Éditeur(s) : Wiley-blackwell Publishing, Inc
Résumé : Recent theoretical and field studies conducted in both terrestrial and marine ecosystems have suggested that diversity could be a more complex and multi-component concept than previously thought. However, it is still poorly understood to what extent the information provided by the various indices is complementary with regard to diversity, and to what extent this complementarity is reproducible in different situations or at different scales of observation. In the present work, we have analysed the reproducibility of the empirical relationships between 11 diversity indices related to four major aspects (components) of species diversity (species richness, rarity, evenness and species taxonomy) in order to determine whether there is a general pattern of redundancy or complementarity in diversity measures that holds across years, areas and spatial scales. We have applied this approach to groundfish diversity through the analysis of 2404 trawl hauls collected during the first large-scale annual surveys carried out using a single sampling design throughout the northern Mediterranean Sea (ranging from 36.3 to 45.7 degrees N, and 5.3 degrees W to 28 degrees E). Whatever the years, areas and scales studied, we found a strong reproducibility in the number and the nature of the main complementary components of diversity. The whole set of diversity indices considered may be roughly split into 6 complementary groups of descriptors. This result highlights that, in contrast to what is still the usual practice, monitoring diversity should not be based on only one or two of the most widely used components, even at large scale. Finally, in a context where developing tools for monitoring diversity is considered as a high priority worldwide, the strong reproducibility of the relationships between diversity indices we observed offers a basis for discussion of the feasibility and relevance of proposing a general shortlist of indices for monitoring diversity at different management scales.
Ecography (0906-7590) (Wiley-blackwell Publishing, Inc), 2010-12 , Vol. 33 , N. 6 , P. 1123-1135

Droits : 2010 The Authors / Ecography
http://archimer.ifremer.fr/doc/00029/14064/11382.pdf
DOI:10.1111/j.1600-0587.2009.06259.x
http://archimer.ifremer.fr/doc/00029/14064/

Éditeur(s) : Wiley-blackwell Publishing, Inc
Résumé : P>Torsvik et al. recently presented a revised model for the opening of the South Atlantic Ocean. According to these authors, this new plate tectonic model is internally consistent and consistent with globally balanced plate motion solutions and takes into account realistic intraplate deformation. However, this model shows a number of kinematic and geological problems that we underline here, together with some comparisons with the new kinematic model recently proposed by Moulin et al.
Geophysical Journal International (0956-540X) (Wiley-blackwell Publishing, Inc), 2010-10 , Vol. 183 , N. 1 , P. 20-28

Droits : info:eu-repo/semantics/openAccess
http://archimer.ifremer.fr/doc/00014/12504/9878.pdf
DOI:10.1111/j.1365-246X.2010.04727.x
http://archimer.ifremer.fr/doc/00014/12504/

Éditeur(s) : HAL CCSD Blackwell Publishing
Résumé : International audience
Pliocene and Pleistocene deposits from Grande-Terre (Guadeloupe archipelago, French Lesser Antilles) provide a remarkable example of an isolated carbonate system built in an active margin setting, with sedimentation both controlled by rapid sea-level changes and tectonic movements. Based on new field, sedimentological and palaeontological analyses, these deposits have been organized into four sedimentary sequences (S1 to S4) separated by three subaerial erosion surfaces (SB0, SB1 and SB2). Sequences S1 and S2 ('Calcaires inférieurs à rhodolithes') deposited during the late Zanclean to early Gelasian (planktonic foraminiferal Zones PL2 to PL5) in low subsidence conditions, on a distally steepened ramp dipping eastward. Red algal-rich deposits, which dominate the western part of Grande-Terre, change to planktonic foraminifer-rich deposits eastward. Vertical movements of tens of metres were responsible for the formation of SB0 and SB1. Sequence S3 ('Formation volcano-sédimentaire', 'Calcaires supérieurs à rhodolithes' and 'Calcaires à Agaricia') was deposited during the late Piacenzian to early Calabrian (Zones PL5 to PT1a) on a distally steepened, red algal-dominated ramp that changes upward into a homoclinal, coral-dominated ramp. Deposition of Sequence S3 occurred during a eustatic cycle in quiet tectonic conditions. Its uppermost boundary, the major erosion surface SB2, is related to the Cala1 eustatic sea-level fall. Finally, Sequence S4 ('Calcaires à Acropora') probably formed during the Calabrian, developing as a coral-dominated platform during a eustatic cycle in quiet tectonic conditions. The final emergence of the island could then have occurred in late Calabrian times.
ISSN: 1469-3496

