03800021] Potential role of aquatic macrophytes in the regulation of cyanobacterial blooms : Allelopathic approach2022-10-06T13:00:23.000+02:002022-10-06T13:00:23.000+02:00In a context of global change, the Aquitaine lake of Parentis-Biscarrosse (France) is subject to a double issue : on the one hand, the proliferation of two species of invasive aquatic macrophytes (E. densa and L. major) and, on the other hand, the upsurge of cyanobacteria blooms. Invasive macrophytes have a high growth rate and a very efficient vegetative reproduction. Recently, modern chemical approaches have shown that this reproductive success could be explained by the secretion of allelopathic compounds which affect the environmental communities. Moreover, studies have also shown that cyanobacteria would be the most sensitive algal group to this kind of interactions. The objective of this study is therefore to characterize by a non-targeted metabolomic approach, the effect of allelopathic compounds produced by E. densa and L. major on the toxigenic cyanobacteria M. aeruginosa. For this purpose, an experiment was carried out by putting in contact this strain of cyanobacteria and extracts of E. densa and L. major. The exposure took place in microcosms (glass balloons), during 96 hours and in a thermoregulated chamber. In a first step, measurements of chlorophyll concentration and photosynthetic yield were performed every day using a PhytoPAM. In a second step, the allelopathic relationships between our organisms were investigated through non-targeted metabolomic analyses. The results obtained indicate an inhibition of the photosynthetic yield of M. aeruginosa for macrophyte extract concentrations of 10g/L. The first results of the metabolomic analyses show a significant discrimination of our conditions, which suggests that there is a sensitivity of the M. aeruginosa metabolome to macrophyte extracts. Currently, the metabolomic analyses are still in progress.https://hal.inrae.fr/hal-03799950[hal-03799950] Metabolomic and photosynthesis responses of freshwater periphyton to natural vs synthetic fungicides2022-10-06T12:38:00.000+02:002022-10-06T12:38:00.000+02:00Agricultural activity leads to the release of thousands of compounds such as fungicides to aquatic ecosystems that might be harmful for exposed organisms such as periphytic microbial communities that play key role in ecosystem functions. Although previous studies have shown adverse effect of fungicides on the structure and functions of periphytic biofilms or their component, there is still a paucity of knowledge on short term molecular/biochemical mechanisms involved in such long term impairment on ecosystem function(s). This is strongly needed to support the discovery of biomarkers allowing the early and sensitive detection of the alteration of ecosystem function. To tackle this challenge, untargeted meta-metabolomics is an approach of choice since it provides a comprehensive picture of the biochemical activity and the phenotype (i.e. molecular phenotype through the identification of metabolites and their pathways) of a community, as a result of interactions with the environment. In this context, the present study aims to highlight the link between short-term response at the molecular level (metabolomics) and long term response at the function level (photosynthesis, microbial activity)of periphytic biofilms to the model fungicides copper (Cu, as natural fungicide) and tebuconazole (TBZ, as synthetic fungicide). To this end, short-term exposure (4h) to serial dilution of Cu and TBZ were first performed under controlled conditions (T°C 18°C, L/d 12:12). Following these exposure, photosynthetic yield using Phyto-PAM (as function) and metabolomics analysis were implemented. The results showed effect of copper on both photosynthetic activity and metabolic pattern whereas only metabolomics responded to tebuconazole. According this first experiment, two concentrations have been selected in order to further implement one month exposure to determine the kinetic of responses and their synchronism. This investigation will provide additional evidence about long-term effect on microbial activity.https://hal.inrae.fr/hal-03799923[hal-03799923] Metabolomics insights in the response and tolerance of stream biofilms to chemical stress in urban context2022-10-06T12:33:40.000+02:002022-10-06T12:33:40.000+02:00Recent evidences hilighted the effect of urban effluent on the structure and functions of dowstream periphytic microbial communities associated to increased tolerance to further chemical stress. Nevertheless, the underlying (molecular) mechanisms of these responses remain poorly understood while usual descriptors provide a partial picture of the phenotype of the communities under chemical stress. In this context, the present study aims to gain knowledge about the molecular/biochemical responses of biofilms under urban stress through the implementation of untargeted metabolomics approach. To do so, following exposure in indoor channels connected to a urban effluent, the metabolomic responses of the biofilms were characterized in parallel of structural and functional responses. First, no significant effects were noted on the photosynthesis, respiration, primary/secondary production, as well as on biomass whereas exposure to the raw effluent led to tolerance acquisition to further chemical stress likely associated to significant shift in the microbial diversity. Then, the metabolomic profiles showed discrepancies between all the tested conditions demonstrating a clear effect of the effluent on the molecular phenotype of the biofilms. Moreover, the clear separation between raw and ultrafiltrated conditions highlighted the potential contribution of the microbes from the effluent in the response. Such pattern paralleled with microbial diversity one. The strong influence of the microbes was further confirmed through HCA showing that control and ultrafiltrated conditions were clustered together.Further trends analysis combined with pathways analysis revealed potential impact on porphyrin and chlorophyll metabolism, among others. Finally, statistical comparison between the metabolomic profiles of raw vs ultrafiltrated conditions highlighted that only 11% down- and 18% up-regulated signals contributed to the tolerance of the biofilm. Overall, this study demonstrates that the metabolomic response is more sensitive than usual descriptors through its ability to discriminate all the experimental conditions. Moreover, our results showed that microbes strongly contribute to these various molecular/biochemical responses, as well as to tolerance acquisition. Further investigations are ongoing to confirm the identity of the candidate metabolites and pathways and discriminate their link to urban microbes vs chemicals associated to the tolerance acquisition to chemical stress.https://hal.inrae.fr/hal-03799916[hal-03799916] Characterization of the metabolomic response of freshwater biofilms to urban wastewater2022-10-06T12:30:08.000+02:002022-10-06T12:30:08.000+02:00Urban wastewater treatment plants (WWTPs) release large amounts of pollutants (e.g. chemicals, microbes) into aquatic environments that may impact exposed organisms. Among these organisms, aquatic biofilms as a complex assemblage of microorganisms with a short life cycle (e.g. microalgae, bacteria, etc.) and by their key role in aquatic ecosystems (e.g. primary production) are relevant and increasingly used to investigate the impact of chemical contamination at the community level. Despite increasing knowledge on the impact of chemical stress on these communities, the underlying (molecular/biochemical) mechanisms remain poorly described while usual descriptors provide a partial picture of phenotype. To tackle this issue, untargeted metabolomics approach is relevant through the simultaneous characterization of chemical exposure and the global response of the whole biofilm. In this context, this study focuses on the characterization of the potential impact of urban (WWTPs) on aquatic periphytic microbial communities by implementing an untargeted metabolomic approach. To do so, colonization/exposure was carried out during 4 weeks at upstream and downstream sites from three WWTPs along a tributary of the Arcachon Basin (Belin Beliet: upstream, Salles: intermediate; Mios: downstream). First, multivariate analyses (PCA and HCA) showed discrepancies in the metabolomics profile between the three WWTPs and between upstream and downtream site of each WWTP. This difference is more marked at the downstream site (Mios), likely because of increasing disturbances along the tributary (e.g detection of pesticides only on the downstream site). Moreover, the strong discrimination between upstream and dowstream sites at Mios suggested that this WWTP is a source of pollutants. At this site, further univariate analysis combined to pathways analysis allowed preliminary annotation (i.e. based only on MS1) that highlighted a potential impact on the respiration and photosynthesis pathways. Further investigations are ongoing to improve the annotation through the analysis of MS² spectra and by using an internal database. Overall, this study confirms the relevance of untargeted metabolomics to highlight potential impact of urban discharges on aquatic microbial communities.https://hal.inrae.fr/hal-03799905[hal-03799905] Characterization of the metabolomic response of freshwater biofilms to urban wastewater2022-10-06T12:25:21.000+02:002022-10-06T12:25:21.000+02:00[...]https://hal.inrae.fr/hal-03799899[hal-03799899] Optimization of the analysis of polar metabolites by implementing HILIC-HRMS based untargeted metabolomics2022-10-06T12:21:57.000+02:002022-10-06T12:21:57.000+02:00La métabolomique non ciblée ambitionne de fournir une vision du métabolome la plus complète possible regroupant des composés avec des propriétés physico-chimiques (e.g. poids moléculaire, log Kow) très variées. Si la spectrométrie de masse haute résolution (HRMS) propose de couvrir en théorie l’intégralité du spectre de composés, il convient de disposer de méthodologies de séparation chromatographique adéquates. Dans ce contexte, la chromatographie d’interaction hydrophile (HILIC) s’est beaucoup développée ces dernières années de par sa capacité à isoler/séparer efficacement les métabolites très polaires (e.g. glucides, acides aminés, acides organiques), mal déconvolués par une séparation en phase inverse -la méthode la plus répandue-. Dans ce contexte, cette étude vise à développer une méthode de séparation HILIC en métabolomique non-ciblée complémentaire de la séparation en phase inverse. Pour ce faire, un mélange de 32 métabolites couvrant différentes classes et polarités a été constitué afin de comparer 27 méthodes HILIC (i.e. combinaison de colonnes de tailles/technologies différentes et de gradient acide/neutre/basique et isocratique). Les 3 meilleures méthodes (BEH amide/HILIC acide, ZIC cHILIC basique) ont ensuite été appliquées à des matrices végétales dopées ou non (tomates et diatomées) afin d’évaluer l’effet matrice sur la séparation du mélange et entreprendre une caractérisation non-ciblée. Les résultats mettent en évidence une plus forte influence de la matrice sur la colonne BEH-amide. Ils montrent également une meilleure répartition des signaux le long du gradient lors du remplacement de l’eau par de l’éthanol avec une force éluante plus faible. La répétabilité et la reproductibilité des méthodes sont en cours d’analyse.https://hal.inrae.fr/hal-03781345[hal-03781345] Can metabolic mri be useful to image tomato metabolism?2022-09-20T13:51:17.000+02:002022-09-20T13:51:17.000+02:00[...]https://hal.inrae.fr/hal-03776494[hal-03776494] A project-scale map of metadata to improve future data management2022-09-13T19:32:41.000+02:002022-09-13T19:32:41.000+02:00Today, the intra-lab application of best practices in the metabolomics field usually guarantees an adequate data exploitation within a single lab. However, the growing interest in multi-analyses designs (e.g. complementary analytical platforms, variety of matrices, multi-omics), as well as the need of data sharing and reuse, increase the difficulty of data management. Indeed, managing the multiplicity and the heterogeneity of information involved is required to achieve relevant knowledge extraction from metabolomics data. Within the MetaboHUB national infrastructure, one objective is to optimize data handling, especially metadata, to facilitate large-scale analyses, multi-platforms studies, and data FAIRisation (Findability, Accessibility, Interoperability, Reusability). In particular, this fits in the MetaboHUB scientific roadmap that promotes the open science development in the field of metabolomics. In the context of metabolomic and lipidomic studies, data production and analysis come along with a large diversity of metadata (data of the data). To identify clearly-defined bottlenecks and targets for future improvement in data management, the objective of this work was to build a metadata map at the scale of a scientific project. Aiming for completeness, this map was constructed in a collaborative and multidisciplinary way involving chemists, biologists, data stewards as well as computer scientists, combining their respective experience and knowledge. Based on the resulting metadata map, targets (areas and topics) to be further investigated were identified, enabling the construction of transversal working groups at the consortium scale. In particular, this work enables to focus efforts on clearly defined issues to improve standardisation of practices regarding data management and metadata documentation. In conclusion, this collaborative map construction has been shown to be an efficient tool to draw a clear « where do we stand / where do we go » picture inside a national infrastructure like MetaboHUB regarding project-scale metadata. This facilitates the definition of a precise data management. Such an approach could be translated within other infrastructures, consortia and/or communities.https://hal.inrae.fr/hal-03757407[hal-03757407] To dissect or not to dissect for fruit spatial metabolomics: tissue profiling or MRI?2022-08-22T17:15:45.000+02:002022-08-22T17:15:45.000+02:00[...]https://hal.inrae.fr/hal-03757356[hal-03757356] To dissect or not to dissect for fruit spatial metabolomics : tissue profiling or MRI2022-08-22T17:07:51.000+02:002022-08-22T17:07:51.000+02:00[...]https://hal.inrae.fr/hal-03757279[hal-03757279] Spatial Localization of Metabollites In Fruits By NMR : Tissue Dissection and Metabolic Profiling Or Non-Invasive Whole Fruite Imaging ?2022-08-22T16:57:07.000+02:002022-08-22T16:57:07.000+02:00[...]https://hal.inrae.fr/hal-03756884[hal-03756884] MRSI vs CEST MRI to understand tomato metabolism during fruit development: Is there a better contrast ?2022-08-22T15:51:32.000+02:002022-08-22T15:51:32.000+02:00[...]https://hal.inrae.fr/hal-03728389[hal-03728389] NMR-based plant metabolomics at Bordeaux Metabolome Facility: 3 short stories2022-07-20T14:18:08.000+02:002022-07-20T14:18:08.000+02:00[...]https://hal.inrae.fr/hal-03728319[hal-03728319] RMN métabolomique, aliments & nutrition : quelques exemples de la plateforme Métabolome-MetaboHUB -Bordeaux2022-07-20T14:04:07.000+02:002022-07-20T14:04:07.000+02:00[...]https://hal.inrae.fr/hal-03728300[hal-03728300] Preliminary results of a MetaboHUB 2.0 inter-laboratory test on 1D 1H NMR metabolite quantification of a synthetic urine.2022-07-20T13:42:57.000+02:002022-07-20T13:42:57.000+02:00[...]https://hal.inrae.fr/hal-03728234[hal-03728234] NMR metabolomics to explore compositional changes in grape berry under heat stress2022-07-20T13:06:07.000+02:002022-07-20T13:06:07.000+02:00Climate change is increasing the frequency of heat waves in the vineyard that alter the metabolism and final composition of grape berries. Here, the metabolic response of short-term stress to high temperature was thus studied using fruiting cuttings of two Vitis vinifera L. varieties, Merlot and Cabernet Sauvignon, grown in a greenhouse. It is noteworthy that Merlot is known to be more sensitive to heat stress than Cabernet Sauvignon in the vineyard. The stress was localised in the cluster level, applied at the late veraison stage for 8 hours, and compared to a control condition. Subsequently, berries were harvested at 1, 2, 4 and 8 hours after the start of the experiment, and their skin and pulp profiled using 1 H-NMR metabolomics of semi-polar extracts. 1D 1 H-NMR spectra of pH-adjusted extracts were acquired with water presaturation at 500 MHz. The raw 1 H-NMR spectra were processed for ppm calibration, global and local baseline correction and local alignment using NMRProcFlow (v1.4.14) online tool (https://nmrprocflow.org). Each spectrum was divided into buckets, i.e. spectral variables, using Extraction of Relevant Variables for Analysis module (ERVA, resolution factor 0.0005, SNR >3) and normalised to total spectrum intensity after removing the pre-saturated residual water, methanol and solvent-impurities regions using NMRProcFlow to create the dataset matrix. After filtering with a SNR >10, this resulted in datasets of 276 variables quantified for the pulp, and 400 variables for the skin. Twenty-five major metabolites were annotated on the 1D spectra, based on 1D and 2D NMR experiments of pulp and skin extracts and comparison with an in-house spectral database, including four soluble sugars and polyol, six organic acids, thirteen amino acids and two phenolics. Two-way ANOVA and ANOVA-PCA of the 1 H-NMR fingerprints showed that the effect of variety was more important than the effect of heat stress and that one variety, Cabernet Sauvignon, was more responsive to elevated temperature in terms of number of variables impacted. The annotated metabolite most affected by stress in Cabernet Sauvignon was trans-caftaric acid, decreased in the pulp, and arginine, decreased in the skin. Overall, our preliminary results highlight spectral variables that could be used as biomarkers of the heat stress susceptibility and could further contribute to the identification of pathways affected by heat stress.https://hal.inrae.fr/hal-03728111[hal-03728111] TOWARDS A METABOLOMIC CHARACTERISATION OF THE GRAPEVINE RESPONSE TO FLAVESCENCE DORÉE INFECTION BY NMR AND LC-MS PROFILING2022-07-20T11:36:35.000+02:002022-07-20T11:36:35.000+02:00Flavescence dorée (FD) is a quarantine disease of grapevine, involving interactions between the plants, leafhopper vectors (phytophagous insect Scaphoideus titanus Ball, Cicadellidae family), and Flavescence dorée phytoplasma. This disease is a major threat to vineyard survival in different European grapegrowing areas. Differences in FD susceptibility between grapevine varieties exist, in terms of multiplication of the associated phytoplasma and its spread in the plant. Cabernet Sauvignon (CS) is highly susceptible to FD, whereas Merlot (M) is less susceptible. The objective of this project is to determine which primary and specialised metabolites are altered in grapevines following infection by FD phytoplasma under controlled conditions. Plants of CS and M were infected with FD phytoplasma on a single leaf via the natural insect vector S. titanus in a high containment greenhouse. Sampling took place 7-day, or 7-week post-inoculation. The leaves were harvested and immediately frozen in liquid N2 to quench metabolism. Phytoplasma titers were determined on fresh powder of each leaf. Metabolomic analyses were performed on a selection of the leaf sample extracts by 1 H-NMR, LC-LTQ/Orbitrap-HRMS, and LC-QqQ-MS. NMR spectra were acquired at 500 MHz and processed using NMRProcFlow (nmrprocflow.org). For both LC-MS, metabolites were separated by reverse-phase chromatography with a H2O/MeCN gradient. Untargeted experiments