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Author Correction: Demonstration of facilitation between microalgae to face environmental stress. In Scientific Reports, vol; 10, n°1, Article : 3557 ; DOI: 10.1038/s41598-020-59860-0 ; WOS:000563252500001 Author Correction: Demonstration of facilitation between microalgae to face environmental stress. In Scientific Reports, vol; 10, n°1, Article : 3557 ; DOI: 10.1038/s41598-020-59860-0 ; WOS:000563252500001The original version of this Article omitted an affiliation for Emna Krichen and the Acknowledgements section contained typographical errors and was incomplete. This erratum is available as an annex file.; International audience; Positive interactions such as facilitation play an important role during the biological colonization and species succession in harsh or changing environments. However, the direct evidence of such ecological interaction in microbial communities remains rare. Using common freshwater microalgae isolated from a High Rate Algal Pond HRAP treating wastewaters, we investigated with both experimental and modeling approaches the direct facilitation between two algal strains during the colonization phase. Our results demonstrate that the first colonization by microalgae under a severe chemical condition arose from the rapid growth of pioneer species such as Chlorella sorokiniana, which facilitated the subsequent colonization of low growth specialists such as Scenedesmus pectinatus. The pioneer species rapidly depleted the total available ammonia nitrogen favoring the specialist species initially inhibited by free ammonia toxicity. This latter species ultimately dominated the algal community through competitive exclusion under low nutrient conditions. We show that microbial successions are not only regulated by climatic conditions but also by interactions between species based on the ability to modify their growth conditions. We suggest that facilitation within the aquatic microbial communities is a widespread ecological interaction under a vast range of environmental stress.

Autophagy is an evolutionarily conserved process of cellular self-eating which emerged these last years as a major adaptive metabolic response to various stresses such as fasting, hypoxia, or environmental pollutants. However, surprisingly very few data is currently available on its role in fish species which are directly exposed to frequent environmental perturbations. Here, we report that the treatment of fasted trout hepatocytes with the autophagy inhibitor Bafilomycine A1 lowered the mRNA levels of many of the gluconeogenesis-related genes and increased those of genes involved in intracellular lipid stores. Concurrently, intracellular free amino acid levels dropped and the expression of the main genes involved in the endoplasmic reticulum (ER) stress exhibited a sharp increase in autophagy inhibited cells. Together these results highlight the strong complexity of the crosstalk between ER, autophagy and metabolism and support the importance of considering this function in future studies on metabolic adaptation of fish to environmental stresses.

This thesis aimed at investigating some of the possible evolutionary benefits of sexual reproduction using both a theoretical and an experimental approach. The first approach consisted in developing evolutionary quantitative genetic models for the evolution of sex. A first model (based on Fisher’s geometrical model) considers an arbitrary number of phenotypic traits under stabilizing selection around a fixed optimum, and explores the effect of mutational bias acting on the traits. A second model represents a phenotypic trait under both stabilizing and directional selection (modeled by a linear, cyclical or stochastic change in the phenotypic optimum). Individual-based simulations showed that in the absence of mutational bias or environmental change, the population evolves towards asexuality. However, with mutational bias, intermediate rates of sex are maintained in the population even when the cost of sex is strong. Higher rates of sex evolve when the phenotypic optimum changes over time. The second part of the thesis consisted in developing an experimental model to test theoretical predictions on the possible benefits of sex, using the facultatively sexual rotifer Brachionus plicatilis. The results demonstrate genetic variation for investment in sex between strains from the same natural population, and the existence of transgenerational maternal effects affecting the rate of sex. Finally, the results from an evolution experiment suggest that sex facilitates adaptation to a stressful environment.; L’objectif de cette thèse était d’étudier les bénéfices évolutifs possibles de la reproduction sexuée par une approche à la fois théorique et expérimentale. La première approche visait au développement de modèles de génétique quantitative pour l’évolution du sexe. Un premier modèle (s’appuyant sur le modèle géométrique de Fisher) considère un nombre arbitraire de traits phénotypiques sous sélection stabilisante autour d’un optimum fixe, et explore l’effet du biais mutationnel agissant sur les traits. Un deuxième modèle représente un trait phénotypique à la fois sous sélection stabilisante et directionnelle (représentée par un déplacement de l’optimum phénotypique de façon linéaire, cyclique ou stochastique). Des simulations individu-centrées ont montré qu’en l’absence de biais ou de changement environnemental, la population évolue vers l’asexualité. Cependant, avec un biais mutationnel, des taux de sexe intermédiaires peuvent évoluer même lorsque le coût du sexe est élevé. Des taux de sexe plus importants peuvent évoluer lorsque l’optimum phénotypique change dans le temps. La deuxième partie de la thèse consistait à développer un modèle expérimental pour tester les prédictions théoriques sur les éventuels avantages du sexe, en utilisant le rotifère à reproduction sexuée facultative Brachionus plicatilis. Les résultats démontrent l’existence de variabilité génétique dans l’investissement pour le sexe, entre des souches d’une même population naturelle, et celle d’effets maternels transgénérationels qui affectent le taux de sexe. Pour finir, les résultats d’une expérience d’évolution suggèrent que le sexe facilite l’adaptation à un environnement stressant.

