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Droughts have recurrently impacted the Amazon rainforests, undermining the forest biomass carbon sink capacity due to a quicker increase of biomass mortality compared to growth. Most global land surface models used for assessments of the Global Carbon Budget and future climate projections have not incorporated drought-induced tree mortality. Their prediction of biomass dynamics are therefore subject to large uncertainties, as a result of (1) lack of explicit simulation of hydraulic transportin the continuum from soil to leaves; (2) lack of process-based equations connecting the impairment of the hydraulic transport system of trees to mortality; (3) lack of representation of mortality across trees sizes. To address these critical research gaps, I improved plant hydraulic representation in ORCHIDEECAN. This model was re-calibrated and evaluated over rainforests in Amazon basin, and applied to simulate the future evolution of biomass dynamics facing droughts. Firstly, I implemented a mechanistic hydraulic architecture that was designed by E. Joetzjer, and a hydraulic-failure related tree mortality module that I designed into ORCHIDEE-CAN. The model was calibrated against the world’s longest running drought manipulation experiment of Caxiuana in the eastern Amazon. Our model produced comparable annual tree mortality rates than the observation andcaptured biomass dynamics. This work provides a basis for further research in assimilating experimental observation data to parameterize the hydraulic failure induced tree mortality. Secondly, I applied ORCHIDEE-CAN-NHA over the Amazon intact rainforest. The model reproduced the drought sensitivity of aboveground biomass (AGB) growth and mortality observed atnetworks of forest inventory plots across Amazon intact forests for the two recent mega-droughts of 2005 and 2010. We predicted a more negative sensitivity of the net biomass carbon sink to water deficits for the recent 2015/16 El Nino, which was the most severe drought in the historical record. In the model, even if climate change with droughts becoming more severe tended to intensify tree mortality, increased CO2 concentration contributed to attenuate the C loss due to mortality by suppressing transpiration.Lastly, I used the ORCHIDEE-CAN-NHA model for future simulations of biomass carbondynamics. Most climate models (ISIMIP2 program) consistently predict a drier trend in northeastern Amazon. The simulation forced by the HadGEM climate model in the RCP8.5 scenario shows the most pronounced drying in eastern and northeastern Amazon, with a cross-over point at which the carbon sink turned to a carbon source in the Guiana Shield and East-central Amazon in the middle of the 21st century. This study sheds light on predicting the future evolution of Amazon rainforest biomass dynamics with an improved process-based model able to reproduce climate-change induced mortality.In the conclusion and outlook sections, future developments and research priorities are proposed, which would improve the reliability and performances of the process-based model presented in this dissertation, allowing to better capture mechanisms that control the evolution of forest biomass dynamics in the face of more frequent drought risks.; Les sécheresses ont eu un impact récurrent sur les forêts tropicales amazoniennes, amenuisant la capacité de puits de carbone de la biomasse forestière. La plupart des modèles globaux de surface terrestre utilisés pour les évaluations du budget mondial du carbone et les projections climatiques futures, n'intègrent pas la mortalité des arbres induite par la sécheresse. Leurs prévisions de la dynamique de la biomasse sont donc sujettes à de grandes incertitudes. Les faiblesses des modèlesglobaux sont liés à : (1) l’absence de la représentation explicite du transport hydraulique; (2) le manque d'équations basées sur les processus à travers la description de la façon dont une altération du système de transport hydraulique des arbres conduit à la mortalité ; (3) le manque de représentation de la mortalité à travers les tailles des arbres. Tout d'abord, j'ai implémenté une architecture hydraulique mécaniste qui a été conçue par E. Joetzjer, et un module de mortalité des arbres que j'ai conçu dans l'ORCHIDEE-CAN-NHA. Notre modèle a produit des taux annuels de mortalité des arbres comparables à ceux observés et a capturé la dynamique de la biomasse. Ce travail fournit une base pour des recherches ultérieures sur l'assimilationdes données d'observation expérimentales afin de paramétrer la mortalité des arbres induite par la défaillance hydraulique.Deuxièmement, j'ai appliqué ORCHIDEE-CAN-NHA sur la forêt tropicale intacte de l'Amazonie. Le modèle a reproduit la sensibilité à la sécheresse de la croissance et de la mortalité de la biomasse aérienne (AGB) observée sur des réseaux de placettes d'inventaire forestier dans les forêts intactes d'Amazonie pour les deux récentes méga-sécheresses de 2005 et 2010. Dans le modèle, même si le changement climatique, avec des sécheresses devenant plus sévères, a eu tendance à intensifier la mortalité des arbres, l'augmentation de la concentration de CO2 a contribué à atténuer la perte de carbone due à la mortalité en supprimant la transpiration. Enfin, j'ai utilisé le modèle ORCHIDEE-CAN-NHA afin de simuler le futur du stockage ducarbone dans la biomasse en Amazonie. La plupart des modèles climatiques (ISIMIP-2) projettent néanmoins de manière cohérente une tendance plus sèche dans le nord-est de l'Amazonie. La simulation forcée par le modèle climatique HadGEM dans le scénario RCP8.5 montre un assèchement plus prononcé dans l'est et le nord-est de l'Amazonie, avec un point d'intersection où le puits de carbone se transforme en source de carbone dans le bouclier guyanais et le centre-est de l'Amazonie, au milieu du 21e siècle. Cette étude permet de prédire l'évolution future de la dynamique de la biomasse de la forêtamazonienne avec un modèle amélioré basé sur les processus, capable de reproduire la mortalité induitepar le changement climatique. Dans les sections conclusion et perspectives, des développements futurs et des priorités de recherche sont proposés, qui amélioreraient la fiabilité et les performances du modèle basé sur les processus présentés dans cette thèse, permettant de mieux capturer les mécanismes qui contrôlent l'évolution de la dynamique de la biomasse forestière face à des risques de sécheresse plus fréquents.

