Résumé : Les mattes de procaryotes constituent une niche écologique diversifiée. peu étudié!<..en mangrove et jamais décrjte dans les Antilles. L'objectif de cette thèse est de décrire les procaryotes filamenteux reposant sur le sédiment marin et de caractériser les interactions entre la matte, milieu et entre les différents micro-organismes. Nous avons d'abord caractérisé les micro-organismes majoritaires de la matte par le séquençage de l'ADNr 16S et des hybridations moléculaires (FISH). Il a ainsi été possible de décrire deux nouvelles espèces de Beggiatoaceae dont la structure a été étudiée par microscopie électronique. De plus, afin de caractériser l'environnement chimique de ces bactéries, des capteurs potentiométriques ont été utilisés. Ils ont permis de démontrer que les Beggiaotaceae oxydaient les sulfures en prélevant l'oxygène du milieu, tandis que des analyses de microscopie couplées à de l'EDX ont mis en évidence des réserves de soufre intracellulaires dans ces bactéries. Le séquençage de l'ADNr 16S des cyanobactéries filamenteuses a mis en évidence quatre nouvelles espèces de l'ord~e des Oscillatoriales. Deux d'entre elles, du genre Planktothricoides ont révélé une toxicité positive sur les Artemia sp:, les deux autres ont été identifiées comme proches d'Oscillatoria spongeliae, une espèce symbiotique d'éponge, bien que les coupes uItrafines d'une de ces souches aient montré une morphologie interne proche des Tychonema. L'analyse des données a permis d'étoffer les connaissances sur les communautés microbiennes de mangrove et constitue une base intéressante de travail sur la contribution des micro-organismes au fonctionnement de l'écosystème mangrove dans son ensemble
Procaryotic mats are ecological niches, occuring in many ecosystems. Those structures are little studied in marine mangrove sediment and have never been described in West Indies. The purpose ofthis thesis is to characterize the interactions between the mat and the environment, and between the different filamentous micro-organisms living into the mat. In a first place, we characterized the mainly micro-organisrns of the mat by sequencing 16S rDNA. We confirmed these sequences by molecular hybridization (FISH) with specific probes designed from sequences obtained. Thus, it was possible to describe two new Beggiatoaceae strains, whose structure has been studied by electronic microscopy. Furthemore, we used potentiometric captors in situ and in laboratory, by creating a mesocosm, in order to define the chemical environment where involved these bacteria. These experiences proved that the Beggiatoaceae of the mat oxidized the sulfur taking the oxygen from the medium, while the microscopic analysis coupled with EDX showed intracellular sulfur granules into the bacteria. The study of the filamentous cyanobacteria of the mat highlighted four new cyanobacteria strains, all studied by electronic rmcroscopy. Two of them belongs to Planktothrlcoides genus and showed positive toxicity on Artemia salina. The others species are close to Oscillatorla spongeliae, a sponge symbiont, nevertheless, one ofthem showed an intemal morphology close to Tychonema. The analysis of the different results adduces sorne knowledge about mangrove microbial communities. Furthermore, this study can be used as an interesting base to study the micro-organisms contribution in functioning mangrove ecosystem

http://www.theses.fr/2013AGUY0614/document

Éditeur(s) : HAL CCSD Wiley
Résumé : International audience
Morphology can be misleading in the representation of phylogenetic relationships, especially in simple organisms like cnidarians and particularly in hydrozoans. These suspension feeders are widely distributed in many marine ecosystems, and the family Aglaopheniidae Marktanner-Turneretscher, 1890 is among the most diverse and visible, especially on tropical coral reefs. The taxonomy of this family is based on morphological characters with emphasis on reproductive structures for the identification of genera. This study is the most comprehensive molecular phylogeny of the Aglaopheniidae to date, including six genera and 38 species, of which 13 were investigated for the first time and sampled on tropical coral reefs throughout the Indo-Pacific region. For newly sampled individuals, we sequenced the 16S rRNA, the nuclear locus comprising the complete ITS1-5.8S rRNA gene-ITS2 and the first intron of the calmodulin nuclear gene. Phylogenetic analyses of the data revealed and confirmed a general polyphyly, or doubtful monophyly, of all sampled genera in tropical regions based on both the mitochondrial and nuclear markers. Our results revealed that several morphological characters used today are unsuited to resolve phylogenetic relationships between species and genera, as well as the high phyletic diversity within this family. Future revision of the classification of this family will require extensive geographic sampling and the use of an integrative approach.
ISSN: 0300-3256

hal-01253738
https://hal.archives-ouvertes.fr/hal-01253738
https://hal.archives-ouvertes.fr/hal-01253738/document
https://hal.archives-ouvertes.fr/hal-01253738/file/Phylogenetic%20relationships%20within%20Aglaopheniidae%20%28Cnidaria%2C._hal.pdf
DOI : 10.1111/zsc.12135