were performed on a UHPLC-ESI-LTQ/Orbitrap-MS with an ESI probe operated in positive mode and processed using MS Dial v4.7 8. Targeted experiments were performed on an LC-QqQ-MS system with a MRM method in positive or negative mode and the quantification by using calibration curves built with standards.The phytoplasma titre data, metabolite quantification data or metabolomic signatures of leaf samples were managed with ODAM tool.https://hal.inrae.fr/hal-03728068[hal-03728068] TOWARDS A METABOLOMIC CHARACTERISATION OF THE GRAPEVINE RESPONSE TO FLAVESCENCE DORÉE INFECTION BY NMR AND LC-MS PROFILING2022-07-20T10:47:00.000+02:002022-07-20T10:47:00.000+02:00[...]https://hal.science/hal-03718267[hal-03718267] Cytotoxic activity of Nep1-like proteins on monocots.2022-07-08T17:50:25.000+02:002022-07-08T17:50:25.000+02:00Necrosis- and ethylene-inducing peptide 1 (Nep1)-like proteins (NLPs) are found throughout several plant-associated microbial taxa and are typically considered to possess cytolytic activity exclusively on dicot plant species. However, cytolytic NLPs are also produced by pathogens of monocot plants such as the onion (Allium cepa) pathogen Botrytis squamosa. We determined the cytotoxic activity of B. squamosa BsNep1, as well as other previously characterized NLPs, on various monocot plant species and assessed the plant plasma membrane components required for NLP sensitivity. Leaf infiltration of NLPs showed that onion cultivars are differentially sensitive to NLPs, and analysis of their sphingolipid content revealed that the GIPC series A : series B ratio did not correlate to NLP sensitivity. A tri-hybrid population derived from a cross between onion and two wild relatives showed variation in NLP sensitivity within the population. We identified a quantitative trait locus (QTL) for NLP insensitivity that colocalized with a previously identified QTL for B. squamosa resistance and the segregating trait of NLP insensitivity correlated with the sphingolipid content. Our results demonstrate the cytotoxic activity of NLPs on several monocot plant species and legitimize their presence in monocot-specific plant pathogens.https://hal.inrae.fr/hal-02798242[hal-02798242] MetaboHUB and RFMF : two tools at the service of metabolomics and fluxomics in France2022-07-04T16:37:48.000+02:002022-07-04T16:37:48.000+02:00MetaboHUB and RFMF are two tools developed in France to serve the scientific community in Metabolomics and Fluxomics (M&F). The French Metabolomics and Fluxomics Network (RFMF, https://www.bordeaux.inra.fr/ifr103/reseau_metabolome/) is a scientific society which contributes to the development of M&F and more broadly to the overall analysis of metabolism in France through various actions: • Foster relationships between French researchers working in the world of M&F (public and private sectors); • Promote and structure education and training in M&F; • Organize and support the organization of conferences in France and abroad; • Encourage the participation of young researchers to national and international conferences through grants; • Allocate funds mission or prizes for accomplished work in M&F. MetaboHUB project (http://www.metabohub.fr/en/) aims at creating a national infrastructure that will place France among the European leaders for advanced research services in M&F. MetaboHUB provides equipment and services to academic research and industrial partners in nutrition, health, agriculture, environment and biotechnology. MetaboHUB is the merging of 4 existing facilities (Bordeaux, Paris-Saclay, Toulouse and Clermont-Ferrand) into a unique infrastructure sharing common regulations and complementary M&F tools. Besides providing state-of-the-art services and support to national and international projects, a major ambition of MetaboHUB is to develop innovative tools and methods to address critical biological questions. MetaboHUB will provide custom solutions for (i) high-throughput, quantitative technologies for biochemical phenotyping of large sets of samples and for systems biology through standardization and combination of state–of-art technologies, (ii) identification of metabolites in human biofluids, plants, microorganisms and animal cell extracts, through the implementation and maintenance of centralized and open spectral repositories for metabolome annotations, (iii) large-scale flux profiling and sub-cellular fluxomics through integration of analytical data from multiple analytical devices, (iv) access to high-impact services to the national scientific community and industrial actors and, (v) attracting and training a new generation of scientists and students.https://hal.inrae.fr/hal-03695453[hal-03695453] PeakForest: a multi-platform digital infrastructure for interoperable metabolite spectral data and metadata management2022-06-14T20:10:39.000+02:002022-06-14T20:10:39.000+02:00Introduction Accuracy of feature annotation and metabolite identification in biological samples is a key element in metabolomics research. However, the annotation process is often hampered by the lack of spectral reference data in experimental conditions, as well as logistical difficulties in the spectral data management and exchange of annotations between laboratories. Objectives To design an open-source infrastructure allowing hosting both nuclear magnetic resonance (NMR) and mass spectra (MS), with an ergonomic Web interface and Web services to support metabolite annotation and laboratory data management. Methods We developed the PeakForest infrastructure, an open-source Java tool with automatic programming interfaces that can be deployed locally to organize spectral data for metabolome annotation in laboratories. Standardized operating procedures and formats were included to ensure data quality and interoperability, in line with international recommendations and FAIR principles. Results PeakForest is able to capture and store experimental spectral MS and NMR metadata as well as collect and display signal annotations. This modular system provides a structured database with inbuilt tools to curate information, browse and reuse spectral information in data treatment. PeakForest offers data formalization and centralization at the laboratory level, facilitating shared spectral data across laboratories and integration into public databases. Conclusion PeakForest is a comprehensive resource which addresses a technical bottleneck, namely large-scale spectral data annotation and metabolite identification for metabolomics laboratories with multiple instruments. PeakForest databases can be used in conjunction with bespoke data analysis pipelines in the Galaxy environment, offering the opportunity to meet the evolving needs of metabolomics research. Developed and tested by the French metabolomics community, PeakForest is freely-available at https://github.com/peakforest .https://hal.inrae.fr/hal-03695147[hal-03695147] MRSI vs CEST MRI to understand tomato metabolism during fruit development: Is there a better contrast?2022-06-14T17:07:59.000+02:002022-06-14T17:07:59.000+02:00[...]https://hal.inrae.fr/hal-03692155[hal-03692155] Exposure & responses of freshwater microbial communities to natural and anthropogenic chemicals2022-06-09T17:30:40.000+02:002022-06-09T17:30:40.000+02:00[...]https://hal.inrae.fr/hal-03691889[hal-03691889] Metabolomics insight into the influence of environmental factors in responses of freshwater biofilms to the model herbicide diuron2022-06-09T16:25:56.000+02:002022-06-09T16:25:56.000+02:00Freshwater biofilms have been increasingly used during the last decade in ecotoxicology due to their ecological relevance to assess the effect(s) of environmental stress at the community level. Despite growing knowledge about the effect of various stressors on the structure and the function of these microbial communities, a strong research effort is still required to better understand their response to chemical stress and the influence of environmental stressors in this response. To tackle this challenge, untargeted metabolomics is an approach of choice because of its capacity to give an integrative picture of the exposure to multiple stress and associated effect as well as identifying the molecular pathways involved in these responses. In this context, the present study aimed to explore the use of an untargeted metabolomics approach to unravel at the molecular/biochemical level the response of the whole biofilm to chemical stress and the influence of various environmental factors in this response. To this end, archived high-resolution mass spectrometry data from previous experiments at our laboratory on the effect of the model photosynthesis inhibitor diuron on freshwater biofilm were investigated by using innovative solutions for OMICs data (e.g., DRomics) and more usual chemometric approaches (multivariate and univariate statistical analyses). The results showed a faster (1 min) and more sensitive response of the metabolome to diuron than usual functional descriptors, including photosynthesis. Also, the metabolomics response to diuron resulted from metabolites following various trends (increasing, decreasing, U/bell shape) along increasing concentration and time. This metabolomics response was influenced by the temperature, photoperiod, and flow. A focus on a plant-specific omega-3 (eicosapentaenoic acid) playing a key role in the trophic chain highlighted the potential relevance of metabolomics approach to establish the link between molecular alteration and ecosystem structure/functioning impairment but also how complex is the response and the influence of all the tested factors on this response at the metabolomics level. Altogether, our results underline that more fundamental researches are needed to decipher the metabolomics response of freshwater biofilm to chemical stress and its link with physiological, structural, and functional responses toward the unraveling of adverse