541 results on '"YAKIMOV, Michail M."'
Search Results
102. Discovery of anaerobic lithoheterotrophic haloarchaea, ubiquitous in hypersaline habitats
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Sorokin, Dimitry Y. (author), Messina, Enzo (author), Smedile, Francesco (author), Roman, Pawel (author), Damsté, Jaap S.Sinninghe (author), Ciordia, Sergio (author), Mena, Maria Carmen (author), Ferrer, Manuel (author), Golyshin, Peter N. (author), Kublanov, Ilya V. (author), Samarov, Nazar I. (author), Toshchakov, Stepan V. (author), La Cono, Violetta (author), Yakimov, Michail M. (author), Sorokin, Dimitry Y. (author), Messina, Enzo (author), Smedile, Francesco (author), Roman, Pawel (author), Damsté, Jaap S.Sinninghe (author), Ciordia, Sergio (author), Mena, Maria Carmen (author), Ferrer, Manuel (author), Golyshin, Peter N. (author), Kublanov, Ilya V. (author), Samarov, Nazar I. (author), Toshchakov, Stepan V. (author), La Cono, Violetta (author), and Yakimov, Michail M. (author)
- Abstract
Hypersaline anoxic habitats harbour numerous novel uncultured archaea whose metabolic and ecological roles remain to be elucidated. Until recently, it was believed that energy generation via dissimilatory reduction of sulfur compounds is not functional at salt saturation conditions. Recent discovery of the strictly anaerobic acetotrophic Halanaeroarchaeum compels to change both this assumption and the traditional view on haloarchaea as aerobic heterotrophs. Here we report on isolation and characterization of a novel group of strictly anaerobic lithoheterotrophic haloarchaea, which we propose to classify as a new genus Halodesulfurarchaeum. Members of this previously unknown physiological group are capable of utilising formate or hydrogen as electron donors and elemental sulfur, thiosulfate or dimethylsulfoxide as electron acceptors. Using genome-wide proteomic analysis we have detected the full set of enzymes required for anaerobic respiration and analysed their substrate-specific expression. Such advanced metabolic plasticity and type of respiration, never seen before in haloarchaea, empower the wide distribution of Halodesulfurarchaeum in hypersaline inland lakes, solar salterns, lagoons and deep submarine anoxic brines. The discovery of this novel functional group of sulfur-respiring haloarchaea strengthens the evidence of their possible role in biogeochemical sulfur cycling linked to the terminal anaerobic carbon mineralisation in so far overlooked hypersaline anoxic habitats., BT/Environmental Biotechnology
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- 2017
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103. Discovery of anaerobic lithoheterotrophic haloarchaea, ubiquitous in hypersaline habitats
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Sorokin, Dimitry Y., Messina, Enzo, Smedile, Francesco, Roman, Pawel, Sinninghe Damsté, J.S., Ciordia, Sergio, Mena, Maria Carmen, Ferrer, Manuel, Golyshin, Peter N., Kublanov, Ilya V., Samarov, Nazar I., Toshchakov, Stepan V., La Cono, Violetta, Yakimov, Michail M., Sorokin, Dimitry Y., Messina, Enzo, Smedile, Francesco, Roman, Pawel, Sinninghe Damsté, J.S., Ciordia, Sergio, Mena, Maria Carmen, Ferrer, Manuel, Golyshin, Peter N., Kublanov, Ilya V., Samarov, Nazar I., Toshchakov, Stepan V., La Cono, Violetta, and Yakimov, Michail M.
