Plastome condensation during adaptation to a heterotrophic lifestyle is generally well understood and lineage-independent models have been derived. However, understanding the evolutionary trajectories of comparatively old heterotrophic lineages that are on the cusp of a minimal plastome, is essential to complement and expand current knowledge. We study Hydnoraceae, one of the oldest and least investigated parasitic angiosperm lineages. Plastome comparative genomics, using seven out of eight known species of the genus Hydnora and three species of Prosopanche, reveal a high degree of structural similarity and shared gene content; contrasted by striking dissimilarities with respect to repeat content [inverted and direct repeats (DRs)]. We identified varying inverted repeat contents and positions, likely resulting from multiple, independent evolutionary events, and a DR gain in Prosopanche. Considering different evolutionary trajectories and based on a fully resolved and supported species-level phylogenetic hypothesis, we describe three possible, distinct models to explain the Hydnoraceae plastome states. For comparative purposes, we also report the first plastid genomes for the closely related autotrophic genera Lactoris (Lactoridaceae) and Thottea (Aristolochiaceae).

The global carbon cycle is subject to intense research, where sources and sinks for greenhouse gases, carbon dioxide in particular, are estimated for various systems and biomes. Lakes have previously been neglected in carbon balance estimations, but have recently been recognized to be significant net sources of CO2. This thesis estimates emission of carbon dioxide (CO2) from boreal lakes and factors regulating the CO2 saturation from field measurements of CO2 concentration along with a number of chemical, biological and physical parameters. Concentration of dissolved organic carbon (DOC) was found to be the most important factor for CO2 saturation in lake water, whereas climatic parameters such as precipitation, temperature and global radiation were less influential. All lakes were supersaturated with and, thus, sources of CO2. Sediment incubation experiments indicated that in-lake mineralization processes during summer stratification mainly occurred in the pelagial. Approximately 10% of the CO2 emitted from the lake surface was produced in epilimnetic sediments. The mineralization of DOC and emission of CO2 from freshwaters was calculated on a catchment basis for almost 80,000 lakes and 21 major catchments in Sweden, together with rates of sedimentation in lakes and export of organic carbon to the sea. The total export of terrestrial organic carbon to freshwaters could thereby be estimated and consequently also the importance of lakes for the withdrawal of organic carbon export from terrestrial sources to the sea. Lakes removed 30-80% of imported terrestrial organic carbon, and mineralization and CO2 emission were much more important than sedimentation of carbon. The carbon loss was closely related to water retention time, where catchments with short residence times (<1 year) had low carbon retentions, whereas in catchments with long residence times (>3 years) a majority of the imported TOC was removed in the lake systems. The Gulf of Bothnia was also studied in this thesis and found to be a net heterotrophic system, emitting large amounts of CO2 to the atmosphere on an annual basis. The rate of CO2 emission was depending on the balance between primary production and bacterial respiration, and the system was oscillating between being a source and a sink of CO2.