This thesis aimed at investigating some of the possible evolutionary benefits of sexual reproduction using both a theoretical and an experimental approach. The first approach consisted in developing evolutionary quantitative genetic models for the evolution of sex. A first model (based on Fisher’s geometrical model) considers an arbitrary number of phenotypic traits under stabilizing selection around a fixed optimum, and explores the effect of mutational bias acting on the traits. A second model represents a phenotypic trait under both stabilizing and directional selection (modeled by a linear, cyclical or stochastic change in the phenotypic optimum). Individual-based simulations showed that in the absence of mutational bias or environmental change, the population evolves towards asexuality. However, with mutational bias, intermediate rates of sex are maintained in the population even when the cost of sex is strong. Higher rates of sex evolve when the phenotypic optimum changes over time. The second part of the thesis consisted in developing an experimental model to test theoretical predictions on the possible benefits of sex, using the facultatively sexual rotifer Brachionus plicatilis. The results demonstrate genetic variation for investment in sex between strains from the same natural population, and the existence of transgenerational maternal effects affecting the rate of sex. Finally, the results from an evolution experiment suggest that sex facilitates adaptation to a stressful environment.; L’objectif de cette thèse était d’étudier les bénéfices évolutifs possibles de la reproduction sexuée par une approche à la fois théorique et expérimentale. La première approche visait au développement de modèles de génétique quantitative pour l’évolution du sexe. Un premier modèle (s’appuyant sur le modèle géométrique de Fisher) considère un nombre arbitraire de traits phénotypiques sous sélection stabilisante autour d’un optimum fixe, et explore l’effet du biais mutationnel agissant sur les traits. Un deuxième modèle représente un trait phénotypique à la fois sous sélection stabilisante et directionnelle (représentée par un déplacement de l’optimum phénotypique de façon linéaire, cyclique ou stochastique). Des simulations individu-centrées ont montré qu’en l’absence de biais ou de changement environnemental, la population évolue vers l’asexualité. Cependant, avec un biais mutationnel, des taux de sexe intermédiaires peuvent évoluer même lorsque le coût du sexe est élevé. Des taux de sexe plus importants peuvent évoluer lorsque l’optimum phénotypique change dans le temps. La deuxième partie de la thèse consistait à développer un modèle expérimental pour tester les prédictions théoriques sur les éventuels avantages du sexe, en utilisant le rotifère à reproduction sexuée facultative Brachionus plicatilis. Les résultats démontrent l’existence de variabilité génétique dans l’investissement pour le sexe, entre des souches d’une même population naturelle, et celle d’effets maternels transgénérationels qui affectent le taux de sexe. Pour finir, les résultats d’une expérience d’évolution suggèrent que le sexe facilite l’adaptation à un environnement stressant.

National audience

As all perennial plants, fruit trees must cope with multiple environmental stresses during their life. The current progressive increase in air temperature makes fruit trees particularly fragile because of their long life during which they might accumulate stresses and the long duration of the selection process to search for more adapted materials. The progressive temperature increase directly impacts the tree phenology, especially their flowering time which results from the regulation of dormancy duration. The ongoing changes endanger the flower quality and the synchronicity of flowering among varieties that is necessary for cross-pollination. Moreover, during summer, despite the irrigation of most orchards, trees must face periods of soil water deficit and/or high temperatures during which the regulation of stomatal closure may impact the tree water use efficiency. Fruit development also depends on the climatic conditions during formation and maturation whereas floral induction occurs for the next season. In this talk, we will briefly review the threats for fruit production and the physiological mechanisms possibly involved that would deserve deep investigations for provid ing a more comprehensive knowledge of fruit tree temperature perception and responses. This knowledge is indeed crucial to draw strategies for the creation of new plant material better adapted to future climatic conditions.