- Abstract
Hypersaline anoxic habitats harbour numerous novel uncultured archaea whose metabolic and ecological roles remain to be elucidated. Until recently, it was believed that energy generation via dissimilatory reduction of sulfur compounds is not functional at salt saturation conditions. Recent discovery of the strictly anaerobic acetotrophic Halanaeroarchaeum compels to change both this assumption and the traditional view on haloarchaea as aerobic heterotrophs. Here we report on isolation and characterization of a novel group of strictly anaerobic lithoheterotrophic haloarchaea, which we propose to classify as a new genus Halodesulfurarchaeum. Members of this previously unknown physiological group are capable of utilising formate or hydrogen as electron donors and elemental sulfur, thiosulfate or dimethylsulfoxide as electron acceptors. Using genome-wide proteomic analysis we have detected the full set of enzymes required for anaerobic respiration and analysed their substrate-specific expression. Such advanced metabolic plasticity and type of respiration, never seen before in haloarchaea, empower the wide distribution of Halodesulfurarchaeum in hypersaline inland lakes, solar salterns, lagoons and deep submarine anoxic brines. The discovery of this novel functional group of sulfur-respiring haloarchaea strengthens the evidence of their possible role in biogeochemical sulfur cycling linked to the terminal anaerobic carbon mineralisation in so far overlooked hypersaline anoxic habitats.
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- 2017
104. Determinants and prediction of esterase substrate promiscuity patterns
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Ministerio de Economía y Competitividad (España), European Commission, Ministerio de Economía, Industria y Competitividad (España), Biotechnology and Biological Sciences Research Council (UK), German Research Foundation, Natural Sciences and Engineering Research Council of Canada, Principado de Asturias, CSIC - Unidad de Recursos de Información Científica para la Investigación (URICI), Martínez-Martínez, Mónica, Coscolín, Cristina, Santiago, Gerard, Chow, Jennifer, Stogios, Peter J., Bargiela, Rafael, Gertler, Christoph, Navarro-Fernández, José, Bollinger, Alexander, Thies, Stephan, Méndez-García, Celia, Popovic, Ana, Brown, Greg, Chernikova, Tatyana, García-Moyano, Antonio, Bjerga, Gro Elin Kjæreng, Pérez-García, Pablo, Hai, Tran, Pozo, Mercedes V. del, Stokke, Runar, Steen, Ida H., Cui, Hong, Xu, Xiaohui, Nocek, Boguslaw P., Alcaide, María, Distaso, Marco, Mesa, Victoria, Peláez, Ana I., Sánchez, Jesús, Buchholz, Patrick C. F., Pleiss, Jürgen, Fernández-Guerra, Antonio, Glöckner, Frank Oliver, Golyshina, Olga V., Yakimov, Michail M., Savchenko, Alexei, Jaeger, Karl-Erich, Yakunin, Alexander F., Streit, Wolfgang R., Golyshin, Peter N., Guallar, Victor, Ferrer, Manuel, INMARE Consortium, Ministerio de Economía y Competitividad (España), European Commission, Ministerio de Economía, Industria y Competitividad (España), Biotechnology and Biological Sciences Research Council (UK), German Research Foundation, Natural Sciences and Engineering Research Council of Canada, Principado de Asturias, CSIC - Unidad de Recursos de Información Científica para la Investigación (URICI), Martínez-Martínez, Mónica, Coscolín, Cristina, Santiago, Gerard, Chow, Jennifer, Stogios, Peter J., Bargiela, Rafael, Gertler, Christoph, Navarro-Fernández, José, Bollinger, Alexander, Thies, Stephan, Méndez-García, Celia, Popovic, Ana, Brown, Greg, Chernikova, Tatyana, García-Moyano, Antonio, Bjerga, Gro Elin Kjæreng, Pérez-García, Pablo, Hai, Tran, Pozo, Mercedes V. del, Stokke, Runar, Steen, Ida H., Cui, Hong, Xu, Xiaohui, Nocek, Boguslaw P., Alcaide, María, Distaso, Marco, Mesa, Victoria, Peláez, Ana I., Sánchez, Jesús, Buchholz, Patrick C. F., Pleiss, Jürgen, Fernández-Guerra, Antonio, Glöckner, Frank Oliver, Golyshina, Olga V., Yakimov, Michail M., Savchenko, Alexei, Jaeger, Karl-Erich, Yakunin, Alexander F., Streit, Wolfgang R., Golyshin, Peter N., Guallar, Victor, Ferrer, Manuel, and INMARE Consortium
- Abstract
Esterases receive special attention because of their wide distribution in biological systems and environments and their importance for physiology and chemical synthesis. The prediction of esterases’ substrate promiscuity level from sequence data and the molecular reasons why certain such enzymes are more promiscuous than others remain to be elucidated. This limits the surveillance of the sequence space for esterases potentially leading to new versatile biocatalysts and new insights into their role in cellular function. Here, we performed an extensive analysis of the substrate spectra of 145 phylogenetically and environmentally diverse microbial esterases, when tested with 96 diverse esters. We determined the primary factors shaping their substrate range by analyzing substrate range patterns in combination with structural analysis and protein–ligand simulations. We found a structural parameter that helps rank (classify) the promiscuity level of esterases from sequence data at 94% accuracy. This parameter, the active site effective volume, exemplifies the topology of the catalytic environment by measuring the active site cavity volume corrected by the relative solvent accessible surface area (SASA) of the catalytic triad. Sequences encoding esterases with active site effective volumes (cavity volume/SASA) above a threshold show greater substrate spectra, which can be further extended in combination with phylogenetic data. This measure provides also a valuable tool for interrogating substrates capable of being converted. This measure, found to be transferred to phosphatases of the haloalkanoic acid dehalogenase superfamily and possibly other enzymatic systems, represents a powerful tool for low-cost bioprospecting for esterases with broad substrate ranges, in large scale sequence data sets.
