Éditeur(s) : Public Library Science
Résumé : Subsurface sediments of the Sonora Margin (Guaymas Basin), located in proximity of active cold seep sites were explored. The taxonomic and functional diversity of bacterial and archaeal communities were investigated from 1 to 10 meters below the seafloor. Microbial community structure and abundance and distribution of dominant populations were assessed using complementary molecular approaches (Ribosomal Intergenic Spacer Analysis, 16S rRNA libraries and quantitative PCR with an extensive primers set) and correlated to comprehensive geochemical data. Moreover the metabolic potentials and functional traits of the microbial community were also identified using the GeoChip functional gene microarray and metabolic rates. The active microbial community structure in the Sonora Margin sediments was related to deep subsurface ecosystems (Marine Benthic Groups B and D, Miscellaneous Crenarchaeotal Group, Chloroflexi and Candidate divisions) and remained relatively similar throughout the sediment section, despite defined biogeochemical gradients. However, relative abundances of bacterial and archaeal dominant lineages were significantly correlated with organic carbon quantity and origin. Consistently, metabolic pathways for the degradation and assimilation of this organic carbon as well as genetic potentials for the transformation of detrital organic matters, hydrocarbons and recalcitrant substrates were detected, suggesting that chemoorganotrophic microorganisms may dominate the microbial community of the Sonora Margin subsurface sediments.
Plos One (1932-6203) (Public Library Science), 2014-08 , Vol. 9 , N. 8 , P. e104427

Droits : This is an open-access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.
http://archimer.ifremer.fr/doc/00203/31408/29801.pdf
DOI:10.1371/journal.pone.0104427
http://archimer.ifremer.fr/doc/00203/31408/

Éditeur(s) : HAL CCSD Oldendorf/Luhe
Résumé : International audience
Large filamentous sulfur-oxidizing bacteria belonging to the Beggiatoacae family can cover large portions of shallow marine sediments surrounding mangroves in Guadeloupe (French West Indies). In order to assess the importance of Beggiatoa mats as an infaunal food source, observations were conducted of the area within mats and at increasing distances from mats. We used natural isotopic compositions and a C-13 enrichment study. Both revealed an ingestion of bacterial mats by associated meiofauna, dominated by rotifers and to a smaller extent by small polychaetes and nematodes. Compared to adjacent sites, sediment covered by bacterial mats presented a higher abundance of diatoms, whereas the total biomass of bacteria did not vary. This constant bacterial abundance suggests that the proportion of organic matter represented by sulfur bacteria is limited compared to the fraction of total bacteria. There was no significant difference in infaunal abundance in mats, suggesting that the availability of this chemosynthetic food resource had a limited local effect. Grazers presented a delta C-13 value increasing with distance from the mat. However, isotopic composition of phospholipid-derived fatty acids specific for diatoms and bacteria revealed that this change is related to modifications of delta C-13 dietary components rather than to changes in diet composition. These complementary methods revealed that the occurrence of sulfur-oxidizing bacterial mats does not necessarily affect grazer abundance and importance of bacteria in their diet. Despite its wide occurrence, Beggiatoa mats would consequently have a minor influence on the structure of the mangrove food web.
ISSN: 0171-8630

hal-01545912
https://hal.archives-ouvertes.fr/hal-01545912
DOI : 10.3354/meps11035

Éditeur(s) : HAL CCSD Ecological Society of America
Résumé : Line transect surveys are widely used in neotropical rainforests to estimate the population abundance of medium- and large-sized vertebrates. The use of indices such as Encounter Rate has been criticized because the probability of animal detection may fluctuate due to the heterogeneity of environmental conditions among sites. In addition, the morphological and behavioral characteristics (biological traits) of species affect their detectability. In this study, we compared the extent to which environmental conditions and species' biological traits bias abundance estimates in terra firme rainforests in French Guiana. The selected environmental conditions included both physical conditions and forest structure covariates, while the selected biological traits included the morphological and behavioral characteristics of species. We used the distance sampling method to model the detection probability as an explicit function of environmental conditions and biological traits and implemented a model selection process to determine the relative importance of each group of covariates. Biological traits contributed to the variability of animal detectability more than environmental conditions, which had only a marginal effect. Detectability was best for large animals with uniform or disruptive markings that live in groups in the canopy top. Detectability was worst for small, solitary, terrestrial animals with mottled markings. In the terra firme rainforests which represent ~80% of the Amazonia and Guianas regions, our findings support the use of relative indices such as the encounter rate to compare population abundance between sites in species-specific studies. Even though terra firme rainforests may appear similar between regions of Amazonia and the Guianas, comparability must be ensured, especially in forests disturbed by human activity. The detection probability can be used as an indicator of species' vulnerability to hunting and, thus, to the risk of local extinction. Only a few biological trait covariates are required to correctly estimate the detectability of the majority of medium- and large-sized vertebrates. Thus, a biological trait model could be useful in predicting the detection probabilities of rare, uncommon or localized species for which few data are available to fit the detection function.
ISSN: 1051-0761

hal-01555267
https://hal.archives-ouvertes.fr/hal-01555267
DOI : 10.1002/eap.1549
PRODINRA : 396614
PUBMED : 28419598

