Les isotopes du fer comme traceurs du cycle du fer dans le secteur Atlantique de l’océan Austral

In wide parts of the ocean, iron is a limiting element for phytoplankton growth due to its very low dissolved concentrations. It is thus a fundamental element of the global carbon cycle and climate. However, its cycle is still not well known. We thus used iron isotopes in order to better constrain its cycle in the Southern Ocean. Our measurement of iron isotopic compositions allowed us to characterize each iron source in this area, but also to evidence processes that we could not have evidenced using iron concentrations only. We have shown that the non reductive release of dissolved iron from the South African margin sediments is a major source of dissolved iron in the vicinity of this margin. A hydrothermal contribution above the mid-oceanic ridge, and lithogenic inputs of different origins in the Weddell Gyre compared to the rest of the section have been characterized. We have estimated the isotopic fractionation factors associated to key processes of the iron cycle, notably in surface waters for the biological uptake of iron by phytoplankton, at intermediate depths for the organic matter remineralization, and in deeper samples for the sorption processes. Our results suggest that the main process releasing dissolved iron in the deep ocean is iron desorption from inorganic particles, contrary to the commonly accepted hypothesis according to which it would be in situ organic matter remineralization.Dans certaines parties de l’océan, le fer est un élément limitant pour la croissance du phytoplancton en raison de ses très faibles concentrations. C’est donc un élément fondamental pour le cycle global du carbone, et par conséquent le climat. Cependant, son cycle est encore mal connu. Nous avons donc utilisé les isotopes du fer afin de mieux contraindre son cycle dans l’océan Austral. Les compositions isotopiques obtenues nous ont permis de caractériser chaque source de fer dans cette zone, mais également de mettre en évidence des processus que nous n’aurions pas pu repérer en utilisant seulement les concentrations du fer. Nous avons ainsi montré que la libération non réductrice de fer dissous depuis les sédiments de la marge sud-africaine est une source majeure de fer dissous à proximité de cette marge. Une contribution hydrothermale au-dessus de la ride médio-océanique, ainsi que des apports lithogéniques de différentes origines entre la Gyre de Weddell et le reste de la section ont également été caractérisés. Nous avons estimé les facteurs de fractionnement isotopique associés à divers processus clés du cycle du fer, notamment pour l’assimilation biologique du fer par le phytoplancton en surface, la reminéralisation de la matière organique aux profondeurs intermédiaires, ainsi que les processus de sorption dans les échantillons profonds. Nos résultats suggèrent que le processus principal libérant du fer dissous en profondeur est un processus de désorption de fer inorganique particulaire, contrairement à l’hypothèse communément admise selon laquelle il s’agirait de la reminéralisation in situ de la matière organique

Carbon allocation to major metabolites in illuminated leaves is not just proportional to photosynthesis when gaseous conditions (CO2 and O2) vary

In gas-exchange experiments, manipulating CO2 and O2 is commonly used to change the balance between carboxylation and oxygenation. Downstream metabolism (utilization of photosynthetic and photorespiratory products) may also be affected by gaseous conditions but this is not well documented. Here, we took advantage of sunflower as a model species, which accumulates chlorogenate in addition to sugars and amino acids (glutamate, alanine, glycine and serine). We performed isotopic labelling with 13CO2 under different CO2/O2 conditions, and determined 13C contents to compute 13C-allocation patterns and build-up rates. The 13C content in major metabolites was not found to be a constant proportion of net fixed carbon but, rather, changed dramatically with CO2 and O2. Alanine typically accumulated at low O2 (hypoxic response) while photorespiratory intermediates accumulated under ambient conditions and at high photorespiration, glycerate accumulation exceeding serine and glycine build-up. Chlorogenate synthesis was relatively more important under normal conditions and at high CO2 and its synthesis was driven by phosphoenolpyruvate de novo synthesis. These findings demonstrate that carbon allocation to metabolites other than photosynthetic end products is affected by gaseous conditions and therefore the photosynthetic yield of net nitrogen assimilation varies, being minimal at high CO2 and maximal at high O2.We thank the Australian Research Council for its support via a Future Fellowship awarded to G.T. under contract FT140100645

