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The richness and structure of symbiont assemblages are shaped by many factors acting at different spatial and temporal scales. Among them, host phylogeny and geographic distance play essential roles. To explore drivers of richness and structure of symbiont assemblages, feather mites and seabirds are an attractive model due to their peculiar traits. Feather mites are permanent ectosymbionts and considered highly host-specific with limited dispersal abilities. Seabirds harbour species-rich feather mite communities and their colonial breeding provides opportunities for symbionts to exploit several host species. To unravel the richness and test the influence of host phylogeny and geographic distance on mite communities, we collected feather mites from 11 seabird species breeding across the Atlantic Ocean and Mediterranean Sea. Using morphological criteria, we identified 33 mite species, of which 17 were new or recently described species. Based on community similarity analyses, mite communities were clearly structured by host genera, while the effect of geography within host genera or species was weak and sometimes negligible. We found a weak but significant effect of geographic distance on similarity patterns in mite communities for Cory’s shearwaters Calonectris borealis. Feather mite specificity mainly occurred at the host-genus rather than at host-species level, suggesting that previously inferred host species-specificity may have resulted from poorly sampling closely related host species. Overall, our results show that host phylogeny plays a greater role than geography in determining the composition and structure of mite assemblages and pinpoints the importance of sampling mites from closely-related host species before describing mite specificity patterns.

International audience; A novel anaerobic methylotrophic halophilic methanogen strain SLHTYRO T was isolated from a deep hypersaline anoxic basin called "Tyro" located in the Eastern Mediterranean Sea. Cells of SLHTYRO T were motile cocci. The strain SLHTYRO T grew between 12 and 37 °C (optimum 30 °C), at pH between 6.5 and 8.2 (optimum pH 7.5) and salinity from 45 to 240 g L −1 NaCl (optimum 135 g L −1). Strain SLHTYRO T was methylotrophic methanogen able to use methylated compounds (trimethylamine, dimethylamine, monomethylamine and methanol). Strain SLHTYRO T was able to grow at in situ hydrostatic pressure and temperature conditions (35 MPa, 14 °C). Phylogenetic analysis based on 16S rRNA gene and mcrA gene sequences indicated that strain SLHTYRO T was affiliated to genus Methanohalophilus within the order Methanosarcinales. It shared >99.16% of the 16S rRNA gene sequence similarity with strains of other Methanohalophilus species. Based on ANIb, AAI and dDDH measurements, and the physiological properties of the novel isolate, we propose that strain SLHTYRO T should be classified as a representative of a novel species, for which the name Methanohalophilus profundi sp. nov. is proposed; the type strain is SLHTYRO T (=DSM 108854 = JCM 32768 = UBOCC-M-3308).

International audience; The parasites of 425 European eels, Anguilla anguilla, were studied between 2009 and 2012 in two Mediterranean coastal lagoons of the island of Corsica, France. An indicator value (IndVal) method was used for analysis, which combines measures of fidelity and specificity. Because of its resilience to detect changes in abundance, IndVal is an effective ecological bioindicator. The IndVal method demonstrated that site, season, silvering stage, and length could influence the occurrence of parasite species in European eel. A randomization test identified ten parasite species as having a significant indicator value for site (lagoons differed principally in salinity: oligohaline to polyhaline for the Biguglia lagoon and polyhaline to euhaline for the Urbino lagoon; the digeneans Bucephalus anguillae and Lecithochirium musculus, the cestodes Bothriocephalus claviceps, Proteocephalus macrocephalus, and larvae of Myzophyllobothrium sp., the nematodes Anguillicoloides crassus, and encysted larvae of Contracaecum sp., the acanthocephalan Acanthocephaloides incrassatus, the monogenean Pseudodactyogyrus anguillae, and the copepod Ergasilus gibbus); one parasite species for the spring season (the acanthocephalan A. incrassatus); six parasite species for silvering stage (yellow, pre-silver, silver; the trematodes B. anguillae and Deropristis inflata, encysted larvae of the nematode Contracaecum sp., the acanthocephalan A. incrassatus, the monogenean P. anguillae, and the copepod E. gibbus); and three parasite species for some of the five length classes (the cestode P. macrocephalus, encysted larvae of the nematode Contracaecum sp., and the monogenean P. anguillae). Data for species composition and infection levels should help to improve the management of parasitism in the populations of European eels.