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
The East Sayan ranges are a key area to understand the interactions between the transpressive deformation linked to the far-field effects of the India-Asia collision and the extension linked to the opening of the Baikal Rift System. The active deformation that affects this range is very recent (around 5 Ma) but occurs in a very complex morphotectonic setting and the understanding of the Tertiary deformation relies entirely on a detailed knowledge of the pre-deformation situation. Using apatite fission track thermochronology, cosmogenic 10Be and morphological study on Tertiary lava flows we demonstrate that prior to the Oligocene the morphology of the East Sayan area was characterized by a wide, constantly rejuvenated erosion surface. Apatite fission track thermal modelling indicates that this surface started to form at least in Late Jurassic-Early Cretaceous (140-120 Ma). The long-term exhumation rates (several tens of million years) derived from apatite fission track data (17.5 m/Ma) and the short-term erosion rates (over a few hundred thousand years) derived from cosmogenic 10Be data (12-20 m/Ma) are coherent implying a near constant mean erosion rate since Late Jurassic. This constant, slow erosion prevented the formation of a lateritic-kaolinic weathering crust on the planation surface. By Oligocene-early Miocene times a long wavelength uplift that remains to be explained, induced incision that created shallow valleys later filled by basaltic lava flows. Finally, the present short-wavelength topography initiated during the Pliocene.
ISSN: 0743-9547

insu-00805603
https://hal-insu.archives-ouvertes.fr/insu-00805603
DOI : 10.1016/j.jseaes.2011.09.017

Éditeur(s) : HAL CCSD
Résumé : International audience
The tropical rainforest of Amazonia is one of the most species-rich ecosystems on earth, with an estimated 16000 tree species. Due to this high diversity, botanical identification of trees in the Amazon is difficult, even to genus, often requiring the assistance of parataxonomists or taxonomic specialists. Advances in informatics tools offer a promising opportunity to develop user-friendly electronic keys to improve Amazonian tree identification.Here, we introduce an original multi-access electronic key for the identification of 389 tree genera occurring in French Guiana terra-firme forests, based on a set of 79 morphological characters related to vegetative, floral and fruit characters. Its purpose is to help Amazonian tree identification and to support the dissemination of botanical knowledge to non-specialists, including forest workers, students and researchers from other scientific disciplines.The electronic key is accessible with the free access software Xper², and the database is publicly available on figshare: https://figshare.com/s/75d890b7d707e0ffc9bf
ISSN: 1314-2011

hal-01392306
https://hal-sde.archives-ouvertes.fr/hal-01392306
DOI : 10.3897/phytokeys.68.8707

Éditeur(s) : HAL CCSD Wiley/Blackwell
Résumé : International audience
Marine fishes exhibit spectacular phenotypic changes during their ontogeny, and the identification of their early stages is challenging due to the paucity of diagnostic morphological characters at the species level. Meanwhile, the importance of early life stages in dispersal and connectivity has recently experienced an increasing interest in conservation programmes for coral reef fishes. This study aims at assessing the effectiveness of DNA barcoding for the automated identification of coral reef fish larvae through large-scale ecosystemic sampling. Fish larvae were mainly collected using bongo nets and light traps around Moorea between September 2008 and August 2010 in 10 sites distributed in open waters. Fish larvae ranged from 2 to 100 mm of total length, with the most abundant individuals being <5 mm. Among the 505 individuals DNA barcoded, 373 larvae (i.e. 75%) were identified to the species level. A total of 106 species were detected, among which 11 corresponded to pelagic and bathypelagic species, while 95 corresponded to species observed at the adult stage on neighbouring reefs. This study highlights the benefits and pitfalls of using standardized molecular systems for species identification and illustrates the new possibilities enabled by DNA barcoding for future work on coral reef fish larval ecology.
ISSN: 1755-098X

hal-01342973
https://hal-univ-perp.archives-ouvertes.fr/hal-01342973
DOI : 10.1111/1755-0998.12293

Éditeur(s) : HAL CCSD American Association of Petroleum Geologists
Résumé : In reservoir engineering, hydrodynamic properties can be estimated from downhole electrical data using heuristic models (e.g., Archie and Kozeny-Carman's equations) relating electrical conductivity to porosity and permeability. Although proven to be predictive for many sandstone reservoirs, the models mostly fail when applied to carbonate reservoirs that generally display extremely complex pore network structures. In this article, we investigate the control of the three-dimensional (3-D) geometry and morphology of the pore network on the electrical and flow properties, comparing core-scale laboratory measurements and 3-D x-ray microtomography image analysis of samples from a Miocene reefal carbonate platform located in Mallorca (Spain). The results show that micrometer- to centimeter-scale heterogeneities strongly influence the measured macroscopic physical parameters that are then used to evaluate the hydrodynamic properties of the rock, and therefore, existing models might not provide accurate descriptions because these heterogeneities occur at scales smaller than those of the integration volume of the borehole geophysical methods. However, associated with specific data processing, 3-D imagery techniques are a useful and probably unique mean to characterize the rock heterogeneity and, thus, the properties variability.
ISSN: 0149-1423

hal-00950066
https://hal.archives-ouvertes.fr/hal-00950066
DOI : 10.1306/05221312134

