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 Cambridge University Press (CUP)
Résumé : Nodulated legume trees comprised 43% of the stand basal area in the low, most frequently flooded microsites, and 23% in higher, drier microsites in a tropical freshwater swamp forest in French Guiana. Dinitrogen fixation in Pterocarpus officinalis, Hydrochorea corymbosa and Inga pilosula was confirmed by acetylene reduction assay (ARA), presence of leghaemoglobin in nodules and the N-15 natural abundance method. The results for Zygia cataractae were inconclusive but suggested N-2 fixation in drier microsites. Nodulated Inga disticha had a N-15-to-N-14 ratio similar to non-N-2-fixing trees, but ARA indicated nitrogenase activity and leghaemoglobin was present in nodules. All bacterial strains were identified as Bradyrhizobium spp. according to the partial 16S rDNA sequences, and they were infective in vitro in the model species Macroptilium atropurpuretan. About 35-50% of N in the leaves of P. officinalis, H. corymbosa and I. pilosula was fixed from the atmosphere. Dinitrogen fixation was estimated to contribute at least 8-13% and 1728% to whole-canopy N in high and low microsites, respectively. Symbiotic N, fixation appears to provide both a competitive advantage to legume trees under N-limited, flooded conditions and an important N input to neotropical freshwater swamp forests.
ISSN: 0266-4674

hal-01189191
https://hal.archives-ouvertes.fr/hal-01189191
PRODINRA : 13151
DOI : 10.1017/S0266467403006059

Éditeur(s) : HAL CCSD AGU and the Geochemical Society
Résumé : International audience
Rainbow is a dome-shaped massif at the 36°14′N nontransform offset along the Mid-Atlantic Ridge. It hosts three ultramafic-hosted hydrothermal sites: Rainbow is active and high temperature; Clamstone and Ghost City are fossil and low temperature. The MoMARDREAM cruises (2007, 2008) presented here provided extensive rock sampling throughout the massif that constrains the geological setting of hydrothermal activity. The lithology is heterogeneous with abundant serpentinites surrounding gabbros, troctolites, chromitites, plagiogranites, and basalts. We propose that a W dipping detachment fault, now inactive, uplifted the massif and exhumed these deep-seated rocks. Present-day deformation is accommodated by SSW-NNE faults and fissures, consistent with oblique teleseismic focal mechanisms and stress rotation across the discontinuity. Faults localize fluid flow and control the location of fossil and active hydrothermal fields that appear to be ephemeral and lacking in spatiotemporal progression. Markers of high-temperature hydrothermal activity (∼350°C) are restricted to some samples from the active field while a more diffuse, lower temperature hydrothermal activity (<220°C) is inferred at various locations through anomalously high As, Sb, and Pb contents, attributed to element incorporation in serpentines or microscale-sulfide precipitation. Petrographic and geochemical analyses show that the dominant basement alteration is pervasive peridotite serpentinization at ∼160–260°C, attributed to fluids chemically similar to those venting at Rainbow, and controlled by concomitant alteration of mafic-ultramafic units at depth. Rainbow provides a model for fluid circulation, possibly applicable to hydrothermalism at oceanic detachments elsewhere, where both low-temperature serpentinization and magmatic-driven high-temperature outflow develop contemporaneously, channeled by faults in the footwall and not along the detachment fault.
ISSN: 1525-2027

hal-01115281
https://hal.archives-ouvertes.fr/hal-01115281
https://hal.archives-ouvertes.fr/hal-01115281/document
https://hal.archives-ouvertes.fr/hal-01115281/file/Andreani_et_al-2014-Geochemistry%2C_Geophysics%2C_Geosystems.pdf
DOI : 10.1002/2014GC005269