Le biome boréal, emmagasinant d’importantes quantités de carbone en son sol et recouvrant une majorité du territoire alaskien, fennoscandien et russe, contribue grandement au système climatique. Toutefois, les variabilités climatiques et les propriétés de l’écosystème, notamment en ce qui a trait à la présence ou l’absence de pergélisol, complexifient la quantification de la variabilité des bilans de carbone du biome boréal, au sein duquel se retrouvent des écosystèmes forestiers, lentiques et de zones humides. Ces bilans de carbone sont grandement influencés par le début et la fin de la saison de croissance photosynthétique, étant à leur tour dépendants de plusieurs variables environnementales telles que la température de l’air et du sol, le contenu du sol en eau, les stades de développement de la végétation, etc. Cette recherche vise à quantifier l’impact de ces variabilités environnementales sur la variabilité des moments où se produisent le début et la fin de la saison de croissance photosynthétique, en distinguant les forêts boréales avec et sans pergélisol. La saison de croissance photosynthétique est caractérisée à partir de la productivité primaire brute dérivée de mesures covariance des turbulences provenant de 40 sites-années d’observation à travers la forêt boréale nord-américaine où l’épinette noire est l’espèce d’arbre dominante. Les variables environnementales considérées étaient les températures de l’air et du sol, les stades de développement de la végétation, le couvert nival, le rayonnement photosynthétiquement actif et le contenu du sol en eau. Le cadre statistique choisi incluait le calcul des coefficients de corrélations de Pearson, l’analyse des points communs et la modélisation par équations structurelles. Les résultats de cette étude montrent que la variabilité du début de la saison de croissance dans les sites sans pergélisol est contrôlée directement par la variabilité annuelle des stades de développement de la végétation ainsi que par le moment où survient le dégel du sol. Ce résultat souligne ainsi l’importance de l’accès à l’eau liquide du sol afin que la végétation initie la photosynthèse. Aucune variable environnementale ne pouvait significativement expliquer le contrôle du début de la photosynthèse au sein des sites avec pergélisol. À l’automne, le contenu du sol en eau ainsi que le début du couvert nival influencent directement la variabilité de la fin de la saison de croissance photosynthétique. Il est alors montré que la disponibilité de l’eau peut mener à une cessation plus hâtive de la photosynthèse à l’automne. L’effet de l’apparition du couvert nival est quant à lui opposé dans les sites avec et sans pergélisol. Son retard dans les sites sans pergélisol témoigne d’une température de l’air suffisamment élevée pour que les précipitations tombent sous forme liquide, prolongeant ainsi les activités photosynthétiques. Son retard dans les sites avec pergélisol signifie plutôt des précipitations neigeuses moindres, retardant ainsi l’apparition d’une couche isolante pour le sol, qui aurait pu allonger la saison de croissance photosynthétique. Cette étude contribue à clarifier les processus contrôlant le début et la fin de la saison de croissance photosynthétique et aidera à améliorer la compréhension des effets des changements climatiques sur la force du puits de carbone de la forêt boréale nord-américaine., The boreal forest, storing large amounts of carbon in its soil and covering a majority of the Alaskan, Canadian, Fennoscandian and Russian territory, is an integral part of the climate system. However, climatic variability and ecosystem properties, particularly with regards to the presence or absence of permafrost, limits our understanding of the carbon balance variability in the boreal biome, which comprises forest, lake and wetland ecosystems. The boreal carbon sink-source strength is greatly influenced by phenological events, including the start and end of the photosynthetic growing season, which are themselves dependent on several environmental variables such as air and soil temperature, soil water content, vegetation development stages, etc. This research aims to provide new insights on the influence of environmental variability on the variability in the timing of the photosynthetic growing season, by broadly distinguishing between boreal forests with and without permafrost. The photosynthetic growing season is characterized using gross primary productivity derived from eddy covariance measurements of net ecosystem carbon dioxide exchange. Data from 40 black spruce- dominated site-years of observation across the North American boreal forest are used. The considered environmental predictors were air and soil temperatures, vegetation development stages, snow cover, photosynthetically active radiation and soil water content. The statistical framework included the calculation of Pearson correlation coefficients, commonality analyses and structural equation modeling. This study shows that the variability in the start of the growing season in permafrost-free sites is directly controlled by the variability in vegetation development stage as well as by the thawing of seasonally frozen ground. This result thus emphasizes the importance of access to liquid soil water for the vegetation to initiate photosynthesis. No environmental variable could significantly explain photosynthesis recovery in sites with permafrost. In fall, the soil water content as well as the start of snow cover directly influence the variability in the end of the photosynthetic growing season. These results suggest that the availability of water can limit photosynthesis in the fall. The effect of snow cover is opposite in sites with and without permafrost. A delay in the appearance of continuous snow cover in sites without permafrost indicates that the air temperature is high enough for precipitation to fall in liquid form and for photosynthesis to continue. In contrast, its delay in sites with permafrost indicates less snowfall, thus delaying the appearance of an insulating layer for the soil, which could have lengthened the photosynthetic growing season. This study sheds light on the controls of the annual variation of the timing of the photosynthetic growing season and will help understanding of the effects of climate change on the strength of the North American boreal forest carbon sink.

A thorough understanding of how tropical forests respond to climate is important to improve ecosystem process models and to reduce uncertainties in current and future global carbon balance calculations. The Amazon rainforest, a major contributor to the global carbon cycle, is subject to strong intra- and interannual variations in climate conditions. Understanding their effect on carbon fluxes between the ecosystem and the atmosphere and on the resulting carbon balance is still incomplete. We examined the long-term (over a 12-year period; 2004-2015) variations in gross primary productivity (GPP), ecosystem respiration (RE) and net ecosystem exchange (NEE) in a tropical rainforest in French Guiana and identified key climatic drivers influencing the changes.The study period was characterized by strong differences in climatic conditions among years, particularly differences in the intensity of the dry and wet seasons, as well as differences in annual carbon fluxes and balance. Annual average GPP varied from 3384.9 g C m(-2) yr(-1) (95% CI [3320.7, 3445.9]) to 4061.2 g C m(-2) yr(-1) (95% CI [3980.1, 4145.0]). RE varied even more than GPP, with a difference of 933.1 C m(-2) yr(-1) between the minimum (3020.6 g C m(-2) yr(-1); 95% CI [2889.4, 3051.3]) and maximum (3953.7 g C m(-2) yr(-1); 95% CI [3887.6, 4019.6]) values. Although NEE showed large interannual variability (nine-fold), from-65.6 g C m(-2) yr(-1) (95% CI [-4.4, -126.0]) to -590.5 g C m(-2) yr(-1) (95% CI [-532.3, -651.6]), the forest remained a carbon sink over the 12-year period.A combination of global radiation (Rg), relative extractable water (REW) and soil temperature (Ts) explained 51% of the daily variations for GPP, 30% for RE and 39% for NEE. Global radiation was always the best predictor of these variations, but soil water content and temperature did also influence carbon fluxes and balance. Seasonally, Rg was the major controlling factor for GPP, RE and NEE during the wet season. During the dry season, variations in carbon fluxes and balance were poorly explained by climate factors. Yet, REW was the key driver of variations in NEE during the dry season.This study highlights that, over the long-term, carbon fluxes and balance in such tropical rainforest ecosystems are largely controlled by both radiation and water limitation. Even though variations in Rg have a greater impact on these fluxes, water limitation during seasonal droughts is enough to reduce ecosystem productivity, respiration and carbon uptake. The reduced precipitation expected in tropical rainforest areas under future climatic conditions will therefore strongly influence carbon fluxes and carbon uptake. This study also highlights the importance for land surface or dynamic global vegetation models to consider the main drivers of carbon fluxes and balance separately for dry and wet seasons.

International audience

International audience; Extreme climatic events (ECEs) such as droughts and heat waves are predicted to increase in intensity and frequency and impact the terrestrial carbon balance. However, we lack direct experimental evidence of how the net carbon uptake of ecosystems is affected by ECEs under future elevated atmospheric CO2 concentrations (eCO2). Taking advantage of an advanced controlled environment facility for ecosystem research (Ecotron), we simulated eCO2 and extreme cooccurring heat and drought events as projected for the 2050s and analyzed their effects on the ecosystem-level carbon and water fluxes in a C3 grassland. Our results indicate that eCO2 not only slows down the decline of ecosystem carbon uptake during the ECE but also enhances its recovery after the ECE, as mediated by increases of root growth and plant nitrogen uptake induced by the ECE. These findings indicate that, in the predicted near future climate, eCO2 could mitigate the effects of extreme droughts and heat waves on ecosystem net carbon uptake.

This study describes how management of grasslands is included in the Organizing Carbon and Hydrology in Dynamic Ecosystems (ORCHIDEE) process-based ecosystem model designed for large-scale applications, and how management affects modeled grassland–atmosphere CO2 fluxes. The new model, ORCHIDEE-GM (grassland management) is enabled with a management module inspired from a grassland model (PaSim, version 5.0), with two grassland management practices being considered, cutting and grazing. The evaluation of the results from ORCHIDEE compared with those of ORCHIDEE-GM at 11 European sites, equipped with eddy covariance and biometric measurements, shows that ORCHIDEE-GM can realistically capture the cut-induced seasonal variation in biometric variables (LAI: leaf area index; AGB: aboveground biomass) and in CO2 fluxes (GPP: gross primary productivity; TER: total ecosystem respiration; and NEE: net ecosystem exchange). However, improvements at grazing sites are only marginal in ORCHIDEE-GM due to the difficulty in accounting for continuous grazing disturbance and its induced complex animal–vegetation interactions. Both NEE and GPP on monthly to annual timescales can be better simulated in ORCHIDEE-GM than in ORCHIDEE without management. For annual CO2 fluxes, the NEE bias and RMSE (root mean square error) in ORCHIDEE-GM are reduced by 53% and 20%, respectively, compared to ORCHIDEE. ORCHIDEE-GM is capable of modeling the net carbon balance (NBP) of managed temperate grasslands (37 ± 30 gC m−2 yr−1 (P < 0.01) over the 11 sites) because the management module contains provisions to simulate the carbon fluxes of forage yield, herbage consumption, animal respiration and methane emissions.