Résumé; Highlighting the role of autophagy in metabolic adaptation of trout hepatocytes to fasting. 13. International Congress on the Biology of Fish

Plants are constantly exposed to environmental stresses and in part due to their sessile nature, they have evolved signal perception and adaptive strategies that are distinct from those of other eukaryotes. This is reflected at the cellular level where receptors and signalling molecules cannot be identified using standard homology-based searches querying with proteins from prokaryotes and other eukaryotes. One of the reasons for this is the complex domain architecture of receptor molecules. In order to discover hidden plant signalling molecules, we have developed a motif-based approach designed specifically for the identification of functional centers in plant molecules. This has made possible the discovery of novel components involved in signalling and stimulus-response pathways; the molecules include cyclic nucleotide cyclases, a nitric oxide sensor and a novel target for the hormone abscisic acid. Here, we describe the major steps of the method and illustrate it with recent and experimentally confirmed molecules as examples. We foresee that carefully curated search motifs supported by structural and bioinformatic assessments will uncover many more structural and functional aspects, particularly of signalling molecules. Keywords: Search motif, Functional centers, Hidden domains, Structural modeling, Molecular docking

International audience; Trees have a long lifespan and must continually adapt to environmental pressures, notably in the context of climate change. Epigenetic mechanisms are doubtless involved in phenotypic plasticity and in stress memory; however, little evidence of the role of epigenetic processes is available for trees growing in fields. Here, we analyzed the possible involvement of epigenetic mechanisms in the winter-dormant shoot apical meristem of Populus × euramericana clones in memory of the growing conditions faced during the vegetative period. We aimed to estimate the range of genetic and environmentally induced variations in global DNA methylation and to evaluate their correlation with changes in biomass production, identify differentially methylated regions (DMRs), and characterize common DMRs between experiments. We showed that the variations in global DNA methylation between conditions were genotype dependent and correlated with biomass production capacity. Microarray chip analysis allowed detection of DMRs 6 months after the stressful summer period. The 161 DMRs identified as common to three independent experiments most notably targeted abiotic stress and developmental response genes. Results are consistent with a winter-dormant shoot apical meristem epigenetic memory of stressful environmental conditions that occurred during the preceding summer period. This memory may facilitate tree acclimation.

International audience; Trees adjust their development to the environmental conditions they experience. Storms events of last decades showed that acclimation of trees to mechanical stresses due to wind is a very important process that allow the trees to sustain for long years. In the future, trees will experience new wind patterns, namely, more often strong winds and fewer daily moderate winds. Moreover, these patterns will go along with drought periods that may interact with the capacity of trees to adjust their growth to mechanical stresses due to wind. It is necessary to understand the mechanisms of wood functional acclimations to environmental conditions in order to predict their behaviour and in order to give foresters and breeders the relevant tools to adapt their forest management. This work aims to study how trees adjust the mechanical and hydraulic functions of their wood to environmental stresses and how this acclimation may be beneficial for the tree to resist to future stresses. In this work, young poplars were grown under controlled climatic conditions that include permanent environmental stress (daily mechanical stress of the stem by bending and/or hydric stress). Then, the properties of wood formed under these stressed conditions were characterized. First, hydraulic conductivity and sensibility to cavitation were measured at the tissue level in order to evaluate the changes in water transport capacity. Secondly, bending tests and Charpy impact tests were carried out at the millimetric scale to locally measure mechanical parameters such as elastic modulus, elastic limit or rupture energy. These experimental data allow to evaluate the impacts of mechanical and water stress on the wood material. At the stem level, they will be merged in an integrative model in order to evaluate the beneficial aspect of wood acclimation for trees.

The honey bee is threatened by biological agents and pesticides that can act in combination to induce synergistic effects on its physiology and lifespan. The synergistic effects of a parasite/pesticide combination have been demonstrated on workers and queens, but no studies have been performed on drones despite their essential contribution to colony sustainability by providing semen diversity and quality. The effects of the Nosema ceranae/fipronil combination on the life traits and physiology of mature drones were examined following exposure under semi-field conditions. The results showed that the microsporidia alone induced moderate and localized effects in the midgut, whereas fipronil alone induced moderate and generalized effects. The parasite/insecticide combination drastically affected both physiology and survival, exhibiting an important and significant generalized action that could jeopardize mating success. In terms of fertility, semen was strongly impacted regardless of stressor, suggesting that drone reproductive functions are very sensitive to stress factors. These findings suggest that drone health and fertility impairment might contribute to poorly mated queens, leading to the storage of poor quality semen and poor spermathecae diversity. Thus, the queens failures observed in recent years might result from the continuous exposure of drones to multiple environmental stressors.

