Cette thèse porte sur l’impact du type de sol sur le fonctionnement biogéochimique d’un écosystème forestier typique d’Europe centrale et occidentale. Pour cette étude, un dispositif expérimental a été mis en place par l’INRA et l’ANDRA au sein d’une hêtraie (Fagus sylvatica) dans la forêt de Montiers-sur-Saulx (Meuse, France) afin de suivre les cycles biogéochimiques entre les différents compartiments de l’écosystème (l’atmosphère, la canopée, la litière et le sol). L’intérêt particulier du site expérimental de Montiers vient du contraste important entre les types de sols pour un même peuplement : rendisol, calci-brunisol et alocrisol/brunisol. Pour la première fois, les stocks et les flux de l’eau et des éléments ont été mesurés et comparés in situ et sur le long terme (entre janvier 2012 et décembre 2015) sur des sols forestiers différents, toutes les autres conditions du site égales par ailleurs (climat, apports atmosphériques, âge et structure du peuplement). Les stocks totaux et échangeables dans le sol et les stocks dans les différents compartiments de la biomasse végétale (branches, tronc, racines grosses et fines) ont été déterminés par le biais d’analyses chimiques et de modélisations. Les flux élémentaires ont été calculés à partir des prélèvements mensuels des solutions de l’écosystème (dépôt atmosphérique, pluviolessivat, écoulement de tronc, solutions libres et liées du sol) et des chutes de litière. Le modèle hydrique BILJOU© a été utilisé pour estimer les composantes du bilan hydrique de l’écosystème. Les résultats montrent que la réserve utile du sol, les stocks des éléments dans le sol, les compositions chimiques des solutions du sol, la stratégie de colonisation racinaire et la production de biomasse pérenne diffèrent fortement en fonction du type de sol. Contrairement à ce que l’on pouvait supposer compte tenu des différences marquées entre les signatures chimiques des solutions des trois sols, les compositions foliaires du peuplement et les flux des éléments hors sol en solution (échange de la canopée, apport au sol) et sous forme solide (chute de litière) ne diffèrent pas ou peu entre les trois stations expérimentales pour la majorité des éléments. La part biologique des cycles minéraux est globalement prédominante et le renouvellement des racines fines représente un flux de recyclage généralement supérieur à la chute de litière aérienne. Nous montrons également que la quantité d’eau transpirée par la canopée, directement liée à la taille de la réserve utile du sol, est le facteur de contrôle principal de la productivité du peuplement à l’échelle annuelle. Des processus d’adaptation du peuplement aux conditions physico-chimiques du sol semblent réduire, voire compenser entièrement, les facteurs secondaires de contrôle de la productivité du peuplement (notamment la disponibilité des nutriments dans le sol). Ainsi un enjeu significatif pour les gestionnaires forestiers pourrait être l’adaptation des pratiques sylvicoles à des parcelles de gestion davantage basées sur les propriétés physiques des sols, et en particulier les profondeurs d’apparition de la roche-mère et de colonisation racinaire / This thesis deals with the impact of soil type on the biogeochemical functioning of a typical forest ecosystem of Central and Western Europe. For this study, a strongly instrumented experimental site was implemented in a beech stand (Fagus sylvatica) within the state forest of Montiers-sur-Saulx (Meuse, France), in order to monitor the biogeochemical cycling between the different compartments of the ecosystem (the atmosphere, the canopy, the forest floor and the soil). The particular value of the Montiers experimental site resides in the strong contrast between soil types under the same beech stand: Rendzic Leptosol, Eutric Cambisol and Dystric Cambisol. For the first time, stocks and fluxes of water and elements were measured and compared in situ and over the long term (from January 2012 to December 2015) on different forest soil types, all other site conditions being equal (climate, atmospheric inputs, stand age and structure). Total and exchangeable pools in the soil and stocks in the different compartments of the vegetation (branches, trunk, fine and coarse roots) were determined via chemical analysis and modelisation. Fluxes of elements were calculated from monthly sampling of the ecosystem’s solutions (atmospheric deposition, throughfall, stemflow, gravitational and bound soil solutions) and of litter fall. The water balance model BILJOU© was used to estimate the different components of the water budget. The results show that the soil water holding capacity, the stocks of elements in the soil, the chemical composition of soil solutions, the rooting strategy and the perennial biomass production differ strongly between soil types. Contrary to what might have been expected in regard to the marked differences between the chemical signatures of the soils solutions in the three soils, the foliar elemental composition of the beech stand and the aboveground fluxes of elements in solution (canopy