Extrait de : Christophe Colomb vu par un marin (Page 312)
Résumé : Gravure représentant une cérémonie en mer en l'honneur des cendres de Christophe Colomb transportées en direction de l'Amérique.
Siècle(s) traité(s) : 16
Droits : Domaine public
Permalien : http://www.manioc.org/images/PAP110640316i1
PAP110640316i1

Éditeur(s) : HAL CCSD Nature Publishing Group
Résumé : International audience
ISSN: 1752-0894

hal-01667978
https://hal.archives-ouvertes.fr/hal-01667978
DOI : 10.1038/s41561-017-0028-x

Éditeur(s) : HAL CCSD Wiley-Blackwell
Résumé : International audience
Marine protist diversity inventories have largely focused on planktonic environments, while benthic protists have received relatively little attention. We therefore hypothesize that current diversity surveys have only skimmed the surface of protist diversity in marine sediments, which may harbor greater diversity than planktonic environments. We tested this by analyzing sequences of the hypervariable V4 18S rRNA from benthic and planktonic protist communities sampled in European coastal regions. Despite a similar number of OTUs in both realms, richness estimations indicated that we recovered at least 70% of the diversity in planktonic protist communities, but only 33% in benthic communities. There was also little overlap of OTUs between planktonic and benthic communities, as well as between separate benthic communities. We argue that these patterns reflect the heterogeneity and diversity of benthic habitats. A comparison of all OTUs against the Protist Ribosomal Reference database showed that a higher proportion of benthic than planktonic protist diversity is missing from public databases; similar results were obtained by comparing all OTUs against environmental references from NCBI's Short Read Archive. We suggest that the benthic realm may therefore be the world's largest reservoir of marine protist diversity, with most taxa at present undescribed.
ISSN: 0168-6496

hal-01383722
http://hal.upmc.fr/hal-01383722
http://hal.upmc.fr/hal-01383722/document
http://hal.upmc.fr/hal-01383722/file/Forster_2016_Benthic_protists.pdf
DOI : 10.1093/femsec/fiw120

Éditeur(s) : HAL CCSD De Gruyter
Résumé : International audience
Coral reefs have undergone profound ecological changes over recent decades. Areas formerly covered by scleractinian coral species are now often overgrown by macroalgae. In Martinique (West Indies), this phenomenon has lead to the colonisation of numerous coral reefs by algae, amongst which Sargassum is one of the most prominent. This study focuses on potential defence molecules produced by Sargassum polyceratium. The hexane dipping method was employed to extract surface molecules on fresh material, and their bioactivities were assessed against bacteria (marine and estuarine), and marine tropical invertebrates wan annelid (Pseudonereis sp.), a bivalve (Codakia orbicularis) and a sea urchin (Diadema antillarum)x. Extracts were active against all microorganisms tested (MICs150 or 300 mg ml-1), early stages of development in Pseudonereis sp. (MICs100 mg ml-1) and embryos of C. orbicularis and D. antillarum (MICs5 mg ml-1), suggesting the production of defence compounds by S. polyceratium.
ISSN: 0006-8055

hal-00746082
https://hal.univ-antilles.fr/hal-00746082
https://hal.univ-antilles.fr/hal-00746082/document
https://hal.univ-antilles.fr/hal-00746082/file/Publication_Sargassum_bortanica_marina.pdf
DOI : 10.1515/BOT.2011.014