Éditeur(s) : Interciencia
Résumé : Zooplankton abundance, biomass and composition were evaluated in various temporal scales in a seasonal coastal upwelling system at Margarita Island, Venezuela. Scales of temporal variation include weeks, months and seasons (relaxation, upwelling and transition). Seasons were delimitated by upwelling index and sea temperature. The sampling period comprise Sept/2002 - July/2003. Zooplankton samplings were made by horizontal trawls (1-10m depth), using 200,mu m nets, 2-6km from the coastal margin. Total abundance show important variation at week scales, with different patterns between locations, while seasonal differences of abundance are marginal. Biomass only shows seasonal variation due significant reduction in the transition season. Zooplankton assemblages show changes at scale of weeks, with different local patterns, and seasonal changes. Changes in assemblage between the relaxation and upwelling seasons include reduction (during upwelling) of abundance in copepods, cladocerans, salpidae, chaetognates, fish and crustacea larvae. Except by cirripedia larvae, those were important in the upwelling assemblages. Transition shows high variation, with reduction of biomass and assemblage composition similar to upwelling, except by an isolated event. Small scale variation in the zooplankton could be related to physical processes at small scales, eg. turbulence, local circulation, small eddies and filaments, and biological response. Additional sources of nutrient input, eg. riverine input and internal waves, could support local plankton productivity and abundance during relaxation. Detection of high variation in zooplankton abundance and composition at small scales, with local interaction, bring a new light over zooplankton estimation in time series in this system.
La abundancia, la biomasa y la composición del zooplancton costero fueron analizadas a varias escalas temporales en un área afectada por surgencia costera estacional (Isla de Margarita, Venezuela); considerando para ello escalas de semanas, meses y periodos, así como la variación local. La estimación del zooplancton fue realizada a partir de arrastres horizontales (1-10m de profundidad) utilizando redes de 200μ entre 2 y 6 km de la línea de costa, entre set/2002 y jul/2003. La abundancia total presentó alta variabilidad a escala de semanas, con patrones diferentes entre localidades, mientras que la diferencia entre periodos es marginal. La biomasa únicamente mostró variación a escala de periodos por una disminución durante el periodo de transición. La composición presentó fluctuaciones a escalas temporales pequeñas, con patrones de variación diferentes localmente, así como a escala de periodos. Los cambios en composición entre el periodo de relajación y el de surgencia incluyen disminución en la abundancia de copépodos, cladóceros, salpas, quetognatos, larvas de peces y crustáceos; excepto por las larvas de cirrípedos que forman un componente importante durante la surgencia. Se postula que procesos físicos a pequeña escala, como la turbulencia, la circulación local o la formación de pequeños giros o filamentos, y los procesos biológicos, condicionan esta elevada variabilidad a escalas pequeñas. La existencia de fuentes de enriquecimiento adicionales como aportes de ríos y ondas internas pudiera condicionar la presencia de elevada abundancia y biomasa, en especial durante periodos de relajación. Los cambios en composición resaltan la importancia del aporte de merozooplancton costero. Palabras clave / Biomasa / Escalas Temporales / Surgencia / Venezuela / Zooplancton Costero /
Interciencia (0378-1844) (Interciencia), 2014-02 , Vol. 39 , N. 2 , P. 122-128

Droits : info:eu-repo/semantics/openAccess
http://archimer.ifremer.fr/doc/00187/29851/28297.pdf
http://archimer.ifremer.fr/doc/00187/29851/

Éditeur(s) : HAL CCSD BioMed Central
Résumé : International audience
BACKGROUND: Sampling design is a key issue when establishing species inventories and characterizing habitats within highly heterogeneous landscapes. Sampling efforts in such environments may be constrained and many field studies only rely on subjective and/or qualitative approaches to design collection strategy. The region of Cacao, in French Guiana, provides an excellent study site to understand the presence and abundance of Anopheles mosquitoes, their species dynamics and the transmission risk of malaria across various environments. We propose an objective methodology to define a stratified sampling design. Following thorough environmental characterization, a factorial analysis of mixed groups allows the data to be reduced and non-collinear principal components to be identified while balancing the influences of the different environmental factors. Such components defined new variables which could then be used in a robust k-means clustering procedure. Then, we identified five clusters that corresponded to our sampling strata and selected sampling sites in each stratum. RESULTS: We validated our method by comparing the species overlap of entomological collections from selected sites and the environmental similarities of the same sites. The Morisita index was significantly correlated (Pearson linear correlation) with environmental similarity based on i) the balanced environmental variable groups considered jointly (p = 0.001) and ii) land cover/use (p-value<0.001). The Jaccard index was significantly correlated with land cover/use-based environmental similarity (p-value = 0.001). CONCLUSIONS: The results validate our sampling approach. Land cover/use maps (based on high spatial resolution satellite images) were shown to be particularly useful when studying the presence, density and diversity of Anopheles mosquitoes at local scales and in very heterogeneous landscapes.
BMC Ecology

pasteur-00914104
https://hal-riip.archives-ouvertes.fr/pasteur-00914104
https://hal-riip.archives-ouvertes.fr/pasteur-00914104/document
DOI : 10.1186/1472-6785-13-45
PUBMED : 24289184

Éditeur(s) : HAL CCSD Nature Publishing Group
Résumé : While Amazonian forests are extraordinarily diverse, the abundance of trees is skewed strongly towards relatively few 'hyperdominant' species. In addition to their diversity, Amazonian trees are a key component of the global carbon cycle, assimilating and storing more carbon than any other ecosystem on Earth. Here we ask, using a unique data set of 530 forest plots, if the functions of storing and producing woody carbon are concentrated in a small number of tree species, whether the most abundant species also dominate carbon cycling, and whether dominant species are characterized by specific functional traits. We find that dominance of forest function is even more concentrated in a few species than is dominance of tree abundance, with only ≈1% of Amazon tree species responsible for 50% of carbon storage and productivity. Although those species that contribute most to biomass and productivity are often abundant, species maximum size is also influential, while the identity and ranking of dominant species varies by function and by region.
ISSN: 2041-1723

hal-01204225
https://hal.archives-ouvertes.fr/hal-01204225
DOI : 10.1038/ncomms7857
PRODINRA : 305614
PUBMED : 25919449

Éditeur(s) : HAL CCSD Ecological Society of America
Résumé : Although niche-based and stochastic processes, including dispersal limitation and demographic stochasticity, can each contribute to community assembly, it is difficult to quantify the relative importance of each process in natural vegetation. Here, we extend Shipley's maxent model (Community Assembly by Trait Selection, CATS) for the prediction of relative abundances to incorporate both trait-based filtering and dispersal limitation from the larger landscape and develop a statistical decomposition of the proportions of the total information content of relative abundances in local communities that are attributable to trait-based filtering, dispersal limitation, and demographic stochasticity. We apply the method to tree communities in a mature, species-rich, tropical forest in French Guiana at 1-, 0.25- and 0.04-ha scales. Trait data consisted of species' means of 17 functional traits measured over both the entire meta-community and separately in each of nine 1-ha plots. Trait means calculated separately for each site always gave better predictions. There was clear evidence of trait-based filtering at all spatial scales. Trait-based filtering was the most important process at the 1-ha scale (34%), whereas demographic stochasticity was the most important at smaller scales (37-53%). Dispersal limitation from the meta-community was less important and approximately constant across scales (similar to 9%), and there was also an unresolved association between site-specific traits and meta-community relative abundances. Our method allows one to quantify the relative importance of local niche-based and meta-community processes and demographic stochasticity during community assembly across spatial and temporal scales.
ISSN: 0012-9658