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
A large sand injectite network is very well exposed in the area of Bevons, Southeast France. The associated sandstone turbiditic channel–fill and the host marls are the Aptian–Albian rocks of the Vocontian Basin. The sand injection network is composed of dykes, sills and sedimentary laccoliths ranging in thickness from mm to pluri–m. The dykes and sills have vertical and horizontal lengths of up to and over 100 m and 1 km, respectively. Outcrop observations show that the architecture and morphology of the sand injectites in the marls is governed by the local stress field during injection, pre–existing faults, the host–rock lithology, compaction, and distance to the potential sand source(s). The main set of dykes is oriented N50–60° perpendicular to the minimum compressive stress σ3 during sand injection. Two other sets of dykes are intruded along pre–existing syn–sedimentary faults oriented N140–150° (set 2) and N90° (set 3) during the Apto–Cenomanian interval. Sills and dykes thin laterally away from their potential sand sources and thin laterally away from them. The vertical thickness variations of the dykes and wings are more complex, as thinning away from the sand sources is often compensated by thickening toward the palaeo–surface. Based on field observations and measurements, we characterized the 3D architecture of the sand injectites and showed that the injectites probably formed due to a forceful injection from an overpressured sand body sealed by low–permeability lithologies.
ISSN: 0191-8141

hal-01243488
https://hal.archives-ouvertes.fr/hal-01243488
DOI : 10.1016/j.jsg.2015.07.001

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Reef positions record the interaction between eustasy and tectonics, and have been used worldwide to characterize vertical deformations of upper-plates at different time-scales and constrain the seismic behavior of megathrusts. Along the Lesser Antilles volcanic arc, high-resolution marine geophysical data were collected on the 2–20 km wide eastern Martinique reef platform to reconstruct its stratigraphic and morphologic history, and understand the influence of local normal faulting, volcanism and plate-scale subduction processes on Holocene and Late Pleistocene reef development. The subsiding Martinique platform's stratigraphy is composed of multiple superimposed sea-level highstand deposits separated by subaerial exposure surfaces of sea-level low stands. The carbonate platform consists of two laterally-extensive carbonate units (unit U2 overlying unit U3) that extend to the platform edge to a depth of − 95 m MSL (mean sea level), and form two morphologic terraces, M2 and M3 respectively. The landward portion of unit U2 is partially overlain between 0 and − 60 m MSL by the living reef tract U1. The current reef is composed of a landward fringing reef, a lagoon and a seaward barrier reef, the latter forming a double-bank barrier around the Caravelle Peninsula. In near-shore multi-channel seismic profiles, a distinct reflector at ~− 35 m MSL, probably a subaerial exposure surface E1, separates the reef sequence formed during the last transgression from a Pleistocene fossil reef tract forming unit U2. Offshore of Mount Pelée volcano (Late Pleistocene), the Holocene reef did not develop above unit U2, whose upper surface is incised by channels and apparent sinkholes. During the Holocene transgression, the possibility of excessive turbidity due to volcanic activity may have inhibited reef development in this area. The un-dated unit U2 probably developed 120–130 ka ago during the last interglacial (MIS 5.5) + 6 m MSL highstand as thick, extensive reefs deposited all along the Lesser Antilles arc. Due to subsidence, MIS 5.5 reefs are not represented by onshore facies, except along the southern Sainte Anne Peninsula where normal faulting and uplift balances island-scale subsidence. Based on unit U2's present elevation and assuming an MIS 5.5 age and + 6 m MSL sea level, Martinique has subsided at maximum 0.3 m/ky, likely due to subduction processes that question the coupling state of the megathrust.
ISSN: 0025-3227

hal-01307036
https://hal.archives-ouvertes.fr/hal-01307036
DOI : 10.1016/j.margeo.2015.08.001

Éditeur(s) : HAL CCSD Wiley-Blackwell
Résumé : International audience
P>Tehran is one of the largest cities in the world (12 million people) facing seismic hazard. Standing at the foothills of Alborz Mountains, the capital of Iran is exposed to potential earthquakes associated with several nearby active faults. Classically mentioned as active features, the Kahrizak, the North Rey and the South Rey scarps cross the town itself and would be the sources of several destructive historical earthquakes. However, the nature of these topographic scarps remains uncertain. To assess whether these features correspond to active faults, we carried out a morphological and stratigraphic study. Our results show that the three scarps define horizontal scarp lines that follow contour lines matching ancient shorelines further East. This point, associated with other morphological characteristics such as the flatness of the upper and the lower surfaces, the long and regular streams that incised the upslope upper surfaces and the fact that the deposits are horizontal and without deformations, suggests in fact that the Kahrizak, the North Rey and the South Rey scarps correspond most likely to ancient shore lines and are not fault scarps.
ISSN: 0954-4879

hal-00496390
https://hal.archives-ouvertes.fr/hal-00496390
DOI : 10.1111/j.1365-3121.2010.00938.x