exchange, stand deposition) and in solid state (litter fall) do not differ significantly between the three experimental stations for the majority of the studied elements. The biological part of the mineral cycles is overall predominant and the recycling through fine roots turnover is generally higher than litter fall. We also show that the quantity of water transpired by the forest canopy, directly linked to the soil water holding capacity, is the primary control factor of the annual stand productivity. Stand adaptation mechanisms to physico-chemical soil properties seemed to reduce, or even entirely compensate for, secondary factors controlling the stand productivity (in particular nutrient availability in the soil). Thus a significant issue for forest managers might be to further adapt forestry practices to management units based on soil physical properties, especially depth to the bedrock and rooting depth

A dinâmica do carbono, nas fases orgânica, inorgânica e gasosa, foi analisada em um ponto na Baía de Caxiuanã e em três pontos no seu afluente Rio Curuá (porções superior, intermediária e inferior) um sistema fluvial de escoamento lento na Amazônia Oriental (Brasil estado do Pará) durante 31 campanhas, de janeiro de 2007 até dezembro de 2009. O objetivo foi avaliar mudanças intra e inter-anuais como função da hidrologia neste preservado rio de água preta. Medições em diferentes profundidades mostraram a formação de estratos físico-químicos, evidenciando o aspecto lêntico nos setores médio e baixo do rio Curuá, com eventos de concentrações extremamente baixas de oxigênio dissolvido durante o período de cheia, como conseqüência da entrada de insumos e da decomposição da matéria orgânica dos ecossistemas terrestres. Devido a esse aspecto, o DOC foi a forma dominante das fases orgânica e inorgânica do carbono, mostrando positiva e significativa correlação com o nível do rio, como resultado de um grande controle de entrada de insumos laterais. As formas particuladas orgânicas não mostraram as mesmas características em nenhum ponto, provavelmente em função da reduzida corrente de água que permite a rápida deposição desses materiais logo após sua entrada no sistema fluvial. As concentrações mais elevadas de CPOC e FPOC observadas na Baía de Caxiuanã parecem ser um sinal da presença de comunidade de fitoplâncton assim como da influência do vento, que ressuspende os sedimentos de fundo nesse ambiente. A concentração de dióxido de carbono exibiu altos valores comparados com a atmosfera, ratificando a bem conhecida característica heterotrófica dos rios amazônicos. Além disso, os baixos níveis de oxigênio observados induziram o consumo de matéria orgânica por bactérias anaeróbias, resultando em altas concentrações de metano, como observado no setor médio do rio Curuá. Assim como ocorreu com as formas particuladas orgânicas, os aspectos ecológicos e geológicos singulares da Baía de Caxiuanã distinguem seu habitat pelos baixos valores de dióxido de carbono quando comparados com a atmosfera, revelando um ambiente com diferente dinâmica biogeoquímica. / Dynamic of carbon, at organic, inorganic, and gas phases, was analyzed in one station at Caxiuanã Bay and three stations on its tributary Curuá River (upper, middle and lower sections) a slow flowing river system in Eastern Amazon (Brazil Pará State) during 31 campaigns, from January 2007 through December 2009. The objective was to evaluate intra and interannual changes as function of hydrology in this undisturbed blackwater river. Measures on different depths showed formation of physicochemical strata, evidencing the lentic aspect on middle and lower sections of Curuá River, with events of extremely low concentrations of dissolved oxygen during high water level, as a consequence of inputs and decomposition of organic matter from terrestrial ecosystems. Due to this aspect, DOC was the dominant form of organic and inorganic carbon phases, showed positive and significant correlation with river stage level for all sites, as result of a large control by lateral inputs. Particulate organic forms did not show the same characteristics in any station, probably as function of reduced water current which enable rapid deposition of these materials soon after their entrance on river system. The higher concentrations of CPOC and FPOC observed at Caxiuanã Bay seem to be a signal of presence of phytoplankton community as well as wind influence which resuspend bottom sediments in this environment. Carbon dioxide concentration on river exhibited higher values compared to atmosphere, ratifying the well-known heterotrophic characteristic of Amazon rivers. Furthermore, observed low levels of oxygen induced organic matter consumption by anaerobic bacteria, resulting in high concentrations of methane, as observed in the middle section of Curuá River. As occurred with particulate organic forms, the singular geologic and ecologic aspects of Caxiuanã Bay distinguish its habitat by low values of carbon dioxide when compared to atmosphere, revealing an environment with different biogeochemical dynamic.