La production de microalgues en hétérotrophie présente plusieurs avantages pour la production de biocarburants par rapport à la production autotrophe, comme une productivité plus importante en termes de biomasse et de lipides. Cependant, le développement industriel de ce procédé est limité par les coûts de productions associés au substrat organique (i.e. glucose) et à ceux liés à la stérilisation des fermenteurs. Les effluents de fermentation sombre, composés principalement d’acétate et de butyrate, pourraient être utilisés comme milieux de culture peu onéreux pour la culture hétérotrophe ou mixotrophe de microalgues. Les objectifs de cette thèse étaient i) de mieux appréhender la croissance algale sur des mélanges variés d’acétate et de butyrate en fonction de la présence ou l’absence de lumière et de la température de croissance et ii) d’évaluer la faisabilité d’utiliser des effluents de fermentation non stérilisés pour soutenir la croissance de microalgues oléagineuses. Tout d’abord, un modèle basé sur des bilans de masse a été construit afin de caractériser la croissance hétérotrophe de Chlorella sorokiniana et Auxenochlorella protothecoides (taux de croissance et rendements) sur des mélanges d’acétate et de butyrate. Les résultats ont montré que le rapport acétate:butyrate et la concentration en butyrate étaient deux paramètres clés pour soutenir la croissance hétérotrophe. Puis, il a été démontré que la présence de lumière et l’utilisation d’une température suboptimale (30 °C) pour la croissance algale permettaient de réduire l’inhibition du butyrate en permettant une production de biomasse autotrophe ou en améliorant la croissance sur acétate. Enfin, il a été montré que les microalgues peuvent être compétitives sur l’acétate lors de la croissance sur des effluents bruts de fermentation sombre en présence de bactéries fermentaires, grâce à la croissance rapide des microalgues sur acétate (1.75 j-1) et à un changement drastique des conditions de culture peu favorables à la croissance des bactéries d’origine fermentaire. / Growing microalgae in heterotrophic mode present several advantages over autotrophic mode such as a higher productivity in terms of biomass and lipids for biofuels production. Nevertheless, this process is limited by the production cost associated with the organic substrate (i.e. glucose) and fermenters sterilization costs. Dark fermentation effluents, mainly composed of acetate and butyrate, could be used as a low-cost medium to grow microalgae heterotrophically or mixotrophically. The aims of this PhD were i) to optimize microalgae growth on various mixtures of fermentations metabolites using the presence or absence light and different cultivation temperatures and ii) to assess the feasibility of using unsterilized fermentation effluents. First, a model based on mass balance was built to characterize heterotrophic growth rates and yields when Chlorella sorokiniana and Auxenochlorella protothecoides were supplemented with different mixtures of acetate and butyrate. Results showed that the acetate:butyrate ratio and the butyrate concentration per se were two key parameters for promoting heterotrophic growth. Then, further studies showed that the presence of light and the use of suboptimal temperature (30 °C) could reduce the butyrate inhibition on growth by either triggering autotrophic production of biomass or enhancing growth on acetate. Finally, it was shown that microalgae could outcompete fermentation bacteria for acetate when growing on raw dark fermentation effluents, thanks to a fast algal growth on acetate (1.75 d-1) and a drastic change of culture conditions to the detrimental of bacterial growth.

Made available in DSpace on 2014-12-17T14:17:54Z (GMT). No. of bitstreams: 1 AdnaLOLF_DISSERT.pdf: 936304 bytes, checksum: 645a4e30c5be1b2d7ff3581233d1e56e (MD5) Previous issue date: 2014-03-31 / Coordena??o de Aperfei?oamento de Pessoal de N?vel Superior / Seed germination and seedling establishment are critical processes for commercial plantation and depend directly on reserve mobilization as a source of cellular fuels and biosynthetic precursors. In this way, we investigated the coordination among reserve mobilization, metabolite partitioning, and mobilizing enzyme activities in Moringa oleifera Lam (moringa) an oil-seeded species employed in biofuel production. Seeds were germinated under controlled conditions and seedlings were grown hydroponically at a greenhouse. Samples were harvested at 0, 4, 8, 10, 12, 16, and 20 days after imbibition (DAI). The contents of dry mass (DM), neutral lipids (NL), soluble proteins (SP), starch, total soluble sugars (TSS), non-reducing sugars (NRS), and