In plant breeding, one of the major challenges of genomic selection is to account for genotype-by-environment (G × E) interactions, and more specifically how varieties are adapted to various environments. Crop growth models (CGM) were developed to model the response of plants to environmental conditions. They can be used to characterize eco-physiological stresses in relation to crop growth and developmental stages, and thereby help to dissect G × E interactions. Our study aims at demonstrating how environment characterization using crop models can be integrated to improve both the understanding and the genomic predictions of G × E interactions. We evaluated the usefulness of using CGM to characterize environments by comparing basic and CGM-based stress indicators, to assess how much of the G × E interaction can be explained and whether gains in prediction accuracy can be made. We carried out a case study in wheat (Triticum aestivum) to model nitrogen stress in a CGM in 12 environments defined by year × location × nitrogen treatment. Interactions between 194 varieties of a core collection and these 12 different nitrogen conditions were examined by analyzing grain number. We showed that (i) CGM based indicators captured the G × E interactions better than basic indicators and that (ii) genomic predictions were slightly improved by modeling the genomic interaction with the crop model based characterization of nitrogen stress. A framework was proposed to integrate crop model environment characterization into genomic predictions. We describe how this characterization promises to improve the prediction accuracy of adaptation to environmental stresses.

A central issue in plant evolutionary ecology is to understand how several coordinated suites of traits (i.e. traits syndrome) may be jointly selected within a single species. This study aims to describe patterns of variation and co-variation of functional traits in a water-stressed tree population and test their relationships with performance traits. Within a Mediterranean population of Fagus sylvatica experiencing recurrent summer droughts, we investigated the phenotypic variation of leaf unfolding phenology, leaf area (LA), leaf mass per area (LMA), leaf water content (LWC), water use efficiency (WUE) estimated by carbon isotopic discrimination (d13C), twig Huber- value (HV: the stem cross-section divided by the leaf area distal to the stem), wood density (WDens), and leaf nitrogen content (Nmass). First, a principal component analysis revealed that two main axes structured the phenotypic variability: the first axis opposed leaf unfolding earliness and LWC to LMA and WUE; the second axis opposed LA to HV. These two axes can be interpreted as the opposition of two strategies (water economy versus water uptake) at two distinct scales (leaf for the first axis and branches for the second axis). Second, we found that LMA, LA, leaf unfolding and LWC responded differently to competition intensity, while WUE, WDens and HV did not correlate with competition. Third, we found that all studied functional traits were related to growth and/or reproductive performance traits and that these relationships were frequently non-linear, showing strong interactions between traits. By highlighting phenotypic clustering of functional traits involved in response to water stress and by evidencing antagonistic selection favouring intermediate trait values as well as trait combinations, our study brought new insights on how natural selection operates on plant functional traits in a stressful environment.

In a warming climate, higher temperatures are likely to modulate positively or negatively the effect of other environmental factors on biota, although such interactions are poorly documented. Here, we explore under controlled conditions the combined effects of two common stressors in freshwater ecosystems, higher temperature and sediment load, on the embryonic development of arctic charr ( Salvelinus alpinus L.). In the warm treatment, embryos had a lower survival, a longer incubation period and a smaller body size with a bigger yolk sac volume. Our data show a significant interaction between temperature and sediment load with temperature increasing dramatically the negative effects of sediment load on fitness-related traits. In the climate change context, these findings highlight the importance of taking into account different thermal scenarios when examining the effect of environmental or anthropogenic stressors.

National audience; Plant response to abiotic stress is a main challenge in a context of global climate change. The understanding of physiological as well as genetic/molecular processes controlling plant‘s response to abiotic stress will help to improve plant breeding. Recently, epigenetic mechanisms such as DNA methylation have been proposed to participate to phenotypic plasticity defines as the different phenotypes for a given genotype in distinct environments is a key process for plant to adapt to their changing environment. This is particularly relevant for perennial plants such as trees that are exposed to repeated fluctuations of their living conditions. In order to assess this question in a perennial plant, we analysed poplar (Populus tremula × Populus alba) RNAi lines inhibited for the DECREASED DNA METHYLATION 1 gene (DDM1, involved in the maintenance of DNA methylation profile). A droughtrewateing experiment was conducted to evaluate the role of DNA methylation in tree phenotypic plasticity. Phenotypic characterization deals with data related to growth, photosynthetic capacities, water-use efficiency, xylem vulnerability to cavitation, xylem anatomy, phytohormones dosage, wood density and Mid Infra-Red spectroscopy (MIRS). Then, epigenomics studies in relation to DNA methylation have been realized: global DNA methylation, Whole Genomic Bisulfite Sequencing (WGBS) and Transposable Elements analyses. Bioinformatics analyses are in progress to identify ‘Differentially Methylated Regions’ in relation to phenotypic plasticity and the role of DNA methylation in memorizing environmental stress.