International audience; Haptophytes are a key phylum of marine protists, including ~300 described morphospecies and 80 morphogenera. We used 454 pyrosequencing on large subunit ribosomal DNA (LSU rDNA) fragments to assess the diversity from size-fractioned plankton samples collected in the Bay of Naples. One group-specific primer set targeting the LSU rDNA D1/D2 region was designed to amplify Haptophyte sequences from nucleic acid extracts (total DNA or RNA) of two size fractions (0.8-3 or 3-20 μm) and two sampling depths [subsurface, at 1 m, or deep chlorophyll maximum (DCM) at 23 m]. 454 reads were identified using a database covering the entire Haptophyta diversity currently sequenced. Our data set revealed several hundreds of Haptophyte clusters. However, most of these clusters could not be linked to taxonomically known sequences: considering OTUs(97%) (clusters build at a sequence identity level of 97%) on our global data set, less than 1% of the reads clustered with sequences from cultures, and less than 12% clustered with reference sequences obtained previously from cloning and Sanger sequencing of environmental samples. Thus, we highlighted a large uncharacterized environmental genetic diversity, which clearly shows that currently cultivated species poorly reflect the actual diversity present in the natural environment. Haptophyte community appeared to be significantly structured according to the depth. The highest diversity and evenness were obtained in samples from the DCM, and samples from the large size fraction (3-20 μm) taken at the DCM shared a lower proportion of common OTUs(97%) with the other samples. Reads from the species Chrysoculter romboideus were notably found at the DCM, while they could be detected at the subsurface. The highest proportion of totally unknown OTUs(97%) was collected at the DCM in the smallest size fraction (0.8-3 μm). Overall, this study emphasized several technical and theoretical barriers inherent to the exploration of the large and largely unknown diversity of unicellular eukaryotes.

We investigated the growth response of the heterotrophic prokaryotic community focusing on Vibrio- and Rhodobacter-related populations (SRF3) to variation in the availability of dissolved organic matter (DOM), population density-dependent effects, and prokaryotic virus (phage) infection in coastal and offshore waters of the NW Mediterranean Sea. We tested the response of the prokaryotic community to three different DOM fractions prepared by ultrafiltration. One of the DOM fractions contained phages (

International audience; A microsporidian of the genus Spraguea was found parasitizing the nervous tissues of Lophius piscatorius collected from various localities in the Mediterranean coastal areas of Tunisia. The tissue localization, the infection focus aspect and sporal dimorphism are characteristics of Spraguea lophii species. Molecular data based on partial sequence of SSUrRNA encoding gene shows few nucleotide polymorphisms, compared to all described Spraguea isolates. Molecular karyotype obtained on pulsed field gel electrophoresis (1D-PFGE) shows a profile with 14 stained bands in the range of 230-880 kbp and a genome size estimated to 6.700 kbp. The rare cutter endonuclease MluI KARD 2-D-PFGE fingerprint shows an extensive chromosome length polymorphism, but the number of chromosome is unchanged and consists of 15 different molecules. The extensive chromosome length polymorphism is associated to a reduced number of genetic events.

A novel sulfate-reducing bacterium, designated C1TLV30T, was isolated from wood falls at a depth of 1693 m in the Mediterranean Sea. Cells were motile vibrios (2–4×0.5 µm). Strain C1TLV30T grew at temperatures between 15 and 45 °C (optimum 30 °C) and at pH 5.4–8.6 (optimum 7.3). It required NaCl for growth (optimum at 25 g NaCl l−1) and tolerated up to 80 g NaCl l−1. Strain C1TLV30T used as energy sources: lactate, fumarate, formate, malate, pyruvate and ethanol. The end products from lactate oxidation were acetate, H2S and CO2 in the presence of sulfate as terminal electron acceptor. Besides sulfate, thiosulfate and sulfite were also used as terminal electron acceptors, but not elemental sulfur, fumarate, nitrate or nitrite. Strain C1TLV30T possessed desulfoviridin and was piezophilic, growing optimally at 10 MPa (range 0–30 MPa). The membrane lipid composition of this strain was examined to reveal an increase in fatty acid chain lengths at high hydrostatic pressures. The G+C content of the genomic DNA was 49.6 % and the genome size was estimated at 3.5±0.5 Mb. Phylogenetic analysis of the SSU rRNA gene sequence indicated that strain C1TLV30T was affiliated to the genus Desulfovibrio with Desulfovibrio profundus being its closest phylogenetic relative (similarity of 96.4 %). On the basis of SSU rRNA gene sequence comparisons and physiological characteristics, strain C1TLV30T ( = DSM 21447T = JCM 1548T) is proposed to be assigned to a novel species of the genus Desulfovibrio, Desulfovibrio piezophilus sp. nov.