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Nitrogen (N) transfer from legume trees to associated crops is a key factor for the N economy of low-input agroforestry systems. In this work, we presented a new approach to estimate N transfer based on the 15N content of root exudates and N released by root turnover of the donor plant (Gliricidia sepium) and the temporal change of the 15N content of the receiver plant (Dichanthium aristatum). The study was carried out in greenhouse using two isotopic methods: 15N leaf feeding (LF) and the natural 15N abundance (NA). Measurements of exudate 15N were made at several dates before and after tree pruning. A time-dependent box model was devised to quantify N transfer in time and to make comparisons between the isotopic methods. In NA, although tree roots and exudates presented a similar 15N signature before tree pruning, exudates were strongly depleted in 15N after pruning. In LF, exudates were always depleted in 15N in relation to tree roots. Hence, the current assumption used in N transfer studies concerning the equal 15N/14N distribution in tissues of the donor plant and in its excreted N was not confirmed in our study. Before pruning, N transfer functioned as a two-N-source system (soil N and exudates N) and both isotopic methods provided similar estimates: 11–12% for LF and 10–15% for NA. Calculations performed with the model indicated that N transfer occurred with small or nil fractionation of 15N in exudates. After pruning, there was a third N source associated with N released from tree root turnover. During this period, the isotopic signature of the receiver plant showed a transient state due to the progressive decrease of 15N content of that N source. The amount of N derived from the tree represented 65% of the total N content of the grass at the end of the experiments.
ISSN: 1161-0301

hal-01082183
https://hal-agroparistech.archives-ouvertes.fr/hal-01082183
DOI : 10.1016/j.eja.2007.03.003

Éditeur(s) : HAL CCSD Elsevier
Résumé : Eperua falcata (Aublet), a late-successional species in tropical rainforest and one of the most abundant tree in French Guiana, has developed an original strategy concerning N-acquisition by largely preferring nitrate, rather than ammonium (H. Schimann, S. Ponton, S. Hattenschwiler, B. Ferry, R. Lensi, A.M. Domenach, J.C. Roggy, Differing nitrogen use strategies of two tropical rainforest tree species in French Guiana: evidence from N-15 natural abundance and microbial activities, Soil Biol, Biochem. 40 (2008) 487-494). Given the preference of this species for nitrate, we hypothesized that root exudates would promote nitrate availability by (a) enhancing nitrate production by stimulating ammonium oxidation or (b) minimizing nitrate losses by inhibiting denitrification. Root exudates were collected in situ in monospecific planted plots. The phytochemical analysis of these exudates and of several of their corresponding root extracts was achieved using UHPLC/DAD/ESI-QTOF and allowed the identification of diverse secondary metabolites belonging to the flavonoid family. Our results show that (i) the distinct exudation patterns observed are related to distinct root morphologies, and this was associated with a shift in the root flavonoid content, (ii) a root extract representative of the diverse compounds detected in roots showed a significant and selective metabolic inhibition of isolated denitrifiers in vitro, and (iii) in soil plots the abundance of nirK-type denitrifiers was negatively affected in rhizosphere soil compared to bulk. Altogether this led us to formulate hypothesis concerning the ecological role of the identified compounds in relation to N-acquisition strategy of this species. (C) 2013 Elsevier Masson SAS. All rights reserved.
ISSN: 0981-9428

hal-01032437
https://hal.archives-ouvertes.fr/hal-01032437
DOI : 10.1016/j.plaphy.2013.05.003

Éditeur(s) : HAL CCSD Wiley
Résumé :  
The symbiotic interactions between Frankia strains and their associated plants from the Casuarinaceae under controlled conditions are well documented but little is known about these interactions under natural conditions. We explored the symbiotic interactions between eight genotypically characterized Frankia strains and five Casuarinaceae species in long-term field trials. Characterization of strains was performed using the polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP) for the nifD-nifK intergenic transcribed spacer (ITS) and 16S-23S ITS. Assessments of the symbiotic interactions were based on nodulation patterns using nodule dry weight and viability, and on actual N-2 fixation using the delta N-15 method. The PCR-RFLP patterns showed that the analyzed strains belonged to the same genotypic group (CeD group), regardless of the host species and environment of origin. The nodule viability index is introduced as a new tool to measure the viability of perennial nodules and to predict their effectiveness. The host Casuarinaceae species was a key factor influencing both the actual N-2-fixing activity of the associated Frankia strain and the viability of nodules within a location. This is the first study providing information on the symbiotic interactions between genotypically characterized Frankia strains and actinorhizal plants under natural conditions. The results revealed a way to improve a long-term management of the Casuarinaceae symbiosis.
ISSN: 0031-9317

hal-01032134
https://hal.archives-ouvertes.fr/hal-01032134
DOI : 10.1111/j.1399-3054.2007.00856.x