hal-00760906
https://hal.archives-ouvertes.fr/hal-00760906
DOI : 10.1111/j.1365-3091.2011.01311.x

Éditeur(s) : Wiley-blackwell Publishing, Inc
Résumé : Vibrioses are the predominant bacterial infections in marine shrimp farms. Vibrio nigripulchritudo is an emerging pathogen of the cultured shrimp Litopenaeus stylirostris in New Caledonia and other regions in the Indo-Pacific. The molecular determinants of V. nigripulchritudo pathogenicity are unknown; however, molecular epidemiological studies have revealed that recent pathogenic V. nigripulchritudo isolates from New Caledonia all cluster into a monophyletic clade and contain a small plasmid, pB1067. Here, we report that a large plasmid, pA1066 (247 kb), can also serve as a marker for virulent V. nigripulchritudo, and that an ancestral version of this plasmid was likely acquired prior to other virulence-linked markers. Additionally, we demonstrate that pA1066 is critical for the full virulence of V. nigripulchritudo in several newly developed experimental models of infection. Plasmid pB1067 also contributes to virulence; only strains containing both plasmids induced the highest level of shrimp mortality. Thus, it appears that these plasmids, which are absent from non-pathogenic isolates, may be driving forces, as well as markers, for the emergence of a pathogenic lineage of V. nigripulchritudo.
Environmental Microbiology (1462-2912) (Wiley-blackwell Publishing, Inc), 2011-02 , Vol. 13 , N. 2 , P. 296-306

Droits : 2010 Society for Applied Microbiology and Blackwell Publishing Ltd
http://archimer.ifremer.fr/doc/00031/14196/11469.pdf
DOI:10.1111/j.1462-2920.2010.02329.x
http://archimer.ifremer.fr/doc/00031/14196/

Éditeur(s) : Wiley-blackwell Publishing, Inc
Résumé : Vibrio splendidus, strain LGP32, is an oyster pathogen associated with the summer mortalities affecting the production of Crassostrea gigas oysters worldwide. Vibrio splendidus LGP32 was shown to resist to up to 10 mu M Cg-Def defensin and Cg-BPI bactericidal permeability increasing protein, two antimicrobial peptides/proteins (AMPs) involved in C. gigas immunity. The resistance to both oyster Cg-Def and Cg-BPI and standard AMPs (polymyxin B, protegrin, human BPI) was dependent on the ompU gene. Indeed, upon ompU inactivation, minimal bactericidal concentrations decreased by up to fourfold. AMP resistance was restored upon ectopic expression of ompU. The susceptibility of bacterial membranes to AMP-induced damages was independent of the ompU-mediated AMP resistance. Besides its role in AMP resistance, ompU proved to be essential for the adherence of V. splendidus LGP32 to fibronectin. Interestingly, in vivo, ompU was identified as a major determinant of V. spiendidus pathogenicity in oyster experimental infections. Indeed, the V. splendidus-induced oyster mortalities dropped from 56% to 11% upon ompU mutation (Kaplan Meier survival curves, P < 0.01). Moreover, in co-infection assays, the ompU mutant was out competed by the wild-type strain with competitive indexes in the range of 0.1-0.2. From this study, ompU is required for virulence of V. splendidus. Contributing to AMP resistance, conferring adhesive properties to V. splendidus, and being essential for in vivo fitness, the OmpU porin appears as an essential effector of the C. gigas/V. splendidus interaction.
Environmental Microbiology (1462-2912) (Wiley-blackwell Publishing, Inc), 2010-04 , Vol. 12 , N. 4 , P. 951-963

