Archaeal Methane Cycling Communities Associated with Gassy Subsurface Sediments of Marennes-Oléron Bay (France)

En libre-accès sur Archimer : http://archimer.ifremer.fr/doc/2009/publication-6165.pdfInternational audienceIn Marennes-Oleacuteron Bay, a macro-tidal bay located on the French Atlantic coast, kilometer-scale acoustic turbidity reveals an accumulation of free gas in the sediment. Large concentrations of organic matter and rapid sedimentation rates provide ideal settings for biogenic methane cycling. We integrate seismic, sedimentologic, biogeochemical and molecular genetic approaches to determine whether microbial methane cycling is involved in this process. Here we show that the acoustic turbidity upper boundary matched with X-ray facies displaying fissures with the highest methane concentrations, demonstrating the existence of methane bubbles in the sediment. 16S rRNA and mcrA gene clone libraries were dominated by sequences affiliated to the three known ANME lineages and to putative methanogens. Sequences related to the marine benthic group B (MBG-B) and miscellaneous crenarchaeotal group (MCG) were also detected. However, the highest methane concentration facies was the only section where active Archaea were detected, using reverse-transcribed rRNA, indicating that these communities were involved either directly or indirectly in the methane cycling process. Moreover, three metabolically active novel uncultivated lineages, related to putative methane cycling Archaea, could be specifically associated to these methane bearing sediments. As methane cycling Archaea are commonly retrieved from deep subseafloor and methane seep sediment, the study of coastal gassy sediments, could therefore help to define the biogeochemical habitats of deep biosphere communities

The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote Small Sub-Unit rRNA sequences with curated taxonomy

The interrogation of genetic markers in environmental meta-barcoding studies is currently seriously hindered by the lack of taxonomically curated reference data sets for the targeted genes. The Protist Ribosomal Reference database (PR2, http://ssu-rrna.org/) provides a unique access to eukaryotic small sub-unit (SSU) ribosomal RNA and DNA sequences, with curated taxonomy. The database mainly consists of nuclear-encoded protistan sequences. However, metazoans, land plants, macrosporic fungi and eukaryotic organelles (mitochondrion, plastid and others) are also included because they are useful for the analysis of high-troughput sequencing data sets. Introns and putative chimeric sequences have been also carefully checked. Taxonomic assignation of sequences consists of eight unique taxonomic fields. In total, 136 866 sequences are nuclear encoded, 45 708 (36 501 mitochondrial and 9657 chloroplastic) are from organelles, the remaining being putative chimeric sequences. The website allows the users to download sequences from the entire and partial databases (including representative sequences after clustering at a given level of similarity). Different web tools also allow searches by sequence similarity. The presence of both rRNA and rDNA sequences, taking into account introns (crucial for eukaryotic sequences), a normalized eight terms ranked-taxonomy and updates of new GenBank releases were made possible by a long-term collaboration between experts in taxonomy and computer scientist

The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote Small Sub-Unit rRNA sequences with curated taxonomy

International audienceThe interrogation of genetic markers in environmental meta-barcoding studies is currently seriously hindered by the lack of taxonomically curated reference data sets for the targeted genes. The Protist Ribosomal Reference database (PR2, http://ssu-rrna.org/) provides a unique access to eukaryotic small sub-unit (SSU) ribosomal RNA and DNA sequences, with curated taxonomy. The database mainly consists of nuclear-encoded protistan sequences. However, metazoans, land plants, macrosporic fungi and eukaryotic organelles (mitochondrion, plastid and others) are also included because they are useful for the analysis of high-troughput sequencing data sets. Introns and putative chimeric sequences have been also carefully checked. Taxonomic assignation of sequences consists of eight unique taxonomic fields. In total, 136 866 sequences are nuclear encoded, 45 708 (36 501 mitochondrial and 9657 chloroplastic) are from organelles, the remaining being putative chimeric sequences. The website allows the users to download sequences from the entire and partial databases (including representative sequences after clustering at a given level of similarity). Different web tools also allow searches by sequence similarity. The presence of both rRNA and rDNA sequences, taking into account introns (crucial for eukaryotic sequences), a normalized eight terms ranked-taxonomy and updates of new GenBank releases were made possible by a long-term collaboration between experts in taxonomy and computer scientists

Interactions entre ciliés et métazoaires dans deux environnements marins contrastés : les sources hydrothermales et les sédiments anoxiques