Éditeur(s) : Elsevier
Résumé : Many fish species are at the southern or northern limit of their distribution range tit the Bay of Biscay, where large-scale hydroclimatic changes have occurred in recent decades. We attempt here to identify the impact of these changes on the fish community of the eastern continental shelf of the Bay of Biscay. Data collected during 14 autumn groundfish surveys in 1973 and from 1987 to 2002 are used. The study area is between latitudes 48 degrees 30'N and 43 degrees 30'N while the depth ranges from 15 to 200 m. Annual abundance indices (number of individuals per km(2)) of 56 fish taxa present on average in at least 5% of the tows are computed. Multivariate analysis is used to detect temporal trends in these species' abundance indices. Assuming that increased water temperature may favour Subtropical species and hinder temperate ones, knowledge about the latitudinal distribution range is used to interpret time trends. Results show an increasing abundance trend with time for fish species having a wide distribution range in latitude (mainly subtropical ones), whereas the abundance of temperate and the least widely distributed species decreased steadily.
ICES Journal of Marine Science (1054-3139) (Elsevier), 2005-10 , Vol. 62 , N. 7 , P. 1436-1443

Droits : 2005 International Council for the Exploration of the Sea Published by Elsevier Ltd.
http://archimer.ifremer.fr/doc/2005/publication-824.pdf
DOI:10.1016/j.icesjms.2005.04.017
http://archimer.ifremer.fr/doc/00000/824/

Éditeur(s) : HAL CCSD Elsevier
Résumé :  
Termites represent one of the most abundant belowground animal taxa in tropical rainforests, where their species richness is much higher than in any other ecosystem. This high diversity in soil ecosystems is however difficult to explain by classical Hutchinsonian niche theory, as there is little evidence for spatial or temporal separation between species. Using delta(13)C and delta(15)N isotopic ratios, we tested if resource partitioning along the humification gradient occurs; in neotropical soldierless termites of the Anoplotermes-group. Two distinct sites were investigated to check if interspecific differences are transposable between sites. Significant differences in delta(15)N were found between species of the Anoplotermes-group. Although some species displayed higher intersite delta(15)N variation than others, species-average delta(15)N values for both sites were highly correlated, showing that sympatric soldierless soil-feeding termites feed on distinct components of the soil. Our data also suggest that some species are more likely to shift along this gradient than others, in response to overall habitat conditions or to the presence of competitors. Feeding niche differentiation can therefore account for the high species richness and diversity of soldierless soil-feeding termites in neotropical rainforests.
ISSN: 0038-0717

hal-01032157
https://hal.archives-ouvertes.fr/hal-01032157
DOI : 10.1016/j.soilbio.2009.07.005

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
The N-S Languedoc volcanic province between the French Massif Central and the Mediterranean Sea is characterized by sporadic scattered low volume (similar to 2 km(3)) and geochemically homogeneous alkali basaltic activity spanning from 161 to 05 Ma The existence of magmatic activity of such a long duration within such a small area (similar to 140 km long and similar to 60 km wide) in spite of the extensive shift to the East of the European plate (about 2500 km during the last 160 Ma) is problematic Trace-element abundances in lavas suggest low degrees of melting (1-5%) in the spinet-garnet transition zone of an enriched Iherzolitic source The lavas display rather large ranges in Sr isotopic ratios (0 70307-0 70436) The Nd-143/Nd-144 ratio variations are smaller (0 51268-0 51300) and these of Pb-206/Pb-204 Pb-208/Pb-204 and Pb-207/Pb-204 are 18 745-19 515 38 53239 228 and 15 567-15 680 respectively The Languedoc lithospheric mantle as sampled by xenoliths is globally similar to the Pyrenees lithosphere The xenoliths show also rather large Sr Nd and Pb isotopic variations (Sr-87/Sr-86 0 70287-0 70578 Nd-143/Nd-144 0 51256-0 51414 Pb-208/Pb-204 37772-39 041 Pb-206/Pb-204 17 901-19 353) except for Pb-207/Pb-204 (15 570-15 620) The Pb-206/Pb-204 and La/Sm ratios are positively correlated both in xenoliths and lavas The increase of the Pb-206/Pb-204 (which could be interpreted as participation of the European Asthenospheric Reservoir EAR) is probably related to volatile-rich (carbonated?) fluid percolation This is corroborated by LILE and HFSE patterns observed in several xenoliths Therefore our data on lavas and xenoliths suggest a lithospheric origin for this long lived magmatism We propose (1) that the role of the asthenosphere in the Languedoc volcanism was restricted to volatile-rich fluid supplying and (2) that the fluid injection within the lithosphere may be related to the arrival of the Central Atlantic Plume head beneath Western Europe about 70 Ma ago In this model the isotopic signature of the oldest lavas (>70 Ma) would be that of the mantle lithosphere inherited from Hercynian processes The signatures of the subsequent lavas would be driven by the metasomatic component stored within the lithosphere and preferentially mobilized during incipient melting This metasomatised lower lithosphere was close to its solidus and small changes in P (or T) triggered incipient melting leading to basaltic volcanism Successive local re adjustments of the lithospheric blocks which accompanied the Meso-Cenozoic evolution of the Thetys Ligurian margin towards the present Mediterranean margin are the probable cause of these changes and so the sporadic volcanic activity in Languedoc is unrelated to deep asthenospheric processes
ISSN: 0024-4937