Droits : 2010 Society for Applied Microbiology and Blackwell Publishing Ltd
http://archimer.ifremer.fr/doc/00003/11421/8044.pdf
DOI:10.1111/j.1462-2920.2009.02138.x
http://archimer.ifremer.fr/doc/00003/11421/

Éditeur(s) : HAL CCSD Blackwell Publishing
Résumé : International audience
In the Causses platform (south-east France), Late Hettangian to Sinemurian deposits were interpreted previously as shallow-water carbonate ramp deposits. A new look at these deposits has shown a fault-controlled mosaic carbonate platform that is different from the carbonate ramp models. Within the platform mosaic, 15 lithofacies have been recognized, which are organized in four facies associations, including peritidal, restricted shallow sub-tidal, sand dunes and sub-tidal shelf facies associations. The rapid lateral and vertical facies changes, and the lack of consistent landward or seaward direction indicated by the pattern of facies changes, question the existence of a shoreline suggested by the traditional models for this region. Instead, the facies organization and cycle stacking pattern suggest deposition in a mosaic of intertidal islands between which sub-tidal restricted or open conditions could coexist in very close proximity. Such a platform mosaic would have been defined by tectonic activities along normal faults which segmented the shallow-water Causses platform. The facies and facies associations are arranged into metre-scale, peritidal and sub-tidal cycles that are also variable. Certain cycles show the same stacking pattern in all the sections and seem to be traceable over tens of kilometres. On the contrary, other cycles cannot be correlated; they are present only in specific sections and have a maximum lateral extension of 1 or 2 km. These metre-scale cycles stack to form four medium-scale cycles bounded by surfaces that display sub-aerial exposure features. Medium-scale cycles stack into two larger-scale cycles (tens of metres thick) and are bounded by well-defined karstic surfaces. Based on their lateral continuity and their stacking pattern, the metre-scale cycles are controlled probably by high frequency eustatic variations overprinting the topographic irregularities formed by differential subsidence of fault-bounded blocks. Episodic fault activities may reorganize the topography so that, even if eustatic changes may still be the major control of cycles, the expression and number of cycles could be different. Cycles of medium and large-scale are interpreted as being allogenic, controlled by changes in eustasy and/or subsidence rates as evidenced by their lateral continuity and the correlations of the large-scale cycles with third-order depositional sequences.
ISSN: 1469-3496

hal-00411940
https://hal.archives-ouvertes.fr/hal-00411940
DOI : 10.1111/j.1365-3091.2007.00896.x

Éditeur(s) : Wiley-blackwell Publishing, Inc
Résumé : We present the results from processing and interpreting five lines from the 1992 Erable multichannel seismic reflection experiment extending from the southeastern margin of Flemish Cap into the northern Newfoundland Basin. These profiles reveal significant along strike variations in the rifting styles experienced by Flemish Cap. In the southwest, a 100-km-wide transition zone is identified between thinned continental crust and thin oceanic crust. Similar to the conjugate Galicia Bank and Iberian margins, this transition zone contains a section of deep basement adjacent to a series of shallower ridges and is interpreted as exhumed serpentinized mantle. Along strike towards the northeast, this transition zone pinches out completely within 100 km and is replaced by thin oceanic crust directly adjacent to thinned continental crust. By interpreting nearby seismic profiles and profiles on the conjugate margins using the same classification criteria, we construct regional maps of the distribution of crustal domains on both sides of the North Atlantic. These maps reveal significant variations in rifting style on the conjugate margins and along strike of each margin and also highlight the role of ancient transfer zones in compartmentalizing these rifting variations into four distinct regions. We propose that the limited localization of shallow topographically high serpentinized peridotite ridges on the Newfoundland-Iberia and Flemish Cap-Galicia Bank conjugate margins, was directly related to an increase in the rate of extension following the separation of Flemish Cap and Galicia Bank which exhumed deeper, less serpentinized mantle.
Geophysical Journal International (0956-540X) (Wiley-blackwell Publishing, Inc), 2010-03 , Vol. 180 , N. 3 , P. 976-U4