Éditeur(s) : HAL CCSD
Résumé : International audience
The tropical rainforest of Amazonia is one of the most species-rich ecosystems on earth, with an estimated 16000 tree species. Due to this high diversity, botanical identification of trees in the Amazon is difficult, even to genus, often requiring the assistance of parataxonomists or taxonomic specialists. Advances in informatics tools offer a promising opportunity to develop user-friendly electronic keys to improve Amazonian tree identification.Here, we introduce an original multi-access electronic key for the identification of 389 tree genera occurring in French Guiana terra-firme forests, based on a set of 79 morphological characters related to vegetative, floral and fruit characters. Its purpose is to help Amazonian tree identification and to support the dissemination of botanical knowledge to non-specialists, including forest workers, students and researchers from other scientific disciplines.The electronic key is accessible with the free access software Xper², and the database is publicly available on figshare: https://figshare.com/s/75d890b7d707e0ffc9bf (doi: 10.6084/m9.figshare.2682550).
ISSN: 1314-2011

hal-01369143
https://hal-sde.archives-ouvertes.fr/hal-01369143
DOI : 10.3897/phytokeys.68.8707

Éditeur(s) : HAL CCSD
Résumé : Sand intrusions (or injectites) are most often the product of post-depositional remobilization of sand leading to its injection into the surrounding rocks. While injectites were recognized for the first time nearly 200 years ago, their emplacement process has been studied for a couple of decades only, since the concepts of deep sea depositional environments have allowed us to better understand their emplacement processes. However, these processes are still relatively poorly understood. Our approach is based on the study of injectites in the Lower Congo Basin from seismic and well data, which we compare to a fossil system in the SE France basin. We have shown that: (1) In buried turbidite channel systems draping deposits on the channel flanks and terraces of channels have the same geophysical signature as 'wing-like' injectites. Finally, the only criterion for identifying seismic injectites is the presence of bedding-discordant seismic reflections, and in the best case the associated uplift of the overlying seismic reflectors. (2) Seismic-scale conical and saucer-shaped sand injectites have been identified in the Lower Congo Basin. The remobilization is likely due to overpressuring induced by the buoyancy effect of hydrocarbons trapped in the margins of a lobe buried underneath 160 m of sediment, followed by the sudden injection of fluidized sand associated with fault reactivation of faults (with a possible role of nearby salt diapirs). (3) A network of injectites (dykes, sills/wings and laccoliths) was formed in the Vocontian basin during the late Albian and/or early Cenomanian, from a lower-middle Albian turbidite channel. The emplacement is probably due to the early compartmentalization of the channel during its burial and the increase of the sedimentation rate generating overpressure; and the subsequent large influx of deep fluids triggering injection. The injection of sand was polyphased: a first episode formed the sills and another emplaced the dykes. Sills/wings and dykes propagated about 2 km laterally away from the parent sand body and about 200 m up to the surface, revealing a much more extended lateral than vertical reach, contrary to the classically accepted idea from the interpretation of seismic data. (4) The emplacement of this large network of injectites was governed by hydrofracturing. Therefore, its morphology is dependent on the host rock heterogeneity (isotropy, fractures), the paleo-stress orientation (ó3 = NW-SE) and the burial depth of the source (300-600 m) at the time of injection. The study of this fossil network allows us to define the relationship between morphology of the injected network and stress state at the time of injection. This relationship can be extrapolated to constrain the morphology of subsurface networks beyond seismicvisibility. (5) Sands injected into low permeability lithologies bear evidence to a major event of fluid escape in the studied basin, but also channeled fluids long after their formation. In this way, injectites both attest to specific episodes of fluid migration in sedimentary basins and contribute to long-lived re-routing of migrating fluids once emplaced. The injection of sand is associated with the sudden escape of fluids, probably resulting from a significant tectonic and/or sedimentary event; in addition, the architecture of injectite networks is governed by the local paleo-stress and heterogeneity in the host rock. Consequently, characterizing injectite networks is an important step in understanding the plumbing systems of continental margins, i.e. the post-depositional evolution of sedimentary basins.
Les intrusions sableuses (ou injectites) sont le plus souvent le produit de la remobilisation post-dépositionnelle des sédiments et de l'injection du sable dans les roches environnantes. Bien que reconnues pour la première fois il y a près de 200 ans, elles ne sont réellement étudiées que depuis quelques dizaines d'années, depuis que les concepts sur les environnements de dépôt dans les domaines marins profonds nous permettent de mieux comprendre les processus de mise en place. Cependant, ces processus restent encore aujourd'hui relativement mal compris. Notre approche repose sur l'étude d'injectites dans le bassin du Bas-Congo a partir de données de sismique et de puits que nous comparerons a un système fossile dans le bassin du SE de la France. Nous avons montre que : (1) Dans des systèmes de chenaux turbiditiques enfouis, les dépôts de drapage sur les marges et terrasses de chenaux présentent la même signature géophysique que les injectites de type "wing". Finalement, le seul critère sismique d'identification des injectites est la présence de réflexions sismiques sécantes vis-a-vis de la stratigraphie associée dans le meilleur des cas au soulèvement des réflecteurs sismiques sus-jacents. (2) Des injectites d'échelle sismique en forme de cône et d'assiette ont été identifiées dans le bassin du Bas-Congo. La remobilisation résulte probablement des pressions anormales induites par l'effet de flottabilité des hydrocarbures piégés dans les marges d'un lobe enfoui sous 160 m de sédiment, puis de l'injection soudaine du sable fluidise associée a la réactivation de failles (possible rôle des diapirs de sel a proximité). (3) Un réseau d'injectites (dykes, sills/wings et laccolites) s'est formé dans le bassin Vocontien entre la fin de l'Albien supérieur et/ou le début du Cénomanien, depuis un chenal turbiditique de l'Albien inférieur-moyen. La mise en place résulte probablement de la compartimentalisation précoce du chenal au cours de son enfouissement et de l'augmentation du taux de sédimentation générant la surpression et de l'apport ulterieur d'importante quantité de fluides profonds déclenchant l'injection. L'injection du sable a été polyphasée : une première injection a formé des sills et une suivante des dykes. Les sills/wings et les dykes se sont propagés latéralement au chenal source sur environ 2 km et vers la surface sur environ 200 m, mettant en évidence une forte remobilisation latérale plutôt que verticale, contrairement a l'idée classiquement admise a partir de l'interprétation des données sismiques. (4) La formation de ce large réseau d'injectites a été gouvernée par des mécanismes d'hydrofracturation. Par conséquent, sa morphologie a été dépendante des hétérogenéités de la roche hôte (milieu isotrope, fracture), des directions de paléo-contraintes (ƒÐ3 = NWSE) et de la profondeur d'enfouissement de la source (300-600 m) au moment de l'injection. L'étude de ce réseau fossile permet de définir les relations entre morphologie du réseau injecté et état de contraintes au moment de l'injection. Cette relation peut être extrapolée de façon à contraindre la morphologie des réseaux de subsurface au-delà de la visibilité sismique. (5) Les sables injectés dans des lithologies de faible perméabilité témoignent d'un épisode d'échappement de fluide important dans les bassins étudiés mais ont aussi guide les fluides longtemps après leur formation. Les injectites contribuent ainsi a l'initiation épisodique et la pérennisation de migrations de fluides dans les bassins sedimentaires. Le processus d'injection est associé a l'échappement brutal de fluides, résultant vraisemblablement d'un évènement tectonique et/ou sédimentaire important, et l'architecture des réseaux d'injectites est gouverné par les paléo-contraintes locales et les hétérogénéités de la roche hôte. Par conséquent, la caractérisation des réseaux d'injectites est une étape importante dans la compréhension de la plomberie des marges, c'est-a-dire l'évolution post-dépôt des bassins sédimentaires.
https://tel.archives-ouvertes.fr/tel-01011486