total free amino acids (TFAA) as the activity of isocitrate lyase (ICL), acid proteases, and amylases were determined. The mobilization of storage proteins was initiated during seed germination whereas the mobilization of storage lipids and starch was triggered throughout seedling establishment although all reserves have been depleted until 20 DAI. The partitioning of DM and metabolites to the roots and the shoots was uneven during seedling establishment. Low shoot/root ratio on the basis of DM could be related to the natural occurrence of moringa in drought climates. In the roots, TSS, NRS, and TFAA were accumulated from 12 to 16 DAI and then were consumed until the end of the experiment. In the shoots, TSS and TFAA were consumed in parallel with NRS accumulation from 12 to 20 DAI. The activity of ICL, acid proteases, and amylases was coordinated with the mobilization of lipids, proteins and starch respectively. Thus, we propose that the patterns of reserve mobilization and metabolite partitioning verified in moringa seem distinct from those found to other tree species and may be involved in metabolic strategies to enable environment colonization / A germina??o da semente e o estabelecimento da pl?ntula s?o processos cr?ticos para o cultivo comercial. Assim, este trabalho tem como objetivo caracterizar a mobiliza??o das reservas e a parti??o dos produtos durante estes processos em moringa, uma esp?cie promissora para a produ??o de biodiesel no Nordeste Brasileiro. Para tanto, as sementes foram germinadas em sistema de rolo sob condi??es controladas (80 ?mol/m2/s, fotoper?odo de 12h e 27?2 ?C) e as pl?ntulas foram transferidas para ?gua destilada em vasos pl?sticos de 1 L de capacidade e mantidas em condi??es de casa de vegeta??o por mais 10 dias. As coletas foram realizadas aos 0, 4, 8, 10, 12, 16 e 20 dias ap?s a embebi??o (DAE), dividindo as pl?ntulas em cotil?dones, parte a?rea e sistema radicular. Foram determinados os conte?dos de massa seca (MS), lip?deos neutros (LN), prote?nas sol?veis (PS), amido, a??cares sol?veis totais (AST), a??cares n?o redutores (ANR) e amino?cidos livres totais (AALT) e as atividades de isocitrato liase (ICL), proteases ?cidas e amilases. A parti??o dos produtos, em termos de MS, ocorreu de forma diferencial, resultando em baixa raz?o parte a?rea/sistema radicular, indicativa de um poss?vel mecanismo de resist?ncia ao d?ficit h?drico. A mobiliza??o das PS foi iniciada na germina??o, enquanto que a mobiliza??o dos LN e do amido foi desencadeada no estabelecimento da pl?ntula, embora todas as reservas tenham sido exauridas at? o 20? DAE, culminando com a expans?o das primeiras folhas. No sistema radicular, houve acumula??o de AST, ANR e AALT do 12? ao 16? DAE e consumo destes metab?litos at? o 20? DAE, enquanto que na parte a?rea, ocorreu diminui??o de AST e AALT em paralelo com o aumento de ANR do 12? ao 20? DAE. As atividades de ICL, proteases ?cidas e amilases ocorreram de forma coordenada com a mobiliza??o de LN, PS e amido, respectivamente. Estes padr?es de mobiliza??o das reservas e parti??o dos metab?litos em moringa se mostraram distintos daqueles verificados para outras esp?cies arb?reas estudadas. ? poss?vel que estes padr?es estejam relacionados com estrat?gias metab?licas utilizadas por esta esp?cie para alcan?ar sucesso durante o estabelecimento da pl?ntula

No description available.

L’estuaire de la Gironde est le plus grand estuaire macrotidal d’Europe formé par la confluence de la Garonne (où se situe l’agglomération de Bordeaux) et de la Dordogne. L’une de ses principales caractéristiques est la présence d’une zone à forte turbidité (bouchon vaseux) où les processus hétérotrophes (dégradation de la matière organique) sont favorisés et où au contraire les processus autotrophes (production primaire) sont limités par le manque de lumière. Ainsi, des déficits en oxygène pouvant être préjudiciables à la vie aquatique se développent systématiquement dans la zone du bouchon vaseux de la Garonne estuarienne. Ces préoccupations environnementales ont donc conduit à étudier en détail dans le cadre de ce travail de doctorat, les facteurs environnementaux qui provoquent ces hypoxies estuariennes. Dans un premier temps, j’ai réalisé un suivi sur le réseau d’eaux urbaines partiellement séparatif et unitaire de la Communauté Urbaine de Bordeaux, de ses stations d’épurations et déversoirs d’orage afin d’appréhender les apports urbains de matières organique et azotées et de les comparer à ceux en provenance du bassin versant amont. Bien que les deux stations d’épuration réalisent des abattements très significatifs sur la matière organique et l’ammonium, il s’avère que les flux vers le milieu