81 research outputs found

    Characterization of Ionizable Groups' Environments in Proteins and Protein-Ligand Complexes through a Statistical Analysis of the Protein Data Bank

    Get PDF
    We conduct a statistical analysis of the molecular environment of common ionizable functional groups in both protein-ligand complexes and inside proteins from the Protein Data Bank (PDB). In particular, we characterize the frequency, type, and density of the interacting atoms as well as the presence of a potential counterion. We found that for ligands, most guanidinium groups, half of primary and secondary amines, and one-fourth of imidazole neighbor a carboxylate group. Tertiary amines bind more rarely near carboxylate groups, which may be explained by a crowded neighborhood and hydrophobic character. In comparison to the environment seen by the ligands, inside proteins, an environment enriched in main-chain atoms is found, and the prevalence of direct charge neutralization by carboxylate groups is different. When the ionizable character of water molecules and phenolic or hydroxyl groups is accounted, considering a high-resolution dataset (less than 1.5 A), charge neutralization could occur for well above 80% of the ligand functional groups considered, but for tertiary amines.Peer reviewe

    Diversité des archées et implication de la composante procaryote dans le cycle biogéochimique du méthane en milieu aquatique continental (études taxonomiques et fonctionnelles dans la colonne d'eau et les sédiments anoxiques du lac Pavin)