tel-01011486
https://tel.archives-ouvertes.fr/tel-01011486
https://tel.archives-ouvertes.fr/tel-01011486/document
https://tel.archives-ouvertes.fr/tel-01011486/file/These_Monnier_2013_banalisee.pdf

Éditeur(s) : HAL CCSD Oxford University Press (OUP)
Résumé : In habitat mosaics, plant populations face environmental heterogeneity over short geographical distances. Such steep environmental gradients can induce ecological divergence. Lowland rainforests of the Guiana Shield are characterized by sharp, short-distance environmental variations related to topography and soil characteristics (from waterlogged bottomlands on hydromorphic soils to well-drained terra firme on ferralitic soils). Continuous plant populations distributed along such gradients are an interesting system to study intrapopulation divergence at highly local scales. This study tested (1) whether conspecific populations growing in different habitats diverge at functional traits, and (2) whether they diverge in the same way as congeneric species having different habitat preferences. Phenotypic differentiation was studied within continuous populations occupying different habitats for two congeneric, sympatric, and ecologically divergent tree species (Eperua falcata and E. grandiflora, Fabaceae). Over 3000 seeds collected from three habitats were germinated and grown in a common garden experiment, and 23 morphological, biomass, resource allocation and physiological traits were measured. In both species, seedling populations native of different habitats displayed phenotypic divergence for several traits (including seedling growth, biomass allocation, leaf chemistry, photosynthesis and carbon isotope composition). This may occur through heritable genetic variation or other maternally inherited effects. For a sub-set of traits, the intraspecific divergence associated with environmental variation coincided with interspecific divergence. The results indicate that mother trees from different habitats transmit divergent trait values to their progeny, and suggest that local environmental variation selects for different trait optima even at a very local spatial scale. Traits for which differentiation within species follows the same pattern as differentiation between species indicate that the same ecological processes underlie intra- and interspecific variation.
ISSN: 0305-7364

hal-01032430
https://hal.archives-ouvertes.fr/hal-01032430
DOI : 10.1093/aob/mct176