hal-00558884
https://hal.archives-ouvertes.fr/hal-00558884
DOI : 10.1016/j.lithos.2010.04.009

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
Résumé : Transposable elements play a major role in the evolution of eukaryotic genomes. Knowing the distribution of transposable elements between different species within the same taxon is essential to study their dynamics and to better understand their role in the evolution of species. Given their abundance, species diversity and living environment, crustaceans are an excellent model for studying comparative genomics of retrotransposons. It is notably in the squat lobsters that the GalEa clade of Superfamily Copia was defined. We studied the distribution of two well-known LTR retrotransposons superfamilies: Gypsy and Copia, in crustaceans. By combining PCRs with degenerate primers and in silico analysis, we identified 35 families of Copia retrotransposons and 46 families of Gypsy retrotransposons in 15 and 18 species of crustaceans (mainly Malacostraca: crabs, shrimp, krill ...). These elements have different distribution and diversity in crustaceans. Gypsy elements appear relatively commonly and diverse in all species. Conversely, the Copia elements seem rare, and consequently more difficult to detect, and are largely dominated by the elements of the clade GalEa. These results suggest two different dynamic strategies for retrotransposons Gypsy (the Red Queen theory) and retrotransposons GalEa (‘domino days spreading’ branching process). In addition, GalEa elements present a great evolutionary success being widely distributed in many branches of metazoans. They are also present in certain red algae and we have also detected them in Fungi. Taking advantage of the large amount of available genomic data, we have studied the distribution of GalEa elements of Fungi, in order to compare it with the results obtained in crustaceans. In fact, they appear only in a large phylum of Ascomycetes, in Pezizomycotina, and they form a monophyletic group within the GalEa. Finally, in the Fungi, the GalEa elements are not majority among Copia retrotransposons. We have therefore initiated a new study in molluscs, to define if the results obtained in crustaceans are a feature of GalEa elements, Malacostraca or metazoans.
Les éléments transposables jouent un rôle majeur dans l’évolution des génomes eucaryotes. La connaissance de la distribution des éléments transposables entre différentes espèces au sein d’un même taxon est une condition essentielle pour étudier leur dynamique et mieux comprendre leur rôle dans l'évolution des espèces. Compte tenu de leur abondance, de leur diversité spécifique et de milieu de vie, les crustacés sont un excellent modèle pour étudier la génomique comparative des rétrotransposons. C’est notamment chez les Galathées qu’a été défini le clade GalEa des éléments de la superfamille des Copia. Nous avons étudié la distribution de deux superfamilles de rétrotransposons à LTR bien connus: les Gypsy et les Copia, au sein des crustacés. En combinant des PCRs avec amorces dégénérées et des analyses in silico, nous avons identifié 35 familles de rétrotransposons Copia et 46 familles de rétrotransposons Gypsy dans respectivement 15 et 18 espèces de crustacés (principalement des malacostracés : crabes, crevettes, krill...). Ces éléments présentent une distribution et une diversité différentes au sein des crustacés. Les éléments Gypsy apparaissent relativement fréquents et diversifiés dans toutes les espèces. A l’inverse, les éléments Copia semblent rares, donc difficilement détectables, et sont largement dominés par les éléments du clade GalEa. Ces résultats suggèrent deux stratégies différentes de dynamique pour les rétrotransposons Gypsy (théorie de la Reine Rouge) et les rétrotransposons GalEa (‘domino days spreading’ branching process). De plus, les éléments GalEa présentent un grand succès évolutif en étant largement distribués dans de nombreuses branches de métazoaires. Ils sont aussi présents chez quelques algues rouges et nous en avons également détecté chez des Fungi. Profitant des nombreuses données génomiques disponibles, nous avons donc étudié la distribution des éléments GalEa de Fungi, dans le but de comparer celle-ci aux résultats obtenus chez les crustacés. En fait, ils n’apparaissent qu’au sein d’un grand embranchement d’ascomycètes, les Pezizomycotina, et ils forment un groupe monophylétique au sein des GalEa. Enfin, chez les Fungi, les éléments GalEa ne sont pas majoritaire parmi les rétrotransposons Copia. Nous avons donc initié une nouvelle étude chez les mollusques, afin de définir si les résultats obtenus chez les crustacés sont une caractéristique des éléments GalEa, des malacostracés ou des métazoaires.
https://tel.archives-ouvertes.fr/tel-01132413