    Get PDF
    Le mĂ©thane, un des principaux gaz Ă  effet de serre, est majoritairement produit et consommĂ© par l'activitĂ© mĂ©tabolique de microorganismes affiliĂ©s aux domaines des Archaea et des Bacteria. Afin d apprĂ©hender le cycle biogĂ©ochimique du mĂ©thane, il est essentiel d identifier l ensemble des acteurs impliquĂ©s dans ce dernier ainsi que les facteurs environnementaux modulant leurs activitĂ©s. Les lacs d eau douce constituent une source importante de mĂ©thane, car, dans ces Ă©cosystĂšmes, les conditions environnementales favorisent la mĂ©thanogenĂšse au dĂ©triment d autres processus terminaux de la dĂ©gradation anaĂ©robie de la matiĂšre organique. Au cours de cette thĂšse, les Ă©tudes sur les communautĂ©s impliquĂ©es dans le cycle biogĂ©ochimique du mĂ©thane ont Ă©tĂ© conduites dans la colonne d eau et les sĂ©diments anoxiques du Lac Pavin (Auvergne), unique lac mĂ©romictique de France. Cet Ă©cosystĂšme a Ă©tĂ© choisi comme site d'Ă©tude en raison des fortes concentrations en mĂ©thane prĂ©sentes dans sa couche d'eau profonde qui contrastent avec les faibles Ă©missions de ce gaz vers l'atmosphĂšre. Ces observations gĂ©ochimiques suggĂšrent une intense activitĂ© de production et de consommation du mĂ©thane, offrant un cadre pertinent pour l Ă©tude des communautĂ©s ciblĂ©es. Les approches molĂ©culaires visant Ă  caractĂ©riser la structure spatiale, la composition, les zones d'activitĂ© et les facteurs (ascendants et descendants) potentiellement impliquĂ©s dans la rĂ©gulation des communautĂ©s de mĂ©thanogĂšnes et de mĂ©thanotrophes ont Ă©tĂ©, au cours de ce travail, systĂ©matiquement associĂ©es Ă  des approches culturales et microcalorimĂ©triques afin d acquĂ©rir des donnĂ©es sur la physiologie des microorganismes impliquĂ©s dans le cycle du mĂ©thane. Les rĂ©sultats obtenus mettent en Ă©vidence que les communautĂ©s de mĂ©thanogĂšnes sont distribuĂ©es sur l ensemble de la colonne d eau anoxique et dans la strate superficielle des sĂ©diments profonds. Ce groupe mĂ©tabolique, essentiellement reprĂ©sentĂ© par des espĂšces affiliĂ©es aux Methanosaetaceae et aux Methanoregulaceae, est particuliĂšrement actif dans la zone benthique qui constituerait la source principale de mĂ©thane dans cet Ă©cosystĂšme. Une nouvelle espĂšce mĂ©thanogĂšne, Methanobacterium lacus, a Ă©tĂ© isolĂ©e de ces sĂ©diments et dĂ©crite, et vient enrichir le faible nombre d'espĂšces mĂ©thanogĂšnes isolĂ©es Ă  ce jour Ă  partir des lacs d'eau douce. L'Ă©tude Ă©cophysiologique de cette souche suggĂšre que la tempĂ©rature pourrait en partie expliquer la faible reprĂ©sentativitĂ© des Methanobacteriales dans cet Ă©cosystĂšme. Une partie du mĂ©thane semble ĂȘtre directement consommĂ©e dans la zone anoxique (pĂ©lagique et benthique). L existence de ce processus d oxydation anaĂ©robie, soutenu par les approches microcalorimĂ©triques, pourrait ĂȘtre, dans les sĂ©diments profonds, sous la dĂ©pendance de lignĂ©es candidates archĂ©ennes dont la physiologie reste encore Ă©nigmatique. Le remplacement progressif des mĂ©thanogĂšnes par 2 lignĂ©es candidates d'archaea (MBG-D et MCG) le long du profil sĂ©dimentaire suggĂšre qu'elle se dĂ©veloppe dans des niche contrastĂ©es. La rĂ©gulation putative des communautĂ©s archĂ©ennes par les virus a Ă©tĂ© analysĂ©e. Cette Ă©tude est la premiĂšre Ă  rapporter la prĂ©sence de particules virales de type "archaeovirus" dans un environnement non-extrĂȘme (en termes de tempĂ©rature, pH et salinitĂ©) ainsi que des particules virales pouvant reprĂ©sentĂ©es de nouvelles familles de virus. Une activitĂ© virale intense est suggĂ©rĂ©e dans ces sĂ©diments par le nombre important de cellules infectĂ©es, comparativement Ă  d'autres sĂ©diments, et par le changement concomitant de la structure de la communautĂ© virale et procaryotique avec la profondeur. Bien qu une partie du mĂ©thane soit probablement oxydĂ©e en anaĂ©robiose, la consommation de ce mĂ©tabolite est principalement dĂ©pendante de l activitĂ© de mĂ©thanotrophes aĂ©robies dominĂ©es par des espĂšces affiliĂ©es au genre Methylobacter, un des principaux genres de mĂ©thanotrophes rencontrĂ© en milieu d eau douce. (...)Methane, a major greenhouse gas, is produced and consumed mainly by the metabolic activity of microorganisms affiliated to the domains Archaea and Bacteria. In order to understand the biogeochemical cycling of methane, it is essential to identify all the biological actors involved, as well as environmental factors modulating their activity. Freshwater lakes are a major source of methane because environmental conditions occurring in these ecosystems favor methanogenesis over other terminal processes of anaerobic degradation of organic matter. In this thesis, studies of communities involved in the biogeochemical cycling of methane were carried out in the water column and anoxic sediment of Lake Pavin (Auvergne), the unique French meromictic lake. This ecosystem has been selected as study site due to the high concentrations of methane in its deep water layer which contrast with the very low emission of this gas in the atmosphere. These geochemical observations suggest an intense activity of production and consumption of methane, providing an appropriate framework for studying the communities involved. Molecular approaches to characterize the spatial structure, composition, activity areas and factors (bottom-up and top-down) potentially involved in the regulation of methanogens and methanotrophs were, in this work, systematically associated to cultural and microcalorimetric approaches to acquire data on the physiology of microorganisms involved in the methane cycle. The results show that methanogens are distributed throughout the permanent anoxic water column (monimolimnion) and mainly in the superficial layer of the sediment situated under the monimolimnion. This metabolic group, mainly represented by species affiliated to Methanosaetaceae and Methanoregulaceae, is particularly active in the benthic zone which would be the main source of methane in this ecosystem. A new species of methanogen, Methanobacterium lacus, was isolated from these sediments and described. It enhances to the small number of methanogenic species isolated to date from freshwater lakes. The ecophysiological study of this strain suggests that the temperature could partly explain the low representation of Methanobacteriales in this ecosystem. A part of the methane appears to be directly consumed in the anoxic zone (pelagic and benthic). The existence of this process of anaerobic oxidation, supported by microcalorimetric approaches, could be in deep sediments, dependent on archaeal candidate lineages whose physiology remains enigmatic. The gradual replacement of methanogens by two archaeal candidate lineages (MBG-D and MCG) along the sedimentary profile suggests that they live in contrasted niche. The putative regulation of the archaeal communities by virus was analyzed. This study has reported the first observations of archaeovirus-like particles in a non-extreme environment (in term of temperature, pH and salinity) and virus-like particles which might represent new viral families. An intense viral activity in these sediments is suggested by i) the important number of visibly infected cells and ii) the concomitant change of the viral and prokaryotic communities with depth. While a fraction of methane is probably oxidized anaerobically, the consumption of this metabolite is mainly dependent on the activity of aerobic methanotrophs dominated by species affiliated to the genus Methylobacter, one of the main types of methanotrophs found in freshwater environments.These methanotrophs have a large area of activity, extending around both sides of the red/ox interface in the water column. This wide distribution may partly explain the low quantity of methane released by the Lake Pavin. (...)CLERMONT FD-Bib.Ă©lectronique (631139902) / SudocSudocFranceF