Éditeur(s) : Gauthier-Villars
Résumé : Cyprideis torosa (Crustacea, Ostracoda), which is well known for its ability to live in a wide range of salinity and for the variability of its ornamentation, was sampled in the paralic environment. in the Camargue (France) and in the area of Santa-Pola (south-east Spain), in ambient waters whose salinity varies from 1 to 120 g/l. The collected valves. which are smooth, punctuated, reticulated or have nodes on their surface, were analyzed by means of spark-source mass spectrometry. We detected twenty-six chemical elements, and found a clear relationship between the chemical composition, the ornamentation of the valves and the environmental parameters. In the oligohaline environment, the carapaces are thick, reticulated or node-bearing ; they are enriched in Si, Al, Fe, Mn and Ba which are terrigenous elements introduced by fresh water. In an open hypersaline environment, the carapaces are reticulated or punctuated ; they are chemically characterized by P, Sr and Li, typical for concentrated seawater. Finally, in a closed hypersaline environment. the collected individuals are smooth, and their carapaces are very thin ; their content S is related to the abundant organic matter provided by the development of algal and cyanobacterial mats. Salinity and confinement, which are the main parameters characteristic of the studied ecosystems, are also the two factors that control the ornamentation of the valves. The chemical analysis and the field observations reveal that the granulometric characteristics of the microhabitats must be considered because they control the exchanges at the water-sediment interface. The anthropic influences on the chemical composition of the carapace must be emphasized: it is possible to detect industrial and domestic wastes. But the ornamentation of the carapace is not related to these pollutants - chiefly heavy metals (Pb, Ni Sn) - and depends mainly on the open or closed character of the ambient environment. The present method highlights, on the basis of the chemical composition, a relationship between ornamentation and environmental parameters. It is particularly efficient in the interpretation of the morphology of the valves in relation to the palaeoenvironment.
Oceanologica Acta (0399-1784) (Gauthier-Villars), 1991 , Vol. 14 , N. 5 , P. 505-514

Droits : info:eu-repo/semantics/openAccess
http://archimer.ifremer.fr/doc/00103/21378/18978.pdf
http://archimer.ifremer.fr/doc/00103/21378/

Éditeur(s) : HAL CCSD World Scientific
Résumé : The present paper presents a laboratory experiment of rip current circulations over a moveable bed. The rip current characteristics over four distinct beach morphologies, exhibiting more or less developed nature-like bar-rip morphology,were investigated. For each video run, the same off shore shore-normal waves were generated by the wave maker with the same mean water level in order to study the sensitivity of the rip current characteristics as a function of the beach morphology only. In each case, a 1-hour video run was used to track a large number (~30) of drifters released within the surf zone. Image coordinates were then rectifie d to still water level Cartesian coordinates to compute drifter velocities, mean characteristics and surf zone rete ntion rates. Results show the presence of classic rip current patterns with counter-rotating cells and a relatively narrowoffshore-directed jet with, for three of the situations, a reasonably symmetric shape. Non-surprisingly, it was found that rip current intensity increases with increasing relative depth of the rip channel. The wave-driven circulations were strongly unstable. Computed standard deviation in fl ow intensity and direction provides high resolution information on the spatial variability of the rip current insta bilities with, for instance, highly-pulsating and weakly directionally variable offshore-directed flow in the rip channel. Conversely to what was previously hypothesized in the literature, there was hardly trace of vortices being shed offs hore and drifters exiting the surf zone compartment were not systematically caught by a pulsating jet. The cause for drifter exiting the semi-enclosed surf zone compartment remains, however, elusive and deserves further investigations. The computed surf zone retention rates (~90%) were of the order of those previously observed in the field, with no clear relationship with the mean rip current velocity or relative depth of the rip channel. Further video-runs will have to be analyzed to explore potential explanations
Proceedings of Coastal Dynamics 2009 Impacts of Human Activities on Dynamic Coastal Processes

ISBN : 978-981-4282-46
hal-00854534
https://hal.archives-ouvertes.fr/hal-00854534

Éditeur(s) : Springer
Résumé : Pearl oysters belonging to the genus Pinctada (Bivalvia: Pteriidae) are widely distributed between the Indo-Pacific and western Atlantic. The existence of both widely distributed and more restricted species makes this group a suitable model to study diversification patterns and prevailing modes of speciation. Phylogenies of eight out of the 11 currently recognised Pinctada species using mitochondrial (cox1) and nuclear (18S rRNA) data yielded two monophyletic groups that correspond to shell size and presence/absence of hinge teeth. Character trace of these morphological characters onto the molecular phylogeny revealed a strong correlation. Pinctada margaritifera appears polyphyletic with specimens from Mauritius grouping in a different clade from others of the French Polynesia and Japan. Hence, P. margaritifera might represent a species complex, and specimens from Mauritius could represent a different species. Regarding the putative species complex Pinctada fucata/Pinctada martensii/Pinctada radiata/Pinctada imbricata, our molecular analyses question the taxonomic validity of the morphological characters used to discriminate P. fucata and P. martensii that exhibited the lowest genetic divergence and are most likely conspecific as they clustered together. P. radiata and P. imbricata were recovered as monophyletic. The absence of overlapping distributions between sister lineages and the observed isolation by distance suggests that allopatry is the prevailing speciation mode in Pinctada. Bayesian dating analysis indicated a Miocene origin for the genus, which is consistent with the fossil record. The northward movement of the Australian plate throughout the Miocene played an important role in the diversification process within Pinctada.
Marine Biotechnology (1436-2228) (Springer), 2011-04 , Vol. 13 , N. 2 , P. 181-192