NNT : 2015PA066017
tel-01132413
https://tel.archives-ouvertes.fr/tel-01132413
https://tel.archives-ouvertes.fr/tel-01132413/document
https://tel.archives-ouvertes.fr/tel-01132413/file/these_archivage_2600252o.pdf

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Deposit feeders are able to process a considerable volume of sediment, containing large 9 quantities of associated bacteria. However, conclusions concerning the trophic role played by 10 benthic bacteria in marine sediments are still not fully elucidated. This study deals with 11 bacterivory by the gastropod Hydrobia ulvae, one of the most abundant deposit-feeding 12 species in intertidal mudflats in Western Europe. Ingestion rates of bacteria were determined 13 during grazing experiments using 15 N pre-enriched bacteria. Grazing experiments were 14 performed in order to measure effects of abiotic (temperature, salinity and luminosity) and 15 biotic (bacterial and algal abundances) factors on ingestion rates of bacteria by H. ulvae of an 16 intertidal mudflat (Brouage, Marennes-Oléron, France). The mean ingestion rate of bacteria 17 by H. ulvae was 1149 ngC ind-1 h-1. The general trend showed a temperature effect with an 18 optimum around 30°C, and the assimilation rate was significantly lower at 5°C. Bacterial 19 assimilation did not significantly differ between salinity 18 and salinity 31. Ingestion was the 20 same in light and in dark conditions. Results were compared with those of other grazing 21 experiments conducted simultaneously in similar conditions with two other grazers with 22 different size and feeding modes: the foraminifera Ammonia tepida and a nematode 23 community from the superficial sediment of the Brouage mudflat. Hydrobia ulvae and 24 nematodes presented a feeding behavior less influenced by environmental changes than A. tepida. Hydrobia ulvae ingested bacteria at a higher rate than smaller meiofaunal grazers and seemed to have a lower ability to selectively ingest diatoms than meiofaunal grazers.
ISSN: 1385-1101

hal-01248039
https://hal.archives-ouvertes.fr/hal-01248039
https://hal.archives-ouvertes.fr/hal-01248039/document
https://hal.archives-ouvertes.fr/hal-01248039/file/Pascal%20et%20al%202008.pdf
DOI : 10.1016/j.seares.2008.05.003