The amount of data obtained by barcoding of prokaryotic 16S rDNA from natural habitats is increasing exponentially. Thus, methods enabling us to extract useful information from these data are of increasing importance. In this thesis microbial communities from water, sludge and drilling dust were analyzed by 16S rDNA sequencing in three geologically well described sedimentary aquifers in Bohemian Massif. The main goal of this research was to establish how different analytical approaches can be useful in interpretation of groundwater biogeochemical processes. Three approaches were used: First, taxonomy and metabolic traits of the most abundant microorganisms were assessed. Second, ordination methods showing metabolic and taxonomic variability between communities were used. Last the analysis of phylogenetic dissimilarity using UniFrac metrics was performed. When analyzing individual localities separately, the shift in microbial community composition corresponds with the change of environmental conditions. The unconstrained ordination method based on the variability in metabolic traits indicated, that sludge samples are more informative than water samples when asking which electron donor is used in microbial communities. On the other hand, unconstrained ordination methods were useless when the...

L’objectif de cette thèse concerne la quantification des flux benthos-pélagiques dans une lagune soumise à un régime climatique tropical rythmé de périodes humides et périodes sèches. La lagune de Terminos, située au sud du golfe du Mexique est le plus vaste écosystème laguno-estuarien du Mexique (2000 km2). Du fait de sa faible profondeur (3.5 m en moyenne), les processus benthiques sont sensés participer activement à l’ensemble du cycle biogéochimique de cet Ecosystème. Les mesures de flux benthiques ont eu lieu au cours de un réseau de 13 stations pendant une saison sèche (mars 2009 et 2010) et une saison humide (octobre 2009 et novembre 2010). Quatre stations ont fait l’objet de mesures plus fréquentes du 2008 au 2010. Des incubations ex-situ de carottes de sédiment prélevées ont permis de mesurer la variabilité spatio-temporelle des taux de respiration benthique (SOD) et des flux de sels nutritifs. Les SOD sont significativement différents entre les périodes sèches et humides (1327±161 et 2248±359 µmol m-2 h-1 respectivement). Les flux de silicates sont significativement plus importants pendant la saison des pluies (89.4±15.9 µmol m-2 h-1) que pendant la saison sèche (46.5±11.4 µmol m-2 h-1). Les flux de phosphates, faibles tout au long des périodes étudiées, n’ont pas montré de différence significative. Les flux d’azote dissous (DIN) sont de même intensité mais de sens opposé (2.9±18.8 µmol m-2 h-1 et 24.3±7.3 µmol m-2 h-1). Ces flux caractérisés par un fort signal saisonnier sont fortement corrélés avec les caractéristiques biogéochimiques des sédiments (Corg, N et chloropigments) et contribuent significativement au bilan du carbone et des éléments associés. / The goal of this study concerns the quantification of sediment-water fluxes in a tropical lagoon under climatic forcing regulated by successive dry and wet periods. Terminos lagoon on the South coast of Gulf of Mexico (Campeche sound) is a shallow (3.5 m) but vast estuarine system (2000 km2) where the sediments are supposed to contribute largely to the overall biogeochemical cycling. Benthic flux measurements were performed twice over a network of 13 stations during dry (March 2009 and 2010) and wet periods (October 2009 and November 2010). A selection of 4 stations from this network were visited more frequently between 2008 and 2010. Sediment Oxygen Demand (SOD) and nutrient fluxes were measured through ex-situ incubations of sediment cores sampled manually. SOD were significantly different between both