outcome pathways (AOP) for key ecosystem functions (e.g., primary production).https://hal.inrae.fr/hal-03677495[hal-03677495] Identifying early metabolite markers of successful graft union formation in grapevine2022-05-24T18:40:25.000+02:002022-05-24T18:40:25.000+02:00Grafting is an important horticultural technique used for many crop species. However, some scion/rootstock combinations are considered as incompatible due to poor graft union formation and subsequently high plant mortality. The early identification of graft incompatibility could allow the selection of non-viable plants before planting and would have a beneficial impact on research and development in the nursery sector. In general, visible phenotypes of grafted plants (size, root number, etc.) are poorly correlated with grafting success, but some studies have suggested that some polyphenols could be used as markers of graft incompatibility several months or years after grafting. However, much of the previous studies into metabolite markers of grafting success have not included all the controls necessary to unequivocally validate the markers proposed. In this study, we quantified 73 primary and secondary metabolites in nine hetero-grafts and six homo-grafted controls 33 days after grafting at the graft interface and in both the scion and rootstock woody tissues. Certain biomarker metabolites typical of a high stress status (such as proline, GABA and pallidol) were particularly accumulated at the graft interface of the incompatible scion/rootstock combination. We then used correlation analysis and generalized linear models to identify potential metabolite markers of grafting success measured one year after grafting. Here we present the first attempt to quantitatively predict graft compatibility and identify marker metabolites (especially asparagine, trans-resveratrol, trans-piceatannol and alpha-viniferin) 33 days after grafting, which was found to be particularly informative for homo-graft combinations.https://hal.science/hal-03626801v2[hal-03626801] Isolation of Plasmodesmata membranes for lipidomic and proteomic analysis2022-04-01T12:30:45.000+02:002022-04-01T12:30:45.000+02:00Plasmodesmata (PD) are membranous intercellular nanochannels crossing the plant cell wall to connect adjacent cells in plants. Our understanding of PD function heavily relies on the identification of their molecular components, these being proteins or lipids. In that regard, proteomic and lipidomic analyses of purified PD represent a crucial strategy in the field. Here we describe a simple two-step purification procedure that allows isolation of pure PD-derived membranes from Arabidopsis suspension cells suitable for "omic" approaches. The first step of this procedure consists on isolating pure cell walls containing intact PD, followed by a second step which involves an enzymatic degradation of the wall matrix to release PD membranes. The PD-enriched fraction can then serve to identify the lipid and protein composition of PD using lipidomic and proteomic approaches, which we also describe in this method article.https://hal.inrae.fr/hal-03592312[hal-03592312] Critical assessment of metabolism and related growth and quality traits in trout fed spirulina-supplemented plant-based diets2022-03-01T12:11:53.000+01:002022-03-01T12:11:53.000+01:00[...]https://hal.inrae.fr/hal-03580569[hal-03580569] When dietary supplements meet metabolomics: A fast-evolving field—A follow-up of ABR volume 67: Metabolomics coming of age with its technological diversity2022-02-18T17:08:42.000+01:002022-02-18T17:08:42.000+01:00Volume 67 of Advances in Botanical Research "Metabolomics coming of age with its technological diversity" edited by Dominique Rolin (series Editors Jean-Pierre Jacquot and Pierre Gadal) was published in 2013 and featured 13 chapters including more than 40 authors with a range of expertise in biology, biochemistry, analytical chemistry, chemometrics and bioinformatics. This volume highlighted the technological diversity of metabolomics approaches that have revolutionized life sciences, more particularly plant biology, providing a deeper understanding of the multifaceted chemical and physiological variety of plant systems. Since its initiation, metabolomics has never failed to deliver further progress in research fields. In this anniversary volume 100 of ABR, a special focus is placed on the contribution of metabolomics to the study of dietary supplements, where Chemistry, Botanics and Physiology cross path. We also highlight the current challenges and future perspectives in this inspiring, fast-evolving area, which holds great promise for unraveling novel mechanisms by which food supplements benefit Human nutrition and health.https://hal.science/hal-03563439[hal-03563439] Phosphoinositides containing stearic acid are required for interaction between Rho GTPases and the exocyst to control the late steps of polarized exocytosis2022-02-09T17:51:55.000+01:002022-02-09T17:51:55.000+01:00Cell polarity is achieved by regulators such as small G proteins, exocyst members and phosphoinositides, with the latter playing a key role when bound to the exocyst proteins Sec3p and Exo70p, and Rho GTPases. This ensures asymmetric growth via the routing of proteins and lipids to the cell surface using actin cables. Previously, using a yeast mutant for a lysophosphatidylinositol acyl transferase encoded by the PSI1 gene, we demonstrated the role of stearic acid in the acyl chain of phosphoinositides in cytoskeletal organization and secretion. Here, we use a genetic approach to characterize the effect on late steps of the secretory pathway. The constitutive overexpression of PSI1 in mutants affecting kinases involved in the phosphoinositide pathway demonstrated the role of molecular species containing stearic acid in bypassing a lack of phosphatidylinositol-4-phosphate (PI(4)P) at the plasma membrane, which is essential for the function of the Cdc42p module. Decreasing the levels of stearic acid-containing phosphoinositides modifies the environment of the actors involved in the control of late steps in the secretory pathway. This leads to decreased interactions between Exo70p and Sec3p, with Cdc42p, Rho1p and Rho3p, because of disruption of the GTP/GDP ratio of at least Rho1p and Rho3p GTPases, thereby preventing activation of the exocyst.https://hal.science/hal-02408567[hal-02408567] Plant lipids: Key players of plasma membrane organization and function2021-12-20T12:10:23.000+01:002021-12-20T12:10:23.000+01:00The plasma membrane (PM) is the biological membrane that separates the interior of all cells from the outside. The PM is constituted of a huge diversity of proteins and lipids. In this review, we will update the diversity of molecular species of lipids found in plant PM. We will further discuss how lipids govern global properties of the plant PM, explaining that plant lipids are unevenly distributed and are able to organize PM in domains. From that observation, it emerges a complex picture showing a spatial and multiscale segregation of PM components. Finally, we will discuss how lipids are key players in the function of PM in plants, with a particular focus on plant-microbe interaction, transport and hormone signaling, abiotic stress responses, plasmodesmata function. The last chapter is dedicated to the methods that the plant membrane biology community needs to develop to get a comprehensive understanding of membrane organization in plants.https://hal.science/hal-03432678[hal-03432678] AP2/ERF transcription factors orchestrate very long chain fatty acid biosynthesis during Arabidopsis lateral root development2021-11-17T14:12:32.000+01:002021-11-17T14:12:32.000+01:00[...]https://hal.science/hal-03360663[hal-03360663] A Lipidomics Approach to Measure Phosphatidic Acid Species in Subcellular Membrane Fractions Obtained from Cultured Cells2021-10-01T01:00:47.000+02:002021-10-01T01:00:47.000+02:00[...]https://hal.science/hal-03349722[hal-03349722] Sphingolipids mediate polar sorting of PIN2 through phosphoinositide consumption at the trans-Golgi network2021-09-20T18:45:42.000+02:002021-09-20T18:45:42.000+02:00Abstract The lipid composition of organelles acts as a landmark to define membrane identity and specify subcellular function. Phosphoinositides are anionic lipids acting in protein sorting and trafficking at the trans -Golgi network (TGN). In animal cells, sphingolipids control the turnover of phosphoinositides through lipid exchange mechanisms at endoplasmic reticulum/TGN contact sites. In this study, we discover a mechanism for how sphingolipids mediate phosphoinositide homeostasis at the TGN in plant cells. Using multiple approaches, we show that a reduction of the acyl-chain length of sphingolipids results in an increased level of phosphatidylinositol-4-phosphate (PtdIns(4)P or PI4P) at the TGN but not of other lipids usually coupled to PI4P during exchange mechanisms. We show that sphingolipids mediate Phospholipase C (PLC)-driven consumption of PI4P at the TGN rather than local PI4P synthesis and that this mechanism is involved in the polar sorting of the auxin efflux carrier PIN2 at the TGN. Together, our data identify a mode of action of sphingolipids in lipid interplay at the TGN during protein sorting.https://hal.inrae.fr/hal-03321074[hal-03321074] Leaf metabolomic data of eight sunflower lines and their sixteen hybrids under water deficit2021-08-26T16:47:08.000+02:002021-08-26T16:47:08.000+02:00This 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.https://hal.inrae.fr/hal-02743576[hal-02743576] Vers une annotation RMN 1D et 2D ciblée à partir de matrices de référence2021-08-17T14:12:10.000+02:002021-08-17T14:12:10.000+02:00[...]https://hal.inrae.fr/hal-03320839[hal-03320839] Another Tale from the Harsh World: How Plants Adapt to Extreme Environments2021-08-16T17:09:47.000+02:002021-08-16T17:09:47.000+02:00The environmental