The GEOTRACES Intermediate Data Product 2014

The GEOTRACES Intermediate Data Product 2014 (IDP2014) is the first publicly available data product of the international GEOTRACES programme, and contains data measured and quality controlled before the end of 2013. It consists of two parts: (1) a compilation of digital data for more than 200 trace elements and isotopes (TEls) as well as classical hydrographic parameters, and (2) the eGEOTRACES Electronic Atlas providing a strongly inter-linked on-line atlas including more than 300 section plots and 90 animated 3D scenes. The IDP2014 covers the Atlantic, Arctic, and Indian oceans, exhibiting highest data density in the Atlantic. The TEI data in the IDP2014 are quality controlled by careful assessment of intercalibration results and multi-laboratory data comparisons at cross-over stations. The digital data are provided in several formats, including ASCII spreadsheet, Excel spreadsheet, netCDF, and Ocean Data View collection. In addition to the actual data values the IDP2014 also contains data quality flags and 1-sigma data error values where available. Quality flags and error values are useful for data filtering. Metadata about data originators, analytical methods and original publications related to the data are linked to the data in an easily accessible way. The eGEOTRACES Electronic Atlas is the visual representation of the IDP2014 data providing section plots and a new kind of animated 3D scenes. The basin-wide 3D scenes allow for viewing of data from many cruises at the same time, thereby providing quick overviews of large-scale tracer distributions. In addition, the 3D scenes provide geographical and bathymetric context that is crucial for the interpretation and assessment of observed tracer plumes, as well as for making inferences about controlling processes

Bioinformatic analysis of ESTs collected by Sanger and pyrosequencing methods for a keystone forest tree species: oak

<p>Abstract</p> <p>Background</p> <p>The Fagaceae family comprises about 1,000 woody species worldwide. About half belong to the <it>Quercus </it>family. These oaks are often a source of raw material for biomass wood and fiber. Pedunculate and sessile oaks, are among the most important deciduous forest tree species in Europe. Despite their ecological and economical importance, very few genomic resources have yet been generated for these species. Here, we describe the development of an EST catalogue that will support ecosystem genomics studies, where geneticists, ecophysiologists, molecular biologists and ecologists join their efforts for understanding, monitoring and predicting functional genetic diversity.</p> <p>Results</p> <p>We generated 145,827 sequence reads from 20 cDNA libraries using the Sanger method. Unexploitable chromatograms and quality checking lead us to eliminate 19,941 sequences. Finally a total of 125,925 ESTs were retained from 111,361 cDNA clones. Pyrosequencing was also conducted for 14 libraries, generating 1,948,579 reads, from which 370,566 sequences (19.0%) were eliminated, resulting in 1,578,192 sequences. Following clustering and assembly using TGICL pipeline, 1,704,117 EST sequences collapsed into 69,154 tentative contigs and 153,517 singletons, providing 222,671 non-redundant sequences (including alternative transcripts). We also assembled the sequences using MIRA and PartiGene software and compared the three unigene sets. Gene ontology annotation was then assigned to 29,303 unigene elements. Blast search against the SWISS-PROT database revealed putative homologs for 32,810 (14.7%) unigene elements, but more extensive search with Pfam, Refseq_protein, Refseq_RNA and eight gene indices revealed homology for 67.4% of them. The EST catalogue was examined for putative homologs of candidate genes involved in bud phenology, cuticle formation, phenylpropanoids biosynthesis and cell wall formation. Our results suggest a good coverage of genes involved in these traits. Comparative orthologous sequences (COS) with other plant gene models were identified and allow to unravel the oak paleo-history. Simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs) were searched, resulting in 52,834 SSRs and 36,411 SNPs. All of these are available through the Oak Contig Browser <url>http://genotoul-contigbrowser.toulouse.inra.fr:9092/Quercus_robur/index.html</url>.</p> <p>Conclusions</p> <p>This genomic resource provides a unique tool to discover genes of interest, study the oak transcriptome, and develop new markers to investigate functional diversity in natural populations.</p