    Comparative genomics highlights the unique biology of Methanomassiliicoccales, a Thermoplasmatales-related seventh order of methanogenic archaea that encodes pyrrolysine

    Get PDF
    BACKGROUND: A seventh order of methanogens, the Methanomassiliicoccales, has been identified in diverse anaerobic environments including the gastrointestinal tracts (GIT) of humans and other animals and may contribute significantly to methane emission and global warming. Methanomassiliicoccales are phylogenetically distant from all other orders of methanogens and belong to a large evolutionary branch composed by lineages of non-methanogenic archaea such as Thermoplasmatales, the Deep Hydrothermal Vent Euryarchaeota-2 (DHVE-2, Aciduliprofundum boonei) and the Marine Group-II (MG-II). To better understand this new order and its relationship to other archaea, we manually curated and extensively compared the genome sequences of three Methanomassiliicoccales representatives derived from human GIT microbiota, “Candidatus Methanomethylophilus alvus", “Candidatus Methanomassiliicoccus intestinalis” and Methanomassiliicoccus luminyensis. RESULTS: Comparative analyses revealed atypical features, such as the scattering of the ribosomal RNA genes in the genome and the absence of eukaryotic-like histone gene otherwise present in most of Euryarchaeota genomes. Previously identified in Thermoplasmatales genomes, these features are presently extended to several completely sequenced genomes of this large evolutionary branch, including MG-II and DHVE2. The three Methanomassiliicoccales genomes share a unique composition of genes involved in energy conservation suggesting an original combination of two main energy conservation processes previously described in other methanogens. They also display substantial differences with each other, such as their codon usage, the nature and origin of their CRISPRs systems and the genes possibly involved in particular environmental adaptations. The genome of M. luminyensis encodes several features to thrive in soil and sediment conditions suggesting its larger environmental distribution than GIT. Conversely, “Ca. M. alvus” and “Ca. M. intestinalis” do not present these features and could be more restricted and specialized on GIT. Prediction of the amber codon usage, either as a termination signal of translation or coding for pyrrolysine revealed contrasted patterns among the three genomes and suggests a different handling of the Pyl-encoding capacity. CONCLUSIONS: This study represents the first insights into the genomic organization and metabolic traits of the seventh order of methanogens. It suggests contrasted evolutionary history among the three analyzed Methanomassiliicoccales representatives and provides information on conserved characteristics among the overall methanogens and among Thermoplasmat

    Genomics and metagenomics of trimethylamine-utilizing Archaea in the human gut microbiome