Cilliates (Ciliophora) are defined as one of the main groups within the eukaryotic systematic. These ubiquitous unicellular microorganisms have adapted to a wide range of habitats (terrestrial, marine and freshwater habitats) using different morphological and physiological strategies, some of which are based on symbiosis. Out of the numerous ecological niches found in the marine environment, two were selected in this study : hydrothermal vents and coastal marine sediments. Morphological observations (live, stained, scanning, and transmission electron microscopy) and molecular genetic analyses (PCR, cloning, sequencing, in situ hybridization) were combined in order to characterise the unicellular eukaryote communities associated with endemic metazoans from these two contrasted environments (hydrothermal bivalves and intertidal polychaetes). The present study (i) compared the distribution of unicellular eukaryotes associated with different deep-sea marine environments (seawater, hydrothermal vents, Bathymodiolus), (ii) revealed new clades within the ciliates detected in hydrothermal bivalves, (iii) redescribed and compared the distribution of astomes, a specific group of ciliates, only found associated with metazoans, (iv) defined endocytoplasmic bacteria as a third partner in this tripartite association. Here we show that a majority of unicellular eukaryotes detected in hydrothermal environments are also widespread in oceanic waters. However, distinct and stable ecological niches, such as endemic bivalves, harbour more specific ciliate communities, either symbiotic and/or parasitic. Moreover, Cirratulidae polychaetes from anoxic coastal sediments are part of a tripartite association with endocommensal ciliates harbouring endocytoplasmic bacteria. The endosymbiotic bacteria, mainly affiliated to Epsilon-Proteobacteria and to a new Proteobacteria clade named Durchoniella Endocytoplasmic Proteobacteria Group (DEPG), were phylogeneticaly distant from any previously described Proteobacteria, suggesting a common evolutionary history. These new models may help to better understand the interactions between eukaryotes and bacteria.Les communautés d’eucaryotes unicellulaires associées à des métazoaires endémiques de deux environnements marins, les sources hydrothermales et les sédiments marins côtiers, ont été caractérisées par des études moléculaires et microscopiques. Ce travail de recherche a permis i) de caractériser et de comparer la distribution des communautés d’eucaryotes unicellulaires associées à différents environnements marins profonds, ii) de mettre en évidence de nouveaux clades, notamment chez les ciliés détectés dans les bivalves hydrothermaux, iii) de redéfinir et de comparer la distribution d’un groupe particulier de ciliés, les astomes, retrouvé uniquement en interaction avec des polychètes, iv) de mettre en évidence dans ces astomes endocommensaux, un troisième degré d’interaction représenté par des bactéries endocytoplasmiques. Ainsi, cette étude montre qu’une majorité d’eucaryotes unicellulaires détectés au niveau des sources hydrothermales sont des organismes cosmopolites des océans. Cependant, des niches écologiques distinctes et stables, représentées par les bivalves endémiques, abritent des communautés de ciliés plus spécifiques. De plus, les polychètes Cirratulidae retrouvés dans les sédiments côtiers réduits abritent un modèle d’interaction tripartite composé d’astomes endocommensaux associés à des bactéries endocytoplasmiques. Ces endosymbiontes sont phylogénétiquement très éloignés des organismes déjà décrits, et pourraient être ainsi les témoins d’une histoire évolutive commune. Ces nouveaux modèles d’étude ouvrent le champ des interactions entre eucaryotes et bactéries

Interactions entre ciliés et métazoaires dans deux environnements marins contrastés (les sources hydrothermales et les sédiments anoxiques)

Les communautés d eucaryotes unicellulaires associées à des métazoaires endémiques de deux environnements marins, les sources hydrothermales et les sédiments marins côtiers, ont été caractérisées par des études moléculaires et microscopiques. Ce travail de recherche a permis i) de caractériser et de comparer la distribution des communautés d eucaryotes unicellulaires associées à différents environnements marins profonds, ii) de mettre en évidence de nouveaux clades, notamment chez les ciliés détectés dans les bivalves hydrothermaux, iii) de redéfinir et de comparer la distribution d un groupe particulier de ciliés, les astomes, retrouvé uniquement en interaction avec des polychètes, iv) de mettre en évidence dans ces astomes endocommensaux, un troisième degré d interaction représenté par des bactéries endocytoplasmiques. Ainsi, cette étude montre qu une majorité d eucaryotes unicellulaires détectés au niveau des sources hydrothermales sont des organismes cosmopolites des océans. Cependant, des niches écologiques distinctes et stables, représentées par les bivalves endémiques, abritent des communautés de ciliés plus spécifiques. De plus, les polychètes Cirratulidae retrouvés dans les sédiments côtiers réduits abritent un modèle d interaction tripartite composé d astomes endocommensaux associés à des bactéries endocytoplasmiques. Ces endosymbiontes sont phylogénétiquement très éloignés des organismes déjà décrits, et pourraient être ainsi les témoins d une histoire évolutive commune. Ces nouveaux modèles d étude ouvrent le champ des interactions entre eucaryotes et bactériesPARIS-BIUSJ-Physique recherche (751052113) / SudocROSCOFF-Observ.Océanol. (292393008) / SudocSudocFranceF