hal-01032424
https://hal.archives-ouvertes.fr/hal-01032424

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Metasedimentary rocks in the transition zone between the Pernambuco-Alagoas Domain and the Sergipano Belt (southern Borborema Province, NE Brazil) were studied in order to place constraints on the geological evolution of this portion of West Gondwana. High-grade metamorphic conditions are recorded by the garnet-sillimanite assemblage and common anatexis in pelitic paragneisses. Two samples dated by LA-ICP-MS in the north yielded a predominance of early Neoproterozoic detrital zircons, with age peaks between 990 Ma and 827 Ma, with the youngest grain suggesting deposition after 670 Ma. Low Th/U zircons (Th/U < 0.1) in these samples display a significant spread in ages, from 691 to 568 Ma. One sample in the south is dominated by a homogenous population of Paleoproterozoic grains, with a 2200 Ma peak. The southernmost sample also contains Paleoproterozoic zircons but the most abundant population is Neoproterozoic, and characterized by age peaks at c. 670, 647 and 623 Ma. These results show that deposition of sediments in the southern PEAL Domain and in the northern Sergipano Belt occurred in the Late Neoproterozoic. The differing age spectra between samples are correlated with potential source rocks in the study area or in its proximity, reflecting variable input from local sources. The data are interpreted to indicate that during the course of an extensional event at c. 673-647 Ma, Tonian granitic intrusions and synextensional metamorphic rocks were unroofed and eroded to provide zircons for sediments deposited in the north, whereas Paleoproterozoic and synextensional magmatic rocks were the main sources for sediments in the south. Peak metamorphic conditions and contractional deformation are constrained to c. 630-600 Ma.
ISSN: 0895-9811

hal-01468011
https://hal.archives-ouvertes.fr/hal-01468011
DOI : 10.1016/j.jsames.2016.09.010

Résumé : Au cours de 325 relevés, 518 observations visuelles et 202 acoustiques ont permis de recenser 4 familles, 14 genres et 17 espèces, représentant un effectif total cumulé de près de 6000 cétacés contactés dans les limites de 15 mille nautiques des côtes en Guadeloupe. Les dauphins (Delphinidëe), constituent 33% des 36 espèces actuellement connues dans le monde. Six espèces plus rares ont été décrites. Parmi les cétacés à fanons, la baleine à bosse (Megaptera novaeangliae) migre dans les eaux côtières de décembre à fin mai et reste l'espèce la plus rencontrée. Grâce à un suivi individuel par télémétrie, il a pu être prouvé qu'au moins un individu de cette espèce pouvait séjourner dans l'archipel plus de huit jours. En 2010, une baleine à bosse de la baie du Moule à été suivie sur plus de 6300 kilomètres jusqu'au sud de l'Islande, vers les Iles Féroé. Une première estimation de stock sur la période de 2008 à 2011 propose que 442 baleines à bosse %CV 19,29 IC95% [302-645] évolueraient dans l'archipel côtier. Les carnïvores sont les plus abondants, avec parmi ceux-ci, le dauphin tacheté pantroplcal (Stenella attenuata) dont l'estimation indique que 270 à 300 individus évolueraient sur 1361 km2 avec une densité relative élevée (0,052 tndtvtdus/km>, %CV 90,16), principalement en-côte-sous-le-vent. L'analyse de la répartition spatiale et des facteurs du milieu indique une sectorisation géographique marquée des populations en zone côtière, avec des distributions influencées spécifiquement par la bathymétrie, la latitude, les distances à la côte et à l'isobathe 200, pour les informations principales et selon les espèces.
In 325 surveys, 518 visuai observations and acoustic 202 have identified four families, 14 genera and 17 species, representing a cumulative total ofnearly 6000 cetaceans assessed within 15 miles of coastal water ofGuadeloupe. Dolphins (Delphinidae), constitute 33% ofthe 36 species currently known in the world. Six rare species have been described. Among the baleen whales, the humpback whale (Megaptera novaeangliae) migrate into coastal waters from December to late May and is the species most encountered. With individual monitoring by telemetry, it has been proved that at least one individual ofthis species could stay in the archipelago over eight days. In 2010, a humpback whale in the Bay ofmold were followed for more than 6300 km to the south ofIceland to the Faroe Islands. A first estimate ofstock over the period 2008 to 20 Il suggests that 442 humpback whales CV% 19.2995% [302-645] would evolve in the coastal archipelago. <..';:-.'") Carnivores are the most abundant, with among them, the spotted dolphin (Stenella attenuata) whose estimate indicates that 270 to 300 individuals are present over 1361 km 2 with a high specifie density (0.052 individuals / km 2,% CV 90, 16), mainly in the Leeward coast. The analysis ofthe spatial distribution and environmental factors indicates a marked geographical sectorisation ofpopulations in coastal areas, with distributions specifically influenced by bathymetry, latitude, distance to the coast and the isobath 200, depending on the species