    Get PDF
    International audienceThe biological significance of Archaea in the human gut microbiota is largely unclear. We recently reported genomic and biochemical analyses of the Methanomassiliicoccales, a novel order of methanogenic Archaea dwelling in soil and the animal digestive tract. We now show that these Methanomassiliicoccales are present in published microbiome data sets from eight countries. They are represented by five Operational Taxonomic Units present in at least four cohorts and phylogenetically distributed into two clades. Genes for utilizing trimethylamine (TMA), a bacterial precursor to an atherosclerogenic human metabolite, were present in four of the six novel Methanomassiliicoccales genomes assembled from ELDERMET metagenomes. In addition to increased microbiota TMA production capacity in long-term residential care subjects, abundance of TMA-utilizing Methanomassiliicoccales correlated positively with bacterial gene count for TMA production and negatively with fecal TMA concentrations. The two large Methanomassiliicoccales clades have opposite correlations with host health status in the ELDERMET cohort and putative distinct genomic signatures for gut adaptation

    Diversity of archaea and implication of prokaryotes in the biochemical cycle of methane in continental aquatic environments : taxonomic and functional studies in the water column and the anoxic sediments of Lake Pavin

    No full text
    Le mĂ©thane, un des principaux gaz Ă  effet de serre, est majoritairement produit et consommĂ© par l'activitĂ© mĂ©tabolique de microorganismes affiliĂ©s aux domaines des Archaea et des Bacteria. Afin d’apprĂ©hender le cycle biogĂ©ochimique du mĂ©thane, il est essentiel d’identifier l’ensemble des acteurs impliquĂ©s dans ce dernier ainsi que les facteurs environnementaux modulant leurs activitĂ©s. Les lacs d’eau douce constituent une source importante de mĂ©thane, car, dans ces Ă©cosystĂšmes, les conditions environnementales favorisent la mĂ©thanogenĂšse au dĂ©triment d’autres processus terminaux de la dĂ©gradation anaĂ©robie de la matiĂšre organique. Au cours de cette thĂšse, les Ă©tudes sur les communautĂ©s impliquĂ©es dans le cycle biogĂ©ochimique du mĂ©thane ont Ă©tĂ© conduites dans la colonne d’eau et les sĂ©diments anoxiques du Lac Pavin (Auvergne), unique lac mĂ©romictique de France. Cet Ă©cosystĂšme a Ă©tĂ© choisi comme site d'Ă©tude en raison des fortes concentrations en mĂ©thane prĂ©sentes dans sa couche d'eau profonde qui contrastent avec les faibles Ă©missions de ce gaz vers l'atmosphĂšre. Ces observations gĂ©ochimiques suggĂšrent une intense activitĂ© de production et de consommation du mĂ©thane, offrant un cadre pertinent pour l’étude des communautĂ©s ciblĂ©es. Les approches molĂ©culaires visant Ă  caractĂ©riser la structure spatiale, la composition, les zones d'activitĂ© et les facteurs (ascendants et descendants) potentiellement impliquĂ©s dans la rĂ©gulation des communautĂ©s de mĂ©thanogĂšnes et de mĂ©thanotrophes ont Ă©tĂ©, au cours de ce travail, systĂ©matiquement associĂ©es Ă  des approches culturales et microcalorimĂ©triques afin d’acquĂ©rir des donnĂ©es sur la physiologie des microorganismes impliquĂ©s dans le cycle du mĂ©thane. Les rĂ©sultats obtenus mettent en Ă©vidence que les communautĂ©s de mĂ©thanogĂšnes sont distribuĂ©es sur l’ensemble de la colonne d’eau anoxique et dans la strate superficielle des sĂ©diments profonds. Ce groupe mĂ©tabolique, essentiellement reprĂ©sentĂ© par des espĂšces affiliĂ©es aux Methanosaetaceae et aux Methanoregulaceae, est particuliĂšrement actif dans la zone benthique qui constituerait la source principale de mĂ©thane dans cet Ă©cosystĂšme. Une nouvelle espĂšce mĂ©thanogĂšne, Methanobacterium lacus, a Ă©tĂ© isolĂ©e de ces sĂ©diments et dĂ©crite, et vient enrichir le faible nombre d'espĂšces mĂ©thanogĂšnes isolĂ©es Ă  ce jour Ă  partir des lacs d'eau douce. L'Ă©tude Ă©cophysiologique de cette souche suggĂšre que la tempĂ©rature pourrait en partie expliquer la faible reprĂ©sentativitĂ© des Methanobacteriales dans cet Ă©cosystĂšme. Une partie du mĂ©thane semble ĂȘtre directement consommĂ©e dans la zone anoxique (pĂ©lagique et benthique). L’existence de ce processus d’oxydation anaĂ©robie, soutenu par les approches microcalorimĂ©triques, pourrait ĂȘtre, dans les sĂ©diments profonds, sous la dĂ©pendance de lignĂ©es candidates archĂ©ennes dont la physiologie reste encore Ă©nigmatique. Le remplacement progressif des mĂ©thanogĂšnes par 2 lignĂ©es candidates d'archaea (MBG-D et MCG) le long du profil sĂ©dimentaire suggĂšre qu'elle se dĂ©veloppe dans des niche contrastĂ©es. La rĂ©gulation