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Grey (Halichoerus grypus) and harbour seals (Phoca vitulina) are sympatric seal species, but they display distinct strategies of habitat use and connectivity between haulout sites. The distribution patterns and variations in relative abundance of both species were investigated along the French coast of the English Channel, at the southern limit of their range where seal numbers are increasing. Regular censuses conducted at all main haulout sites in mainland France showed significant seasonal variations at most sites, with more harbour seals counted during summer (breeding and moulting seasons), and more grey seals during summer only in the eastern English Channel. Trends in maximum haulout numbers at haulout sites showed a significant increase over the last five years, ranging from 9.7 to 30.9% per year for harbour seals, and from 5.8% (in the western English Channel) to 49.2% (in the eastern English Channel) per year for grey seals. These rates of increase in grey seal numbers are not linked to local pup production and most probably result from seal movements from the southwest British Isles and the North Sea, respectively. Aerial surveys conducted across the English Channel showed that most seal observations at sea were concentrated in the north-eastern English Channel. Telemetry showed that the 28 harbour seals tracked remained highly coastal, within a radius of 100 km from their haulout sites, and did not move to other known colonies. Grey seals moved much greater distances, reaching up to 1200 km from their capture site. More than half of the 45 grey seals tracked crossed the English Channel, especially during the breeding season, moving to known colonies in the southwest British Isles and the North Sea. Combining individual tracks and long-term surveys of the seal populations allowed a better understanding of the dynamics of these populations and their connectivity at a larger regional scale. The findings provide direct information for the management of grey and harbour seals within the frame of the Marine Strategy Framework Directive, and highlight focus areas where potential interactions between the two species should be monitored.
ISSN: 0967-0645

hal-01509674
https://hal.archives-ouvertes.fr/hal-01509674
DOI : 10.1016/j.dsr2.2017.04.004

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Background : Biological communities are normally composed of a few abundant and many rare species. This pattern is particularly prominent in microbial communities, in which most constituent taxa are usually extremely rare. Although abundant and rare subcommunities may present intrinsic characteristics that could be crucial for understanding community dynamics and ecosystem functioning, microbiologists normally do not differentiate between them. Here, we investigate abundant and rare subcommunities of marine microbial eukaryotes, a crucial group of organisms that remains among the least-explored biodiversity components of the biosphere. We surveyed surface waters of six separate coastal locations in Europe, independently considering the picoplankton, nanoplankton, and microplankton/mesoplankton organismal size fractions.Results : Deep Illumina sequencing of the 18S rRNA indicated that the abundant regional community was mostly structured by organismal size fraction, whereas the rare regional community was mainly structured by geographic origin. However, some abundant and rare taxa presented similar biogeography, pointing to spatiotemporal structure in the rare microeukaryote biosphere. Abundant and rare subcommunities presented regular proportions across samples, indicating similar species-abundance distributions despite taxonomic compositional variation. Several taxa were abundant in one location and rare in other locations, suggesting large oscillations in abundance. The substantial amount of metabolically active lineages found in the rare biosphere suggests that this subcommunity constitutes a diversity reservoir that can respond rapidly to environmental change.Conclusions : We propose that marine planktonic microeukaryote assemblages incorporate dynamic and metabolically active abundant and rare subcommunities, with contrasting structuring patterns but fairly regular proportions, across space and time.
ISSN: 0960-9822

hal-01149637
http://hal.upmc.fr/hal-01149637
http://hal.upmc.fr/hal-01149637/document
http://hal.upmc.fr/hal-01149637/file/Logares_et_al_CurrentBiol_accepted.pdf
DOI : 10.1016/j.cub.2014.02.050

Éditeur(s) : HAL CCSD
Résumé : Genetic structure of Hylesia metabus (Lepidoptera: Saturniidae), moths responsible for lepidopterism outbreaks in French Guiana and Venezuela. . ICE 2016; XXV International Congress of Entomology
ICE 2016; XXV International Congress of Entomology
Orlando, United States

hal-01607289
https://hal.archives-ouvertes.fr/hal-01607289
DOI : 10.1603/ICE.2016.113657
PRODINRA : 396124

Éditeur(s) : HAL CCSD WILEY-BLACKWELL Wiley
Résumé : International audience
Connectivity among populations determines the dynamics and evolution of populations, and its assessment is essential in ecology in general and in conservation biology in particular. The robust basis of any ecological study is the accurate delimitation of evolutionary units, such as populations, metapopulations and species. Yet a disconnect still persists between the work of taxonomists describing species as working hypotheses and the use of species delimitation by molecular ecologists interested in describing patterns of gene flow. This problem is particularly acute in the marine environment where the inventory of biodiversity is relatively delayed, while for the past two decades, molecular studies have shown a high prevalence of cryptic species. In this study, we illustrate, based on marine case studies, how the failure to recognize boundaries of evolutionary-relevant unit leads to heavily biased estimates of connectivity. We review the conceptual framework within which species delimitation can be formalized as falsifiable hypotheses and show how connectivity studies can feed integrative taxonomic work and vice versa. Finally, we suggest strategies for spatial, temporal and phylogenetic sampling to reduce the probability of inadequately delimiting evolutionary units when engaging in connectivity studies.
ISSN: 0962-1083

hal-01218810
https://hal.archives-ouvertes.fr/hal-01218810
DOI : 10.1111/mec.13048