International audience

Precise descriptions of forest productivity, biomass, and structure are essential for understanding ecosystem responses to climatic and anthropogenic changes. However, relations between these components are complex, in particular for tropical forests.[br/] We developed an approach to simulate carbon dynamics in the Amazon rainforest including around 410 billion individual trees within 7.8 million km(2). We integrated canopy height observations from space-borne LIDAR in order to quantify spatial variations in forest state and structure reflecting small-scale to large-scale natural and anthropogenic disturbances. Under current conditions, we identified the Amazon rainforest as a carbon sink, gaining 0.56 GtC per year. This carbon sink is driven by an estimated mean gross primary productivity (GPP) of 25.1 tC ha(-1) a(-1), and a mean woody aboveground net primary productivity (wANPP) of 4.2 tC ha(-1) a(-1). We found that successional states play an important role for the relations between productivity and biomass. Forests in early to intermediate successional states are the most productive, and woody above-ground carbon use efficiencies are non-linear. Simulated values can be compared to observed carbon fluxes at various spatial resolutions (> 40 m). Notably, we found that our GPP corresponds to the values derived from MODIS. For NPP, spatial differences can be observed due to the consideration of forest successional states in our approach. We conclude that forest structure has a substantial impact on productivity and biomass. It is an essential factor that should be taken into account when estimating current carbon budgets or analyzing climate change scenarios for the Amazon rainforest.

Key message [br/] We developed precise, consistent, generic, and robust biomass equations for seven aboveground tree components of sessile and pedunculate oaks. These equations can be used to accurately estimate carbon stocks and fluxes in and out of the forest. [br/] Context[br/] Large uncertainties still persist when using existing biomass equations for larger scale applications. [br/] Aims [br/] The objective of this study was to test two contrasting modeling approaches to obtain biomass estimates of various components (stem, stem wood, stem bark, crown, and three branch categories) for Quercus petraea and Quercus robur and to compare them in terms of predictive capacity, genericity, consistency, and robustness. [br/] Methods [br/] All models were calibrated on a total of 117 oak trees sampled over a wide range of sites and stands and further tested on an independent data set of 33 trees. The “empirical” approach consisted in declining a common allometric equation based on two variables (diameter at breast height and total height) into all its possible forms and selecting the final model on purely statistical performances; the “structural” method was based on the fitting of a priori dedicated model forms for each component to allow a clear interpretation of the model parameters. [br/] Results [br/] For the stem components, both approaches resulted in similar statistical performances despite difference in model forms and number of parameters. Although equally performant on the validation data set for the total crown, only the structural model gave satisfactory results when applied to the independent data set. Both approaches failed to accurately predict the branch fractions on the validation data set. [br/] Conclusion [br/] Using physically based model forms increased the robustness of the biomass equations.

Background: Capturing the response of forest ecosystems to inter-annual climate variability is a great challenge. In this study, we tested the capability of an individual-based forest gap model to display carbon fluxes at yearly and daily time scales. The forest model was applied to a spruce forest to simulate the gross primary production (GPP), respiration and net ecosystem exchange (NEE). We analyzed how the variability in climate affected simulated carbon fluxes at the scale of the forest model.[br/][br/] Results: Six years were simulated at a daily time scale and compared to the observed eddy covariance (EC) data. In general, the seasonal cycle of the individual carbon fluxes was correctly described by the forest model. However, the estimated GPP differed from the observed data on the days of extreme climatic conditions. Two new parameterizations were developed: one resulting from a numerical calibration, and the other resulting from a filtering method. We suggest new parameter values and even a new function for the temperature limitation of photosynthesis.[br/][br/] Conclusions: The forest model reproduced the observed carbon fluxes of a forest ecosystem quite well. Of the three parameterizations, the calibrated model version performed best. However, the filtering approach showed that calibrated parameter values do not necessarily correctly display the individual functional relations. The concept of simulating forest dynamics at the individual base is a valuable tool for simulating the NEE, GPP and respiration of forest ecosystems.

Background Evergreen coniferous forests contain high stocks of organic matter. Significant carbon transformations occur in litter and soil of these ecosystems, making them important for the global carbon cycle. Due to seasonal allocation of photosynthates to roots, carbon availability changes seasonally in the topsoil. The aim of this paper was to describe the seasonal differences in C source utilization and the involvement of various members of soil microbiome in this process. Results Here, we show that microorganisms in topsoil encode a diverse set of carbohydrate-active enzymes, including glycoside hydrolases and auxiliary enzymes. While the transcription of genes encoding enzymes degrading reserve compounds, such as starch or trehalose, was high in soil in winter, summer was characterized by high transcription of ligninolytic and cellulolytic enzymes produced mainly by fungi. Fungi strongly dominated the transcription in litter and an equal contribution of bacteria and fungi was found in soil. The turnover of fungal biomass appeared to be faster in summer than in winter, due to high activity of enzymes targeting its degradation, indicating fast growth in both litter and soil. In each enzyme family, hundreds to thousands of genes were typically transcribed simultaneously. Conclusions Seasonal differences in the transcription of glycoside hydrolases and auxiliary enzyme genes are more pronounced in soil than in litter. Our results suggest that mainly fungi are involved in decomposition of recalcitrant biopolymers in summer, while bacteria replace them in this role in winter. Transcripts of genes encoding enzymes targeting plant biomass biopolymers, reserve compounds and fungal cell walls were especially abundant in the coniferous forest topsoil. Electronic supplementary material The online version of this article (10.1186/s40168-017-0340-0) contains supplementary material, which is available to authorized users.

A mechanistic description of the global COS cycle consistent with atmospheric measurements and its potential to evaluate gross primary production of vegetation models. European Geosciences Union General Assembly 2016

A Land Data Assimilation System (LDAS) able to ingest surface soil moisture (SSM) and Leaf Area Index (LAI) observations is tested at local scale to increase prediction accuracy for water and carbon fluxes. The ISBA-A-gs Land Surface Model (LSM) is used together with LAI and the soil water content observations of a grassland at the SMOSREX experimental site in southwestern France for a seven-year period (2001–2007). Three configurations corresponding to contrasted model errors are considered: (1) best case (BC) simulation with locally observed atmospheric variables and model parameters, and locally observed SSM and LAI used in the assimilation, (2) same as (1) but with the precipitation forcing set to zero, (3) real case (RC) simulation with atmospheric variables and model parameters derived from regional atmospheric analyses and from climatological soil and vegetation properties, respectively. In configuration (3) two SSM time series are considered: the observed SSM using Thetaprobes, and SSM derived from the LEWIS L-band radiometer located 15 m above the ground. Performance of the LDAS is examined in the three configurations described above with either one variable (either SSM or LAI) or two variables (both SSM and LAI) assimilated. The joint assimilation of SSM and LAI has a positive impact on the carbon, water, and heat fluxes. It represents a greater impact than assimilating one variable (either LAI or SSM). Moreover, the LDAS is able to counterbalance large errors in the precipitation forcing given as input to the model.