Droits : 2010 RAS
http://archimer.ifremer.fr/doc/00001/11202/7876.pdf
DOI:10.1111/j.1365-246X.2009.04477.x
http://archimer.ifremer.fr/doc/00001/11202/

Éditeur(s) : Wiley-blackwell Publishing, Inc
Résumé : Red shrimp, Farfantepenaeus brasiliensis, larvae's response to different concentrations of live foods (diatoms Chaetoceros gracilis: 20-100 x 103 cells/mL; flagellate Tetraselmis chuii: 2-10 x 103 cells/mL and Artemia nauplii [NA]: 1-5 NA/mL) was investigated in three experiments. Experimental assessments were based on four variables: survival rate, weight gain, development index (DI), and resistance to salinity stress. A combination of C. gracilis 80 x 103 cells/mL, T. chuii 2 x 103 cells/mL, and Artemia 4 NA/mL provided the best experimental response. Specifically, F. brasiliensis larvae fed with the above-mentioned optimal concentrations of microalgae and Artemia grew faster and reached the postlarval stage in less time (168 h) than larvae in other feeding regimes evaluated. The effect of C. gracilis concentration on larval growth, survival, and the DI demonstrated that microalgae-based foods could be a highly productive alternative to more traditional aquaculture feeding regimes.
Journal Of The World Aquaculture Society (0893-8849) (Wiley-blackwell Publishing, Inc), 2010-06 , Vol. 41 , N. 3 , P. 402-410

Droits : Copyright by the World Aquaculture Society 2010
http://archimer.ifremer.fr/doc/00028/13928/11639.pdf
DOI:10.1111/j.1749-7345.2010.00381.x
http://archimer.ifremer.fr/doc/00028/13928/

Éditeur(s) : Wiley-blackwell Publishing, Inc
Résumé : Seagrasses structure some of the world's key coastal ecosystems presently in decline due to human activities and global change. The ability to cope with environmental changes and the possibilities for shifts in distribution range depend largely on their evolvability and dispersal potential. As large-scale data usually show strong genetic structure for seagrasses, finer-grained work is needed to understand the local processes of dispersal, recruitment and colonization that could explain the apparent lack of exchange across large distances. We aimed to assess the fine-grained genetic structure of one of the most important and widely distributed seagrasses, Zostera marina, from seven meadows in Brittany, France. Both classic population genetics and network analysis confirmed a pattern of spatial segregation of polymorphism at both regional and local scales. One location exhibiting exclusively the variety 'angustifolia' did not appear more differentiated than the others, but instead showed a central position in the network analysis, confirming the status of this variety as an ecotype. This phenotypic diversity and the high allelic richness at nine microsatellites (2.33-9.67 alleles/locus) compared to levels previously reported across the distribution range, points to Brittany as a centre of diversity for Z. marina at both genetic and phenotypic levels. Despite dispersal potential of several 100 m, a significant pattern of genetic differentiation, even at fine-grained scale, revealed 'genetic patchiness'. Meadows seem to be composed of a mosaic of clones with distinct origins in space and time, a result that calls into question the accuracy of the concept of populations for such partially clonal species.
Molecular Ecology (0962-1083) (Wiley-blackwell Publishing, Inc), 2010-06 , Vol. 19 , N. 12 , P. 2394-2407

Droits : 2010 Blackwell Publishing Ltd
http://archimer.ifremer.fr/doc/00006/11690/8499.pdf
DOI:10.1111/j.1365-294X.2010.04649.x
http://archimer.ifremer.fr/doc/00006/11690/