fluctuations of a constantly evolving world can mould a changing context, often unfavourable to sessile organisms that must adjust their resource allocation between both resistance or tolerance mechanisms and growth. Plants bear the fascinating ability to survive and thrive under extreme conditions, a capacity that has always attracted the curiosity of humans, who have discovered and improved species capable of meeting our physiological needs. In this context, plant research has produced a great wealth of knowledge on the responses of plants to a range of abiotic stresses, mostly considering model species and/or controlled conditions. However, there is still minimal comprehension of plant adaptations and acclimations to extreme environments, which cries out for future investigations. In this article, we examined the main advances in understanding the adapted traits fixed through evolution that allowed for plant resistance against abiotic stress in extreme natural ecosystems. Spatio-temporal adaptations from extremophile plant species are described from morpho-anatomical features to physiological function and metabolic pathways adjustments. Considering that metabolism is at the heart of plant adaptations, a focus is given to the study of primary and secondary metabolic adjustments as well as redox metabolism under extreme conditions. This article further casts a critical glance at the main successes in studying extreme environments and examines some of the challenges and opportunities this research offers, especially considering the possible interaction with ecology and metaphenomics.https://hal.inrae.fr/hal-03107184[hal-03107184] Maize metabolome and proteome responses to controlled cold stress partly mimic early‐sowing effects in the field and differ from those of Arabidopsis2021-04-22T15:39:04.000+02:002021-04-22T15:39:04.000+02:00In Northern Europe, sowing maize one-month earlier than current agricultural practices may lead to moderate chilling damage. However, studies of the metabolic responses to low, non-freezing, temperatures remain scarce. Here, genetically-diverse maize hybrids (Zea mays, dent inbred lines crossed with a flint inbred line) were cultivated in a growth chamber at optimal temperature and then three decreasing temperatures for two days each, as well as in the field. Leaf metabolomic and proteomic profiles were determined. In the growth chamber, 50% of metabolites and 18% of proteins changed between 20 and 16°C. These maize responses, partly differing from those of Arabidopsis to short-term chilling, were mapped on genome-wide metabolic maps. Several metabolites and proteins varied similarly for all temperature decreases: seven MS-based metabolite signatures and two proteins involved in photosynthesis decreased continuously. Several metabolites or proteins increasing in the growth-chamber chilling conditions showed similar trends in the early-sowing field experiment, including trans-aconitate, three hydroxycinnamate derivatives, a benzoxazinoid, a sucrose synthase, lethal leaf-spot 1 protein, an allene oxide synthase, several glutathione transferases and peroxidases. Hybrid groups based on field biomass were used to search for the metabolite or protein responses differentiating them in growth-chamber conditions, which could be of interest for breeding. This article is protected by copyright. All rights reserved.https://hal.science/hal-03189252[hal-03189252] Biophysical analysis of the plant-specific GIPC sphingolipids reveals multiple modes of membrane regulation2021-04-03T01:15:41.000+02:002021-04-03T01:15:41.000+02:00[...]https://hal.inrae.fr/hal-03163223[hal-03163223] Putative imbalanced amino acid metabolism in rainbow trout long term fed a plant-based diet as revealed by 1 H-NMR metabolomics2021-03-09T11:35:56.000+01:002021-03-09T11:35:56.000+01:00The long-term effect of a plant (P)-based diet was assessed by proton nuclear magnetic resonance (1 H-NMR) metabolomics in rainbow trout fed a marine fish meal (FM)-fish oil (FO) diet (M), a P-based diet and a control commercial-like diet (C) starting with the first feeding. Growth performances were not heavily altered by long-term feeding on the P-based diet. An 1 H-NMR metabolomic analysis of the feed revealed significantly different soluble chemical compound profiles between the diets. A set of soluble chemical compounds was found to be specific either to the P-based diet or to the M diet. Pterin, a biomarker of plant feedstuffs, was identified both in the P-based diet and in the plasma of fish fed the P-based diet. 1 H-NMR metabolomic analysis on fish plasma and liver and muscle tissues at 6 and 48 h post feeding revealed significantly different profiles between the P-based diet and the M diet, while the C diet showed intermediate results. A higher amino acid content was found in the plasma of fish fed the P-based diet compared with the M diet after 48 h, suggesting either a delayed delivery of the amino acids or a lower amino acid utilisation in the P-based diet. This was associated with an accumulation of essential amino acids and the depletion of glutamine in the muscle, together with an accumulation of choline in the liver. Combined with an anticipated absorption of methionine and lysine supplemented in free form, the present results suggest an imbalanced essential amino acid supply for protein metabolism in the muscle and for specific functions of the liver.https://hal.inrae.fr/hal-03149808[hal-03149808] Untangling plant immune responses through metabolomics2021-02-23T13:14:22.000+01:002021-02-23T13:14:22.000+01:00Plant metabolomics is a set of fast-moving, analytical and chemometric tools and methods for plant functional genomics, phenotyping and systems biology. This multidisciplinary “omics” science can deliver qualitative and quantitative data that provide a detailed description of biochemical systems that are influenced by environmental changes, such as plant–pathogen interactions. This chapter examines key insights and recent outputs in the field of phytopathological metabolomics with a specific focus on the perturbations of primary compounds involved in central metabolism and infection-related metabolites including phytohormones. Priming of plant immune responses is also considered through the angle of metabolomics. Furthermore, the chapter highlights the recurring challenges in the distinction of host and pathogen metabolomes and the hurdles of metabolome annotation. The chapter concludes with perspectives indicating key avenues in ongoing efforts to decode metabolic landscapes of plants under biotic stress conditions.https://hal.science/hal-03136737[hal-03136737] Décryptage métabolomique de la réponse écosystémique des biofilms dulcicoles à la pollution chimique2021-02-09T22:32:52.000+01:002021-02-09T22:32:52.000+01:00[...]https://hal.inrae.fr/hal-03125729[hal-03125729] Precautions of a revisited protocol for 1D 1H-NMR profiling of plant samples from extract preparation to spectra processing. Preliminary results of an inter laboratory experiments.2021-01-29T17:33:49.000+01:002021-01-29T17:33:49.000+01:00[...]https://hal.inrae.fr/hal-03125712[hal-03125712] Combined metabolomic and proteomic profiling of maize leaf to reveal metabolic responses to cold temperatures2021-01-29T17:20:17.000+01:002021-01-29T17:20:17.000+01:00[...]https://hal.inrae.fr/hal-03125691[hal-03125691] NMRProcFlow: An easy GUI tool dedicated to 1D NMR spectra processing (1H & 13C) for Metabolomics2021-01-29T17:03:42.000+01:002021-01-29T17:03:42.000+01:00[...]https://hal.science/hal-01366193[hal-01366193] Highly Repeatable Dissolution Dynamic Nuclear Polarization for Heteronuclear NMR Metabolomics2021-01-21T15:53:32.000+01:002021-01-21T15:53:32.000+01:00At natural C-13 abundance, metabolomics based on heteronuclear NMR is limited by sensitivity. We have recently demonstrated how hyperpolarization by dissolution dynamic nuclear polarization (D-DNP) assisted by cross-polarization (CP) provides a reliable way of enhancing the sensitivity of heteronudear NMR in dilute mixtures of metabolites. In this Technical Note, we evaluate the precision of this experimental approach, a critical point for applications to metabolomics. The higher the repeatability, the greater the likelihood that one can detect small biologically relevant differences between samples. The average repeatability of our state-of-the-art D-DNP NMR equipment for samples of metabolomic relevance (20 mg dry weight tomato extracts) is 3.6% for signals above the limit of quantification (LOQ) and 6.4% when all the signals above the limit of detection (LOD) are taken into account. This first report on the repeatability of D-DNP highlights the compatibility of the technique with the requirements of metabolomics and confirms its potential as an analytical tool for such applications.https://inserm.hal.science/inserm-03103515[inserm-03103515] Ral GTPases promote breast cancer metastasis by controlling biogenesis and organ targeting of exosomes2021-01-08T11:56:54.000+01:002021-01-08T11:56:54.000+01:00Cancer extracellular vesicles (EVs) shuttle at distance and fertilize pre-metastatic niches facilitating subsequent seeding by tumor cells. However, the link between EV secretion mechanisms and their capacity to form pre-metastatic niches remains obscure. Using mouse models, we show that GTPases of the Ral family control, through the phospholipase D1, multi-vesicular bodies homeostasis and tune the biogenesis and secretion of pro-metastatic EVs. Importantly, EVs from RalA or RalB depleted cells have limited organotropic capacities in vivo and are less efficient in promoting metastasis. RalA and RalB reduce the EV levels of the adhesion molecule MCAM/CD146, which favors EV-mediated metastasis by allowing EVs targeting to the lungs. Finally, RalA, RalB and MCAM/CD146, are factors of poor prognosis in breast cancer patients. Altogether, our study identifies RalGTPases as