A Monte Carlo-based calibration and uncertainty assessment was performed for heat, water and carbon (C) fluxes, simulated by a soil-plant-atmosphere system model (CoupModel), in mown grassland. Impact of different multi-objective and multi-criteria constraints was investigated on model performance and parameter behaviour. Good agreements between hourly modelled and measurement data were obtained for latent and sensible heat fluxes (R2?=?0.61, ME?=?0.48?MJ?m-2?day-1), soil water contents (R2?=?0.68, ME?=?0.34%) and carbon-dioxide flux (R2?=?0.60, ME?=?-0.18?g?C?m-2?day-1). Multi-objective and multi-criteria constraints were efficient in parameter conditioning, reducing simulation uncertainty and identifying critical parameters. Enforcing multi-constraints separately on heat, water and C processes resulted in the highest model improvement for that specific process, including some improvement too for other processes. Imposing multi-constraints on all groups of variables, associated with heat, water and C fluxes together, resulted in general effective parameters conditioning and model improvement. Uncertainty-based modelling was done for heat, water and carbon flux in grassland.Multi-objective and multi-criteria were enforced to constrain model simulations.Multi-objective and multi-criteria constraints were effective in model calibration.Different multi-constraints conditioned model parameters differently.Different multi-constraints improved the model performance in different way.

Tree secondary growth is responsible for woody biomass accumulation and is a major component of carbon storage in forest ecosystems. Environmental constraints on secondary growth in Mediterranean ecosystems must, however, be described in more to details to better understand how they will be modified by climate change. This dissertation aims at studying the functional responses of Mediterranean holm oak (Quercus ilex) to seasonal and inter-annual climate variations through the study of carbon allocation to secondary growth. Different experimental approaches, at spatial scales ranging from tree rings to the ecosystem and at temporal scales from the day to several decades, were used to identify the main environmental constraints (water availability, temperature warming, competition) to secondary growth and carbon isotopic composition of tree rings. The phenology of stem growth shows evidence for a direct environmental control on annual growth by winter temperature and summer drought that is more limiting than the carbon supply from photosynthesis. Climate change from 1968 to 2013 resulted in earlier water limitation on secondary growth, which was compensated by earlier growth onset, due to warmer winter temperature, and higher water use efficiency, due to increased atmospheric CO2 concentration. Thinning reduced tree mortality and increased stem growth, so thinning management in old holm oak coppices could prepare the ecosystem to better withstand the increasing drought forecasted for the Mediterranean region., La croissance secondaire est à l'origine de l'accumulation de biomasse pérenne par les arbres et détermine en partie la capacité des écosystèmes forestiers à stocker du carbone. Cependant, les contraintes environnementales sur la croissance en milieu méditerranéen sont encore mal décrites et nous ne savons pas comment les changements climatiques futurs vont les modifier. L'objectif de la thèse est de déterminer, principalement à partir de l'étude de l'allocation du carbone à la croissance secondaire, les réponses fonctionnelles saisonnières et interannuelles du chêne vert (Quercus ilex L.) aux variations climatiques en région méditerranéenne. L'utilisation de différentes approches expérimentales, à des échelles spatiales allant du cerne à l'écosystème et à des échelles temporelles allant de la journée à plusieurs dizaines d'années, a permis de mettre en évidence l'effet de différentes contraintes environnementales (disponibilité en eau, réchauffement de la température, et densité du peuplement) sur la croissance secondaire et la composition isotopique du cerne. L'étude de la phénologie de la croissance montre que celle-ci est contrôlée directement par les températures hivernales et le déficit hydrique, plus que par la disponibilité en éléments carbonés issus de la photosynthèse. De 1968 à 2013, les changements climatiques ont entrainé une contrainte hydrique de plus en plus précoce qui s'est trouvée compensée par un début de croissance initié plus tôt dans l'année, sous l'effet du réchauffement des températures hivernales, et une meilleure efficacité d'utilisation de l'eau, sous l'effet de l'augmentation de la concentration en CO2 atmosphérique. La réduction de la mortalité et l'augmentation de la croissance observée dans des parcelles éclaircies montre que cette pratique sylvicole permet de préparer les taillis de chêne vert à l'intensification de la sècheresse prévue pour la région méditerranéenne.

International audience; Predicting ecosystem responses to global change has become a major challenge, particularly as terrestrial ecosystems contribute to the mitigation of global climate change through carbon sequestration. Plant traits are major surrogates of ecosystem physiology may thus help to predict carbon (C) fluxes and their consequences for the delivery of ecosystem services (e.g. C sequestration) across climatic gradients and in changing environments. However, linkages between community abundance-weighted means (CWM) of plant functional traits and ecosystem C fluxes have rarely been tested. It is also not known to what degree traits, which are typically measured at a defined point in time, are suitable for predicting annual C fluxes. We analysed the relationships between ecosystem fluxes and community level plant traits for 13 European grasslands under contrasting climate and management regimes, using multiyear eddy covariance data. Plant traits (specific leaf area SLA, leaf dry matter content LDMC, specific root length SLR) were determined at peak biomass. Analyses showed that GPPmax (at maximum radiation) was related to SLA, SRL and LDMC across sites and management, where GPPmax was an excellent indicator for annual GPP. Similar relations were found between for root density (and -diameter) and ecosystem respiration. Ecosystems respiration at GPPmax was also in line with annual respiration, indicating the strong predictive potential of plant community traits. Our study therefore suggests that above- and belowground community level plant traits are well suited surrogates for predicting ecosystem C fluxes at peak biomass and at annual scale.

Following a volcanic eruption which killed almost 2000 people in Cameroon in 1986, the Délégation aux Risques Majeurs, a French Government Agency, requested a report evaluating the risks of a similar eruption of CO2 in Auvergne: this volcanic province of the French "Massif Central" has structures comparable with those which were at the location of the Cameroon eruption. The lake Pavin, 90 m deep, located in a volcanic crater, is of meromictic type: the annual circulation of water is incomplete with the deep layer, (60-90 m), remains stagnant year to year. This property was confirmed by ten profiles of the content of 3H of the water column. A weak inflow of water (about 0.1m3.m2.yr') at the bottom of the lake plays an important role in the geochemistry of the system. Application of the ofFick's laws estimates the influence of advection and diffusion in particular for conservative components such as I8O, Na*. Carbon isotopes measurements on total dissolved inorganic carbon and on dissolved gases (CO2 and CH4) showed that the deep carbon contribution comprising about 20 % due to fermentation of organic matter, 10% dissolved inorganic carbon in the advective water inflow and 70% by CO2 ofmagmatic origin. This contribution of mantle fluids was confirmed by 3He/4He measurement. If quantity of CO 2 dissolved at -90 m does not exceed 1 LCO2.LH2ó' whereas its solubility is, with 5 °C, of 1.5 LCO2.LH2O'.bar', it would be interesting to follow thepH deep water, not only of Pavin but also of the other deep lakes from Auvergne (Godivelle, Issarlès, Tazenat, Chau- vet) likely to transform into carbon dioxide tank., Résumé À la suite d'une éruption volcanique qui provoqua la mort de près de 2000 personnes au Cameroun en 1986, la Délégation aux Risques Majeurs demanda un rapport sur l'évaluation des risques d'une éruption de CO2 en Auvergne dans la mesure où cette province volcanique du Massif Central français présente des appareils et des lacs comparables à ceux qui furent à l'origine de la catastrophe de Nyos. Le lac Pavin, profond de 90 m, situé dans un cratère volcanique est de type méromictique car la circulation annuelle des eaux est incomplète et la couche profonde, de -60 à -90 m, reste stagnante d'une année sur l'autre. Cette méromicticité a été confirmée par une dizaine de profils de la teneur en 3H de la colonne d'eau. L'étude de ces profils de 3H a permis de mettre en évidence un flux d'eau profonde à la base du monimolimnion qui, s'il est faible (0,1 m3.m2.an"'), joue un rôle important dans la géochimie du système par l'apport d'éléments en solution. L'application des lois de Fick permet d'estimer les effets d'advection et de diffusion notamment pour les éléments ayant un comportement chimique conservatif (18O, Na% etc.). La mesure des isotopes du carbone sur le carbone minéral total dissous et sur les gaz (CO2 et CH4) a permis de montrer que l'apport profond de carbone comprend trois sources : 20 % dus à la fermentation méthanique de la matière organique, 10 % de carbone minéral total dissous dans le flux d'eau advectif du fond et 70 % de CO2 d'origine magmatique. Cet apport de fluides mantelliques est confirmé par la mesure du rapport isotopique 3He/4He. Si la quantité de CO2 dissous à -90 m ne dépasse pas 1 Lcqj.Ljko"1 alors que sa solubilité est, à 5 °C, de 1,5 LCO2.LH2O1.bar1, il serait intéressant de suivre le pH des eaux profondes, non seulement du lac Pavin mais aussi des autres lacs profonds d'Auvergne (Godivelle, Issarlès, Tazenat, Chau- vet) car ils sont susceptibles de se transformer en réservoir de gaz carbonique., Olive Philippe, Boulègue Jacques. Étude biogéochimique d'un lac méromictique : le lac Pavin, France / Biogeochemical study of a meromictic lake: Pavin lake, France. In: Géomorphologie : relief, processus, environnement, Octobre-décembre, vol. 10, n°4. pp. 305-316.