Éditeur(s) : HAL CCSD Wiley-Blackwell
Résumé : International audience
Although protists are critical components of marine ecosystems, they are still poorly characterized. Here we analysed the taxonomic diversity of planktonic and benthic protist communities collected in six distant European coastal sites. Environmental deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) from three size fractions (pico-, nano- and micro/mesoplankton), as well as from dissolved DNA and surface sediments were used as templates for tag pyrosequencing of the V4 region of the 18S ribosomal DNA. Beta-diversity analyses split the protist community structure into three main clusters: picoplankton-nanoplankton-dissolved DNA, micro/mesoplankton and sediments. Within each cluster, protist communities from the same site and time clustered together, while communities from the same site but different seasons were unrelated. Both DNA and RNA-based surveys provided similar relative abundances for most class-level taxonomic groups. Yet, particular groups were overrepresented in one of the two templates, such as marine alveolates (MALV)-I and MALV-II that were much more abundant in DNA surveys. Overall, the groups displaying the highest relative contribution were Dinophyceae, Diatomea, Ciliophora and Acantharia. Also, well represented were Mamiellophyceae, Cryptomonadales, marine alveolates and marine stramenopiles in the picoplankton, and Monadofilosa and basal Fungi in sediments. Our extensive and systematic sequencing of geographically separated sites provides the most comprehensive molecular description of coastal marine protist diversity to date.
ISSN: 1462-2912

hal-01191731
http://hal.upmc.fr/hal-01191731
http://hal.upmc.fr/hal-01191731/document
http://hal.upmc.fr/hal-01191731/file/Massana_2015_Marine_protist.pdf
DOI : 10.1111/1462-2920.12955

Éditeur(s) : HAL CCSD American Society for Biochemistry and Molecular Biology
Résumé : International audience
Neuroglobins, previously thought to be restricted to vertebrate neurons, were detected in the brain of a photosymbiotic acoel, Symsagittifera roscoffensis, and in neurosensory cells of the jellyfish Clytia hemisphaerica. For the neuroglobin of S. roscoffensis, a member of a lineage that originated either at the base of the bilateria or of the deuterostome clade, we report the ligand binding properties, crystal structure at 2.3 Å, and brain immunocytochemical pattern. We also describe in situ hybridizations of two neuroglobins specifically expressed in differentiating nematocytes (neurosensory cells) and in statocytes (ciliated mechanosensory cells) of C. hemisphaerica, a member of the early branching animal phylum cnidaria. In silico searches using these neuroglobins as queries revealed the presence of previously unidentified neuroglobin-like sequences in most metazoan lineages. Because neural systems are almost ubiquitous in metazoa, the constitutive expression of neuroglobin-like proteins strongly supports the notion of an intimate association of neuroglobins with the evolution of animal neural systems and hints at the preservation of a vitally important function. Neuroglobins were probably recruited in the first protoneurons in early metazoans from globin precursors. Neuroglobins were identified in choanoflagellates, sponges, and placozoans and were conserved during nervous system evolution. Because the origin of neuroglobins predates the other metazoan globins, it is likely that neuroglobin gene duplication followed by co-option and subfunctionalization led to the emergence of globin families in protostomes and deuterostomes (i.e. convergent evolution).
ISSN: 0021-9258

hal-01020584
http://hal.upmc.fr/hal-01020584
http://hal.upmc.fr/hal-01020584/document
http://hal.upmc.fr/hal-01020584/file/Rosko_jbc_revised.pdf
DOI : 10.1074/jbc.M112.407601