dry and wet seasons (1327±161 and 2248±359 µmol m-2 h-1 respectively). Silicates fluxes were significantly more intense during the wet season (89.4±15.9 µmol m-2 h-1) than during the dry one (46.5±11.4 µmol m-2 h-1). Phosphate fluxes, low during all periods did not show a temporal trend. Finally DIN fluxes showed a net uptake during the wet season (2.9±18.8 µmol m-2 h-1) and conversely an efflux during the dry season (24.3±7.3 µmol m-2 h-1). These fluxes depicted a pronounced seasonal signal, showed a significant correlation to sediment characteristics (Corg, N and chloropigments) and finally contributed to the overall carbon and nutrient budget of the lagoon.

Les cycles biogéochimiques du carbone et des éléments biogènes (Si, N, P) ont été étudiés en lien avec la dynamique nutritionnelle du phytoplancton dans le système naturellement fertilisé des Kerguelen. Cette étude s'inscrit dans le programme KEOPS2, qui a ciblé le nord-est du plateau des Kerguelen au début de la saison productive. La comparaison avec une zone HNLC limitée en fer a confirmé certaines des précédentes observations réalisées au cours des expériences de fertilisations artificielles et naturelles : le fer stimule clairement la croissance du phytoplancton et plus particulièrement celle des diatomées. Les zones naturellement fertilisées se sont en effet caractérisées par des biomasses en chlorophylle a et en silice biogénique 3-10 fois supérieures à la zone non-fertilisée et, par de fortes vitesses de production de silice biogénique atteignant des valeurs rarement observées dans l'océan Austral. La zone HNLC s'est caractérisée quant à elle par une population nanoplanctonique principalement composée de nanoflagellés autotrophes non siliceux. Ces travaux soulignent l'importance d'étudier la composition spécifique des populations de diatomées pour comprendre leurs implications dans les cycles du C et du Si. Nos observations ont montré que les caractéristiques physiologiques des diatomées conditionnent directement l'export de matière en profondeur dans la région des Kerguelen. Cette idée a notamment été illustrée par l'étude de l'évolution saisonnière du bloom au sud-est du plateau. / Biogeochemical cycles of carbon, silicon, nitrogen and phosphorus were studied in relation to the nutritional dynamics of phytoplankton in the naturally iron-fertilized region of Kerguelen, in the Southern Ocean. This study was conducted in the framework of the KEOPS 2 program which took place in the northeastern part of the Kerguelen Plateau in early austral spring (October-November 2011). The comparison between this iron-fertilized region and an iron-limited HNLC (High Nutrient Low Chlorophyll) area confirmed some previous observations from artificial and natural fertilization experiments: iron availability clearly stimulates phytoplankton growth and especially diatom growth. Iron-fertilized regions were characterized by 3-10 fold higher chlorophyll a and biogenic silica biomasses than the iron-limited area, as well as higher biogenic silica production rates reaching values rarely observed in the Southern Ocean. The HNLC area was characterized by a nanoplanktonic assemblage mainly composed of non-siliceous autotrophic nanoflagellates. Our results highlight the importance of studying the specific composition of diatom assemblages to better understand their impact on the C and Si biogeochemical cycles. Our observations showed that physiological traits of diatoms directly drove matter export to depth in the Kerguelen region. This idea was illustrated through the seasonal evolution of the south-eastern bloom by combining our data with KEOPS 1 data. In this region, a shift in the diatom assemblage was observed in parallel to an evolution of the vertical flux of matter, and of uptake and particulate matter ratios Si:C:N.