naturel restent importants, notamment durant les périodes estivales, pendant lesquelles des orages peuvent engendrer des déversements d’effluents non traités. Ensuite, des expériences d’incubations ont permis de mettre en évidence le caractère fortement labile de cette matière organique urbaine. Le carbone organique dissous et l’ammonium, contenus dans les eaux usées, sont des composés fortement consommateurs en oxygène. Des expériences de respirométrie ont également permis d’estimer les taux de consommation en oxygène nettement plus importants dans les effluents urbains que dans les eaux de la Gironde. Enfin, l’analyse des données du réseau de mesures en continu de la qualité physico-chimique des eaux MAGEST (MArel Gironde ESTuaire) a démontré que l’estuaire subit dans sa section garonnaise des périodes d’hypoxie lors d’étiages prononcés, la masse d’eau la plus affectée par ces désoxygénations étant celle qui oscille aux alentours de l’agglomération de Bordeaux. Si ces résultats démontrent l’impact significatif de l’agglomération Bordelaise, le traitement statistique des données MAGEST pour la période 2005-2011 montre que les phénomènes de désoxygénation sont accrus en période d’étiage prononcé, en présence du bouchon vaseux et lorsque la température de l’eau est élevée. Dans ces conditions, l’oxygène dissous, déjà présent en faible quantité, peut être rapidement consommé lors d’apports supplémentaires d’eaux urbaines non traitées qui ont lieu pendant de fortes précipitations orageuses. Ce travail démontre également que le type de traitement biologique des eaux usées employé par les stations d’épuration et les capacités de stockage temporaire d’eaux d’orages ont un rôle critique sur les bilans de ces composés rejetés dans le milieu naturel. Enfin, ce travail permet de proposer aux gestionnaires des stratégies de rejets des effluents à court et moyen terme, en fonction des conditions hydrologiques et physico-chimiques du milieu, dans le but de limiter leur impact sur l’oxygénation des eaux estuariennes de la Garonne. / The Gironde Estuary is the largest macrotidal estuary in Western Europa, formed by the Garonne River (where the urban area of Bordeaux is located) and the Dordogne River. One of its main characteristics is the presence of a Turbidity Maximum Zone (TMZ) where heterotrophic processes (organic matter decomposition) are favored and where low penetration of light limits autotrophic processes (photosynthetic activity). Low dissolved oxygen (DO) that could impact aquatic biota occurred exclusively in the fluvial, low salinity and high turbidity sections of the estuary. These environmental concerns have led to study in detail in this work factors that cause estuarine hypoxia. First, I have estimated organic matter and ammonium fluxes from urban inputs in separate and combined sewer network of the Urban Community of Bordeaux, its wastewater treatment plants (WWTP) and combined sewer overflow, to compare them to the upstream watershed inputs. Even if the two WWTPs succeed in significant reduction in organic matter and ammonium contents of effluents, discharges into estuarine waters are important especially during summer, periods while storm events can generate untreated effluent inputs. This work demonstrates the high lability of this urban organic matter through incubation experiments. The dissolved organic carbon and ammonium contents in wastewater consume oxygen. Respirometry experiments allowed us to estimate higher oxygen uptake rates in wastewater than in the waters of the Gironde Estuary. Finally, the analysis of 7-yr data series from the continuous monitoring of the physico-chemical water quality (MAGEST network: MArel Gironde ESTuary) highlights periods of hypoxia in the upstream section of the estuary during pronounced low water around the Bordeaux conurbation. Statistical treatments of the 7-yr time series of DO concentration demonstrate the significant impact of the Bordeaux metropolitan area as it appears that the under-oxygenations increase during marked low water, in the presence of the TMZ, when the water temperature is high, and where the dissolved oxygen content is already low and can be quickly consumed after untreated storm water discharges. This study also shows that the nature of biological treatment used by the WWTPs and the temporary storage capacity of storm water have a critical role in the release of such compounds into the environment. This work finally provides strategies for effluent discharges to water managers, to short and medium terms, based on hydrological and physico-chemical conditions of the environment in order to limit their impact on the water oxygenation of the Garonne River.