The GEOTRACES Intermediate Data Product 2014

The GEOTRACES Intermediate Data Product 2014 (IDP2014) is the first publicly available data product of the international GEOTRACES programme, and contains data measured and quality controlled before the end of 2013. It consists of two parts: (1) a compilation of digital data for more than 200 trace elements and isotopes (TEIs) as well as classical hydrographic parameters, and (2) the eGEOTRACES Electronic Atlas providing a strongly inter-linked on-line atlas including more than 300 section plots and 90 animated 3D scenes. The IDP2014 covers the Atlantic, Arctic, and Indian oceans, exhibiting highest data density in the Atlantic. The TEI data in the IDP2014 are quality controlled by careful assessment of intercalibration results and multi-laboratory data comparisons at cross-over stations. The digital data are provided in several formats, including ASCII spreadsheet, Excel spreadsheet, netCDF, and Ocean Data View collection. In addition to the actual data values the IDP2014 also contains data quality flags and 1-? data error values where available. Quality flags and error values are useful for data filtering. Metadata about data originators, analytical methods and original publications related to the data are linked to the data in an easily accessible way. The eGEOTRACES Electronic Atlas is the visual representation of the IDP2014 data providing section plots and a new kind of animated 3D scenes. The basin-wide 3D scenes allow for viewing of data from many cruises at the same time, thereby providing quick overviews of large-scale tracer distributions. In addition, the 3D scenes provide geographical and bathymetric context that is crucial for the interpretation and assessment of observed tracer plumes, as well as for making inferences about controlling processes

Investigation of Arabidopsis thaliana (L.) Heynh phenotypic variability and characterization of drought stress effects on photosynthesis and leaf sugar content of Col-0, Mt-0 and Shahdara ecotypes

Compte tenu des changements climatiques annoncés, les végétaux risquent d'être confrontés, dans un proche avenir, à des épisodes de sécheresse sévères de plus en plus fréquents. Afin de prédire l'impact de telles contraintes sur la productivité et le rendement des plantes cultivées, il convient d'étudier l'effet du manque d'eau sur l'activité photosynthétique, le transport et l'accumulation des sucres. Dans un premier temps, la croissance, le développement, la biomasse et la photosynthèse de huit écotypes d'Arabidopsis thaliana ont été caractérisés. Trois de ces écotypes (Col-0, Mt-0 et Shahdara) ont ensuite été soumis à une période de déficit hydrique. Une chute du contenu relatif en eau des rosettes (RWC), de la conductance stomatique (gs) et de l'assimilation nette (AN) a été observée précocement chez Mt-0, écotype initialement caractérisé par une très faible efficience de l'utilisation de l'eau (AN/E). En réponse au stress, l'analyse des courbes AN/Ci de chaque écotype montrait que la limitation stomatique s'accompagne rapidement de limitations métaboliques (baisse de la Vcmax). En fin de stress hydrique, une diminution des réserves en amidon a conduit dans tous les cas à une accumulation de saccharose dans les feuilles. Les expressions des gènes codant les principaux transporteurs foliaires de sucres (polyols, hexoses et saccharose) étaient quant à eux différemment affectés par le manque d'eau. Shahdara, qui est parvenu à conserver un RWC relativement élevé, est l'écotype qui a le mieux toléré la contrainte hydrique. À l'opposé, Mt-0 présentait, en fin de stress, une inhibition de l'AN couplée à des altérations majeures et irréversibles des photosystèmes II (chutes de qP et de Fv/Fm).Considering the predicted climate changes, plants are likely to face, in the future, severe and frequent droughts. In order to evaluate the impact of such stress on productivity and crop yield, the effect of water shortage on photosynthetic activity, sugar transport and accumulation was investigated. Firstly, growth, development, biomass and photosynthesis of eight Arabidopsis thaliana ecotypes have been characterised. Secondly, three of them (Col-0, Mt-0 and Shahdara) were subjected to drought stress. The relative water content (RWC), the stomatal conductance (gs) and the net assimilation (AN) decreased early in rosette leaves of Mt-0 which was initially characterized by a very low water use efficiency (AN/E). In response to drought, AN/Ci curves analysis for each ecotype showed that stomatal limitation was quickly related with metabolic limitations (lower Vcmax). At the end of the stress, reduced starch content always led to a sucrose accumulation in leaves. The expression of genes encoding the main leaf sugar carriers (polyols, hexoses and sucrose) was differently impaired by the water shortage. Shahdara, that managed to maintain a relatively high RWC, was the most tolerant ecotype to water stress. In contrast, at the end of the stress, Mt-0 exhibited an AN inhibition together with significant and irreversible photosystem II alterations (drop of both qP and Fv/Fm)