Summary: This thesis is focused on collecting information on the importance of dead wood on biogeochemical cycles of chemical elements in the mountain forest ecosystems of central Europe. The goal of this thesis was to determine the concentration of various elements(C, N, P, Ca, Mg, K, Na, Mn, Al, Fe) in the coarse woody debris of spruce samples of different age, stage of decomposition which were collected in different localities in the national park Šumava. Another goal was to determine the speed of which these elements are released from the dead wood. The information on the quantity of different elements and the speed of their release is currently lacking and could lead to better understanding of various biogeochemical cycles of elements in the mountain forest. During the decomposition the concentration of the elements N, P, Al and Fe increased whereas the Kalium concentration decreased. The other elements' (C, N, Ca, Mg, Mn) concentrations varied. Carbon constituted approximately 50% of weight in all of the samples analyzed. We carried out a laboratory experiment based on decomposition of dead wood samples in various stage of decay during a period of six months. The released concentration of CO2 was measured at two to four weeks intervals. The release of CO2 continually decreased during the experiment.....

Cette thèse met en perspective un ensemble d’éléments des scénarios socio-économiques sous l’angle de la modélisation du climat. Ces éléments contribuent à améliorer la compréhension de l’état actuel des sciences du climat en ce qui concerne les scénarios. En parallèle, ces éléments montrent le potentiel du récent modèle compact du système Terre OSCAR v2.2.Le premier élément concerne l’incertitude des émissions. Bien que les inventaires d’émissions soient incertains, nous ignorons dans quelle mesure ces incertitudes affectent les projections climatiques. Nous quantifions cet impact pour les émissions des énergies fossiles, la principale cause du changement climatique. Nous montrons que ces incertitudes dans les émissions sont amenées à augmenter avec l’utilisation des énergies fossiles non-conventionnelles, mais qu’elles n’augmentent pas de manière significative l’incertitude dans les projections climatiques. Ceci est vrai pour la majeure partie des variables, comme l’augmentation de la température moyenne de surface, mais pas pour certaines qui sont d’intérêt pour la qualité de l’air.Le second élément est une analyse climatique des récents scénarios Shared Socio-Economic Pathways. Nous identifions des failles dans la base de données, que nous comblons. Sur cette base, nous calculons les projections climatiques des scénarios SSP. Nous montrons la présence d’incohérence dans l’utilisation des émissions CO2 dues à l’utilisation des terres (LUC) calculées par les modèles intégrés (IAMs) et des variables associées à l’utilisation des terres. Nous identifions des compromis dans les réductions d’émissions pour l’atténuation du changement climatique. Nous réévaluons de manière plus robuste les budgets carbone. Les incertitudes dans les élévations de températures sont examinées en détail.Le troisième élément concerne les émissions négatives. La plupart des scénarios qui limitent le changement climatique bien en dessous de 2°C par rapport au préindustriel, respectant ainsi l’Accord de Paris, utilisent des émissions négatives. A l’aide d’une version développée de OSCAR v2.2, nous calculons les implications pour le système Terre de plusieurs aspects des techniques d’absorption de dioxyde de carbone (CDR). Nous identifions les réversibilités des différentes parties du système terre, et évaluons le potentiel de refroidissement de ces techniques. Nous montrons aussi que la reforestation pourrait être moins apte à atténuer le changement climatique, du fait du changement dans l’albedo de surface. Par ailleurs, le potentiel d’alcalinisation des eaux de surfaces pour atténuer le changement climatique pourrait être inférieur à celui initialement estimé.Dans l’ensemble, cette thèse identifie des défauts dans le développement actuel des scénarios. Certains ne constituent pas un problème pour les projections climatiques, comme les incertitudes dans le calcul des émissions. D’autres nécessitent une attention particulière, comme le calcul des émissions CO2 dues au LUC par les IAMs ou l’éventuelle surestimation des capacités des techniques de CDR. Ce travail renforce l’urgence du besoin d’atténuation du changement climatique. / This thesis puts into perspective different elements of socio-economic