This is an author manuscript that has been accepted for publication in International Journal of Systematic and Evolutionary Microbiology, copyright Society for General Microbiology, but has not been copy-edited, formatted or proofed. Cite this article as appearing in International Journal of Systematic and Evolutionary Microbiology. This version of the manuscript may not be duplicated or reproduced, other than for personal use or within the rule of 'Fair Use of Copyrighted Materials' (section 17, Title 17, US Code), without permission from the copyright owner, Society for General Microbiology. The Society for General Microbiology disclaims any responsibility or liability for errors or omissions in this version of the manuscript or in any version derived from it by any other parties. The final copy-edited, published article, which is the version of record, can be found at http://mic.sgmjournals.org, and is freely available without a subscription.; International audience; A novel aerobic, heterotrophic, prosthecate bacterium, designated 26III/A02/215(T), was isolated from surface water of the north-western Mediterranean Sea. Cells stained Gram-negative and were straight to slightly curved rods, forming red colonies on agar plates. The strain grew at 15-37 degrees C inclusive (optimum 30 degrees C) and grew optimally at seawater salinity. Growth was observed on organic acids, amino acids and complex organic substrates. The fatty acids (>5 %) detected in strain 26III/A02/215(T) were C(17 : 1)omega6c, C(18 : 1)omega7c and C(17 : 0). The lipid pattern indicated the presence of phosphatidylglycerol, glucuronopyranosyldiglyceride, monoglycosyldiglyceride, an unidentified glycolipid and three unidentified phospholipids. Phosphatidylethanolamine and diphosphatidylglycerol were absent. Ubiquinone Q-10 was the only respiratory lipoquinone. The G+C content of the genomic DNA was 46.8 mol%. Comparative 16S rRNA gene sequence analysis indicated that strain 26III/A02/215(T) belonged to the Hyphomonas-Hirschia-Robiginitomaculum branch of the order Caulobacterales. This affiliation was consistent with the results of polar lipid analyses. Among this group, the novel isolate was most closely related to Robiginitomaculum antarcticum (93.9 % 16S rRNA gene sequence similarity to the type strain). On the basis of genotypic, chemotaxonomic and phenotypic distinctness, we propose a novel genus, Hellea gen. nov., with Hellea balneolensis sp. nov. as the type species. The type strain of Hellea balneolensis is 26III/A02/215(T) (=DSM 19091(T) =CIP 109500(T) =OOB 269(T)).

En libre-accès sur Archimer : http://archimer.ifremer.fr/doc/2008/publication-5294.pdf; International audience; Two novel Gram-negative bacteria, designated strains DR41_21(T) and DR41_18(T), were isolated from coastal, surface waters of the north-western Mediterranean Sea. The cells were motile, pleomorphic rods, 2.9 microm long and 0.9 microm wide and formed cream colonies on marine agar medium. The G+C content of the genomic DNA was 60 mol%. Phylogenetic analysis of 16S rRNA gene sequences positioned the isolates in the class Alphaproteobacteria within the family Rhodospirillaceae. The 16S rRNA gene sequence similarity of the two strains was 98.8 % but DNA-DNA hybridization indicated only 55 % relatedness. Strain DR41_21(T) was able to denitrify and possessed nirK and nosZ genes, unlike strain DR41_18(T), which possessed only nirK. These isolates represent two novel species of a new genus, Nisaea gen. nov., for which the names Nisaea denitrificans sp. nov. and Nisaea nitritireducens sp. nov. are proposed. The type strain of Nisaea denitrificans is DR41_21(T) (=DSM 18348(T)=CIP 109265(T)=OOB 129(T)) and the type strain of Nisaea nitritireducens is DR41_18(T) (=DSM 19540(T)=CIP 109601(T)=OOB 128(T)).

International audience; The spatial distribution of parasite communities from teleost fishes (Diplodus vulgaris, Mullus surmuletus, Pagellus erythrinus, Phycis phycis, Scorpaena scrofa and Symphodus tinca) was studied in the Bonifacio Strait Marine Reserve (Corsica Island) with different protection levels. Canonical correspondence analysis was used to study spatial patterns and to quantify the importance of site influence on parasite communities. To supplement these results, we used the indicator species analysis (Indval) to identify parasite species as bioindicators of a given ecosystem. Moreover, fish spatial distribution in the marine reserve was evaluated in order to link parasite species occurrence and fish abundance. Several parasite species were associated with a specific site, and some of them were considered as site bioindicators, especially in the western part of the protected area (Bruzzi and Moines Islands). However, the relative abundance of fish followed a different spatial pattern. Stronger fish abundance was observed in the eastern part of the reserve (Lavezzi Islands). The parasite species were correlated to sites inside as well outside the reserve. The parasite distribution seemed not to be influenced by the protection status of the site. Furthermore, in our study, most of the parasite species were not linked to a site. The most important factor influencing their distribution was host specificity. This suggested that the parasite life traits history remained a fundamental determinant in the community composition.