Plant sulphur metabolism is stimulated by photorespiration

Intense efforts have been devoted to describe the biochemical pathway of plant sulphur (S) assimilation from sulphate. However, essential information on metabolic regulation of S assimilation is still lacking, such as possible interactions between S assimilation, photosynthesis and photorespiration. In particular, does S assimilation scale with photosynthesis thus ensuring sufficient S provision for amino acids synthesis? This lack of knowledge is problematic because optimization of photosynthesis is a common target of crop breeding and furthermore, photosynthesis is stimulated by the inexorable increase in atmospheric CO2. Here, we used high-resolution S-33 and C-13 tracing technology with NMR and LC-MS to access direct measurement of metabolic fluxes in S assimilation, when photosynthesis and photorespiration are varied via the gaseous composition of the atmosphere (CO2, O-2). We show that S assimilation is stimulated by photorespiratory metabolism and therefore, large photosynthetic fluxes appear to be detrimental to plant cell sulphur nutrition

13C Isotope Labelling to Follow the Flux of Photorespiratory Intermediates

International audienceMeasuring the carbon flux through metabolic pathways in intact illuminated leaves remains challenging because of, e.g., isotopic dilution by endogenous metabolites, the impossibility to reach isotopic steady state, and the occurrence of multiple pools. In the case of photorespiratory intermediates, our knowledge of the partitioning between photorespiratory recycling, storage, and utilization by other pathways is thus rather limited. There has been some controversy as to whether photorespiratory glycine and serine may not be recycled, thus changing the apparent stoichiometric coefficient between photorespiratory O2 fixation and CO2 release. We describe here an isotopic method to trace the fates of glycine, serine and glycerate, taking advantage of positional 13C content with NMR and isotopic analyses by LC–MS. This technique is well-adapted to show that the proportion of glycerate, serine and glycine molecules escaping photorespiratory recycling is very small

Lien entre la forme locale de la surface libre et les pressions d'impact générées par une vague déferlante sur un ouvrage

International audienc

Simulation d'impact d'une vague déferlante sur une structure en vibration

Ce travail présente l'étude de l'impact d'une vague déferlante sur une structure en vibration par la simulation numérique des équations de Navier-Stokes avec une suivi d'interface de type VOF (code THETIS). Il fait suite au travail de thèse de Cyril Mokrani (2012) dans lequel une validation précise de l'outil numérique avait été réalisée dans le contexte de l'impact hydrodynamique. On a ainsi montré l'importance d'une description très précise de l'interface locale à l'impact pour que la prévision du pic de pression soit correcte. Nous souhaitons maintenant nous focaliser sur la méthode et les résultats que nous avons obtenus dans le cadre de l'impact sur une structure vibrante. La méthode d'interaction fluide structure que nous avons développé s'appuie uniquement sur le code Navier-Stokes THETIS. Dans un premier temps, on cherche à simuler une structure à un seul degré de liberté en translation, et ce, de manière totalement implicite. Pour cela, nous simulons dans la méthode VOF ce solide rigide par une phase fluide à viscosité infinie. Une force de rappel proportionnelle au déplacement peut être ajoutée sous la forme d'une force volumique dans la phase 'solide'. Nous présenterons des exemples de simulations qui valide cette approche. Cette méthode peut également permettre d'approcher un solide déformable en flexion si l'on considère celui-ci comme un empilement vertical de solides rigides chacun affecté d'une force de rappel, cette dernière étant elle même calculée à l'aide d'une matrice de souplesse et des déplacements des solides voisins. Nous proposons également de développer cette idée durant la conférence et de montrer les premiers résultats basés sur cette approche