BFP - Equipe OrFE; Plant growth and crop yield are negatively affected by a reduction in water availability. However, a clear understanding of how growth is regulated under nonlethal drought conditions is lacking. Recent advances in genomics, phenomics, and transcriptomics allow in-depth analysis of natural variation. In this study, we conducted a detailed screening of leaf growth responses to mild drought in a worldwide collection of Arabidopsis thaliana accessions. The genetic architecture of the growth responses upon mild drought was investigated by subjecting the different leaf growth phenotypes to genome-wide association mapping and by characterizing the transcriptome of young developing leaves. Although no major effect locus was found to be associated with growth in mild drought, the transcriptome analysis delivered further insight into the natural variation of transcriptional responses to mild drought in a specific tissue. Coexpression analysis indicated the presence of gene clusters that co-vary over different genetic backgrounds, among others a cluster of genes with important regulatory functions in the growth response to osmotic stress. It was found that the occurrence of a mild drought stress response in leaves can be inferred with high accuracy across accessions based on the expression profile of 283 genes. A genome-wide association study on the expression data revealed that trans regulation seems to be more important than cis regulation in the transcriptional response to environmental perturbations.

Book of abstracts p. 85-86Book of abstracts p. 85-86; Genomic random regression for adaptation breeding: Whole-genome prediction of the reaction norms to environmental stress in bread wheat (Triticum aestivum L.). EUCARPIA Biometrics in Plant Breeding

Cytokinins are phytohormones that regulate many developmental and environmental responses. The Medicago truncatula cytokinin receptor MtCRE1 (Cytokinin Response 1) is required for the nitrogen-fixing symbiosis with rhizobia. As several cytokinin signaling genes are modulated in roots depending on different biotic and abiotic conditions, we assessed potential involvement of this pathway in various root environmental responses. Phenotyping of cre1 mutant roots infected by the Gigaspora margarita arbuscular mycorrhizal (AM) symbiotic fungus, the Aphanomyces euteiches root oomycete, or subjected to an abiotic stress (salt), were carried out. Detailed histological analysis and quantification of cre1 mycorrhized roots did not reveal any detrimental phenotype, suggesting that MtCRE1 does not belong to the ancestral common symbiotic pathway shared by rhizobial and AM symbioses. cre1 mutants formed an increased number of emerged lateral roots compared to wild-type plants, a phenotype which was also observed under non-stressed conditions. In response to A. euteiches, cre1 mutants showed reduced disease symptoms and an increased plant survival rate, correlated to an enhanced formation of lateral roots, a feature previously linked to Aphanomyces resistance. Overall, we showed that the cytokinin CRE1 pathway is not only required for symbiotic nodule organogenesis but also affects both root development and resistance to abiotic and biotic environmental stresses.