Éditeur(s) : HAL CCSD Elsevier Masson
Résumé : International audience
In vertebrates, brain functional asymmetries are widespread and increase brain performance. Some species of fishes are known to have brain asymmetries; however, little information is available on brain lateralization in coral reef fishes and the impact this could have during the recruitment phase. In this study, soldierfish, Myripristis pralinia, at the larval and juvenile stage recognized conspecifics through visual cues. Larvae with the ablation of either the right or left telencephalic hemisphere lost the attraction towards conspecific cues. In contrast, juveniles with the ablation of the right (but not left) telencephalic hemisphere still displayed a preference towards conspecific visual cues. These results suggest the left telencephalic hemisphere is responsible for the lateralization process used in the visual recognition of coral reef fish juveniles. The determinism of lateralized perception of conspecifics during fish ontogeny may be a consequence of genetic factors, linked with the metamorphosis processes and/or environmental factors such as predation at recruitment.
ISSN: 0003-3472

hal-01340504
https://hal-univ-perp.archives-ouvertes.fr/hal-01340504
DOI : 10.1016/j.anbehav.2016.04.011

Éditeur(s) : HAL CCSD Nature Publishing Group
Résumé : International audience
ISSN: 1752-0894

hal-01668923
https://hal.archives-ouvertes.fr/hal-01668923
DOI : 10.1038/s41561-017-0028-x

Éditeur(s) : HAL CCSD Inter-Research
Résumé : International audience
The effects of global change are particularly serious in areas where range shiftsof species are physically constrained such as the Ligurian Sea, which is one ofthe coldest sectors of the Mediterranean. In this basin, historical informationon water temperature (from the sea surface down to 75 m depth) dates backto the 1950s. Early studies also recorded warm-water species occurrence.Thanks to these data we provide the first detailed characterization of watertemperature variation from 1958 up to 2010 in the layer 0–75 m depth. Wecoupled this analysis with the available information on rocky reef epibenthiccommunities (literature review from 1955 to 1964 and field data from 1980 to2010). The analysis of water temperature revealed several patterns of variation:a cooling phase from 1958 to 1980, a phase of rapid warming from 1980 to1990 and a phase of slower warming from 1990 to 2010. Inter-annual variationin temperature increased over the entire period for the water layer down to20 m. Warm-water native and alien species richness increased during thewarming phases. Literature estimates suggest a decrease in warm-water nativespecies richness during the cooling phase. The analysis of quantitative data collectedin the early 1990s and late 2000s indicated a decrease in the cover ofwarm-water native species on shallow rocky reefs and an increase in deeperwaters. We argue that increased inter-annual variation in water temperaturemay disadvantage native warm-water species in shallow waters. Our resultsindicate that the effect of temperature rises in cold, constrained basins may bemore complex than the simple prediction of species changing their geographicalrange according to their thermal limits.
Marine Ecology Progress Series

hal-01239259
https://hal-univ-perp.archives-ouvertes.fr/hal-01239259
DOI : 10.1111/maec.12277