Droits : Springer Science+Business Media, LLC 2010
http://archimer.ifremer.fr/doc/00035/14635/14015.pdf
DOI:10.1007/s10126-010-9278-y
http://archimer.ifremer.fr/doc/00035/14635/

Éditeur(s) : HAL CCSD
Résumé : International audience
The carbon capture and storage is considered as one of the solutions of reducing the effects of global warming. It consists in injecting large quantities of CO 2 in supercritical form directly into deeply located geological formations. One of the methods involves sequestration in the carbonate sedimentary rocks (sandstones and limestones) which are considered as a promising solution. The morphology of the pore network and solid skeleton defines important macroscopic prop-erties of the rock (permeability, stiffness). Modelling at micro scale of random heterogeneous materials (porous media) should be based on morphological and statistical characterisation 1,2 of the investigated microstructure. The work is focused on a reconstruction method by grains deposit 3 , for various range of pa-rameters, to obtain equivalent model of natural rock samples (oolitic limestone and fontainebleau sandstone). Generated samples satisfy morphological and statistical informations 4 which were obtained by 3D image analysis of X-ray tomography of the natural rock samples. For validation of the modelling numerical computations of mechanical and transfer properties are also provided.
14th European Mechanics of Materials Conference - EMMC14
Gothembourg, Sweden

hal-01103163
https://hal.archives-ouvertes.fr/hal-01103163

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
The nucleation and growth processes of spherulitic alkali feldspar have been investigated in this study through X-ray microtomography and electron backscatter diffraction (EBSD) data. Here we present the first data on Shape Preferred Orientation (SPO) and Crystal Preferred Orientation (CPO) of alkali feldspar within spherulites. The analysis of synchrotron X-ray microtomography and EBSD datasets allowed us to study the morphometric characteristics of spherulites in trachytic melts in quantitative fashion, highlighting the three-dimensional shape, preferred orientation, branching of lamellae and crystal twinning, providing insights about the nucleation mechanism involved in the crystallization of the spherulites. The nucleation starts with a heterogeneous nucleus (pre-existing crystal or bubble) and subsequently it evolves forming “bow tie” morphologies, reaching radially spherulitic shapes in few hours. Since each lamella within spherulite is also twinned, these synthetic spherulites cannot be considered as single nuclei but crystal aggregates originated by heterogeneous nucleation. A twin boundary may have a lower energy than general crystal–crystal boundaries and many of the twinned grains show evidence of strong local bending which, combined with twin plane, creates local sites for heterogeneous nucleation.This study shows that the growth rates of the lamellae (10− 6–10− 7 cm/s) in spherulites are either similar or slightly higher than that for single crystals by up to one order of magnitude. Furthermore, the highest volumetric growth rates (10− 11–10− 12 cm3/s) show that the alkali feldspar within spherulites can grow fast reaching a volumetric size of ~ 10 μm3 in 1 s.
ISSN: 0024-4937

hal-01172356
https://hal.archives-ouvertes.fr/hal-01172356
DOI : 10.1016/j.lithos.2014.12.003

Éditeur(s) : HAL CCSD Public Library of Science
Résumé : International audience
We studied the diversity within the former genus Gymnangium in the South West IndianOcean by using an integrative approach of both traditional (morphology-based) and modernmolecular taxonomy. Nine species were recorded in the material collected. A total of 97 16Smitochondrial DNA sequences and 54 Calmodulin nuclear sequences from eight Gymnangium/Taxella species were analyzed. We found both morphological and molecular differencesin the studied Gymnangium species that make it necessary to split the genus. It isproposed to revalidate the genus Taxella which is currently regarded as a synonym ofGymnangium. Two species of the genus Taxella (T. eximia and T. gracilicaulis), until nowregarded as distinct species based on morphological characteristics, cluster together in onephylogenetic clade. Possible explanations are discussed. Two species from Madagascarnew to science are herein described and rare species from the Indian Ocean islands are redescribed.
ISSN: 1932-6203

hal-01564043
https://hal-univ-perp.archives-ouvertes.fr/hal-01564043
DOI : 10.1371/journal.pone.0174244