Plants unlike other living forms are sessile thereby facing severe biotic and abiotic stresses. Plants have evolved different efficient defence responses which thrive upon a number of intrinsic factors, such as genotypic and phenotypic constitutions and developmental circumstances, and extrinsic factors like severity and duration of the stresses. Stress management uses molecular and biochemical level controls, the competence, and speed, at which a stress signal is perceived and transmitted to generate stress signal molecules and activate stress-protective mechanisms. A well-concerted action of the plants' competence at morphological, physiological, biochemical, and molecular strata regulates numerous adaptive responses to biotic and abiotic stresses. Genetic manipulations of signalling networks have been widely used to improve plant productivity under stressful conditions. Advanced biotechnological application will enable maintaining agriculture in a sustainable manner. In this special issue, we present two reviews and four research papers which address genomic, molecular, and physiological regulations as well as signalling networks dealing with plant responses to abiotic and biotic factors. Climate change, desertification, and the rise in human population have put a severe load on agriculture and are deteriorating crop productivity. In recent years, numerous molecular and metabolic pathways involved in plant responses and adaptation to various types of environmental stresses have been identified and reported. Among hundreds of metabolic pathways identified, the role of polyamines in stress management to enhance plant acclimation and adaptation is emerging rapidly. In this special issue, a timely review by P. Rangan et al. (2014) summarizes our knowledge on biosynthesis and catabolism of polyamines and highlights recent progress in elucidating the functions of polyamines in regulation of plant responses to abiotic stresses. Given a huge genetic variation among plant species, the authors also discuss a systematic approach based on polyamine-mediated enhancement of stress tolerance which might be used as a potential strategy for screening and identification of natural variants within existing crop species. The identified genotypes that possess compatible allelic variants could be then used for the improvement of stress tolerance. Plant-microbe interactions are at the core of symbiotic, parasitic, or mutualistic plant-microbe relationships. These interactions have displayed a unique way of mutualistic communications for a resource sharing. To shed light on the topic, a detailed review of M. Libault (2014) explains the unique mechanisms in using legumes to interact with bacteria. Leguminous plants have developed a mutualistic symbiotic relationship with rhizobium (a type of soil bacteria). Upon bacterial infection, a new root organ called nodule is developed that enables the leguminous plants to access a steady source of nitrogen through the fixation and assimilation of the atmospheric N2 by the symbiotic bacteria. In return, the bacteria also get benefit from the symbiotic plants that provide photosynthesis product to bacteria as source of carbon. Environmental stress or climate change, which influences the concentration of the atmospheric carbon dioxide (CO2), will have a significant impact on plant photosynthesis. As a consequence, this will affect the nitrogen and carbon metabolism, leading to altered nitrogen fixation efficiency. The key regulatory mechanisms controlling carbon/nitrogen balances with particular attention to legume nodulation are reviewed by coeditor M. Libault in his review article. In addition, readers can also get an overview about the effect of the change in CO2 level on nitrogen fixation efficiency through this review, giving rise to idea as to how we could mitigate the impact of the change in atmospheric CO2 concentration. Besides the change in atmospheric CO2 level, water deficit is one of the major constraints for nodulation, and, as a consequence for plant productivity. This topical issue is presented here by a research article of S. Sulieman et al. (2014). In their study, the authors assessed the growth and nodulation attributes of two soybean varieties DT2008 and Williams 82 (W82), which have contrasting drought-tolerant capacity, in a symbiotic association with Bradyrhizobium japonicum under drought and subsequent rehydration. The authors aimed to understand the correlation between N2 fixation efficiency and differential drought-responsive phenotypes of DT2008 and W82. Their results also provide genetic resources and basis foundation for further genomic research that would lead to better understanding of mechanisms involved in regulation of N2 fixation in soybean under drought at molecular level. Heavy metal pollution has been a matter of grave concern. Until recently, efforts have been mainly restricted to phytoremediation of soils using plant species with high metal uptake capacity such as Brassica species. Chromium (Cr) is a highly phytotoxic heavy metal affecting crop productivity and human health via entering the food chain. Phytoremediation of Cr-polluted soils has been mostly demonstrated in using herbaceous plants, whereas use of cotton cultivars in Cr phytoremediation is least explored. In the present issue, M. K. Daud et al. (2014) have shown the potentials of two transgenic cotton cultivars (J208 and Z905) and their hybrid line (ZD14) in Cr phytoremediation using a multiple biomarker approach. Their work showed that these cotton cultivars and hybrid line could effectively uptake and sequestrate Cr in dead parts of the plants, such as vacuole and cell wall, besides having a more highly accelerated antioxidant system. This study thus proposes a new role of cotton cultivars in phytoremediation of Cr-polluted soils. The interactions between macro- and micronutrient homeostases have been reported in many physiological and nutritional situations. N. Bouain et al. (2014) studied the interaction between phosphate (Pi) and zinc (Zn) homeostasis in two lettuce varieties. The results revealed that the variation in Pi and Zn supplies affects the biomass and photosynthesis as well as the dynamics of Pi transport in a contrasting manner between the two varieties, indicating a genetic basis for such physiological responses. On the basis of their results, the authors proposed a working model of how Pi and Zn signalling pathways are integrated into functional networks to control plant growth. Salinity is a major abiotic stress worldwide claiming agriculture lands and affecting productivity. Research paper by A. Matsui et al. (2014) investigated salt stress in Arabidopsis. The authors reported that the tasiRNA-ARF pathway is involved in controlling floral architecture in plants under drought and high salinity. The ta-siRNA biosynthesis mutants and mutated ARF3-overexpressing plants showed short stamen under drought and salt stress, which hampered self-pollination. This study reports for the first time that a type of ta-siRNAs (tasiRNA-ARF) plays an important role in maintaining normal stamen growth and fertilization under drought and high salinity.

In response to different environmental stresses, eIF2 alpha phosphorylation represses global translation coincident with preferential translation of ATF4, a master regulator controlling the transcription of key genes essential for adaptative functions. Here, we establish that the eIF2 alpha/ATF4 pathway directs an autophagy gene transcriptional program in response to amino acid starvation or endoplasmic reticulum stress. The eIF2 alpha-kinases GCN2 and PERK and the transcription factors ATF4 and CHOP are also required to increase the transcription of a set of genes implicated in the formation, elongation and function of the autophagosome. We also identify three classes of autophagy genes according to their dependence on ATF4 and CHOP and the binding of these factors to specific promoter cis elements. Furthermore, different combinations of CHOP and ATF4 bindings to target promoters allow the trigger of a differential transcriptional response according to the stress intensity. Overall, this study reveals a novel regulatory role of the eIF2 alpha-ATF4 pathway in the fine-tuning of the autophagy gene transcription program in response to stresses.