En libre-accès sur Archimer : http://archimer.ifremer.fr/doc/2008/publication-5292.pdf; International audience; A novel aerobic, Gram-negative bacterium, designated strain CM41_14b(T), was isolated from surface waters in the coastal north-western Mediterranean Sea. Cells were non-motile, straight rods, 2.6 microm long and 0.7 microm wide and formed pale-orange colonies on marine agar medium. The G+C content of the genomic DNA was 39 mol%. Phylogenetic analysis based on the 16S rRNA gene sequence placed the strain within the genus Balneola (phylum Bacteroidetes). On the basis of 16S rRNA gene sequence comparisons, and physiological and biochemical characteristics, the isolate represents a novel species for which the name Balneola alkaliphila sp. nov. is proposed. The type strain is CM41_14b(T) (=DSM 19538(T)=CIP 109603(T)=OOB 103(T)).

En libre-accès sur Archimer : http://archimer.ifremer.fr/doc/2008/publication-4193.pdf; International audience; A novel aerobic, Gram-negative bacterium, designated 3X/A02/235T, was isolated from the surface of coastal waters in the north-western Mediterranean Sea. Cells were motile, straight rods, 1.6 microm long and 0.5 microm wide, and formed cream colonies on marine agar medium. The G+C content of the genomic DNA was 61 mol%. Phylogenetic analysis of the 16S rRNA gene sequence placed the strain in the class Gammaproteobacteria and within the family Alteromonadaceae. On the basis of 16S rRNA gene sequence comparisons and physiological and biochemical characteristics, this isolate represents a novel species of a novel genus, for which the name Haliea salexigens gen. nov., sp. nov. is proposed. The type strain of Haliea salexigens is 3X/A02/235T (=DSM 19537T =CIP 109602T =MOLA 286T).

International audience; The cadmium, lead, copper, and zinc levels were measured in six organs (lung, liver, kidney, skin, muscle, and bone) from 18 specimens of toothed whales, belonging to five species, found stranded along the Corsican coast between November 1993 and December 1998. The five species examined were the bottlenose dolphin Tursiops truncatus, the common dolphin Delphinus delphis, the striped dolphin Stenella coeruleoalba, the pilot whale Globicephala melas, and the Risso's dolphin Grampus griseus. The values obtained demonstrate that there is a great variability in the accumulation of toxic metals. A comparison of the values with those obtained in other geographical regions also demonstrates an extensive variability in metal levels. The presence of metals in the stomach contents of three of the individuals studied shows that the food source is responsible for a significant input of pollutants to the whales. Measured pollutant levels in whales are thus the result of an accumulation occurring throughout the animal's life.

International audience; OBJECTIVES: We sought to describe the various cardiovascular complications that occurred in the Lyon Diet Heart Study (a secondary prevention trial testing the protective effects of a Mediterranean type of diet), to analyze their relations with the associated drug treatments and to gain insights into the possible mechanisms underlying the beneficial effects of certain nutriments. BACKGROUND: Dietary habits are implicated in coronary heart disease, and the traditional Mediterranean diet is thought to be cardioprotective. However, the exact mechanisms of this protection are unknown. METHODS: A total of 605 patients (303 control subjects and 302 study patients) were studied over a mean period of 27 months. Major primary end points (cardiovascular death and nonfatal acute myocardial infarction), secondary end points (including unstable angina, stroke, heart failure and embolisms) and minor end points (stable angina, need for myocardial revascularization, postangioplasty restenosis and thrombophlebitis) were analyzed separately and in combination. RESULTS: When major primary and secondary end points were combined, there were 59 events in control subjects and 14 events in the study patients, showing a risk reduction of 76% (p < 0.0001). When these end points were combined with the minor end points, there were 104 events in control subjects and 68 events in the study patients, giving a risk reduction of 37% (p < 0.005). By observational analysis, only aspirin among the medications appeared to be significantly protective (risk ratio after adjustment for prognosis factors 0.45; 95% confidence interval 0.25 to 0.80). CONCLUSIONS: These data show a protective effect of the Mediterranean diet. However, the risk reduction varied depending on the type of end point considered. Our hypothesis is that different pathogenetic mechanisms were responsible for the development of the various complications. It is likely that certain nutriments characteristic of the Mediterranean diet (omega-3 fatty acids, oleic acid antioxidant vitamins) have specific cardioprotective effects.