http://www.theses.fr/2012AGUY0520/document

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
A suite of eclogite xenoliths from the Roberts Victor kimberlite (South Africa) is remarkable for its high abundances of base metal sulfides (BMS; up to 2 modal %). However, while sulfides are nearly ubiquitous in Type I eclogites (garnet > 0.07% Na2O), Type II eclogites (garnet < 0.07% Na2O) systematically lack sulfides. Two different sulfide assemblages are recognised within the Type I xenolith suite. Both populations are polyphase Cu-Ni-Fe sulfides, one characterised by the pyrrhotite (Po) + pentlandite (Pn) + chalcopyrite (Cp) assemblage and the other by the smythite/violarite (Smy/Vi) + (Ni)pyrite (Py) + Cp assemblage. The latter is the most abundant assemblage and reflects the supergene alteration of the "primary" Po + Pn + Cp assemblage. This process overprints the original composition of the sulfides by remobilising elements such as S, Fe, Ni, Se and Te. In the Type I eclogites, BMS occur as inclusions within silicates (garnet and clinopyroxene) and as interstitial grains. No chemical differences were observed between enclosed and interstitial sulfides. However, their relative abundances are correlated, indicating a similar origin. The Po + Pn + Cp assemblage is identical to eclogitic sulfides previously described in some Roberts Victor diamonds. Silicate-enclosed sulfides could appear to be early phases, but they are restricted to the outer parts of the silicate grains, suggesting a late incorporation during partial recrystallisation of silicate phases, induced by fluid-rock percolation-reaction during a metasomatic event. Positive whole-rock correlations between Se and (La/Sm)N⁎ and between Cu and ΣLREEN⁎ indicate a direct link between sulfide content and the enrichment of Mg + incompatible elements in the Type I eclogites, further supporting a metasomatic origin of the sulfide component. Similarly, a negative correlation between ΣLREEN⁎ and Cucpx implies that the metasomatic agent was at least partially composed of S-rich fluid (e.g. H2S, SO2) that reacted with the rock and leached Cu out of the silicates. The coupling between sulfides and LREE in the Type I eclogites, as well as the absence of sulfides and metasomatic features (e.g. unequilibrated grain boundaries, melt pockets, fluid inclusions, phlogopite) in the Type II eclogites, demonstrate that Type II eclogites did not undergo such a metasomatic event and therefore may represent the less-modified protoliths of Type I eclogites.
ISSN: 0009-2541

hal-00903856
https://hal.archives-ouvertes.fr/hal-00903856
DOI : 10.1016/j.chemgeo.2013.06.015

Éditeur(s) : CNEXO
Résumé : This book constitutes the first of a series of three volumes, the purpose of which is to cover the principal methods used in fish population dynamics. It is devoted to the definition of the main concepts, ami the presentation of the usual mathematical models. The second volume will deal with the fitting of the models, and the estimation of parameters. The third will be devoted to sampling problems. These volumes will be recollections of communications presented during ad hoc seminars, hold in Brest (GSG/COB) in 1980 and 1981. The first part deals with the basic concepts related to the two components whose relationship is being described by the population dynamics, namely the fish stock, to its relations with biological populations, and to the partition of catchabtiity into its components (vulnerability, availability...). The second chapter of this part is devoted to the quantification of exploitation. This leads to a discussion of nominal and effective fishing effort and fishing intensity. A brief review of the use of catch per unit of effort as an index of abundance is followed by a discussion of the concept of fishing power. The second part starts with some general remarks on mathematical modelling (chapter III), then comes to the two classical categories of models : global (surplus production) models (chapter IV), and structural models (chapter V). Chapter IV is mainly a review, based upon the SCHAEFER and PELLATOMLINSON models. Some less classical formulas from the recent literature are also introduced. Attention is paid to the underlying hypotheses and to the limitation of such models. The reader is finally referred to papers presenting the developments that could make it possible to overcome some of these limitations. Chapter V is based upon the classical BEVERTON and HOLT and RlCKER models, and the yield per recruit concepts. This field is however inlarged. Other commonly used variants of structural models are presented with an effort being made to clarify the real differences between all these variants. Special attention is also paid to so-called regenerative models and to the use of spawing-biomass or fecundity per recruit, which are likely to become commonly used in the coming years. In all cases, special attention is paid to the presentation of the basic formulas, that the reader might have to use if faced with a practical problem. Finally, a discussion of the underlying hypotheses takes place, before a brief review of the main developments, where the reader is referred to the appropriate literature.
Ce livre constitue le premier volet d'un tryptique destiné à effectuer une revue des méthodes essentielles en dynamique des populations marines exploitées. Il est consacré à la définition des concepts de base, à la présentation des modèles courants. Dans la discussion des concepts, ce volume s'attache à clarifier les notions relatives aux deux parties dont les relations font l'objet de la dynamique des populations exploitées : le stock et la flottille de pêche. Ceci amène notamment à préciser la définition d'un stock, sa relation avec la notion de population biologique, à analyser les problèmes de définition de la capturabilité. Les concepts d'intensité, d'effort, de puissance de pêche, une analyse des relations entre abondance et capture par unité d'effort sont ensuite présentés. Après une brève réflexion générale sur la modélisation, la deuxième partie de cet ouvrage présente les modèles eux-mêmes, en abordant successivement les modèles dits globaux et structuraux. Un effort est fait pour couvrir non seulement les versions les plus anciennes, mais aussi les variantes récentes, pour détailler les relations entre ces différentes variantes, offrir un formulaire de base, enfin, discuter les hypothèses majeures et les prolongements souhaitables ou en cours.
Publications du C.N.E.X.O. Série "Rapports scientifiques et techniques" (0339-2899) (CNEXO), 1981 , N. 45 , P. 1-120

Droits : Centre National pour l'Exploitation des Océans, 1981
http://archimer.ifremer.fr/doc/1981/rapport-1126.pdf
http://archimer.ifremer.fr/doc/00000/1126/

Éditeur(s) : Elsevier Science Bv
Résumé : Fluid escape structures on the Nile Deep Sea Fan were investigated during the MEDIFLUX MIMES expedition in 2004. Mud volcanoes, pockmarks and authigenic carbonate structures were surveyed for the first time with a high-resolution deep-towed 75 kHz sidescan sonar and a 2-8 kHz Chirp sediment echosounder. In combination with existing multibeam bathymetry and detailed seafloor in situ geological observations, these new data allowed detailed seep analyses. About 60 gas flares were detected acoustically in the water column from the sidescan sonar raw data at water depths from 770 to 1700 m. These gas flares coincide at the seabed with 1) the centres of the mud volcanoes where mud is also extruded, 2) the borders of the mud volcanoes where the emitted gases contribute to the precipitation of authigenic carbonates, and 3) to the edges of broad sheets of authigenic carbonates. Subsurface sediments are commonly disturbed by ascending fluids throughout the delta, with an abundance of seep-related carbonate structures on the seafloor. The feeder channels below mud volcanoes, similar to the gas conduits below the widespread carbonate crust structures and pockmarks, are relatively narrow and, for the vast majority of them, do not exceed a few metres in diameter. The seeps on the Nile Deep Sea Fan clearly follow lineations on the seafloor that we can relate to faults. (C) 2010 Elsevier B.V. All rights reserved.
Marine Geology (0025-3227) (Elsevier Science Bv), 2010-09 , Vol. 275 , N. 1-4 , P. 1-19