putative des communautĂ©s archĂ©ennes par les virus a Ă©tĂ© analysĂ©e. Cette Ă©tude est la premiĂšre Ă  rapporter la prĂ©sence de particules virales de type "archaeovirus" dans un environnement non-extrĂȘme (en termes de tempĂ©rature, pH et salinitĂ©) ainsi que des particules virales pouvant reprĂ©sentĂ©es de nouvelles familles de virus. Une activitĂ© virale intense est suggĂ©rĂ©e dans ces sĂ©diments par le nombre important de cellules infectĂ©es, comparativement Ă  d'autres sĂ©diments, et par le changement concomitant de la structure de la communautĂ© virale et procaryotique avec la profondeur. Bien qu’une partie du mĂ©thane soit probablement oxydĂ©e en anaĂ©robiose, la consommation de ce mĂ©tabolite est principalement dĂ©pendante de l’activitĂ© de mĂ©thanotrophes aĂ©robies dominĂ©es par des espĂšces affiliĂ©es au genre Methylobacter, un des principaux genres de mĂ©thanotrophes rencontrĂ© en milieu d’eau douce. (...)Methane, a major greenhouse gas, is produced and consumed mainly by the metabolic activity of microorganisms affiliated to the domains Archaea and Bacteria. In order to understand the biogeochemical cycling of methane, it is essential to identify all the biological actors involved, as well as environmental factors modulating their activity. Freshwater lakes are a major source of methane because environmental conditions occurring in these ecosystems favor methanogenesis over other terminal processes of anaerobic degradation of organic matter. In this thesis, studies of communities involved in the biogeochemical cycling of methane were carried out in the water column and anoxic sediment of Lake Pavin (Auvergne), the unique French meromictic lake. This ecosystem has been selected as study site due to the high concentrations of methane in its deep water layer which contrast with the very low emission of this gas in the atmosphere. These geochemical observations suggest an intense activity of production and consumption of methane, providing an appropriate framework for studying the communities involved. Molecular approaches to characterize the spatial structure, composition, activity areas and factors (bottom-up and top-down) potentially involved in the regulation of methanogens and methanotrophs were, in this work, systematically associated to cultural and microcalorimetric approaches to acquire data on the physiology of microorganisms involved in the methane cycle. The results show that methanogens are distributed throughout the permanent anoxic water column (monimolimnion) and mainly in the superficial layer of the sediment situated under the monimolimnion. This metabolic group, mainly represented by species affiliated to Methanosaetaceae and Methanoregulaceae, is particularly active in the benthic zone which would be the main source of methane in this ecosystem. A new species of methanogen, Methanobacterium lacus, was isolated from these sediments and described. It enhances to the small number of methanogenic species isolated to date from freshwater lakes. The ecophysiological study of this strain suggests that the temperature could partly explain the low representation of Methanobacteriales in this ecosystem. A part of the methane appears to be directly consumed in the anoxic zone (pelagic and benthic). The existence of this process of anaerobic oxidation, supported by microcalorimetric approaches, could be in deep sediments, dependent on archaeal candidate lineages whose physiology remains enigmatic. The gradual replacement of methanogens by two archaeal candidate lineages (MBG-D and MCG) along the sedimentary profile suggests that they live in contrasted niche. The putative regulation of the archaeal communities by virus was analyzed. This study has reported the first observations of archaeovirus-like particles in a non-extreme environment (in term of temperature, pH and salinity) and virus-like particles which might represent new viral families. An intense viral activity in these sediments is suggested by i) the important number of visibly infected cells and ii) the concomitant change of the viral and prokaryotic communities with depth. While a fraction of methane is probably oxidized anaerobically, the consumption of this metabolite is mainly dependent on the activity of aerobic methanotrophs dominated by species affiliated to the genus Methylobacter, one of the main types of methanotrophs found in freshwater environments.These methanotrophs have a large area of activity, extending around both sides of the red/ox interface in the water column. This wide distribution may partly explain the low quantity of methane released by the Lake Pavin. (...