Éditeur(s) : Pergamon-elsevier Science Ltd
Résumé : We report rare earth element (REE) and neodymium (Nd) isotope data for the organic fraction of sediments collected from various depositional environments, i.e. rivers (n=25), estuaries (n=18), open-ocean settings (n=15), and cold seeps (n=12). Sedimentary Organic Matter (SOM) was extracted using a mixed hydrogen peroxide/nitric acid solution (20%-H2O2 – 0.02M-HNO3), after removal of carbonate and oxy-hydroxide phases with dilute hydrochloric acid (0.25M-HCl). A series of experimental tests indicate that extraction of sedimentary organic compounds using H202 may be complicated occasionally by partial dissolution of sulphide minerals and residual carbonates. However, this contamination is expected to be minor for REE because measured concentrations in H2O2 leachates are about two-orders of magnitude higher than in the above mentioned phases. The mean REE concentrations determined in the H2O2 leachates for samples from rivers, estuaries, coastal seas and open-ocean settings yield relatively similar levels, with ΣREE = 109 ± 86 ppm (mean ± s; n=58). The organic fractions leached from cold seep sediments display even higher concentration levels (285 ± 150 ppm; mean ± s; n=12). The H2O2 leachates for most sediments exhibit remarkably similar shale-normalized REE patterns, all characterized by a mid-REE enrichment compared to the other REE. This suggests that the distribution of REE in leached sedimentary organic phases is controlled primarily by biogeochemical processes, rather than by the composition of the source from which they derive (e.g. pore, river or sea- water). The Nd isotopic compositions for organic phases leached from river sediments are very similar to those for the corresponding detrital fractions. In contrast, the SOM extracted from marine sediments display εNd values that typically range between the εNd signatures for terrestrial organic matter (inferred from the analysis of the sedimentary detrital fractions) and marine organic matter (inferred from the analysis of local surface seawater). A notable exception is the case of organic matter (OM) fractions leached from cold seep sediment samples, which sometimes exhibit εNd values markedly different from both terrigenous and surface seawater signatures. This suggests that a significant fraction of organic compounds in these sediments may be derived from chemosynthetic processes, recycling pore water REE characterized by a distinct isotopic composition. Overall, our results confirm that organic matter probably plays an important role in the oceanic REE budget, through direct scavenging and remineralization within the water column. Both the high REE abundances and the shape of shale-normalized patterns for leached SOM also suggest that OM degradation in sub-surface marine sediments during early diagenesis could control, to a large extent, the distribution of REE in pore waters. Benthic fluxes of organic-bound REE could hence substantially contribute to the exchange processes between particulates and seawater that take place at ocean margins. Neodymium isotopes could provide useful information for tracing the origin (terrestrial versus marine) and geographical provenance of organic matter, with potential applications in paleoceanography. In particular, future studies should further investigate the potential of Nd isotopes in organic compounds preserved in sedimentary records for reconstructing past variations of surface ocean circulation.
Geochimica Et Cosmochimica Acta (0016-7037) (Pergamon-elsevier Science Ltd), 2014-09 , Vol. 140 , P. 177-198

Droits : 2014 Elsevier Ltd. All rights reserved.
http://archimer.ifremer.fr/doc/00191/30250/28682.pdf
DOI:10.1016/j.gca.2014.05.016
http://archimer.ifremer.fr/doc/00191/30250/

