Plant central metabolism generates reactive oxygen species (ROS), which are key regulators that mediate signalling pathways involved in developmental processes and plant responses to environmental fluctuations. These highly reactive metabolites can lead to cellular damage when the reduction-oxidation (redox) homeostasis becomes unbalanced. Whilst decades of research have studied redox homeostasis in leaves, fundamental knowledge in fruit biology is still fragmentary. This is even more surprising when considering the natural profusion of fruit antioxidants that can process ROS and benefit human health. In this review, we explore redox biology in fruit and provide an overview of fruit antioxidants with recent examples. We further examine the central role of the redox hub in signalling during development and stress, with particular emphasis on ascorbate, also referred to as vitamin C. Progress in understanding the molecular mechanisms involved in the redox regulations that are linked to central metabolism and stress pathways will help to define novel strategies for optimising fruit nutritional quality, fruit production and storage.

Current crop yield of the best ideotypes is stagnating and threatened by climate change. In this scenario, understanding wild plant adaptations in extreme ecosystems offers an opportunity to learn about new mechanisms for resilience. Previous studies have shown species specificity for metabolites involved in plant adaptation to harsh environments.Here, we combined multispecies ecological metabolomics and machine learning-based generalized linear model predictions to link the metabolome to the plant environment in a set of 24 species belonging to 14 families growing along an altitudinal gradient in the Atacama Desert.Thirty-nine common compounds predicted the plant environment with 79% accuracy, thus establishing the plant metabolome as an excellent integrative predictor of environmental fluctuations. These metabolites were independent of the species and validated both statistically and biologically using an independent dataset from a different sampling year. Thereafter, using multiblock predictive regressions, metabolites were linked to climatic and edaphic stressors such as freezing temperature, water deficit and high solar irradiance.These findings indicate that plants from different evolutionary trajectories use a generic metabolic toolkit to face extreme environments. These core metabolites, also present in agronomic species, provide a unique metabolic goldmine for improving crop performances under abiotic pressure.

Tomato is a major crop suffering substantial yield losses from diseases, as fruit decay at a postharvest level can claim up to 50% of the total production worldwide. Due to the environmental risks of fungicides, there is an increasing interest in exploiting plant immunity through priming, which is an adaptive strategy that improves plant defensive capacity by stimulating induced mechanisms. Broad-spectrum defence priming can be triggered by the compound ß-aminobutyric acid (BABA). In tomato plants, BABA induces resistance against various fungal and bacterial pathogens and different methods of application result in durable protection. Here, we demonstrate that the treatment of tomato plants with BABA resulted in a durable induced resistance in tomato fruit against Botrytis cinerea, Phytophthora infestans and Pseudomonas syringae. Targeted and untargeted metabolomics were used to investigate the metabolic regulations that underpin the priming of tomato fruit against pathogenic microbes that present different infection strategies. Metabolomic analyses revealed major changes after BABA treatment and after inoculation. Remarkably, primed responses seemed specific to the type of infection, rather than showing a common fingerprint of BABA-induced priming. Furthermore, top-down modelling from the detected metabolic markers allowed for the accurate prediction of the measured resistance to fruit pathogens and demonstrated that soluble sugars are essential to predict resistance to fruit pathogens. Altogether, our results demonstrate that metabolomics is particularly insightful for a better understanding of defence priming in fruit. Further experiments are underway in order to identify key metabolites that mediate broad-spectrum BABA-induced priming in tomato fruit.

Ammonium (NH 4 +)-based fertilization efficiently mitigates the adverse effects of nitrogen fertilization on the environment. However, high concentrations of soil NH 4 + provoke growth inhibition, partly caused by the reduction of cell enlargement and associated with modifications of cell composition, such as an increase of sugars and a decrease in organic acids. Cell expansion depends largely on the osmotic-driven enlargement of the vacuole. However, the involvement of subcellular compartmentation in the adaptation of plants to ammonium nutrition has received little attention, until now. To investigate this, tomato (Solanum lycopersicum) plants were cultivated under nitrate and ammonium nutrition and the fourth leaf was harvested at seven developmental stages. The vacuolar expansion was monitored and metabolites and inorganic ion contents, together with intracellular pH, were determined. A data-constrained model was constructed to estimate subcellular concentrations of major metabolites and ions. It was first validated at the three latter developmental stages by comparison with subcellular concentrations obtained experimentally using nonaqueous fractionation. Then, the model was used to estimate the subcellular concentrations at the seven developmental stages and the net vacuolar uptake of solutes along the developmental series. Our results showed ammonium nutrition provokes an acidification of the vacuole and a reduction in the flux of solutes into the vacuoles. Overall, analysis of the subcellular compartmentation reveals a mechanism behind leaf growth inhibition under ammonium stress linked to the higher energy cost of vacuole expansion, as a result of alterations in pH, the inhibition of glycolysis routes and the depletion of organic acids.

Introduction 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.

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

Strawberry 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.

<p>During the process of photosynthesis, leaves capture CO<sub>2</sub> from the atmosphere and rapidly convert it into a diverse array of primary and secondary metabolites. Plants maintain a core set of metabolic pathways that ensure the basic building blocks of life that are available for each plant species to function. However, as plants evolved on land, they began to allocate this carbon (C) to innovative secondary metabolites and organs (cuticles, roots, wood) that protected them from abiotic stress (UV radiation, aridity, freezing) and biotic attack (fungal pathogens and insect/animal herbivory). As plants expanded over the land surface and occupied different niches, the amount of C fixed by plants varied and the types of secondary compounds synthesised by plants began to differ. Little is known about the metabolic profiles of the dominant European tree species and how variable the metabolomes of individual tree species are to changes in site conditions such as nutrient availability or soil moisture status. This study took advantage of recent advances in high-resolution mass spectrometry (HRMS) and bioinformatic tools to compare the leaf metabolomes of 14 commercially important tree species grown across three common gardens. Alongside the metabolic profiles, important chemical and morphological data were also collected from the trees during sampling, including targeted analysis of specific leaf metabolites such as proteins and phenolic compounds to obtain quantitative information on how their concentrations varied between tree species and site. Our analysis showed that the metabolomes of each tree species statistically differ from one another, and this dissimilarity was highly conserved at all three sites, even though tree growth and mortality rates varied between species and site. Our analysis also clearly highlighted distinct metabolome shifts between angiosperm and gymnosperm tree species, with angiosperms displaying greater concentrations of chlorophyll and amino acids alongside lower C/N ratios. These differences were also accompanied by discrepancies in an important set of secondary metabolites detected with the metabolomic technique. Furthermore, we also found that certain secondary compounds were essential in distinguishing between deciduous and evergreen species or families where targeted analysis could not detect significant differences. Our results indicate that temperate tree species may have conserved chemical 'fingerprints' that provide information on fundamental differences in the activity of certain plant metabolic pathways. This thus provides a promising tool to investigate how and why different plant species allocate C differently over the growing season and defend themselves against diverse abiotic and biotic pressures.</p>