Éditeur(s) : HAL CCSD Société Géologique de France
Résumé : International audience
The seaward extension of onshore formations and structures were previously almost unknown in Provence. The interpretation of 2D high-resolution marine seismic profiles together with the integration of sea-bottom rock samples provides new insights into the stratigraphic, structural and paleogeographic framework of pre-Messinian Salinity Crisis (MSC) deposits of the Provence continental shelf. Seven post-Jurassic seismic units have been identified on seismic profiles, mapped throughout the offshore Provence area and correlated with the onshore series. The studied marine surface and sub-surface database provided new insights into the mid and late Cretaceous paleogeography and structural framework as well as into the syn-and post-rift deformation in Provence. Thick (up to 2000 m) Aptian-Albian series whose deposition is controlled by E-W-trending faults are evidenced offshore. The occurrence and location of the Upper Cretaceous South-Provence basin is confirmed by the thick (up to 1500 m) basinal series downlaping the Aptian-Albian unit. This basin was fed in terrigenous sediments by a southern massif (" Massif Méridional ") whose present-day relict is the Paleozoic basement and its sedimentary cover from the Sicié imbricate. In the bay of Marseille, thick syn-rift (Rupelian to Aquitanian) deposition occurred (>1000 m). During the rifting phase, syn-sedimentary deformations consist of dominant N040 to N060 sub-vertical faults with a normal component and N050 drag-synclines and anticlines. The syn-rift and early post-rift units (Rupelian to early Burdigalian) are deformed and form a set of E-W-trending en echelon folds that may result from sinistral strike-slip reactivation of N040 to N060 normal faults during a N-S com-pressive phase of early-to-mid Burdigalian age (18-20 Ma). Finally, minor fault reactivation and local folding affect post-rift deposits within a N160-trending corridor localized south of La Couronne, and could result from a later, post-Burdigalian and pre-Pliocene compressive phase.
Cadre tectonostratigraphique des formations anté-pliocènes du plateau continental de Provence (golfe du Lion oriental, SE France) Mots-clés. – Géologie marine, Tectonostratigraphie, Stratigraphie sismique, Paléogéographie crétacée, Rifting oligo-miocène, Compression post-rift Résumé. – Le prolongement en mer des formations et des structures provençales était jusqu'alors largement inconnu.L'interprétation de profils de sismique-réflexion marine 2D et l'intégration de dragages et carottages du fond-marin ont permis d'apporter des éléments nouveaux concernant le cadre stratigraphique, structural et paléogéographique des dé-pôts anté-Messiniens du plateau continental de Provence. Sept unités sismiques post-jurassiques ont été identifiées sur les profils sismiques, cartographiées à travers le plateau continental et corrélées avec les séries affleurant à terre. Une épaisse unité apto-albienne (jusqu'à 2000 m) dont le dépôt est contrôlé par des failles E-W a été mise en évidence en mer. L'existence d'un bassin subsident au Crétacé supérieur sur le plateau continental de Provence a été confirmée par le développement d'une épaisse série de bassin (jusqu'à 1500 m) reposant en downlap sur l'Apto-Albien. Le socle mé-tamorphique de l'écaille de Sicié et sa couverture sédimentaire peut être considéré comme une relique allochtone du « Massif Méridional » ayant alimenté le Bassin sud-provençal en éléments terrigènes au Crétacé supérieur. Dans la rade de Marseille, une épaisse unité syn-rift (Rupélien à Aquitanien) a été mise en évidence (>1000 m), structurée en une série de synformes en échelon d'axe E-W et affectée par des failles d'orientation dominante N040 à N060. Sur le flanc sud des synformes, la formation de plis d'axe N050 est associée à une déformation syn-sédimentaire. La formation des synformes en échelon d'axe E-W résulterait d'une réactivation en décrochement des failles N040 à N060 pendant une phase de compression N-S dont l'âge est compris entre le Burdigalien inférieur et moyen (18-20 Ma). Enfin, les dépôts post-rift sont affectés par des déformations mineures (réactivation de failles et plis associés), le long d'un couloir d'orientation N160 à l'ouest de la baie de Marseille, attribuables à une phase de compression post-burdigalienne et anté-pliocène.
ISSN: 0037-9409

hal-01463727
https://hal-amu.archives-ouvertes.fr/hal-01463727
https://hal-amu.archives-ouvertes.fr/hal-01463727/document
https://hal-amu.archives-ouvertes.fr/hal-01463727/file/Fournier_et_al_Provence_2016.pdf
DOI : 10.2113/gssgfbull.187.4-5.187

Éditeur(s) : HAL CCSD Springer Verlag
Résumé : International audience
The release of polycyclic aromatic hydrocarbons (PAHs) into the environment has increased very substantially over the last decades. PAHs are hydrophobic molecules which can accumulate in high concentrations in sediments acting then as major secondary sources. Fish contamination can occur through contact or residence nearby sediments or though dietary exposure. In this study, we analyzed certain physiological traits in unexposed fish (F1) issued from parents (F0) exposed through diet to three PAH mixtures at similar and environmentally relevant concentrations but differing in their compositions. For each mixture, no morphological differences were observed between concentrations. An increase in locomotor activity was observed in larvae issued from fish exposed to the highest concentration of a pyrolytic (PY) mixture. On the contrary, a decrease in locomotor activity was observed in larvae issued from heavy oil mixture (HO). In the case of the third mixture, light oil (LO), a reduction of the diurnal activity was observed during the setup of larval activity. Behavioral disruptions persisted in F1-PY juveniles and in their offspring (F2). Endocrine disruption was analyzed using cyp19a1b:GFP transgenic line and revealed disruptions in PY and LO offspring. Since no PAH metabolites were dosed in larvae, these findings suggest possible underlying mechanisms such as altered parental signaling molecule and/or hormone transferred in the gametes, eventually leading to early imprinting. Taken together, these results indicate that physiological disruptions are observed in offspring of fish exposed to PAH mixtures through diet.
ISSN: 0944-1344