Droits : 2010 Elsevier B.V. All rights reserved.
http://archimer.ifremer.fr/doc/00013/12457/9766.pdf
DOI:10.1016/j.margeo.2010.04.003
http://archimer.ifremer.fr/doc/00013/12457/

Éditeur(s) : HAL CCSD Ocean Drilling Programm
Résumé : This paper provides a summary of postcruise scientific results from Ocean Drilling Program (ODP) Leg 209 available to date, building upon shipboard observations and syntheses summarized in the Leg 209 Initial Results volume. During Leg 209, 19 holes were drilled at 8 sites along the Mid-Atlantic Ridge from 14°43´ to 15°44´N, mainly in residual mantle peridotite intruded by gabbroic rocks, in order to understand the tectonic and structural processes responsible for formation of oceanic lithosphere with abundant residual peridotite exposed on the seafloor coupled with a relatively low proportion of volcanic rocks. Based on proportions of recovered lithologies, the entire area may be underlain by mantle peridotite with ~20%–40% gabbroic intrusions and impregnations. Impregnated peridotites with olivine + two pyroxenes + plagioclase + spinel that apparently formed in equilibrium probably record crystallization from primitive mid-ocean-ridge basalt at pressures of 0.5–0.6 GPa. Metamorphic equilibria record isobaric cooling to ~1100°C at this pressure. Thus, the conductively cooled thermal boundary layer beneath the Mid-Atlantic Ridge in this region is >15 km thick. Combined crystallization and reaction with residual peridotite formed a series of impregnated peridotites recording increasing Na content at nearly constant Mg#; this process could explain some of the variation in fractionation-corrected Na (e.g., Na = 8.0) observed in mid-ocean-ridge basalts. Clinopyroxene textures and compositions record such impregnation processes, and they are particularly well documented for Site 1274. Other Leg 209 gabbroic rocks formed from extensive crystallization of highly evolved melts, indicating that a substantial proportion of melt entering the thermal boundary layer crystallizes entirely beneath the seafloor, with no volcanic equivalent. Alteration of peridotites occurred over a range of temperatures and is the result of three distinct processes: rock-dominated serpentinization with formation of brucite in olivine-rich lithologies, fluid-dominated serpentinization with formation of magnetite and no brucite, and fluid-dominated talc alteration with addition of SiO2 as well as H2O and oxygen. The latter two processes also exhibit detectable trace element metasomatism that is distinct in its character from the igneous impregnation described in the previous paragraph. Microstructures show that most residual peridotites were not ductilely deformed at temperatures less than ~1200°C. Structural and paleomagnetic data require tectonic rotations of relatively undeformed blocks; some rotations probably exceeded 60° around nearly horizontal axes parallel to the rift axis. Rotations occurred along several generations of high-temperature mylonitic shear zones extending deeper than 15 km depth and numerous faults at lower temperature. Early formed shear zones and faults were passively rotated around later features; such a process could have produced low-angle fault surfaces without slip on low-angle faults. This region provides end-member examples of processes that are common at many or most slow-spreading ridges. Osmium isotope ratios indicate an ancient history of depletion for residual peridotites from the 14°–16°N region along the Mid-Atlantic Ridge. Though depleted Os isotope ratios in peridotite have been reported elsewhere along the global ridge system, the values from this region are among the most depleted. In general, Os isotope ratios from mid-ocean-ridge basalts are systematically more radiogenic than Os isotope ratios from ridge peridotite samples, suggesting a polygenetic heterogeneous source for mid-ocean-ridge basalts. Geochemical studies of zircons from Leg 209 gabbroic rocks and impregnated peridotites, together with other ridge and arc-related zircons, indicate that ridge zircons have systematically lower fractionation-corrected U and Th concentrations compared to arc zircons. This observation provides a tool for interpreting the tectonic provenance of ancient detrital zircons and indicates an arclike provenance for Hadean detrital zircons. Geobiological studies and aerobiological studies were also undertaken during Leg 209. The geobiological work found no measurable microbial enhancement of olivine dissolution rate, possibly because the samples from Leg 209 were sterile. The aerobiological study determined that dust from North Africa, collected from the derrick of the JOIDES Resolution during Leg 209, contains a variety of abundant microorganisms.
Proceedings ODP, scientific results, 209

hal-00407966
https://hal.archives-ouvertes.fr/hal-00407966
DOI : 10.2973/odp.proc.sr.209.001.2007

Éditeur(s) : HAL CCSD Ecological Society of America
Résumé : Tropical plant diversity is extraordinarily high at both local and regional scales. Many studies have demonstrated that natural enemies maintain local diversity via negative density dependence, but we know little about how natural enemies influence beta-diversity across habitats and/or regions. One way herbivores could influence plant beta-diversity is by driving allocation trade-offs that promote habitat specialization across resource gradients. We therefore predicted that increasing resource availability should be accompanied by increasing herbivory rates and decreasing plant allocation to defense. Second, relative abundances within plant lineages are predicted to reflect patterns of habitat specialization and allocation trade-offs. A phylogenetic context is vital not only to compare homologous plant traits (including defense strategies) across habitat types, but also to connect evolutionary trade-offs to patterns of species diversification in each phylogenetic lineage. We tested these predictions for trees in white-sand, clay terra firme, and seasonally flooded forests in Peru and French Guiana that represent the range of soil fertility, forest structure, and floristic compositions found throughout the Amazon region. We established 74 0.5-ha plots in these habitats and sampled all trees. Within 12 representative plots we marked newly expanding leaves of 394 saplings representing 68 species, including the most abundant species in each plot in addition to species from five focal lineages: Swartzia and Inga (Fabaceae), Protieae (Burseracaeae), Bombacoideae (Malvaceae), and Micropholis (Sapotaceae). We measured total leaf production rates for each sapling and calculated relative herbivory impact as the ratio between herbivory rate and leaf production rate. Herbivory rates averaged 2.1% per month, did not correlate with leaf production rate, and were similar across habitats. Relative herbivore impacts exceeded leaf production rates for most species. Leaf production rate averaged 2.8%, was significantly higher in seasonally flooded forests than the other two habitats, and exhibited significant correlations with specific leaf area. Species with high herbivory rates exhibited significantly lower relative abundances in terra firme forests. Overall, focal species within lineages present contrasting patterns regarding their herbivory rates and leaf production rate within habitats. These results highlight why a lineage-based approach is necessary when attempting to connect hypotheses regarding evolutionary trade-offs to community assembly patterns.
ISSN: 0012-9658