central molecules linking the mechanisms of EVs secretion and cargo loading to their capacity to disseminate and induce pre-metastatic niches in a CD146 dependent manner.https://hal.inrae.fr/hal-03101885[hal-03101885] MRSI vs CEST MRI to understand tomato metabolism in ripening fruit: is there a better contrast?2021-01-07T13:20:46.000+01:002021-01-07T13:20:46.000+01:00Besides structural information, magnetic resonance imaging (MRI) is crucial to reveal the presence and gradients of metabolites in organs constituted of several tissues. In plant science, such knowledge is key to better understand fruit development and metabolism. Routine methods based on fixation for cytological studies or dissection for metabolite measurements induce biases and plant sample destruction. Magnetic resonance spectroscopy imaging (MSRI) leads to one NMR spectrum per pixel while chemical exchange saturation transfer (CEST) MRI allows mapping metabolites having exchangeable protons. As both methods present different advantages and drawbacks, we compared them to map metabolites in ripe tomato fruits. We demonstrated that MRSI was difficult to interpret due to large spatial chemical shift variations while CEST MRI produced promising image mapping of the main carbohydrates and amino acids. It showed that glucose/fructose was mostly located in the locular tissue, whereas glutamate/glutamine/GABA was found inside the columella.Graphical abstract.https://hal.inrae.fr/hal-03058513[hal-03058513] NMR-based metabolomics workflow for quality and effect assessment of alternative plant-based diets in rainbow trout.2020-12-11T19:31:07.000+01:002020-12-11T19:31:07.000+01:00[...]https://normandie-univ.hal.science/hal-02525074[hal-02525074] Chromogranin A preferential interaction with Golgi phosphatidic acid induces membrane deformation and contributes to secretory granule biogenesis2020-12-09T17:01:37.000+01:002020-12-09T17:01:37.000+01:00Chromogranin A (CgA) is a key luminal actor of secretory granule biogenesis at the trans‐Golgi network (TGN) level but the molecular mechanisms involved remain obscure. Here, we investigated the possibility that CgA acts synergistically with specific membrane lipids to trigger secretory granule formation. We show that CgA preferentially interacts with the anionic glycerophospholipid phosphatidic acid (PA). In accordance, bioinformatic analysis predicted a PA‐binding domain (PABD) in CgA sequence that effectively bound PA (36:1) or PA (40:6) in membrane models. We identified PA (36:1) and PA (40:6) as predominant species in Golgi and granule membranes of secretory cells, and we found that CgA interaction with these PA species promotes artificial membrane deformation and remodeling. Furthermore, we demonstrated that disruption of either CgA PABD or phospholipase D (PLD) activity significantly alters secretory granule formation in secretory cells. Our findings show for the first time the ability of CgA to interact with PLD‐generated PA, which allows membrane remodeling and curvature, key processes necessary to initiate secretory granule budding.https://hal.science/hal-02997549[hal-02997549] Plant lipids: Key players of plasma membrane organization and function2020-11-10T11:22:48.000+01:002020-11-10T11:22:48.000+01:00The Plasma Membrane (PM) is a key structure protecting the cell, regulating nutrient exchanges and acting as a control tower allowing the cell to perceive signals. Plasma comes from the greek πλάσμα meaning "which molds", meaning that the PM takes the shape of the cell by delimitating it. The PM harbors the appropriate signaling cascades allowing adaptive responses ensuring proper cell functions in a continuously fluctuating environment, crucial for cell survival. To address this challenge, the PM needs to be both stable and robust yet incredibly fluid and adaptable. This amazing combination of long-term stability and short-term dynamics in order to adapt to signals relies on its fascinating molecular organization. PMs are extremely complex systems, harboring many different molecular species of lipids in which heterogeneity is more likely to occur than homogeneity. In plants as in animals, the recent development of proteomics, lipidomics and methods to visualize lipids and proteins in vivo has greatly increased our knowledge of the PM. Corresponding Author Sébastien Mongrandhttps://hal.science/hal-02992204[hal-02992204] Immunopurification of Intact Endosomal Compartments for Lipid Analyses in Arabidopsis2020-11-06T13:01:24.000+01:002020-11-06T13:01:24.000+01:00[...]https://hal.inrae.fr/hal-02983822[hal-02983822] Plant Nitrate Reductases Regulate Nitric Oxide Production and Nitrogen-Fixing Metabolism During the Medicago truncatula–Sinorhizobium meliloti Symbiosis2020-10-30T13:14:42.000+01:002020-10-30T13:14:42.000+01:00Nitrate reductase (NR) is the first enzyme of the nitrogen reduction pathway in plants, leading to the production of ammonia. However, in the nitrogen-fixing symbiosis between legumes and rhizobia, atmospheric nitrogen (N 2) is directly reduced to ammonia by the bacterial nitrogenase, which questions the role of NR in symbiosis. Next to that, NR is the best-characterized source of nitric oxide (NO) in plants, and NO is known to be produced during the symbiosis. In the present study, we first surveyed the three NR genes (MtNR1, MtNR2, and MtNR3) present in the Medicago truncatula genome and addressed their expression, activity, and potential involvement in NO production during the symbiosis between M. truncatula and Sinorhizobium meliloti. Our results show that MtNR1 and MtNR2 gene expression and activity are correlated with NO production throughout the symbiotic process and that MtNR1 is particularly involved in NO production in mature nodules. Moreover, NRs are involved together with the mitochondrial electron transfer chain in NO production throughout the symbiotic process and energy regeneration in N 2-fixing nodules. Using an in vivo NMR spectrometric approach, we show that, in mature nodules, NRs participate also in the regulation of energy state, cytosolic pH, carbon and nitrogen metabolism under both normoxia and hypoxia. These data point to the importance of NR activity for the N 2-fixing symbiosis and provide a first explanation of its role in this process.https://hal.inrae.fr/hal-02936725[hal-02936725] Leaf metabolite profiling reveals biochemical diversities within wheat genetic resources2020-09-11T17:59:26.000+02:002020-09-11T17:59:26.000+02:00[...]https://hal.inrae.fr/hal-02927022[hal-02927022] Proton-NMR Metabolomics of Rainbow Trout Fed a Plant-Based Diet Supplemented with Graded Levels of a Protein-Rich Yeast Fraction Reveal Several Metabolic Processes Involved in Growth2020-09-01T14:06:36.000+02:002020-09-01T14:06:36.000+02:00Background Plant raw materials are commonly used in aquafeeds, as marine resources are unsustainable. However, full plant-based diets lead to poorer fish growth performance. Objective We aimed to understand the metabolic effects of a yeast fraction as a protein supplement in a plant-based diet and to integrate such effects with phenotypic traits as a new approach to assess the interest of this raw material. Methods Juvenile (49 g) rainbow trout (Oncorhynchus mykiss) were fed graded levels of a yeast protein-rich fraction (5% YST05, 10% YST10, 15% YST15) in a plant-based diet (PB) for 84 d. Final body weight, feed conversion ratio, and hepatosomatic and viscerosomatic indexes were measured. Plasma, liver, and muscle 1H-NMR fingerprints were analyzed with principal component analyses, and their metabolite patterns were clustered according to the yeast level to identify concomitant metabolic effects. A regression modeling approach was used to predict tissue metabolite changes from plasma fingerprints. Results In tissues, the patterns of metabolite changes followed either linear trends with the gradual inclusion of a yeast fraction (2 patterns out of 6 in muscle, 1 in liver) or quadratic trends (4 patterns in muscle, 5 in liver). Muscle aspartate and glucose (395 and 138% maximum increase in relative content compared with PB, respectively) revealing modification in energy metabolism, as well as modification of liver betaine (163% maximum increase) and muscle histidine (57% maximum decrease) related functions, indicates that the yeast fraction could improve growth in several ways. The highest correlation between measured and predicted metabolite intensities in a tissue based on plasma fingerprints was observed for betaine in liver (r = 0.80). Conclusions These findings herald a new approach to assess the plurality of metabolic effects induced by diets and establish the optimal level of raw materials. They open the way for using plasma as a noninvasive matrix in trout nutrition studies.https://hal.inrae.fr/hal-02914290[hal-02914290] The tomato Guanylate-Binding Protein SlGBP1 enables fruit tissue differentiation by maintaining endopolyploid cells in a non-proliferative state2020-08-11T17:35:23.000+02:002020-08-11T17:35:23.000+02:00Cell fate maintenance is an integral part of plant cell differentiation and the production of functional cells, tissues, and organs. Fleshy fruit development is characterized by the accumulation of water and solutes in the enlarging cells of parenchymatous tissues. In tomato (Solanum lycopersicum), this process is associated with endoreduplication in mesocarp cells. The mechanisms that preserve this developmental program, once initiated, remain unknown. We show here that analysis of a previously identified tomato ethyl methanesulfonate-induced mutant that exhibits abnormal mesocarp cell differentiation could help elucidate determinants of fruit cell fate maintenance. We identified and validated the causal locus through mapping-by-sequencing and gene editing, respectively, and performed metabolic, cellular, and transcriptomic analyses of the mutant phenotype. The data indicate that