Predicting regional and global carbon (C) and water dynamics on grasslands has become of major interest, as grasslands are one of the most widespread vegetation types worldwide, providing a number of ecosystem services (such as forage production and C storage). The present study is a contribution to a regional-scale analysis of the C and water cycles on managed grasslands. The mechanistic biogeochemical model PaSim (Pasture Simulation model) was evaluated at 12 grassland sites in Europe. A new parameterization was obtained on a common set of eco-physiological parameters, which represented an improvement of previous parameterization schemes (essentially obtained via calibration at specific sites). We found that C and water fluxes estimated with the parameter set are in good agreement with observations. The model with the new parameters estimated that European grassland are a sink of C with 213?g?C?m-2?yr-1, which is close to the observed net ecosystem exchange (NEE) flux of the studied sites (185?g?C?m-2?yr-1 on average). The estimated yearly average gross primary productivity (GPP) and ecosystem respiration (RECO) for all of the study sites are 1220 and 1006?g?C?m-2?yr-1, respectively, in agreement with observed average GPP (1230?g?C?m-2?yr-1) and RECO (1046?g?C?m-2?yr-1). For both variables aggregated on a weekly basis, the root mean square error (RMSE) was ~5-16?g?C?week-1 across the study sites, while the goodness of fit (R2) was ~0.4-0.9. For evapotranspiration (ET), the average value of simulated ET (415?mm?yr-1) for all sites and years is close to the average value of the observed ET (451?mm?yr-1) by flux towers (on a weekly basis, RMSE~2-8?mm?week-1; R2?=?0.3-0.9). However, further model development is needed to better represent soil water dynamics under dry conditions and soil temperature in winter. A quantification of the uncertainties introduced by spatially generalized parameter values in C and water exchange estimates is also necessary. In addition, some uncertainties in the input management data call for the need to improve the quality of the observational system. A mechanistic biogeochemical pasture simulation model (PaSim) is improved by using a common set of eco-physiological parameters.PaSim was evaluated at 12 grassland sites in Europe, performing regional-scale analysis of carbon and water cycles.PaSim estimated that European grasslands are a carbon sink of 213?g?C?m-2?yr-1.PaSim overestimated the soil water content during dry periods.

International audience

We evaluate the ISBACC (Interaction Soil Biosphere Atmosphere Carbon Cycle) land surface model (LSM) over the Amazon forest, and propose a revised parameterization of photosynthesis, including new soil water stress and autotrophic respiration (RA) functions. The revised version allows the model to better capture the energy, water and carbon fluxes when compared to five Amazonian flux towers. The performance of ISBACC is slightly site dependent although similar to the widely evaluated LSM ORCHIDEE (Organizing Carbon and Hydrology In Dynamic Ecosystems – version 1187), which is based on different assumptions. Changes made to the autotrophic respiration functions, including a vertical profile of leaf respiration, lead to yearly simulated carbon use efficiency (CUE) and carbon stocks which is consistent with an ecophysiological meta-analysis conducted on three Amazonian sites. Despite these major improvements, ISBACC struggles to capture the apparent seasonality of the carbon fluxes derived from the flux tower estimations. However, there is still no consensus on the seasonality of carbon fluxes over the Amazon, stressing a need for more observations as well as a better understanding of the main drivers of autotrophic respiration.

Impacts des modes de gestion des prairies temporaires sur l'évolution des stocks de carbone et les flux environmentaux. Scéance de l'académie d'Agriculture de France : Prairies, environnement et territoires

Les flux de carbone et les paramètres environnementaux relevées de manière continue de 2004 à 2012 sur le site Guyaflux dans la forêt tropicale humide de Paracou en Guyane Française ont été l’objet d’une étude dans le but de mieux comprendre l’influence du climat sur les bilans de carbone entre la forêt et l’atmosphère. J’ai eu deux approches statistiques complémentaires dans le cadre de cette étude en utilisant des méthodes adaptées aux séries temporelles d’une part et des méthodes corrélatives d’autre part. J’ai ainsi pu mettre en évidence que le rayonnement global est le principal facteur explicatif des bilans de carbone saisonniers et de leurs variations inter-annuelles. Ce travail a par ailleurs permis d’observer que contrairement à ce qui était attendu, la saison humide était responsable de la plus large partie du puits de carbone annuel. Ce comportement particulier devra être expliqué par des études complémentaires.