Éditeur(s) : HAL CCSD Oxford University Press (OUP)
Résumé : International audience
Two types of olivine occur in kimberlites from Greenland, Canada and southern Africa. The first, xenocrystic olivine, displays several different forms. Most distinctive are 'nodules', a term we use to describe the large (1-5 mm), rounded, single crystals or polycrystalline aggregates that are a common constituent of many kimberlites. Olivine compositions are uniform within single nodules but vary widely from nodule to nodule, from Fo81 to 93. Within many nodules, sub- to euhedral asymmetric tablets have grown within larger anhedral olivine grains. Dislocation structures, particularly in the anhedral grains, demonstrate that this olivine was deformed before being incorporated into the kimberlite magma. Olivine grains in the kimberlite matrix between the nodules have morphologies similar to those of the tablets, suggesting that most matrix olivine grains are parts of disaggregated nodules. We propose that a sub- to euhedral form is not sufficient to identify phenocrysts in kimberlites and provide some criteria, based on morphology, internal deformation and composition, that distinguish phenocrysts from xenocrysts. The second type of olivine is restricted to rims surrounding xenocrystic grains. Only this olivine crystallized from the kimberlite magma. Major and trace element data for the rim olivine are used to calculate the composition of the parental kimberlite liquid, which is found to contain between about 20 and 30% MgO. The bulk compositions of many kimberlites contain higher MgO contents as a result of the presence of xenocrystic olivine. The monomineralic, dunitic, character of the nodules, and the wide range from Fo-rich to Fo-poor olivine compositions, provide major constraints on the origin of the nodules. Dunite is a relatively rare rock in the mantle and where present its olivine is persistently Fo-rich. The dunitic source of the nodules in kimberlites lacked minerals such as pyroxene and an aluminous phase, which make up about half of most mantle-derived rocks. It appears that these minerals were removed from the mantle peridotite that was to become the source of the nodules, and the Fo content of the retained olivine was modified during interaction with CO2-rich fluids whose arrival at the base of the lithosphere immediately preceded the passage of the kimberlite magmas. Fragments of the resultant dunite were entrained into the kimberlite, where they were retained both as intact nodules and as disaggregated grains in the matrix.
ISSN: 0022-3530

insu-00543321
https://hal-insu.archives-ouvertes.fr/insu-00543321
BIBCODE : 10.1093/petrology/egp080
DOI : 10.1093/petrology/egp080

Éditeur(s) : HAL CCSD
Résumé :   Diplôme : DEA
il s'agit d'un type de produit dont les métadonnées ne correspondent pas aux métadonnées attendues dans les autres types de produit : DISSERTATION
Links between architectural stages of development (ASD), photosynthetic capacities and leaf characteristics in Tachigali melinonii (Caesalpiniaceae) were investigated in the tropical forest of French Guiana. Three ASD were sampled under three light conditions to elucidate the impact of ASD- and light-related changes on photosynthetic functional traits. Photosynthetic parameters (maximum rate in RubisCO carboxylation (Vcmax) and maximum rate of electron transport (Jmax) were estimated by adjusting a biochemical model (Farquhar et al., 1980) to response curves of CO2 assimilation rate to intercellular CO2 concentration, under saturated light. In addition, N and C foliar concentrations were analysed and N allocations to the carboxylation and bioenergetic processus of photosynthesis were calculated using the model of Niinemets and Tenhunen (1997). The variations in ecophysiological parameters observed were due to leaf anatomical and structural changes instead of changes in photosynthetic components, suggesting adjustments to light conditions. Tachigali melinonii thus appears to display morphological and anatomical plasticity at different ASDs and under different light conditions.
Une espèce forestière de Guyane Française, Tachigali melinonii (Caesalipiniaceae), a été choisie afin de regarder la variation des traits fonctionnels relatifs à la photosynthèse en fonction de la disponibilité en lumière et en fonction de son stade de développement architectural. Du fait du tempérament de l'espèce vis-à-vis de la lumière de type «struggling gambler» (ombrage nécessaire aux jeunes stades puis développement en pleine lumière), trois stades clefs de développement parmi la séquence de différenciation de l'espèce ainsi que trois environnements lumineux ont été choisis. Les capacités photosynthétiques foliaires ont été estimées à partir de l'ajustement de paramètres du modèle biochimique de photosynthèse foliaire (Farquhar et al. 1980) sur des courbes de réponses de l'assimilation de CO² (A) à des concentrations intracellulaires en CO² (Ci) croissantes, en condition de lumière saturante. La vitesse maximale de carboxylation Vcmax et le flux maximal d'électrons photosynthétiques Jmax ont ainsi été estimés et ensuite reliés aux caractéristiques structurales foliaires, notamment la concentration en azote, en carbone ainsi qu'avec la densité et l’épaisseur. Les fractions d'azote allouées aux processus photosynthétiques de carboxylation et de bioénergétique ont été calculées. Des variations, dues à un effet du stade de développement sur les paramètres étudiés ainsi qu’à un effet de la quantité de lumière disponible, ont été constatées. Ces variations sont surtout liées à des ajustements anatomiques et structuraux foliaires et non à des modifications de l’appareil photosynthétique. Tachigali melinonii semble donc modifier ses caractéristiques structurales foliaires en fonction de son stade de développement, ce qui suppose un contrôle ontogénique partiel, et en fonction de la disponibilité en lumière.
https://hal.archives-ouvertes.fr/hal-01189520

hal-01189520
https://hal.archives-ouvertes.fr/hal-01189520
PRODINRA : 44951