hal-01032418
https://hal.archives-ouvertes.fr/hal-01032418

Éditeur(s) : Ecole nationale supérieure agronomique de Rennes
Résumé : Describe and gain understanding on fluctuations in animal population over time and space is a central goal of population ecology. This is also crucial to ensure the sustainable management of exploited resources, particularly those with complex population dynamics such as the bluefin tuna. The goal of this work is to collect bluefin tuna catches from the ancestral Mediterranean and Atlantic trap fisheries to (i) characterise long-term fluctuations in bluefin tuna population migrating in the Mediterranean, (ii) analyse their causes et (iii) assess their implications for fisheries management. The bluefin tuna main biological and ecological characteristics are first detailed. Then, the first part presents the trap fishery, and the process of collect and validation of the historical catches. This leads to develop a data base of 54 time-series more than 20 years long, the longest ones spanning about four centuries. Mean historical catches were around 15 000 tons/year ([7 000;25 000]). Time-series are analysed in a second part. Temporal variability of trap catches may be decomposed in three components: 100-year-long periodic fluctuations, 20-year cycles and inter-annual variations. These medium- to long-term fluctuations, representing more than 50% of the variability in the time-series, were synchronous all around the western Mediterranean and adjacent North Atlantic. In contrast, short-term variability was synchronous at a local scale only. It is argued that long-term fluctuations in trap catches could be considered as a proxy for those in abundance, and a synthetic time-series is computed to depict them. Biological and ecological processes that could cause such long-term fluctuations are discussed in a third part. We tested whether long-term fluctuations in Atlantic bluefin tuna might be related to large-scale environmental changes, using long time-series of the North Atlantic Oscillation (NAO), the Length of the Day index (LOD, a proxy of the atmospheric circulation index ACI) and the temperature. Spectral analyses of trap catches, LOD and temperature displayed similar spectra with peak at low frequency, whereas those of the NAO exhibited a broad band spectrum. Regression analyses and tests of correlation did not reveal any clear relationship between trap catches on the one hand and NAO and LOD on the other hand. In contrast, long-term fluctuations in trap catches appear to be negatively and significantly related to long-term trends in temperature. Underlying processes that could explain such a relationship are discussed, with special focus on changes in migration patterns. Finally, implications of such fluctuations in term of fisheries management are discussed in a fourth part. A simulation framework, in which a simulated population dynamics model is coupled with a VPA, is built to test the pertinence of the diagnostic of stock assessment according to different scenarios on fluctuations origins and population status. In the hypothesis of fluctuations linked to variations in the recruitment, VPA appears able to reconstruct the fluctuations but the predictions may be biased if natural fluctuations are not taking into account. In the hypothesis of fluctuations linked to changes in migration pattern, VPA is not able to reconstruct the population dynamics. In a precautionary approach, quotas which follow may be unsuitable in the best case, at worst dangerous if they are defined in comparison with a reference point. The concept of cible reference points, fixe and unique over time, appears not relevant for bluefin tuna; estimate trajectory reference pertinent may prove to be more pertinent.
Décrire et comprendre les fluctuations spatio-temporelles des espèces animales constituent les enjeux majeurs de l'écologie. La question est également cruciale pour réussir la gestion durable des ressources exploitées, en particulier celle du thon rouge, grand pélagique migrateur à la dynamique complexe. L'objectif de ce travail est de collecter les captures historiques de thon rouge par les madragues méditerranéennes et proche atlantiques pour (i) caractériser les fluctuations à long terme de la population migrante en Méditerranée, (ii) étudier leur déterminisme et (iii) évaluer leurs implications en terme de gestion des pêcheries. Après avoir décrit les principales caractéristiques biologiques et écologiques du thon rouge, la première partie présente la pêcherie à la madrague, puis le processus de collecte et de validation des données historiques de captures. Ce dernier conduit à la mise en place d'une base de données de 54 séries de plus de 20 ans, dont les plus longues s'étendent sur près de 4 siècles. Les productions historiques sont estimées à environ 15 000 tonnes/an ([7 000;25 000]). Les séries historiques de captures sont analysées dans la seconde partie. Leur variabilité temporelle peut être décomposée en trois composantes : de larges cycles pseudo-séculaires, des variations périodiques d'une vingtaine d'années et des fluctuations inter-annuelles. Les fluctuations à moyen et long terme, expliquant plus de la moitié de la variance des séries, sont synchrones à l'échelle du bassin méditerranéen occidental et du proche Atlantique. La variabilité inter-annuelle, en revanche, n'est synchrone qu'à une échelle locale. On montre finalement que les fluctuations à long terme des captures peuvent être considérées comme de bons indices des tendances des abondances de la population de thons rouges migrants en Méditerranée. Une série synthétique est construite pour les décrire. Les processus biologiques et écologiques susceptibles d'être à l'origine de ces fluctuations sont discutés dans la troisième partie. L'hypothèse d'un forçage environnemental à grande échelle est testée en utilisant des indices à long terme de l'Oscillation Nord Atlantique (NAO), de la longueur du jour (LOD, un indicateur de l'indice de circulation atmosphérique ACI) et de la température. Les analyses spectrales sur les séries de captures, du LOD et des températures révèlent des spectres similaires, avec un pic sur les basses fréquences, alors que celles sur le NAO conduisent à une large bande spectrale. Les régressions et les tests de corrélations ne montrent aucune relation significative entre les captures par les madragues et le NAO et le LOD. En revanche, les fluctuations à long terme des captures apparaissent significativement et négativement corrélées avec les fluctuations à long terme des températures. Les processus sous-jacents susceptibles d'expliquer une telle relation, en particulier des changements migratoires, sont discutés. Finalement, les implications des fluctuations pour la gestion de la pêcherie sont discutées dans une quatrième partie. Un cadre de simulation, couplant un modèle de dynamique de population à une VPA, est élaboré pour tester la pertinence des diagnostics d'évaluation de stock selon différents scénarios d'origine des fluctuations et d'état de la population. Dans l'hypothèse de fluctuations liées à des variations du recrutement, la VPA apparaît capable de reconstruire les fluctuations mais les prédictions sont biaisées lorsqu'il n'est pas tenu compte des fluctuations naturelles du stock. Dans l'hypothèse de fluctuations liées à des changements migratoires, la VPA est alors incapable de reproduire la dynamique de la population. Dans une approche de précaution, les quotas qui en découlent peuvent se révéler au mieux inappropriés, au pire dangereux s'ils sont définis par rapport à un point de référence. Ce concept de point cible, fixe et unique dans le temps, apparaît inapproprié pour le thon rouge ; estimer des "trajectoires de référence" serait sans doute plus pertinent.