Soil organic carbon (SOC) concentrations and greenhouse gas (GHG) emissions are not uniform across the landscape, but assemble in “hotspots” in specific areas. These differences are mainly driven by human-induced activities such as agricultural management. 40-50% of the Earth’s land surface is under agricultural land-use, for instance cropland, managed grassland and permanent crops including agro-forestry and bio-energy crops. Furthermore, 62% of the global soil C stock is SOC and the soil stores more than 3 times more C than the atmosphere. Thus, C sequestration in agricultural soil has a potentially important role in increasing SOC storage and GHG mitigation, and there is considerable interest in understanding the effects of agricultural management on SOC and GHG fluxes in both grasslands and croplands, in order to better assess the uncertainty and vulnerability of terrestrial SOC reservoirs. For the sake of discovering the agricultural management practices relating to the effective and sustainable C sequestration in agricultural lands in Europe, simulating future terrestrial C stocks and GHG budgets under varied agricultural management systems in major European ecosystems is essential. Using models is a useful method with the purpose of this and abundant studies have carried out. However, many model results have not been validated with reliable observed long-term data, while other studies have reported a strong impact of model initialisation on model result. Nevertheless, predictions of annual to decadal variability in the European terrestrial C and GHG ressources largely rely on model results. Consequently, finding the most appropriate and comprehensive model initialisation method for obtaining reliable model simulations became important, especially for process-based ecosystem models. In recent years, Zimmermann et al. (2007) have succeed in initialising the Rothamsted Carbon model (RothC) using a physical and chemical soil fractionation method. For that reason, we hypothesised that measured detailed SOC data would be useful to initialise ecosystem models, and this hypothesis should be tested for different process-based models and agricultural land-use and management. (...); La concentration de Carbone organique de sol (COS) et les émissions de gaz à effet de serre (GES) ne sont pas uniformes à travers l’espace, mais se regroupent en “hotspots” dans des endroits spécifiques. Ces différences s’expliquent principalement par les activités anthropiques telles que la gestion agricole. 40-50% de la surface de la Terre est utilisé par l’agriculture, par exemple les terres cultivées, les prairies gérées et cultures permanentes, y compris l’agro-foresterie et de bio-cultures énergétiques. En outre, 62% du carbone globale est COS, et le sol conserve plus que 3 fois plus de C que l’atmosphère. Ainsi, la séquestration du carbone dans les sols agricoles joue un rôle potentiellement important dans l’augmentation de stockage de COS et l’atténuation des GES, et il y a un intérêt considérable pour comprendre les effets de la gestion agricole sur le COS et les flux de GES aux prairies et terres cultivées, afin de mieux évaluer l’incertitude et la vulnérabilité des réservoirs de COS. Afin de découvrir les pratiques de gestion agricole qui contribuent à la séquestration efficace et durable du carbone aux terres agricoles en Europe, il est essentiel de simuler les stocks futurs de carbone terrestriel et les budgets de GES par rapport aux systèmes de gestion agricole variés sur les grands écosystèmes européens. Dans ce contexte, la modélisation est une méthode utile, et la modélisation a déjà été utilisée dans beaucoup d’études. Cependant beaucoup de résultats de la modélisation n’ont pas encore été validés avec les données mesurées sur l’horizon long-terme, et d’ailleurs d’autres études ont constaté un fort impact de l’initialisation du modèle sur le résultat du modèle. Néanmoins, la variabilité des prévisions annuelles et décennales concernant le C et le GES en Europe dépendent des résultats du modèle. Par conséquence, il est important de trouver la meilleure méthode d’initialisation des modèles pour obtenir des résultats des modèles fiables, notamment pour les modèles d’écosystèmes dits “process-based”. Au cours des dernières années, Zimmermann et al. (2007) a réussit à initialiser le modèle de Rothamsted carbone (RothC) en utilisant une méthode (physique et chimique) de fractionation des sols. Pour cette raison, j’ai fait l’hypothèse que les données COS détaillées seraient utiles pour initialiser des modèles d’écosystème, et que cette hypothèse doit être testée avec les modèles différents par rapport aux gestions agricoles différentes. Les buts de cette thèse sont les suivants: i) évaluation des influences des gestions agricoles sur le stockage de COS, en utilisant des approches expérimentales et des approches de modélisation; et ii) déterminer la meilleur méthode d’initialisation des modèles. (...)

The carbon isotope composition of the CO2 efflux (δ13CE) from ecosystem components is widely used to investigate carbon cycles and budgets at different ecosystem scales. δ13CE, was considered constant but is now known to vary along seasons. The seasonal variations have rarely been compared among different ecosystem components. We aimed to characterise simultaneously the seasonal dynamics of δ13CE in different compartments of two temperate broadleaved forest ecosystems. Using manual chambers and isotope ratio mass spectrometry, we recorded simultaneously δ13CE and δ13C of organic matter in sun leaves, current-year twigs, trunk bases and soil in an oak and a beech forest during 1 year. In the two forests, δ13CE displayed a larger variability in the tree components than in the soil. During the leafy period, a pronounced vertical zonation of δ13CE was observed between the top (sun leaves and twigs with higher values) and bottom (trunk and soil with lower values) of the ecosystem. No correlation was found between δ13CE and δ13C of organic matter. Causes for these seasonal variations and the vertical zonation in isotope signature are discussed. Our study shows clear differences in values as well as seasonal dynamics of δ13CE among different components in the two ecosystems. The temporal and local variation of δ13CE cannot be inferred from organic matter signature or CO2 emission rates.

National audience

The development of a new organ is the results of coordinated events of cell division and expansion. Fruit growth starts immediately after bloom with intensive cell division. As development proceeds, the proliferative activity of cells progressively slows down giving way to a phase of pure cell enlargement, during fruit growth and ripening. Modeling the way cell division and expansion progress together is crucial to understand the emergence of specific morphological traits ( fruit size, weight, shape and texture) and their dependence on environmental factors. Models already exist for cell division and late fruit growth ( cell expansion), but the coupling of the two processes have not been addressed yet in fruit. Here we propose a first integrated model of tomato fruit development, explicitly coupling cell proliferation and expansion. The model is used to predict the evolution of cell number, size and ages during fruit development, under different environmental conditions.

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.

National audience; Une des attentes forte de la société et des décideurs politiques est de mieux comprendre et de pouvoir anticiper les réponses des agro-écosystèmes aux changements climatiques et atmosphériques anticipés. La prévision sur le long-terme de ces impacts sur la contribution des agro-écosystèmes à l’effet de serre et sur leur potentiel d’atténuation des émissions permis par le stockage de carbone dans la matière organique des sols repose nécessairement sur l’utilisation de modèles ; ce type d’outil permettant de confronter ses sorties (résultats) aux données observes ou mesurés dans des situations réelles, et d’en tirer des questionnements sur notre capacité à comprendre ou à prédire le système étudié.

L’objectif principal de ce travail était de caractériser la variabilité saisonnière des échanges gazeux des arbres de la canopée en forêt tropicale humide guyanaise confrontés à des saisons sèches. L’étude s’est orientée sur (i) la description des amplitudes de fonctionnement des arbres de la canopée en conditions hydriques non-limitantes, au niveau foliaire et ligneux, (ii) la caractérisation du déficit hydrique saisonnier du sol et son impact sur le statut hydrique des arbres, (iii) la mesure des flux gazeux carbonés et hydriques au cours des saisons sèches dans deux habitats contrastés du point de vue hydrique, afin de préciser leur sensibilité et réponse à la sècheresse. Nous avons mis en évidence une très forte variabilité des échanges gazeux foliaires des arbres de la canopée, en conditions environnementales similaires. Ces résultats confirment la forte variabilité inter-arbre observée précédemment pour les compositions isotopiques ou chimiques des feuilles, et les compromis entre acquisition et conservation des ressources au niveau des feuilles et des troncs, mais nous avons montré par ailleurs qu’à l’échelle de l’arbre, ces compromis sont totalement indépendants entre le compartiment feuille et tronc. Nos résultats montrent qu’une proportion non négligeable d’arbres ne subit pas de sécheresse marquée en saison sèche, malgré la forte diminution de la teneur en eau du sol en surface. Nous faisons l’hypothèse que ces arbres possèdent alors des racines en profondeur qui leur permettent d’accéder aux horizons qui restent humides malgré la faible pluviométrie. Durant les longues saisons sèches, nous observons une diminution de l’assimilation nette de CO2 foliaire, de l’efflux de CO2 des troncs ou de la densité de flux de sève, et dans une moindre mesure de la respiration foliaire, pour une majorité d’arbres. Néanmoins, de grandes différences de réponse à la sècheresse du sol ont été observées, suggérant des sensibilités et des mécanismes de réponse différents entre ces arbres. De plus, ces variations sont plus importantes, et concernent un nombre plus important d’arbres, quand l’intensité de la sécheresse est plus forte (2008 par rapport à 2007). Ces résultats sont cohérents avec les variations saisonnières des échanges gazeux entre l’écosystème et l’atmosphère. Ils montrent que les variations à l’échelle de l’écosystème résultent de la réponse à la sécheresse d’une partie seulement des arbres, et non de l’ensemble de la communauté. En habitat de bas-fond (SFF, Seasonal Flooded Forest), nous montrons une plus faible diminution des flux carbonés et hydriques en saison sèche, suggérant un accès pour ces arbres aux horizons humides, proches de la nappe phréatique (-1.0 m de profondeur environ). Par ailleurs, nos résultats suggèrent pour certains arbres un effet négatif des conditions d’anoxie sur ces flux en saison des pluies. D’autres arbres néanmoins ne montrent pas de réponse à ces conditions d’anoxie, suggérant une forte tolérance. Si l’accentuation de l’intensité des saisons sèches en forêt tropicale humide Amazonienne, comme suggérée par les modèles climatiques, se confirme au cours des prochaines décennies, ce travail suggère des réponses différenciées entre espèces à ces contraintes, qui pourraient se traduire par une modification rapide de la composition spécifique des forêts, au profit des espèces plus résistantes aux contraintes hydriques., The aim of this work was to characterize the seasonal variations in leaf and trunk gas exchange of tropical rainforest canopy trees exposed to dry seasons. This study focused on (i) describing the functional variability of leaf and wood characteristics of canopy trees, (ii) defining soil water deficit in dry season, (iii) measuring gas exchange (CO2 and H2O) at the leaf and trunk level during dry seasons in a Terra firme forest and in a seasonally flooded forest in order to specify their sensitivity and response to drought. We showed large differences in morphological and functional traits among canopy trees and strong correlations among traits, and pointed that trade-offs at the leaf or the trunk levels are independent. Our results showed that part of the studied trees do not encounter a large reduction in soil water content during dry seasons, suggesting that they display deep rooting systems. During long dry periods, we recorded a decrease in leaf photosynthesis, trunk CO2 efflux or sap flow density, and foliar respiration to a lesser extent, for a majority of the trees. Nevertheless, large differences among trees in their response to these conditions were observed, suggesting distinct sensitivities and response to soil drought among trees. Furthermore, these variations were greatest when soil drought was highest (2008 as compared to 2007). In seasonally flooded forest, the decrease in gas exchange was less, suggesting that these trees do have access to wet layers during the dry season, close to the groundwater. However, during wet seasons, we observed a negative effect of anoxia for some trees, whereas others did not display any response, suggesting large differences in tolerance to anoxia among trees abundant in these seasonally flooded forests. We conclude that would seasonal soil droughts increase over the next decades, large vegetation changes might occur because of the large differences among trees in their functional response to soil drought conditions.