Éditeur(s) : Wiley-blackwell Publishing, Inc
Résumé : Aims: A description of bacterial pathogens in shrimp ponds is necessary to understand their pathogenesis. Vibrio nigripulchritudo was shown to contain saprophytic and pathogenic strains among New Caledonian isolates. We established a method to map the development of V. nigripulchritudo in pond sediments at three different genetic levels: the species level, then at the pathogenic cluster level and finally at the plasmid level, present only in all highly pathogenic isolates. Methods and Results: PCR methods were applied to shrimp pond sediments both before and after a mortality outbreak. Using crude samples, the species V. nigripulchritudo is not detected at first (0/42 samples at day 56 post stocking) but appears frequently in the sediments after the mortality event (30/42 at day 107). The distribution of strains from the pathogenic cluster of V. nigripulchritudo also follows this pattern. In contrast, the pSFn1 virulence-associated plasmid was detected in one sample at day 56 and none at day 107. An enrichment method was developed to lower the detection limits of our assays. After enrichment, the species V. nigripulchritudo was detected in all samples at both dates. The number of samples positive for pSFn1 was 42/42 samples at day 56 and 29/42 at day 107. Conclusions: These results show that the sediments contain V. nigripulchritudo, notably pathogenic strains. Surprisingly, the virulence-associated plasmid pSFn1 found in all V. nigripulchritudo isolated from moribund shrimp appears less frequently in sediments, possibly being useless or even detrimental to its recipient bacteria in this environment. Significance and Impact of the Study: This study confirms the presence of pathogenic V. nigripulchritudo strains in shrimp pond sediment before a mortality outbreak complying with a previous hypothesis that sediments could be the infecting reservoir. After the outbreak, both total V. nigripulchritudo and pathogenic strains populations have largely increased, possibly contributing to the recurrent mortality observed in this shrimp vibriosis.
Journal Of Applied Microbiology (1364-5072) (Wiley-blackwell Publishing, Inc), 2010-06 , Vol. 108 , N. 6 , P. 2003-2011

Droits : 2010 The Society for Applied Microbiology - Wiley-Blackwell
http://archimer.ifremer.fr/doc/00004/11484/8177.pdf
DOI:10.1111/j.1365-2672.2009.04601.x
http://archimer.ifremer.fr/doc/00004/11484/

Éditeur(s) : Wiley-blackwell Publishing, Inc
Résumé : Primary production must constrain the amount of fish and invertebrates available to expanding fisheries; however the degree of limitation has only been demonstrated at regional scales to date. Here we show that phytoplanktonic primary production, estimated from an ocean-colour satellite (SeaWiFS), is related to global fisheries catches at the scale of Large Marine Ecosystems, while accounting for temperature and ecological factors such as ecosystem size and type, species richness, animal body size, and the degree and nature of fisheries exploitation. Indeed we show that global fisheries catches since 1950 have been increasingly constrained by the amount of primary production. The primary production appropriated by current global fisheries is 17-112% higher than that appropriated by sustainable fisheries. Global primary production appears to be declining, in some part due to climate variability and change, with consequences for the near future fisheries catches.
Ecology Letters (1461-023X) (Wiley-blackwell Publishing, Inc), 2010-04 , Vol. 13 , N. 4 , P. 495-505

Droits : 2010 Blackwell Publishing Ltd/CNRS
http://archimer.ifremer.fr/doc/00002/11294/7836.pdf
DOI:10.1111/j.1461-0248.2010.01443.x
http://archimer.ifremer.fr/doc/00002/11294/

Éditeur(s) : HAL CCSD Blackwell Publishing
Résumé : International audience
The study of eight stratigraphic sections at the margin of the semi-enclosed Zsambek Basin (Hungary) allows the sedimentary anatomy of oolitic-bioclastic systems in the Sarmatian of the Central Paratethys to be reconstructed. The mollusc, foraminiferal and ostracod associations indicate that the carbonate systems are Latest Badenian to Late Sarmatian in age. The Lower-Upper Sarmatian deposits are organized in superimposed subaqueous dunes prograding towards the basin on a low-angle ramp. During the Late Sarmatian, the ramp underwent subaerial erosion linked to a moderate relative fall in sea-level. Lagoonal deposits were later formed and microbial-nubeculariid-bryozoan-serpulid buildups were emplaced. The 'abnormal' marine conditions of the Sarmatian, conducive to the development of a poorly diversified flora and fauna and dominant non-skeletal grains, are linked to fluctuating salinities, mesotrophic to eutrophic conditions and perhaps high alkalinity.
ISSN: 1469-3496

hal-00429337
https://hal.archives-ouvertes.fr/hal-00429337
DOI : 10.1111/j.1365-3091.2009.01055.x