Redescription and phylogenetic analyses of Durchoniella spp. (Ciliophora, Astomatida) associated with the polychaete Cirriformia tentaculata (Montagu, 1808)

Microscopic and phylogenetic analyses were performed on endocommensal astome ciliates retrieved from the middle intestine of a marine cirratulid polychaete, Cirriformia tentaculata, collected in the bay of Roscoff (English Channel, Northwest French coast) and on the Southwest English coast. Three morphotypes of the astome genus Durchoniella were identified, two corresponding to described species (the type species Durchoniella brasili (Léger and Duboscq, 1904) de Puytorac, 1954 and Durchoniella legeriduboscqui de Puytorac, 1954) while a third morphotype remains undescribed. Their small subunit (SSU) rRNA gene sequences showed at least 97.2% identity and phylogenetic analyses grouped them at the base of the subclass Scuticociliatia (Oligohymenophorea), as a sister lineage to all astomes from terrestrial oligochaete annelids. Ultrastructural examination by transmission electron microscopy and fluorescence in situ hybridization analyses revealed the presence of endocytoplasmic cocci and rod-shaped bacteria surrounded by a very thin membrane. These endocytoplasmic bacteria may play a role in the association between endocommensal astome ciliates and cirratulid polychaetes inhabiting in anoxic coastal sediments

KBE009: An antimalarial bestatin-like inhibitor of the Plasmodium falciparum M1 aminopeptidase discovered in an Ugi multicomponent reaction-derived peptidomimetic library

Malaria is a global human parasitic disease mainly caused by the protozoon Plasmodium falciparum. Increased parasite resistance to current drugs determines the relevance of finding new treatments against new targets. A novel target is the M1 alanyl-aminopeptidase from P. falciparum (PfA-M1), which is essential for parasite development in human erythrocytes and is inhibited by the pseudo-peptide bestatin. In this work, we used a combinatorial multicomponent approach to produce a library of peptidomimetics and screened it for the inhibition of recombinant PfA-M1 (rPfA-M1) and the in vitro growth of P. falciparum erythrocytic stages (3D7 and FcB1 strains). Dose-response studies with selected compounds allowed identifying the bestatin-based peptidomimetic KBE009 as a submicromolar rPfA-M1 inhibitor (Ki =0.4μM) and an in vitro antimalarial compound as potent as bestatin (IC50 =18μM; without promoting erythrocyte lysis). At therapeutic-relevant concentrations, KBE009 is selective for rPfA-M1 over porcine APN (a model of these enzymes from mammals), and is not cytotoxic against HUVEC cells. Docking simulations indicate that this compound binds PfA-M1 without Zn2+ coordination, establishing mainly hydrophobic interactions and showing a remarkable shape complementarity with the active site of the enzyme. Moreover, KBE009 inhibits the M1-type aminopeptidase activity (Ala-7-amido-4-methylcoumarin substrate) in isolated live parasites with a potency similar to that of the antimalarial activity (IC50 =82μM), strongly suggesting that the antimalarial effect is directly related to the inhibition of the endogenous PfA-M1. These results support the value of this multicomponent strategy to identify PfA-M1 inhibitors, and make KBE009 a promising hit for drug development against malaria. © 2017 Elsevier Ltd

How deep can ectomycorrhizas go? A case study on Pisolithus down to 4 meters in a Brazilian eucalypt plantation

International audienceDespite the strong ecological importance of ectomycorrhizal (ECM) fungi, their vertical distribution remains poorly understood. To our knowledge, ECM structures associated with trees have never been reported in depths below 2 meters. In this study, fine roots and ECM root tips were sampled down to 4-m depth during the digging of two independent pits differing by their water availability. A meta-barcoding approach based on Illumina sequencing of internal transcribed spacers (ITS1 and ITS2) was carried out on DNA extracted from root samples (fine roots and ECM root tips separately). ECM fungi dominated the root-associated fungal community, with more than 90% of sequences assigned to the genus Pisolithus. The morphological and barcoding results demonstrated, for the first time, the presence of ECM symbiosis down to 4-m. The molecular diversity of Pisolithus spp. was strongly dependent on depth, with soil pH and soil water content as primary drivers of the Pisolithus spp. structure. Altogether, our results highlight the importance to consider the ECM symbiosis in deep soil layers to improve our understanding of fine roots functioning in tropical soils