    A microbe that uses crude oil to make methane

    No full text
    International audienceA microorganism that dwells in an underground oil reservoir has been found to degrade various petroleum compounds and use them to produce methane through a previously unreported biochemical pathway

    Diversité des archées et implication de la composante procaryote dans le cycle biogéochimique du méthane en milieu aquatique continental : études taxonomiques et fonctionnelles dans la colonne d'eau et les sédiments anoxiques du lac Pavin

    Get PDF
    Methane, a major greenhouse gas, is produced and consumed mainly by the metabolic activity of microorganisms affiliated to the domains Archaea and Bacteria. In order to understand the biogeochemical cycling of methane, it is essential to identify all the biological actors involved, as well as environmental factors modulating their activity. Freshwater lakes are a major source of methane because environmental conditions occurring in these ecosystems favor methanogenesis over other terminal processes of anaerobic degradation of organic matter. In this thesis, studies of communities involved in the biogeochemical cycling of methane were carried out in the water column and anoxic sediment of Lake Pavin (Auvergne), the unique French meromictic lake. This ecosystem has been selected as study site due to the high concentrations of methane in its deep water layer which contrast with the very low emission of this gas in the atmosphere. These geochemical observations suggest an intense activity of production and consumption of methane, providing an appropriate framework for studying the communities involved. Molecular approaches to characterize the spatial structure, composition, activity areas and factors (bottom-up and top-down) potentially involved in the regulation of methanogens and methanotrophs were, in this work, systematically associated to cultural and microcalorimetric approaches to acquire data on the physiology of microorganisms involved in the methane cycle. The results show that methanogens are distributed throughout the permanent anoxic water column (monimolimnion) and mainly in the superficial layer of the sediment situated under the monimolimnion. This metabolic group, mainly represented by species affiliated to Methanosaetaceae and Methanoregulaceae, is particularly active in the benthic zone which would be the main source of methane in this ecosystem. A new species of methanogen, Methanobacterium lacus, was isolated from these sediments and described. It enhances to the small number of methanogenic species isolated to date from freshwater lakes. The ecophysiological study of this strain suggests that the temperature could partly explain the low representation of Methanobacteriales in this ecosystem. A part of the methane appears to be directly consumed in the anoxic zone (pelagic and benthic). The existence of this process of anaerobic oxidation, supported by microcalorimetric approaches, could be in deep sediments, dependent on archaeal candidate lineages whose physiology remains enigmatic. The gradual replacement of methanogens by two archaeal candidate lineages (MBG-D and MCG) along the sedimentary profile suggests that they live in contrasted niche. The putative regulation of the archaeal communities by virus was analyzed. This study has reported the first observations of archaeovirus-like particles in a non-extreme environment (in term of temperature, pH and salinity) and virus-like particles which might represent new viral families. An intense viral activity in these sediments is suggested by i) the important number of visibly infected cells and ii) the concomitant change of the viral and prokaryotic communities with depth. While a fraction of methane is probably oxidized anaerobically, the consumption of this metabolite is mainly dependent on the activity of aerobic methanotrophs dominated by species affiliated to the genus Methylobacter, one of the main types of methanotrophs found in freshwater environments.These methanotrophs have a large area of activity, extending around both sides of the red/ox interface in the water column. This wide distribution may