Contents Summary 349 I. Leaf growth: volume, structures, water and carbon 349 II. Coupling water and carbon limitations through the Lockhart model? 350 III. ABA signalling pathway as a hub to coordinate water and carbon relations 353 IV. Leaf venation: just a two-way pipe network? 354 V. Leaf ontogeny orchestrates the actors involved in the control of leaf growth 355 VI. The growing leaf in a changing world 360 VII. Conclusion 361 Acknowledgements 362 References 362 Summary Leaf growth is the central process facilitating energy capture and plant performance. This is also one of the most sensitive processes to a wide range of abiotic stresses. Because hydraulics and metabolics are two major determinants of expansive growth (volumetric increase) and structural growth (dry matter increase), we review the interaction nodes between water and carbon. We detail the crosstalks between water and carbon transports, including the dual role of stomata and aquaporins in regulating water and carbon fluxes, the coupling between phloem and xylem, the interactions between leaf water relations and photosynthetic capacity, the links between Lockhart's hydromechanical model and carbon metabolism, and the central regulatory role of abscisic acid. Then, we argue that during leaf ontogeny, these interactions change dramatically because of uncoupled modifications between several anatomical and physiological features of the leaf. We conclude that the control of leaf growth switches from a metabolic to a hydromechanical limitation during the course of leaf ontogeny. Finally, we illustrate how taking leaf ontogeny into account provides insights into the mechanisms underlying leaf growth responses to abiotic stresses that affect water and carbon relations, such as elevated CO2, low light, high temperature and drought.

Human-induced environmental stress may lead to rapid evolutionary processes, and can affect the ability of natural populations to respond to other environmental change or stress. We used quantitative genetics tools, pesticide exposure and a gradient of biotic stress to investigate these questions in the freshwater snail Lymnaea stagnalis. The study focused on the genetic component of variance for life-history traits within populations, and the ability of different lines to respond differently to stress. The effect of parental exposure to a xenobiotic stress on the reaction norm of the progeny to another stress was also estimated (parental non-genetic effect). First, under laboratory conditions, inter-family variance suggested significant heritability for most traits. Second, under outdoor exposure to various pesticides, variation among families was significant for individual growth. Clutch size and hatching rate of the clutches laid in the laboratory after exposure showed similar results, and moreover, family interacted significantly with pesticides. Third, under a gradient of biotic stress (food and competition), inter-family variation was again significant for growth, and a significant interaction with biotic stress was observed for juvenile growth and ultimate size. Family heterogeneity and family × environment interactions indicate the possibility of differential evolutionary responses among lines, through different reaction norms. Stressful conditions did not affect the estimated heritability, and for pesticides, no transgenerational effect was detected on progeny growth in response to the biotic stress. Focused on short-term evolutionary responses, the present study illustrates a possible way of incorporating evolutionary approaches into ecotoxicological risk assessment procedures, for example, by accounting for inter-family variation.