disruption of the SlGBP1 gene, encoding GUANYLATE BINDING PROTEIN1, induces early termination of endoreduplication followed by late divisions of polyploid mesocarp cells, which consequently acquire the characteristics of young proliferative cells. This study reveals a crucial role of plant GBPs in the control of cell cycle genes, and thus, in cell fate maintenance. We propose that SlGBP1 acts as an inhibitor of cell division, a function conserved with the human hGBP-1 protein.https://hal.inrae.fr/hal-02904041[hal-02904041] Biomass composition explains fruit relative growth rate and discriminates climacteric from non-climacteric species2020-07-21T17:46:52.000+02:002020-07-21T17:46:52.000+02:00To understand the mechanisms that link metabolism to phenotypes, which would help to target breeding strategies, eight fleshy fruit species were compared during development and ripening. Three herbaceous (eggplant, pepper, cucumber), three tree (apple, peach, clementine) and two vine (kiwifruit, grape) species were selected for their diversity. Fruit fresh weight and biomass composition including the major soluble and insoluble components were determined throughout fruit development and ripening. Best fitting models of fruit weight were used to estimate relative growth rate (RGR), which was significantly correlated with several biomass components, especially protein content (R=84) stearate (R=0.72), palmitate (R=0.72) and lignocerate (R=0.68). Moreover, the strong link between biomass composition and RGR was further evidenced by generalised linear models that predicted RGR with R-values exceeding 0.9. Fruit comparison also showed that climacteric fruit (apple, peach, kiwifruit) contained more non-cellulosic cell-wall-glucose and -fucose and starch than non-climacteric fruit. The rate of starch net accumulation was also higher in climacteric fruit. These results suggest that the way biomass is constructed has a major influence on performance, especially growth rate.https://hal.inrae.fr/hal-02810647[hal-02810647] The Lipid World Concept of Plant Lipidomics2020-06-06T10:43:43.000+02:002020-06-06T10:43:43.000+02:00Lipidomics has emerged as a new field that allows using various approaches to the chemical structures and the quantitative composition of more than a hundred lipid molecular species constituting the cellular lipidome. The increase of the performance of lipidomic analysis has resulted in recent developments in electrospray ionization mass spectrometry (ESI/MS) and rapid scanning tandem spectrometers that are capable of detecting and quantifying lipids at high sensitivity in an online high-performance chromatography. In this review, after a short description of the characteristic lipid classes of the plant kingdom, different approaches of 'lipidomics' will be addressed, including sample preparation (extractions, sample storage), MS analysis (ionization sources, shotgun lipidomics by direct infusion using tandem-in-space instruments and high-resolution systems and the use of separative methods before MS studies). Common fragmentation modes (MRM, CID including HCD) to determine molecular structures of lipid families in plants are also developed. The different principles of MS lipid analyses are briefly described and the different strategies using HPLC and MS/MS to quantify the different plant lipid molecular species are presented.https://hal.inrae.fr/hal-02666886[hal-02666886] Gene and Metabolite Regulatory Network Analysis of Early Developing Fruit Tissues Highlights New Candidate Genes for the Control of Tomato Fruit Composition and Development2020-05-31T11:34:41.000+02:002020-05-31T11:34:41.000+02:00Variations in early fruit development and composition may have major impacts on the taste and the overall quality of ripe tomato (Solanum lycopersicum) fruit. To get insights into the networks involved in these coordinated processes and to identify key regulatory genes, we explored the transcriptional and metabolic changes in expanding tomato fruit tissues using multivariate analysis and gene-metabolite correlation networks. To this end, we demonstrated and took advantage of the existence of clear structural and compositional differences between expanding mesocarp and locular tissue during fruit development (12–35 d postanthesis). Transcriptome and metabolome analyses were carried out with tomato microarrays and analytical methods including proton nuclear magnetic resonance and liquid chromatography-mass spectrometry, respectively. Pairwise comparisons of metabolite contents and gene expression profiles detected up to 37 direct gene-metabolite correlations involving regulatory genes (e.g. the correlations between glutamine, bZIP, and MYB transcription factors). Correlation network analyses revealed the existence of major hub genes correlated with 10 or more regulatory transcripts and embedded in a large regulatory network. This approach proved to be a valuable strategy for identifying specific subsets of genes implicated in key processes of fruit development and metabolism, which are therefore potential targets for genetic improvement of tomato fruit quality.https://hal.science/hal-02637416[hal-02637416] Different species of phosphatidic acid are produced during neuronal growth and neurosecretion2020-05-28T01:00:10.000+02:002020-05-28T01:00:10.000+02:00Although originally restricted to their structural role as major constituents of membranes, lipids are now well-defined actors to integrate intracellular or extracellular signals. Accordingly, it has been known for decades that lipids, especially those coming from diet, are important to maintain normal physiological functions and good health. This is especially the case to maintain proper cognitive functions and avoid neuronal degeneration. But besides this empiric knowledge, the exact molecular nature of lipids in cellular signaling, as well as their precise mode of action are only starting to emerge. The recent development of novel pharmacological, molecular, cellular and genetic tools to study lipids in vitro and in vivo has contributed to this improvement in our knowledge. Among these important lipids, phosphatidic acid (PA) plays a unique and central role in a great variety of cellular functions. This article will review the different findings illustrating the involvement of PA generated by phospholipase D (PLD) and diacylglycerol kinases (DGK) in the different steps of neuronal development and neurosecretion. We will also present lipidomic evidences indicating that different species of PA are synthesized during these two key neuronal phenomena.https://hal.inrae.fr/hal-02627233[hal-02627233] PhenoMeNal: processing and analysis of metabolomics data in the cloud2020-05-26T21:36:03.000+02:002020-05-26T21:36:03.000+02:00Background Metabolomics is the comprehensive study of a multitude of small molecules to gain insight into an organism's metabolism. The research field is dynamic and expanding with applications across biomedical, biotechnological, and many other applied biological domains. Its computationally intensive nature has driven requirements for open data formats, data repositories, and data analysis tools. However, the rapid progress has resulted in a mosaic of independent, and sometimes incompatible, analysis methods that are difficult to connect into a useful and complete data analysis solution. Findings PhenoMeNal (Phenome and Metabolome aNalysis) is an advanced and complete solution to set up Infrastructure-as-a-Service (IaaS) that brings workflow-oriented, interoperable metabolomics data analysis platforms into the cloud. PhenoMeNal seamlessly integrates a wide array of existing open-source tools that are tested and packaged as Docker containers through the project's continuous integration process and deployed based on a kubernetes orchestration framework. It also provides a number of standardized, automated, and published analysis workflows in the user interfaces Galaxy, Jupyter, Luigi, and Pachyderm. Conclusions PhenoMeNal constitutes a keystone solution in cloud e-infrastructures available for metabolomics. PhenoMeNal is a unique and complete solution for setting up cloud e-infrastructures through easy-to-use web interfaces that can be scaled to any custom public and private cloud environment. By harmonizing and automating software installation and configuration and through ready-to-use scientific workflow user interfaces, PhenoMeNal has succeeded in providing scientists with workflow-driven, reproducible, and shareable metabolomics data analysis platforms that are interfaced through standard data formats, representative datasets, versioned, and have been tested for reproducibility and interoperability. The elastic implementation of PhenoMeNal further allows easy adaptation of the infrastructure to other application areas and omics research domains.https://amu.hal.science/hal-02487236[hal-02487236] Metabolomic characterization of sunflower leaf allows discriminating genotype groups or stress levels with a minimal set of metabolic markers2020-05-26T10:34:16.000+02:002020-05-26T10:34:16.000+02:00This study underlines the potential of metabolic markers for discriminating genotype groups and environmental conditions. Their potential use for prediction is discussed.https://hal.inrae.fr/hal-02565229[hal-02565229] Using metabolomic data to predict Maize yield2020-05-06T14:00:14.000+02:002020-05-06T14:00:14.000+02:00[...]https://hal.inrae.fr/hal-02565126[hal-02565126] Polyphenol profiles of just pruned grapevine canes from wild vitis accessions and vitis vinifera cultivars2020-05-06T13:03:21.000+02:002020-05-06T13:03:21.000+02:00Grapevine canes are an abundant byproduct of the wine industry. The stilbene contents of Vitis vinifera cultivars have been largely studied, but little is known about the stilbene contents of wild Vitis accessions. Moreover, there have only been few studies on the quantification of other phenolic