Droits : info:eu-repo/semantics/openAccess
http://archimer.ifremer.fr/doc/2003/these-65.pdf
http://archimer.ifremer.fr/doc/00000/65/

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Subcutaneous fat tissues from an indigenous fat-type breed and an intensively-lean selected breed were studied in juvenile pigs. Combining DIGE with bioinformatics and target analyses of key genes, enzymes or terminal routes, this study identifies metabolic and homeostatic processes, response to organic substances, and acute-phase responses as the main pathways whose proteins were regulated in association with adiposity. Breed-related differences in abundance and activities of malic enzyme and glucose-6-phosphate dehydrogenase NADPH-supplying enzymes suggested up-regulation of the lipogenic pathway to dispose for a greater adiposity. Over-abundance in the lipolytic protein carboxylesterase-1 was revealed in fat-type piglets. A panel of pro- and anti-inflammatory proteins such as serpins, had an altered abundance in the fat-type piglets, suggesting adverse consequences of fat accumulation even in early post-weaning stages. Propensity to low-grade inflammation in fat pigs was reinforced by the up-regulation of genes encoding pro-inflammatory cytokines IL6 and TNF-α in these piglets. Differential abundance in annexin-A5 and pericentrin suggested a positive regulation of cell apoptosis in lean piglets. Our results are relevant in the context of data linking the accretion of body lipids to the physiology and pathology of adipose tissue in models other than rodents for a better control of human health and nutrition.
ISSN: 1874-3919

hal-01122161
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01122161
PUBMED : 22061664
DOI : 10.1016/j.jprot.2011.10.012

Éditeur(s) : Springer
Résumé : The distribution of summer phytoplankton across the Straits of Magellan (SOM) was studied with the aims of tracing differences among the distinct subregions of the area and contributing to the knowledge of its biodiversity. Samples collected at 25 stations were observed and counted in light microscopy. Selected samples were observed with transmission electron microscopy. The main unifying feature of the phytoplankton in the SOM was the high abundance and numerical dominance of small-sized (<10 μm) eukaryotic species, among which coccoid cells of <3 μm size were predominant (56.2 ± 30.6 of the total phytoplankton abundance). They mostly belonged to the prasinophyte Pycnococcus provasolii, which was abundant (0.8–6,834 cells × 103 ml−1) at all stations with the exception of those in proximity to the Atlantic entrances, where it was not recorded. Small-sized (<3 and 3–5 μm) diatoms (Minidiscus trioculatus, Lennoxia faveolata and other undetermined centric species) attained high densities (<3,757 cells 103 ml−1) especially at stations of the Patagonian sectors, whereas microplanktonic diatoms were only found at the two entrances of the Straits. Dinoflagellates were constituted mainly by >10 μm forms in the Andean subregion and <10 μm naked species in the Patagonian subregion, contributing up to 75.9 and 41.8% of the total carbon in these two areas, respectively. In the Patagonian subregion, flagellates mainly constituted by <5 μm forms and by cryptomonads <10 μm comprised up to 53.9% of the total biomass. Several species identified in this study have never been reported in other investigations in the SOM, while others, including Pycnococcus provasolii and Lennoxia faveolata, have rarely been recorded elsewhere. Overall, the summer phytoplankton of the Straits does not resemble that of any other region of the world’s seas. Although some of the predominant species might have been overlooked elsewhere, their abundance and relative importance apparently constitute a distinctive feature of the SOM.
Polar Biology (0722-4060) (Springer), 2011 , Vol. 34 , N. 9 , P. 1269-1284

Droits : The Author(s) 2010. This article is published with open access at Springerlink.com
http://archimer.ifremer.fr/doc/00026/13722/10828.pdf
DOI:10.1007/s00300-010-0937-2
http://archimer.ifremer.fr/doc/00026/13722/

Éditeur(s) : Gauthier-Villars
Résumé : Several models for the evolution of complex life histories have assumed a carrying capacity for both larval and postlarval stages. In addition, the densities of larvae in laboratory experiments are often so high that there is competition for food. Published values for maximal clearance rates and estimated abundances of larvae suggest that these assumptions and experimental conditions are unrealistic for most marine larvae. For most ciliated larvae, maximum clearance rates are at most a few mi of water daily, and their estimated larval concentrations are at most one to several larvae per liter. Therefore these larvae appear to be too scarce for their grazing to affect their food supply. Larvae of most species are also scarce relative to co-occurring planktonic animals that feed on particles in the same size range. Larvae of many species are scarce relative to co-occurring larvae with a similar feeding apparatus. These observations suggest that larvae of most species have a negligible effect on their food supply. Exceptions could occur when a single species of larva dominates the zooplankton; such circumstances appear to be rare, although extreme aggregations of larvae dominated by a single species could be missed by pump or net samples. Analogous but more conjectural arguments can be made for density-dependent attraction of predators to larval prey. These inferences apply to single species, not to meroplanktonic larvae as a whole: in some coastal waters, larvae of benthic invertebrates comprise a large portion of the multicellular planktonic animals. Also, a species' larval growth may be food-limited in many waters, even when the abundance of food is independent of the abundance of its larvae.
Oceanologica Acta (0399-1784) (Gauthier-Villars), 1996 , Vol. 19 , N. 3-4 , P. 399-407

Droits : info:eu-repo/semantics/openAccess
http://archimer.ifremer.fr/doc/00094/20495/18164.pdf
http://archimer.ifremer.fr/doc/00094/20495/