partly explain the low quantity of methane released by the Lake Pavin. (...)Le mĂ©thane, un des principaux gaz Ă  effet de serre, est majoritairement produit et consommĂ© par l'activitĂ© mĂ©tabolique de microorganismes affiliĂ©s aux domaines des Archaea et des Bacteria. Afin d’apprĂ©hender le cycle biogĂ©ochimique du mĂ©thane, il est essentiel d’identifier l’ensemble des acteurs impliquĂ©s dans ce dernier ainsi que les facteurs environnementaux modulant leurs activitĂ©s. Les lacs d’eau douce constituent une source importante de mĂ©thane, car, dans ces Ă©cosystĂšmes, les conditions environnementales favorisent la mĂ©thanogenĂšse au dĂ©triment d’autres processus terminaux de la dĂ©gradation anaĂ©robie de la matiĂšre organique. Au cours de cette thĂšse, les Ă©tudes sur les communautĂ©s impliquĂ©es dans le cycle biogĂ©ochimique du mĂ©thane ont Ă©tĂ© conduites dans la colonne d’eau et les sĂ©diments anoxiques du Lac Pavin (Auvergne), unique lac mĂ©romictique de France. Cet Ă©cosystĂšme a Ă©tĂ© choisi comme site d'Ă©tude en raison des fortes concentrations en mĂ©thane prĂ©sentes dans sa couche d'eau profonde qui contrastent avec les faibles Ă©missions de ce gaz vers l'atmosphĂšre. Ces observations gĂ©ochimiques suggĂšrent une intense activitĂ© de production et de consommation du mĂ©thane, offrant un cadre pertinent pour l’étude des communautĂ©s ciblĂ©es. Les approches molĂ©culaires visant Ă  caractĂ©riser la structure spatiale, la composition, les zones d'activitĂ© et les facteurs (ascendants et descendants) potentiellement impliquĂ©s dans la rĂ©gulation des communautĂ©s de mĂ©thanogĂšnes et de mĂ©thanotrophes ont Ă©tĂ©, au cours de ce travail, systĂ©matiquement associĂ©es Ă  des approches culturales et microcalorimĂ©triques afin d’acquĂ©rir des donnĂ©es sur la physiologie des microorganismes impliquĂ©s dans le cycle du mĂ©thane. Les rĂ©sultats obtenus mettent en Ă©vidence que les communautĂ©s de mĂ©thanogĂšnes sont distribuĂ©es sur l’ensemble de la colonne d’eau anoxique et dans la strate superficielle des sĂ©diments profonds. Ce groupe mĂ©tabolique, essentiellement reprĂ©sentĂ© par des espĂšces affiliĂ©es aux Methanosaetaceae et aux Methanoregulaceae, est particuliĂšrement actif dans la zone benthique qui constituerait la source principale de mĂ©thane dans cet Ă©cosystĂšme. Une nouvelle espĂšce mĂ©thanogĂšne, Methanobacterium lacus, a Ă©tĂ© isolĂ©e de ces sĂ©diments et dĂ©crite, et vient enrichir le faible nombre d'espĂšces mĂ©thanogĂšnes isolĂ©es Ă  ce jour Ă  partir des lacs d'eau douce. L'Ă©tude Ă©cophysiologique de cette souche suggĂšre que la tempĂ©rature pourrait en partie expliquer la faible reprĂ©sentativitĂ© des Methanobacteriales dans cet Ă©cosystĂšme. Une partie du mĂ©thane semble ĂȘtre directement consommĂ©e dans la zone anoxique (pĂ©lagique et benthique). L’existence de ce processus d’oxydation anaĂ©robie, soutenu par les approches microcalorimĂ©triques, pourrait ĂȘtre, dans les sĂ©diments profonds, sous la dĂ©pendance de lignĂ©es candidates archĂ©ennes dont la physiologie reste encore Ă©nigmatique. Le remplacement progressif des mĂ©thanogĂšnes par 2 lignĂ©es candidates d'archaea (MBG-D et MCG) le long du profil sĂ©dimentaire suggĂšre qu'elle se dĂ©veloppe dans des niche contrastĂ©es. La rĂ©gulation putative des communautĂ©s archĂ©ennes par les virus a Ă©tĂ© analysĂ©e. Cette Ă©tude est la premiĂšre Ă  rapporter la prĂ©sence de particules virales de type "archaeovirus" dans un environnement non-extrĂȘme (en termes de tempĂ©rature, pH et salinitĂ©) ainsi que des particules virales pouvant reprĂ©sentĂ©es de nouvelles familles de virus. Une activitĂ© virale intense est suggĂ©rĂ©e dans ces sĂ©diments par le nombre important de cellules infectĂ©es, comparativement Ă  d'autres sĂ©diments, et par le changement concomitant de la structure de la communautĂ© virale et procaryotique avec la profondeur. Bien qu’une partie du mĂ©thane soit probablement oxydĂ©e en anaĂ©robiose, la consommation de ce mĂ©tabolite est principalement dĂ©pendante de l’activitĂ© de mĂ©thanotrophes aĂ©robies dominĂ©es par des espĂšces affiliĂ©es au genre Methylobacter, un des principaux genres de mĂ©thanotrophes rencontrĂ© en milieu d’eau douce. (...