This PhD work aimed at studying the functioning of the Ascophyllum nodosum zone, a macroalgal belt characteristic of the midintertital zone of sheltered rocky shores from the North Atlantic coasts. This study allowed to establish (1) the stocks of A. nodosum available for harvesting along the Brittany coast (France) together with the algal and animal communities; (2) a heterotrophic annual carbon budget for the A. nodosum zone, dominated by the fluxes due to the canopy; (3) the general trophic web architecture of the zone, characterized by the use of most of the sources of organic matter instead of being only based on the main primary producers of the zone; (4) the effect of partially or totally harvesting the canopy on the specific and functional diversity and the metabolism of the zone. It was also possible to compare the matabolism of the zone to that of other neighbouring canopy covered zone and to the metabolism of a zone without canopy. This study allowed better identifying the functional role of the canopy on the regulation of the biodiversity and on the functioning of rocky shores.; L'objectif de ce travail de thèse était l'étude du fonctionnement de la zone à Ascophyllum nodosum, une ceinture algale caractéristique de la zone médiolittorale des estrans rocheux abrités des côtes de l'Atlantique Nord. Cette étude a permis d'établir (1) l'état des stocks d'A. nodosum disponibles à la récolte le long des côtes de Bretagne et des communautés algales et animales associées ; (2) un bilan annuel de carbone de la zone à A. nodosum hétérotrophe, dominé par le flux dus à la canopée ; (3) l'architecture générale du réseau trophique de la zone, basée sur l'utilisation de la plupart des sources de matière organique et pas seulement sur celle des principaux producteurs primaires ; (4) l'effet de la récolte partielle ou totale de la canopée sur la diversité spécifique, fonctionnelle et le métabolisme de la zone. Il a également été possible de comparer le métabolisme de la zone à celui d'autres ceintures algales voisines et à une zone dépourvue de canopée. Cette étude a permis de mieux préciser le rôle fonctionnel joué par la canopée sur la régulation de la biodiversité et sur le fonctionnement des estrans rocheux.

This PhD work aimed at studying the functioning of the Ascophyllum nodosum zone, a macroalgal belt characteristic of the midintertital zone of sheltered rocky shores from the North Atlantic coasts. This study allowed to establish (1) the stocks of A. nodosum available for harvesting along the Brittany coast (France) together with the algal and animal communities; (2) a heterotrophic annual carbon budget for the A. nodosum zone, dominated by the fluxes due to the canopy; (3) the general trophic web architecture of the zone, characterized by the use of most of the sources of organic matter instead of being only based on the main primary producers of the zone; (4) the effect of partially or totally harvesting the canopy on the specific and functional diversity and the metabolism of the zone. It was also possible to compare the matabolism of the zone to that of other neighbouring canopy covered zone and to the metabolism of a zone without canopy. This study allowed better identifying the functional role of the canopy on the regulation of the biodiversity and on the functioning of rocky shores.; L'objectif de ce travail de thèse était l'étude du fonctionnement de la zone à Ascophyllum nodosum, une ceinture algale caractéristique de la zone médiolittorale des estrans rocheux abrités des côtes de l'Atlantique Nord. Cette étude a permis d'établir (1) l'état des stocks d'A. nodosum disponibles à la récolte le long des côtes de Bretagne et des communautés algales et animales associées ; (2) un bilan annuel de carbone de la zone à A. nodosum hétérotrophe, dominé par le flux dus à la canopée ; (3) l'architecture générale du réseau trophique de la zone, basée sur l'utilisation de la plupart des sources de matière organique et pas seulement sur celle des principaux producteurs primaires ; (4) l'effet de la récolte partielle ou totale de la canopée sur la diversité spécifique, fonctionnelle et le métabolisme de la zone. Il a également été possible de comparer le métabolisme de la zone à celui d'autres ceintures algales voisines et à une zone dépourvue de canopée. Cette étude a permis de mieux préciser le rôle fonctionnel joué par la canopée sur la régulation de la biodiversité et sur le fonctionnement des estrans rocheux.

International audience

Wildfire may lead to long-term soil carbon gain or loss, depending on the ability of the system to conserve chemically stable black carbon (BC). Rainfall events can lead to erosion of this organic matter form deposited on the soil surface. The objective of this study was to quantify horizontal as well as vertical BC transport during a rainfall simulation experiment with sandy soil in northern Senegal. The conceptual approach consisted of artificial burning of harvested residues, which were subsequently exposed to two different rainfall regimes: with and without occurrence of splash. After the rainfall simulation experiment, we quantified the total amount of carbon added to the soil and chemically recalcitrant black carbon (BC) (1) exported from the plots, (2) infiltated into the soil and (3) remaining on the soil surface. Transport processes affected around 40-60 % of the total carbon and BC added. Our results showed that 30 % of the total carbon added by the fire was exported from the site, whereas another 15 % were vertically transported into the soil. BC, which represented about 40 % of the total carbon added, was transported in higher proportions compared to total C (horizontally as well as vertically) when the splash erosion was allowed to occurr. The preferential export of BC was strongly dependent on the rainfall regime: when splash erosion was suppressed, BC export was greatly reduced, whereas BC infiltration increased compared to rainfall with splash occurring.We conclude that water erosion of BC during rainfall events after wildfire is an important factor determining the fate of potentially stable carbon in the ecosystem.