Éditeur(s) : HAL CCSD Blackwell Publishing
Résumé : International audience
Differentiating between forced regressive deposits from deglacial periods inhigh latitude domains and forced regressive deposits from the onset of glacialperiods in low latitude domains is fundamental for the accurate interpretationof glacial cycles within the geological record and then for thereconstruction of palaeogeography and palaeo-climate. A forced regressivedeglacial sequence is documented from the Lake Saint-Jean basin (Quebec,Canada). In this area, the Late Pleistocene to Holocene sediments haverecorded the Laurentide ice sheet retreat accompanied by the invasion ofmarine waters (Laflamme Gulf) from ca 129 cal kyr BP. Subsequently, fluviodeltaicand coastal prograding wedges were deposited; they followed thebase-level fall due to glacio-isostatic rebound. This succession, representinga transition from glacial to post-glacial periods within a previously glaciatedarea, was investigated through recent mapping, preserved landforms, faciesanalysis, and new optical stimulated luminescence and radiocarbon dates.Three basin-scale geological sections share a common lower part made ofisolated ice-contact fan deposits overlying bedrock. Throughout the entirebasin, ice-contact fans are capped by glacimarine muds. Above, fluvial andcoastal prograding systems were deposited and evolved through four steps:(i) deltaic systems progressively increased in width; (ii) coastal influence onsedimentation increased; (iii) hydrographic drainage systems became moreorganised; and (iv) deltas graded from steep (Gilbert delta) to low-angle foresets(mouth-bar delta). Deposited during the base-level fall from glacioisostaticrebound, the complete succession has been designated as a singlefalling stage system tract referred to as a deglacial falling stage system tract.It is representative of a deglaciation sequence in areas previously covered byice during glacial periods (i.e. medium to high latitude domains). Diagnosticcriteria are provided to identify such a deglacial falling stage system tract inthe geological record, which may aid identification of previously unknownglacial cycles.
ISSN: 1469-3496

insu-01184731
https://hal-insu.archives-ouvertes.fr/insu-01184731
DOI : 10.1111/sed.12196

Éditeur(s) : Wiley-blackwell Publishing, Inc
Résumé : Oceanic larvae of the European (Anguilla anguilla) and American (A. rostrata) eels have to cross the Atlantic Ocean from the Sargasso Sea to European or North American coasts before entering continental habitats. In some European rivers, eel recruitment is now < 1% of levels in the 1980s. A better understanding of the effects of anthropogenic pressures and environmental fluctuations on eel larvae and subsequent recruitment is a prerequisite to build efficient management plans. The present paper provides insight into the critical oceanic phase of the eel life cycle with a focus on the duration of the larval migration whose estimates varies between 7 months and more than 2 years in both species. Does this range correspond to a natural variability in larval duration or does it stem from methodological artefacts? We first review the different methods used to estimate the duration of larval migration and critically describe their possible sources of misinterpretation. We then evaluate the consistency of these methods with the current knowledge about the ecology and physiology of eel larvae and the physical oceanography. While a moderate discrepancy in migration duration was found between methods for the American eel, the discrepancy was large in the European eel. In this species, otolith microstructure studies indicated migration durations between 7 and 9 months, while other methods pointed to durations of about 2 years. We show that estimates in favour of a long migration duration seem more robust to methodological caveats than methods estimating short durations of migration.
Fish And Fisheries (1467-2960) (Wiley-blackwell Publishing, Inc), 2010-09 , Vol. 11 , N. 3 , P. 289-306

Droits : 2010 Blackwell Publishing Ltd.
http://archimer.ifremer.fr/doc/00011/12208/9033.pdf
DOI:10.1111/j.1467-2979.2010.00362.x
http://archimer.ifremer.fr/doc/00011/12208/