Éditeur(s) : Elsevier
Résumé : Introduction of non-indigenous species can alter marine communities and ecosystems. In shellfish farming, transfer of livestock, especially oysters, is a common practice and potentially constitutes a pathway for non-indigenous introductions. Many species of seaweeds are believed to have been accidentally introduced in association with these transfers, but there is little direct evidence. We experimentally simulated the transfer of oysters from the Thau Lagoon (France). These transfers involved increasing periods of aerial emersion and additional brine and hot water treatments. The brine and hot water treatments were evaluated as a means of reducing the probability of algal introductions with oyster transfers. Shells were cultured for 40 days in experimental tanks to identify the macroalgae likely to be introduced with any oyster transfer. A total of 57 macroalgal taxa, including 16 taxa not indigenous to the Thau Lagoon, were recorded across all treatments and experiments. The abundance of some species increased in several cases following aerial emersion. Elimination treatments (immersion in brine or hot water) significantly reduced algal diversity, with hot water treatments resulting in no species or only tubular Ulva spp. present. The results support the hypothesis that oyster transfers are effective as primary and secondary vectors of macroalgal introductions. Relatively simple changes to the transfer practice (particularly hot water treatments) are suggested as a means of reducing the risk of non-indigenous algal introductions.
Biological Conservation (0006-3207) (Elsevier), 2007-06 , Vol. 137 , N. 2 , P. 237-247

Droits : 2007 Elsevier Ltd All rights reserved.
http://archimer.ifremer.fr/doc/2007/publication-2779.pdf
DOI:10.1016/j.biocon.2007.02.001
http://archimer.ifremer.fr/doc/00000/2779/

Éditeur(s) : Université de La Rochelle
Résumé : Shrimp aquaculture in New Caledonia is a developing industry, exclusively based on the species Litopenaeus stylirostris. However, it is subject to mortalities during grow out as observed all over the world. Since 1993, shrimp reared during the cold period are affected by a disease named "syndrome 93". As a consequence, the whole industry has become seasonal and produces essentially during the warm season. The climatic conditions during the periods of transition between the two main seasons could be responsible for an environmental stress and the origin reason for mortality outbreaks. Stocking density is the main risk factor. It increases the probability of the appearance and development of the epizooty in the pond. The "Summer Syndrome", a septicemic vibriosis caused by Vibrio nigripulchritudo, was identified for the first time in December 1997 in an intensive shrimp farm (DF). It has become enzootic ever since and is expressed after 50d of rearing. Since 2003, two others farms located near DF have developed the disease. As a consequence, the summer syndrome is considered to be a potential threat for all the industry. Between 1991 and 2005, the increase of feed input and nitrogen levels in feed has led to a significant increase in the growth rate over the years in the farms affected by the disease. In consequence, an early eutrophication of the water is observed, which is concomitant with the beginning of the mortality outbreaks. An early eutrophication and the virulence level of the pathogen are considered as the main risk factors of the disease. Factors may act synergistically to explain the summer syndrome. As part of a multidisciplinary approach (pathology – physiology – environment), two high-frequency surveys were carried out to analyse the pond ecosystem. Since the feed quantity increases with the biomass of shrimp, the eutrophication level of the pond ecosystem will also tend to increase with the duration of rearing. During the first part of the rearing, the abundance of each picoplankton type is exceptionally high and picophytoplankton dominated the autotrophic compartment. The nanophytoplankton dominated the second part of the rearing and was more unstable. The shift from pico to nanophytoplankton could be considered as an environmental stress and was observed in relation to the beginning of the mortalities, whatever the disease. Shift intensity could play a role by inducing directly or indirectly a stress for shrimp and/or a growth and/or virulence factors of the pathogen. Results from sediment studies show that mortality was best characterized by TAN concentration in pore water and even more when the TAN concentration was high. TAN and pH are potential stress factors for shrimp reared in ponds affected by these diseases.
L'aquaculture mondiale de crevettes est un secteur à très forte croissance. Toutefois, les problèmes liés aux maladies dans les élevages ne cessent d'augmenter depuis 1980. Au cours du développement de la filière de Nouvelle-Calédonie, deux épisodes saisonniers de mortalités associées à la présence de Vibrio pathogènes sont apparus et ont fortement perturbé les techniques et les schémas de production. Les premières mortalités hivernales, décrites sous le nom de « syndrome 93 » ont été observées en mai 1993. Elles ont affecté depuis tous les élevages de saison froide de toutes les fermes de production. Les conditions climatiques pendant les périodes de transitions entre les deux principales saisons caractérisant le climat de la Nouvelle-Calédonie, seraient responsables d'un stress environnemental à l'origine du déclenchement du syndrome 93. La densité initiale d'ensemencement, apparaît comme le principal facteur de risque, augmentant la probabilité d'apparition de la maladie et l'ampleur de ses effets. Le « syndrome d'été » a été identifié pour la première fois en 1997 dans une ferme pratiquant une production intensive. Il s'est déclaré depuis 2003 dans deux autres fermes géographiquement proches. Les mortalités apparaissent 58 jours en moyenne après l'ensemencement des post-larves dans les bassins. La recherche d'une croissance maximale des animaux a induit, avec les années, une intensification progressive du système caractérisée par une augmentation de la quantité d'aliment distribuée. L'examen des données historiques fait apparaître une eutrophisation du milieu de plus en plus précoce concomitante au déclenchement des mortalités. En l'état actuel de nos connaissances, cette évolution précoce de l'écosystème en présence de façon récurrente de la souche hautement pathogène du Vibrio incriminé et à une période où la fréquence des mues des crevettes est élevée, constitue le principal facteur de risque de la maladie. Avec l'apport croissant en aliment, la colonne d'eau évolue vers une autotrophie croissante alors que le sédiment devient de plus en plus hétérotrophe au fur et à mesure que l'élevage progresse. Au cours du processus d'eutrophisation, le compartiment autotrophe montre une succession de deux assemblages. Le picophytoplancton domine sur la première partie de l'élevage et laisse place à du nanophytoplancton en seconde partie. Cette phase de transition, concomitante à l'apparition des mortalités quel que soit le syndrome, caractérise un stress environnemental dont l'intensité pourrait favoriser ou non le déclenchement des mortalités. Les suivis de différents indicateurs dans les sédiments - pH, potentiel d'oxydoréduction et concentration en ammoniaque dans l'eau interstitielle – indiquent dans les bassins déclarant les épizooties des conditions qui ont été définies expérimentalement comme potentiellement plus stressantes pour les animaux.

Droits : info:eu-repo/semantics/openAccess
http://archimer.ifremer.fr/doc/2007/these-2643.pdf
http://archimer.ifremer.fr/doc/00000/2643/