Résumé : Fishing crayfish on the gulf's mudflats is a traditional business practised by 450 boats of 12 to 18 metres in length and employs 2,500 sailors. In the north of the gulf, this activity is exclusive, in the south, immature hake are also caught, because the crayfish areas coincide, in part, with the nurseries of the northern stock of this species. Management of these fisheries, called mixed, of crayfish and hake is one of the greatest problems of the Gulf of Gascony. All assessments tend to show the responsibility of the crayfish boats in the future of the hake stock. The solution is likely to pass through a generalised increase of the 80 mm meshing that would lead, eventually, the hake stock yield to its maximum, but would eliminate a great many trades that are only practicable for the moment by using small meshing: crayfish boats, shrimp boats, etc. It was shown moreover that the times of maximum abundance of hake and crayfish do not necessarily coincide. Indeed, hake does not swim along the bottom but rather moves in the channel of water. There are therefore definitely crayfish areas and hake areas, but overlapping such that a ship passing from one to the other during a single pass cannot judge in advance the immediate composition of its catch. The method used for describing these mixed fisheries and providing a solution to their problems of management relies on simulations aided by a bio-economic model known as "compartmental". This structure was adopted to be able to take into account all possible scenarios of the fleets' strategies. The fishery is first divided into geographic elements corresponding to the specific sedimentary structures where the stocks of exploited species are concentrated, the major constraint being the limits of these elements corresponding to those usually employed in fishing statistics, since it is based on these statistics that we can determine the fleets' profiles and their target species. The ratios between the fleet and the species are measured by calculating the fishing power.
La pêche de la langoustine sur les vasières du golfe est une activité traditionnelle pratiquée par 450 bateaux de 12 à 18 mètres et occupe 2500 marins . Dans le nord du golfe, cette activité est exclusive, vers le sud, elle s'accompagne de la capture de merlus immatures, car les zones à langoustine coïncident, pour partie, avec les nourriceries du stock nord de cette espèce. La gestion de ces pêcheries, dites mixtes, de langoustine et de merlu est un des problèmes les plus importants du golfe de Gascogne. Toutes les évaluations tendent à montrer la responsabilité des langoustiniers dans le devenir du stock de merlu. La solution passerait par une augmentation généralisée du maillage à 80 mm qui conduirait, à terme, le rendement du stock de merlu à son maximum, mais ferait disparaître quantité de métiers qui ne sont praticables pour le moment que par l'emploi de petits maillages : langoustiniers, crevettiers etc.. Il a été montré par ailleurs que les abondances maximales de merlu et de langoustine ne coïncident pas obligatoirement. En effet, le merlu n'est pas posé sur le fond mais se déplace dans la tranche d'eau. Il existe donc bien des zones à langoustine et des zones à merlu, mais imbriquées de telle sorte qu'un navire passant de l'une à l'autre au cours d'un même trait ne peut préjuger de la composition immédiate de sa capture. La méthode retenue pour décrire ces pêcheries mixtes et fournir une solution à leurs problèmes de gestion repose sur des simulations à l'aide d'un modèle bio-économique dit " à compartiments". Cette structure a été adoptée pour permettre la prise en compte de tous les cas de figures possibles de stratégies des flottilles. La pêcherie est d'abord divisée en éléments géographiques correspondant à des structures sédimentaires particulières où se concentrent les stocks d'espèces exploitées, la contrainte majeure étant les limites de ces éléments correspondant à celles habituellement employées dans les statistiques de pêche, puisque c'est à partir de ces statistiques que l'on peut déterminer le profil des flottilles et de leurs espèces cîbles. Les rapports entre la flottille et l'espèce sont mesurés par le calcul des puissances de pêche. Chaque compartiment est, sur une base trimestrielle, le résultat de la superposition d'un élément géographique, d'une flottille, d'une espèce ou d'un groupe d'espèces-cibles. L'association espèce-flottille définit le métier. Les stocks sont dits mobiles quand ils recouvrent par le biais des migrations la totalité de la pêcherie, immobiles quand il n'existe pas d'échanges entre éléments géographiques. Dans le deuxième cas, la mortalité par pêche est ventilée au prorata des captures sur chaque stock élémentaire. A l'intérieur de chaque composante un navire a le choix entre poissons démersaux, poissons de fond ou langoustine. L'inflexion de comportement dans les simulations est gouvernée par deux paramètres qui leur permettent d'orienter leur effort vers d'autres cibles pour optimiser leurs bénéfices. On connaît pour chaque flottille les éléments de coûts de production dérivés des comptes d'exploitation de l'année en cours. Pour chaque espèce, le chiffre d'affaire est le produit du prix prédit par l'équation des prix et des quantités débarquées. Les bénéfices escomptés sont déduits de ces deux valeurs. Les simulations ont porté sur diverses hypothèses : - maillage de 50 mm pour la langoustine et 65 mm pour le poisson ; - l'augmentation de l'effort ; - stratégies visant au profit maximal avec ou sans quota sur le merlu. Dans tous les cas, à terme, les schémas classiques des conséquences des procédures de gestion sont vérifiés : les brusques augmentations de maillage créent des situations transitoires catastrophiques mais permettent d'espérer au bout de 15 ans des soldes tout à fait attirants. Les conséquences d'une augmentation de l'effort agissent dans le sens inverse : augmentation immédiate du solde global, pertes à long terme. Enfin quand on laisse les flottilles suivre une stratégie "libre" orientée vers des bénéfices optimaux, les soldes sont importants car il existe toujours un report très marqué vers le merlu, dans les limites d'un quota quand on l'impose. Les phénomènes biologiques sont aisément prévisibles et théoriquement contrôlables. La stratégie des flottilles l'est beaucoup moins et dépend du contexte politico-économique. Le modèle présenté ici peut donner des réponses au gestionnaire et à l'économiste.

Droits : info:eu-repo/semantics/openAccess
http://archimer.ifremer.fr/doc/1988/rapport-2569.pdf
http://archimer.ifremer.fr/doc/00000/2569/