scenarios from a climate change modelling point of view. These elements contribute at improving the comprehension of the current state of climate sciences regarding the scenarios. In the meantime, these elements demonstrate the potential of the recent reduced-form Earth System Model OSCAR v2.2.The first element concerns the uncertainty of emissions. Although emission inventories are uncertain, we ignore what impact on climate change have these uncertainties. We quantify this impact for fossil-fuel emissions, the major contributor to climate change. We show that the uncertainties in emissions are expected to increase with the use of non-conventional fuels, but that they do not increase significantly the uncertainty from Earth system modelling in variables, such as the increase in global surface temperature.The second element is a climate assessment of the recent Shared Socio-economic Pathways (SSP) scenarios. We identify loopholes in the SSP database, and we complete it to calculate the climate projections under these scenarios. Our conclusions suggest inconsistencies in CO2 emissions from Land Use Change (LUC) calculated by the Integrated Assessment Models and in the associated land variables. We identify trade-offs between greenhouse gases in the mitigation of climate change. Using a robust assessment, new carbon budgets are proposed. The uncertainties in increases in global surface temperature are discussed.The third element concerns the negative emissions. Most climate scenarios limiting global warming well below 2°C above preindustrial levels, thus respecting the Paris Agreement, use negative emissions. Using a developed version of OSCAR v2.2, we evaluate the implications for the Earth system of different aspects of different Carbon Dioxide Removal (CDR) technologies. We identify the reversibility in the different components of the Earth system and calculate the cooling potential of carbon dioxide removal technologies. We also show that the potential of afforestation/reforestation techniques may be impeded by the change in albedo, and that the potential of oceanic enhanced weathering may be lower than expected.Overall, this thesis identifies loopholes in the current development of scenarios. Some do not hinder current conclusions regarding climate change, such as the uncertainties in emission inventories. Others call for further analysis, such as the inconsistencies in the use of CO2 emissions from LUC or the eventual overestimation of the potential of some CDR technologies. It emphasizes the need for an urgent mitigation of climate change.

Thesis (Ph. D.)--Joint Program in Chemical Oceanography (Massachusetts Institute of Technology, Dept. of Earth, Atmospheric, and Planetary Sciences; and the Woods Hole Oceanographic Institution), 2007. / Includes bibliographical references (p. 215-225). / The five noble gases (helium, neon, argon, krypton, and xenon) are biologically and chemically inert, making them ideal oceanographic tracers. Additionally, the noble gases have a wide range of solubilities and molecular diffusivities, and thus respond differently to physical forcing. Tritium, an isotope of hydrogen, is useful in tandem with its daughter helium-3 as a tracer for water mass ages. In this thesis, a fourteen month time-series of the five noble gases, helium-3 and tritium was measured at the Bermuda Atlantic Time-series Study (BATS) site. The time-series of five noble gases was used to develop a parameterization of air-sea gas exchange for oligotrophic waters and wind speeds between 0 and 13 m s-1 that explicitly includes bubble processes and that constrains diffusive gas exchange to ± 6% and complete and partial air injection processes to ± 15%. Additionally, the parameterization is based on weeks to seasonal time scales, matching the time scales of many relevant biogeochemical cycles. The time-series of helium isotopes, tritium, argon, and oxygen was used to constrain upper ocean biological production. Specifically, the helium flux gauge technique was used to estimate new production, apparent oxygen utilization rates were used to quantify export production, and euphotic zone seasonal cycles of oxygen and argon were used to determine net community production. The concurrent use of these three methods allows examination of the relationship between the types of production and begins to address a number of apparent inconsistencies in the elemental budgets of carbon, oxygen, and nitrogen. / by Rachel H.R. Stanley. / Ph.D.

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