hal-01121865
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01121865
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01121865/document
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01121865/file/Exposures%20of%20zebrafish_accepted.pdf
DOI : 10.1007/s11356-015-4157-8

Éditeur(s) : HAL CCSD
Résumé : International audience
Fish is a rich source of essential nutrients for fetal development, but in contrast, it is also a well-known route of exposure to environmental pollutants. We assessed whether fish intake during pregnancy is associated with fetal growth and the length of gestation in a panel of European birth cohort studies. The study sample of 151,880 mother-child pairs was derived from 19 population-based European birth cohort studies. Individual data from cohorts were pooled and harmonized. Adjusted cohort-specific effect estimates were combined by using a random- and fixed-effects meta-analysis. Women who ate fish >1 time/wk during pregnancy had lower risk of preterm birth than did women who rarely ate fish (≤ 1 time/wk); the adjusted RR of fish intake >1 but <3 times/wk was 0.87 (95% CI: 0.82, 0.92), and for intake ≥ 3 times/wk, the adjusted RR was 0.89 (95% CI: 0.84, 0.96). Women with a higher intake of fish during pregnancy gave birth to neonates with a higher birth weight by 8.9 g (95% CI: 3.3, 14.6 g) for >1 but <3 times/wk and 15.2 g (95% CI: 8.9, 21.5 g) for ≥ 3 times/wk independent of gestational age. The association was greater in smokers and in overweight or obese women. Findings were consistent across cohorts. This large, international study indicates that moderate fish intake during pregnancy is associated with lower risk of preterm birth and a small but significant increase in birth weight.
The American Journal of Clinical Nutrition

hal-01118513
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01118513
PUBMED : 24335057
DOI : 10.3945/ajcn.113.067421

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
During the last decade, the interaction of deep processes in the lithosphere and mantle with surface processes (erosion, climate, sea-level, subsidence, glacio-isostatic readjustment) has been the subject of heated discussion. The use of a multidisciplinary approach linking geology, geophysics, geodesy, modelling, and geotechnology has led to the awareness of coupled deep and surface processes. Deep earth dynamics (topography, erosion, tectonics) are strongly connected to natural hazards such as earthquakes, landslides, and tsunamis; sedimentary mass transfers have important consequences on isostatic movements and on georesources, geothermal energy repartitions. The ability to read and understand the link between deep Earth dynamics and surface processes has therefore important societal impacts. Ground-truthing at carefully-selected sites of investigation is imperative to better understand these connections.Due to its youth (<30 Ma) and its subsidence history, the almost land-locked Gulf of Lion–Sardinia continental margins system provides a unique record of sedimentary deposition from the Miocene to present. Due to its high subsidence rate, palaeoclimatic variations, tectonic events and vertical evolution are all recorded here at very high resolution. The late Miocene isolation and desiccation of the Mediterranean, the youngest and most catastrophic event, the Messinian Salinity Crisis (MSC), induced drastic changes in marine environments: widespread deposition of evaporite (gypsum, anhydrite and halite) in the central basin, and intense subaerial erosion along its periphery. These extraordinary mass transfers from land to sea induced strong isostatic re-adjustments that are archived in the sedimentary record and represent a window to the lithospheric rheology and the deep processes.The GOLD (Gulf of Lion Drilling) project, proposes to explore this unique sedimentary record as well as the nature of the deep crustal structure, providing valuable information about the mechanisms underlying vertical motions in basins and their margins.
ISSN: 0264-8172

insu-01197393
https://hal-insu.archives-ouvertes.fr/insu-01197393
https://hal-insu.archives-ouvertes.fr/insu-01197393/document
https://hal-insu.archives-ouvertes.fr/insu-01197393/file/Rabineau%20et%20al.-final-MPG2014_REVISED-FINAL-No-Marked_FINAL%2BFigures.pdf
DOI : 10.1016/j.marpetgeo.2015.03.018