National audience

The data quality and the selection of the correct Eddy Covariance (EC) records become an important step in the CO2 flux determination procedure. An innovative combination of existing assessment tests is used to give a relatively complete evaluation of the net ecosystem exchange measurements. For the 2005 full-leaf season at the Hesse site, the percentage of bad quality data is relatively high (59.6%) especially during night-time (68.9%). This result strengthens the importance of the data gap filling method. The filtering used does not lead to a real improvement of the accuracy of the relationship between the CO2 fluxes and the climatic factors. The soil respiration spatial heterogeneity (on a site with relatively homogenous vegetation pattern) seems to be too important to allow this improvement. However, the data rejected present some common characteristics. Their removal lead to a 10% increase in the total amount of CO2 respired (Reco) and photosynthesised (GPP) during the 2005 full-leaf season. Consequently the application of our combination of multiple quality tests is able improve the inter-annual analysis. The question of a systematic application on the large database like the CarboEurope and FLUXNET is legitimate.

International audience; This work proposed a model of tomato growth adapted from the Fishman and Genard model developed to predict carbon and water accumulation in peach fruit. The main adaptations relied on the literature on tomato and mainly concerned: (i) the decrease in cell wall extensibility coefficient during fruit development; (ii) the increase in the membrane reflection coefficient to solute from 0 to 1, which accounted for the switch from symplasmic to apoplasmic phloem unloading, and (iii) the negative influence of the initial fruit weight on the maximum rate of active carbon uptake based on the assumption of higher competition for carbon among cells in large fruits containing more cells. A sensitivity analysis was performed and the model was calibrated and evaluated with satisfaction on 17 experimental datasets obtained under contrasting environmental (temperature, air vapour pressure deficit) and plant (plant fruit load and fruit position) conditions. Then the model was used to analyse the variations in the main fluxes involved in tomato fruit growth and accumulation of carbon in response to virtual carbon and water stresses. The conclusions are that this model, integrating simple biophysical laws, was able to simulate the complex fruit behaviour in response to external or internal factors and thus it may be a powerful tool for managing fruit growth and quality

Predicting the response of grazed grasslands to elevated C02 is of central importance in global change research as grasslands represent 20% of the worlds land area and grassland soils are a major sink for carbon (C). Grasslands responses to elevated C02 are strongly controlled by the availability of other nutrients and nitrogen (N) in particular. There have been many previous studies of N cycling in grasslands exposed to elevated C02 but none of these experiments were grazed. In this thesis I present data on C02 effects on N cycling from an experimental system (FACE: Free Air Carbon dioxide Enrichment) that enabled grazing to be included. The thesis focuses on the effects of elevated C02 on the different processes involved in organic matter (OM) returns from the plant to the soil and the consequences for N availability. In Chapter 1, it was shown that e1evated C02 modified N returns by grazing animals by altering the partitioning of N between faeces and urine creating a potential for enhanced N losses at elevated C02. Plant litter decomposition rates were, at the ecosystem scale, not affected by elevated C02 (Chapter 3), but a marked increase in the organic matter fluxes, from roots, led to an accumulation of coarse OM in the soil (Chapter 4). In Chapter 5, using 14C and 15N labelling, I compared short-term (plant mediated) and long-term (soil mediated) effects of elevated C02 on soil OM dynamics and concluded that soil OM accumulation under elevated C02 was not caused by C or N limitation but probably by the availability of other nutrients. The thesis demonstrates that the inclusion of grazing animals can strongly modify N cycling under elevated C02. As most grasslands are grazed, the prediction of grassland responses to elevated CO2 must be derived from systems in whichanimais are an integral part., Prédire la réponse des prairies pâturées à une élévation de la concentration en CO2 revêt une importance majeure dans la mesure où cet écosystème représente environ 20% de la surface terrestre non immergée mais aussi, parce que les sols prairiaux représentent un puit majeur de carbone (C). La réponse des prairies à un enrichissement en CO2 est fortement contrôlée par la disponibilité des autres nutriments et en particulier l'azote (N). De nombreuses expériences ont par le passé étudié le cycle de l'azote en prairie sous CO2 enrichi mais aucunes de ces études n'a inclus le pâturage. Dans le cadre de cette thèse, je présente des données concernant les effets du CO2 sur le cycle de l'N provenant d'un système expérimental (FACE: enrichissement en dioxyde de carbone à l'air libre) permettant d'inclure des ruminants. Cette thèse est dédiée à l'étude des effets de l'élévation en CO2 sur les différents processus impliqués dans les retours de matière organique (MO) de la plante vers le sol et leurs conséquences pour la disponibilité en N. Dans le Chapitre 1, il a été montré que le CO2 pouvait modifier les retours d'N par les ruminants en affectant la partition d'N entre l'urine et les faeces, ce qui induisait des pertes d'N potentiellement accrues. La décomposition de la litière végétale, considérée à l'échelle de l'écosystème, n'a pas été affectée par le CO2 (Chapitre 3) mais une forte augmentation du volume de MO retournant au sol depuis les racines a induit une accumulation de MO grossière dans le sol (Chapitre 4). Au cours du Chapitre 5, à l'aide d'un double marquage isotopique 14C et 15N, nous avons comparé les effets court terme (transmis par la plante) et long terme (transmis par le sol) du CO2 sur la dynamique de la MO du sol et il a été conclu que l'accumulation de MO n'était pas causée par une limitation en C ou en N mais probablement par la disponibilité en autres nutriments. Cette thèse démontre que l'inclusion des ruminants peut fortement modifier la réponse des prairies au CO2. Dans la mesure où ce mode d'utilisation des pâtures est largement majoritaire, prédire les réponses des pâtures à un enrichissement en CO2 doit provenir de systèmes où les ruminants sont partie intégrante.

Diplôme : Dr. d'Universite

A method involving labeling to isotopic steady state and modeling of the tricarboxylic acid cycle has been used to identify the respiratory substrates in lettuce embryos during the early steps of germination. We have compared the specific radioactivities of aspartate and glutamate and of glutamate C-1 and C-5 after labeling with different substrates. Labeling with [U-14C]acetate and 14CO2 was used to verify the validity of the model for this study; the relative labeling of aspartate and glutamate was that expected from the normal operation of the tricarboxylic acid cycle. After labeling with 14CO2, the label distribution in the glutamate molecule (95% of the label at glutamate C-1) was consistent with an input of carbon via the phosphoenolpyruvate carboxylase reaction, and the relative specific radioactivities of aspartate and glutamate permitted the quantification of the apparent rate of the fumarase reaction. CO2 and intermediates related to the tricarboxylic acid cycle were labeled with [U-14C]acetate, [1-14C] hexanoate, or [U-14C]palmitic acid. The ratios of specific radioactivities of asparate to glutamate and of glutamate C-1 to C-5 indicated that the fatty acids were degraded to acetyl units, suggesting the operation of beta-oxidation, and that the acety-CoA was incorporated directly into citrate. Short-term labeling with [1-14C]hexanoate showed that citrate and glutamate were labeled earlier than malate and aspartate, showing that this fatty acid was metabolized through the tricarboxylic acid cycle rather than the glyoxylate cycle. This was in agreement with the flux into gluconeogenesis compared to efflux as respiratory CO2. The fraction of labeled substrate incorporated into carbohydrates was only about 5% of that converted to CO2; the carbon flux into gluconeogenesis was determined after labeling with 14CO2 and [1-14C]hexanoate from the specific radioactivity of aspartate C-1 and the amount of label incorporated into the carbohydrate fraction. It was only 7.4% of the efflux of respiratory CO2. The labeling of alanine indicates a low activity of either a malic enzyme or the sequence phosphoenolpyruvate carboxykinase/pyruvate kinase. After labeling with [U-14C]glucose, the ratios of specific radioactivities indicated that the labeled carbohydrates contributed less than 10% to the flux of acetyl-CoA. The model indicated that the glycolytic flux is partitioned one-third to pyruvate and two-thirds to oxalacetate and is therefore mainly anaplerotic. The possible role of fatty acids as the main source of acetyl-CoA for respiration is discussed.