compounds in just pruned grapevine canes. In our study, we investigated the polyphenol profile of 51 genotypes belonging to 15 Vitis spp. A total of 36 polyphenols (20 stilbenes, 6 flavanols, 7 flavonols, and 3 phenolic acids) were analyzed by high-performance liquid chromatography coupled with a triple quadrupole mass spectrometer. Our results suggest that some wild Vitis accessions could be of interest in terms of the concentration of bioactive polyphenols and that flavanols contribute significantly to the antioxidant activity of grapevine cane extracts. To the best of our knowledge, this is the most exhaustive study of the polyphenolic composition of grapevine canes of wild Vitis spp.https://hal.inrae.fr/hal-02556668[hal-02556668] Characterization of GMO or glyphosate effects on the composition of maize grain and maize-based diet for rat feeding2020-04-28T13:22:15.000+02:002020-04-28T13:22:15.000+02:00[...]https://hal.science/hal-02510451[hal-02510451] First Community-Wide, Comparative Cross-Linking Mass Spectrometry Study2020-03-17T19:15:15.000+01:002020-03-17T19:15:15.000+01:00The number of publications in the field of chemical cross-linking combined with mass spectrometry (XL-MS) to derive constraints for protein three-dimensional structure modeling and to probe protein–protein interactions has increased during the last years. As the technique is now becoming routine for in vitro and in vivo applications in proteomics and structural biology there is a pressing need to define protocols as well as data analysis and reporting formats. Such consensus formats should become accepted in the field and be shown to lead to reproducible results. This first, community-based harmonization study on XL-MS is based on the results of 32 groups participating worldwide. The aim of this paper is to summarize the status quo of XL-MS and to compare and evaluate existing cross-linking strategies. Our study therefore builds the framework for establishing best practice guidelines to conduct cross-linking experiments, perform data analysis, and define reporting formats with the ultimate goal of assisting scientists to generate accurate and reproducible XL-MS results.https://hal.science/hal-02408581[hal-02408581] PUCHI regulates very long chain fatty acid biosynthesis during lateral root and callus formation2019-12-13T10:41:52.000+01:002019-12-13T10:41:52.000+01:00Lateral root organogenesis plays an essential role in elaborating plant root system architecture. In Arabidopsis, the AP2 family transcription factor PUCHI controls cell proliferation in lateral root primordia. To identify potential targets of PUCHI, we analyzed a time course transcriptomic dataset of lateral root formation. We report that multiple genes coding for very long chain fatty acid (VLCFA) biosynthesis enzymes are induced during lateral root development in a PUCHI-dependent manner. Significantly, several mutants perturbed in VLCFA biosynthesis show similar lateral root developmental defects as puchi-1. Moreover, puchi-1 roots display the same disorganized callus formation phenotype as VLCFA biosynthesis-deficient mutants when grown on auxin-rich callus-inducing medium. Lipidomic profiling of puchi-1 roots revealed reduced VLCFA content compared with WT. We conclude that PUCHI-regulated VLCFA biosynthesis is part of a pathway controlling cell proliferation during lateral root and callus formation.https://hal.science/hal-02179541[hal-02179541] Apport de la métabolomique par 1H-RMN pour le développement de nouveaux aliments chez la truite arc en ciel2019-07-10T22:07:21.000+02:002019-07-10T22:07:21.000+02:00Apport de la métabolomique par 1H-RMN pour le développement de nouveaux aliments chez la truite arc en ciel. 6. Journées de la Recherche Filière Piscicolehttps://hal.univ-lorraine.fr/hal-01557364[hal-01557364] Non-structural carbohydrates in woody plants compared among laboratories2017-07-06T12:33:20.000+02:002017-07-06T12:33:20.000+02:00Non-structural carbohydrates (NSC) in plant tissue are frequently quantified to make inferences about plant responses to environmental conditions. Laboratories publishing estimates of NSC of woody plants use many different methods to evaluate NSC. We asked whether NSC estimates in the recent literature could be quantitatively compared among studies. We also asked whether any differences among laboratories were related to the extraction and quantification methods used to determine starch and sugar concentrations. These questions were addressed by sending sub-samples collected from five woody plant tissues, which varied in NSC content and chemical composition, to 29 laboratories. Each laboratory analyzed the samples with their laboratory-specific protocols, based on recent publications, to determine concentrations of soluble sugars, starch and their sum, total NSC. Laboratory estimates differed substantially for all samples. For example, estimates for Eucalyptus globulus leaves (EGL) varied from 23 to 116 (mean = 56) mg g(-1) for soluble sugars, 6-533 (mean = 94) mg g-1 for starch and 53-649 (mean = 153) mg g-1 for total NSC. Mixed model analysis of variance showed that much of the variability among laboratories was unrelated to the categories we used for extraction and quantification methods (method category R-2 = 0.05-0.12 for soluble sugars, 0.10-0.33 for starch and 0.01-0.09 for total NSC). For EGL, the difference between the highest and lowest least squares means for categories in the mixed model analysis was 33 mg g-1 for total NSC, compared with the range of laboratory estimates of 596 mg g-1. Laboratories were reasonably consistent in their ranks of estimates among tissues for starch (r = 0.41-0.91), but less so for total NSC (r = 0.45-0.84) and soluble sugars (r = 0.11-0.83). Our results show that NSC estimates for woody plant tissues cannot be compared among laboratories. The relative changes in NSC between treatments measured within a laboratory may be comparable within and between laboratories, especially for starch. To obtain comparable NSC estimates, we suggest that users can either adopt the reference method given in this publication, or report estimates for a portion of samples using the reference method, and report estimates for a standard reference material. Researchers interested in NSC estimates should work to identify and adopt standard methods.https://hal.science/hal-01214152[hal-01214152] Workflow4Metabolomics: A collaborative research infrastructure for computational metabolomics2015-10-09T22:15:08.000+02:002015-10-09T22:15:08.000+02:00In the context of an emergent and fast evolving science, the development of various tools dedicated to metabolomic data processing and data analysis increased. Because metabolomic analyses require a variety of steps involving various disciplines from analytical chemistry to statistics and bioinformatics, it requires many skills and expertise. However, despite this abundance of tools, standardization is lacking in these diversity of programs, as well as infrastructure to handle and link the different steps of metabolomic analyses. We recently implemented Workflow4Metabolomics (W4M), a collaborative online platform hosting and providing a full pipeline for metabolomics from data preprocessing to annotation including statistical analysis. It is not designed to respond to only one specific type of metabolomic analysis, but to cover a maximum range of possible approaches - as metabolomics is a complex science that can be studied through various complementary analytical techniques. Thus, more than just gathering programs, W4M provides relevant combinations of generic and specific tools, a large part of which being developed and sustained by the partners providing this virtual research environment (VRE). Moreover, using Galaxy, a web-based platform technology, W4M provides modules from various sources and of various types. This platform allows hosted tools to be run and linked together via an instinctive and ergonomic interface, which is beneficial for both beginners and experts in metabolomics. W4M gets its strength from the collaboration of complementary teams from bioinformatics and metabolomics environment. Initiated by the collaboration between two platforms, it gathers today six research teams and platforms with a higher diversity in skills and expertise. It allows a continuous enrichment in the service provided, with addition of new modules and new possible workflows dedicated to cover a large scope of the increasing needs of the metabolomic community. Moreover, the ‘open-source’ aspect of this platform allows to open it to new collaborators bringing specific expertise that can be highlighted and disseminated in the metabolomic communityhttps://hal.science/hal-00874715[hal-00874715] Carotenoid profiling of tropical root crop chemotypes from Vanuatu, South Pacific2013-10-18T16:13:48.000+02:002013-10-18T16:13:48.000+02:00Tropical root and tuber crops are staple foods in developing countries where they are the main source of carbohydrates and a potential source of secondary metabolites such as carotenoids. Enhancing carotenoid content has considerable potential for improving human nutrition in these areas. Except for cassava and sweet potato, carotenoid content has not been evaluated in large germplasm collections. We describe a simple HPLC-DAD-based protocol for the reliable characterization of carotenoids in root crops. Less than 5% variation in carotenoid content was found among samples collected from tubers of the same plant or from clones of the same genotype. Carotenoids were evaluated in 153 accessions representing 10 different species. Each species had a specific profile of carotenoids, and accessions of the same species differed greatly in their individual content. The database assembled during this study represents a useful tool for nutritionists and breeders working on biofortification of root crops with carotenoids.