    An archaeal origin of the Wood-Ljungdahl H4MPT branch and the emergence of bacterial methylotrophy

    No full text
    International audienceThe tetrahydromethanopterin (H 4 MPT) methyl branch of the Wood-Ljungdahl pathway is shared by archaeal and bacterial metabolisms that greatly contribute to the global carbon budget and greenhouse gas fluxes: methanogenesis and methylotrophy, including methanotrophy 1-3. It has been proposed that the H 4 MPT branch dates back to the last universal common ancestor 4-6. Interestingly, it has been identified in numerous recently sequenced and mostly uncultured non-methanogenic and non-methylotrophic archaeal and bacterial lineages, where its function remains unclear 5,7. Here, we have examined the distribution and phylogeny of the enzymes involved in the H 4 MPT branch and the biosyn-thesis of its cofactors in over 6,400 archaeal and bacterial genomes. We find that a full Wood-Ljungdahl H 4 MPT pathway is widespread in Archaea and is likely ancestral to this domain, whereas this is not the case for Bacteria. Moreover, the inclusion of recently sequenced lineages leads to an important shortening of the branch separating Archaea and Bacteria with respect to previous phylogenies of the H 4 MPT branch. Finally, the genes for the pathway are colocalized in many of the recently sequenced archaeal lineages, similar to bacteria. Together, these results weaken the last universal common ancestor hypothesis and rather favour an origin of the H 4 MPT branch in Archaea and its subsequent transfer to Bacteria. We propose a scenario for its potential initial role in the first bacterial recipients and its evolution up to the emergence of aerobic methylotrophy. Finally, we discuss how an ancient horizontal transfer not only triggered the emergence of key metabolic processes but also important transitions in Earth's history. The Wood-Ljungdahl (WL) pathway consists of the reversible reduction of CO 2 into the carbonyl and methyl moieties of acetyl-coenzyme A (acetyl-CoA) through two separate (carbonyl and methyl) branches 8 (Fig

    Copper-Catalyzed Oxyalkynylation of C-S Bonds in Thiiranes and Thiethanes with Hypervalent Iodine Reagents

    No full text
    We report the oxyalkynylation of thiiranes and thietanes using ethynylbenziodoxolone reagents (EBXs) to readily access functionalized building blocks bearing an alkynyl, a benzoate, and an iodide group. The reaction proceeds with high atom efficiency most likely through an alkynyl-episulfonium intermediate. The transformation is copper-catalyzed and compatible with a large array of thiiranes and thietanes
    • 

    corecore