Éditeur(s) : HAL CCSD Wiley/Blackwell
Résumé : International audience
Photosynthetic eukaryotes have a critical role as the main producers in most ecosystems of the biosphere. The ongoing environmental metabarcoding revolution opens the perspective for holistic ecosystems biological studies of these organisms, in particular the unicellular microalgae that often lack distinctive morphological characters and have complex life cycles. To interpret environmental sequences, metabarcoding necessarily relies on taxonomically curated databases containing reference sequences of the targeted gene (or barcode) from identified organisms. To date, no such reference framework exists for photosynthetic eukaryotes. In this study, we built the PhytoREF database that contains 6490 plastidial 16S rDNA reference sequences that originate from a large diversity of eukaryotes representing all known major photosynthetic lineages. We compiled 3333 amplicon sequences available from public databases and 879 sequences extracted from plastidial genomes, and generated 411 novel sequences from cultured marine microalgal strains belonging to different eukaryotic lineages. A total of 1867 environmental Sanger 16S rDNA sequences were also included in the database. Stringent quality filtering and a phylogeny-based taxonomic classification were applied for each 16S rDNA sequence. The database mainly focuses on marine microalgae, but sequences from land plants (representing half of the PhytoREF sequences) and freshwater taxa were also included to broaden the applicability of PhytoREF to different aquatic and terrestrial habitats. PhytoREF, accessible via a web interface (http://phytoref.fr), is a new resource in molecular ecology to foster the discovery, assessment and monitoring of the diversity of photosynthetic eukaryotes using high-throughput sequencing.
ISSN: 1755-098X

hal-01149047
http://hal.upmc.fr/hal-01149047
http://hal.upmc.fr/hal-01149047/document
http://hal.upmc.fr/hal-01149047/file/Decelle_2015_PhytoREF.pdf
DOI : 10.1111/1755-0998.12401

Éditeur(s) : HAL CCSD Société Géologique de France
Résumé : Pages 72, 1 CD
International audience
Mémoire de la Société Géologique n.s.

hal-00593502
https://hal-brgm.archives-ouvertes.fr/hal-00593502

Éditeur(s) : HAL CCSD Inter-Research
Résumé : International audience
Ecological connectivity is important for effective marine planning and biodiversity conservation. Our aim was to identify factors important in influencing variation in benthic community structure on shallow rocky reefs in 2 regions of the Mediterranean Sea with contrasting oceanographic regimes. We assessed beta (β) diversity at 146 sites in the littoral and shallow sub-littoral from the Adriatic/Ionian Seas (eastern region) and Ligurian/Tyrrhenian Seas (western region) using a null modelling approach to account for variation in species richness. The distance decay relationship between species turnover within each region and geographic distance by sea was determined using generalised linear models. Mantel tests were used to examine correlations between β diversity and connectivity by ocean currents, estimated from Lagrangian dispersal simulations. Variation in β diversity between sites was partitioned according to environmental and spatial components using a distance-based redundancy approach. Species turnover along a gradient of geographic distance was greater by a factor of 3 to 5 in the western region than the eastern region, suggesting lower con-nectivity between sites. β diversity was correlated with connectivity by ocean currents at both depths in the eastern region but not in the western region. The influence of spatial and environmental predictors of β diversity varied considerably between regions, but was similar between depths. Our results highlight the interaction of oceanographic, spatial and environmental processes influencing benthic marine β diversity. Persistent currents in the eastern region may be responsible for lower observed β diversity compared to the western region, where patterns of water circulation are more variable.
Marine Ecology Progress Series

Droits : http://creativecommons.org/licenses/by/
hal-01357935
https://hal-univ-perp.archives-ouvertes.fr/hal-01357935
https://hal-univ-perp.archives-ouvertes.fr/hal-01357935/document
https://hal-univ-perp.archives-ouvertes.fr/hal-01357935/file/m553p001.pdf
DOI : 10.3354/meps11783