The visual quality of fresh potatoes, Solanum tuberosum, became a dominant criterion and a significative economical issue in potato market. According the vegetative reproduction of this species, requirements for visual quality are also needed for potato seed tubers. As an organ for reserve and propagation, the tuber grows underground and is in contact with soil-borne microorganisms, making it potentially exposed to blemishes, for the majority of which the origin is still unclear.The objective of this work is to make an inventory of those tuber blemishes, to characterize them and determine their causes. After the establishment of consensual nomenclature and classification of the blemishes, two hypotheses were formulated: (1) blemishes are due to pathogenic attacks and/or (2) they result from a response of the plants to environmental stresses. The assessment of the first hypothesis allowed identifying a wide diversity of microorganisms living on the blemished tuber surface. Their pathogenicity was tested by several biological assays that allowed producing blemishes on progeny tubers and fulfilling the Koch's postulates for the fungus Rhizoctonia solani causing sclerotia. For many other blemishes no clear relationship was established between a microorganism and a blemish. A study of the microbial structure of the geocaulosphere of tubers blemished or not, showed that bacterial and fungal communities adopted different dynamics during the growing season and according to the sanitary status of the seed tuber, but no causality link could have been drawn. On the other hand, an increase of R. solani population around blemished tubers was observed. The diversity of strains of R. solani originating from France and from Europe and associated to the blemished tubers was characterized. The phylogenetic relationships between the strains were independent of the geographical origin and of the host cultivar, thus the existence of frequent genetic events and genetic mixing between the populations of R. solani was suggested. Concerning the potential implication of different abiotic factors, a survey conducted with farmers showed the implication of soil pH, some cultural practices, including the choice of the susceptible cultivars and meteorological conditions on the occurrence of some blemishes. This work made clear the blemish nomenclature, confirmed the implication of R. solani in the occurrence of some blemishes and suggested new hypotheses concerning the occurrence of blemishes as a plant response to a stressful environment. Thus, a path was opened toward the resolution of the issue asked by all the potato community, responsible for the marketing of a mass consumption fresh product and answering to market requirements related to visual and culinary qualities and to environmental friendly modes of production., La qualité de présentation d'une pomme de terre de consommation, Solanum tuberosum L., commercialisée en produit frais est devenue une exigence et un enjeu économique significatif dans les relations commerciales. Compte tenu du mode de reproduction par voie végétative de cette espèce, ces exigences sont également imposées au tubercule de semence. Organe de réserve et de propagation, le tubercule est produit sous terre, ce qui l'expose aux microorganismes telluriques et le rend potentiellement porteur d'altérations superficielles dont l'origine n'est pas encore clairement identifiée pour certaines d'entre elles. L'objectif de ce travail est de recenser et de caractériser ces altérations superficielles du tubercule et d'en déterminer les causes. Après l'établissement d'une nomenclature et d'une classification consensuelles des défauts observables sur tubercule, deux hypothèses ont été formulées et testées: (1) les défauts sont d'origine pathogène et/ou (2) ils résultent d'une réponse de la plante à des stress environnementaux. L'évaluation de la première hypothèse a mené à l'identification d'une grande diversité de microorganismes vivant à la surface des tubercules altérés. Leur pouvoir pathogène a été testé par une série de tests biologiques. Ceux-ci ont permis de reproduire les défauts sur des tubercules néoformés et de vérifier les postulats de Koch pour le champignon Rhizoctonia solani responsable de la formation de sclérotes. Pour bon nombre d'autres défauts visuels, aucune relation claire entre un microorganisme et une altération n'a pu être établie. Une étude de la structure des communautés microbiennes de la géocaulosphère de tubercules, altérés ou non, a démontré que les communautés fongiques et bactériennes se comportaient selon des dynamiques différentes au cours de la culture et en fonction de l'état sanitaire du tubercule de semence mais aucune relation de causalité n'a pu être mise en évidence. Il a par contre été noté une augmentation de la population de R. solani autour des tubercules altérés. La diversité des isolats d’origine française et européenne associés aux altérations des tubercules a donc été caractérisée. Elle révèle l'existence de relations phylogénétiques indépendantes de l'origine géographique et du cultivar hôte et suggère l'existence de d'événements génétiques fréquents et d'un brassage génétique entre les populations de R. solani. Le test de la seconde hypothèse a consisté à rechercher une implication potentielle de différents facteurs abiotiques dans la formation des altérations superficielles. L'analyse d'une enquête menée auprès d'agriculteurs a mis en évidence l'implication du pH, de certaines pratiques culturales, de la sensibilité de cultivars et de conditions météorologiques particulières dans l'occurrence de certains défauts. Ce travail a permis de clarifier la nomenclature des altérations, de confirmer l'implication de R. solani dans l'apparition de certaines d'entre elles et d'envisager de nouvelles hypothèses quant à la formation de défauts suite à une réponse de la plante à un stress environnemental. Ainsi, une voie a été ouverte vers la résolution de la problématique posée par toute une filière professionnelle, responsable de la mise en marché d'un produit frais de grande consommation, et répondant aux exigences du marché en matière de présentation, qualité culinaire et, mode de production respectueux de l'environnement.

Mes travaux portent sur l'étude du développement et de la réponse des plantes à des stress environnementaux, à l'aide d'approches de protéomique membranaire. Les travaux de ma thèse ont démontré que la sensibilité à l'auxine de la H+-ATPase plasmique change au cours du développement de la plante. A l'issue de ma thèse, j'ai entrepris l'étude de mutants de développement d'Arabidopsis par le classement de leurs profils d'électrophorèse bidimensionnelle, ce qui a permis d'interpréter plusieurs phénotypes mutants. Par la suite, j'ai participé à l'étude du protéome de la membrane plasmique d'Arabidopsis et optimisé la desciption du protéome hydrophobe de cette membrane. J'ai ensuite utilisé cette approche pour étudier la régulation post-traductionnelle d'une famille de protéines membranaires facilitant le transport d'eau, les aquaporines, en réponse à des stress environnementaux. La découverte de la méthylation de certaines aquaporines et de multiples sites de phosphorylation sont des résultats originaux. Mon projet de recherche sera centré sur l'étude du rôle de ces modifications par le biais de i) l'identification de méthyltransférases d'aquaporines, ii) la caractérisation de protéines en interaction avec les domaines modifiés des aquaporines iii) la recherche de conditions environnementales susceptibles de moduler l'activité des aquaporines par méthylation et phosphorylation.

Foliar surface physiology in relation to environmental stress. TREE PHYSIOLOGY MEETING