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- 2017
105. Diversity of glycosyl hydrolases from cellulose-depleting communities enriched from casts of two earthworm species
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Beloqui, Ana, Nechitaylo, Taras Y., Lopez-Cortes, Nieves, Golyshina, Olga V., Ferrer, Manuel, Golyshin, Peter N., Ghazi, Azam, Guazzaroni, Maria-Eugenia, Polaina, Julio, Strittmatter, Axel W., Reva, Oleg, Waliczek, Agnes, and Yakimov, Michail M.
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Biological diversity -- Analysis ,Carbohydrates -- Health aspects ,Hydrolases -- Analysis ,Enzymes -- Analysis ,Biological sciences - Abstract
Carbohydrate-modifying enzymes are retrieved through the activity screening of metagenomic fosmid libraries from cellulose-depleting microbial communities established with the fresh casts of two earthworm species, Aporrectodea caliginosa and Lumbricus terrestris, as inocula. Sequence analysis is performed for large contiguous DNA fragments of fasmids harboring the genes for glycosyl hydrolases (GHs) to associate them with the organism that might produce them, which is complemented by conventional small-subunit (SSU) rRNA clone library sequencing analysis.
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- 2010
106. Analysis of defence systems and a conjugative IncP-1 plasmid in the marine polyaromatic hydrocarbons-degrading bacterium Cycloclasticus sp. 78-ME
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Yakimov, Michail M., Crisafi, Francesca, Messina, Enzo, Smedile, Francesco, Lopatina, Anna, Denaro, Renata, Pieper, Dietmar H., Golyshin, Peter N., Giuliano, Laura, and Helmholtz Centre for infection research, Inhoffenstr. 7, 38124 Braunschweig, Germany.
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multiple defence systems ,Genomic Islands ,Genes, Bacterial ,DNA Restriction-Modification Enzymes ,Seawater ,Piscirickettsiaceae ,CRISPR-Cas Systems ,Cycloclasticus sp. 78-ME ,Biotransformation ,Hydrocarbons ,Plasmids - Abstract
Marine prokaryotes have evolved a broad repertoire of defence systems to protect their genomes from lateral gene transfer including innate or acquired immune systems and infection-induced programmed cell suicide and dormancy. Here we report on the analysis of multiple defence systems present in the genome of the strain Cycloclasticus sp. 78-ME isolated from petroleum deposits of the tanker 'Amoco Milford Haven'. Cycloclasticus are ubiquitous bacteria globally important in polyaromatic hydrocarbons degradation in marine environments. Two 'defence islands' were identified in 78-ME genome: the first harbouring CRISPR-Cas with toxin-antitoxin system, while the second was composed by an array of genes for toxin-antitoxin and restriction-modification proteins. Among all identified spacers of CRISPR-Cas system only seven spacers match sequences of phages and plasmids. Furthermore, a conjugative plasmid p7ME01, which belongs to a new IncP-1θ ancestral archetype without any accessory mobile elements was found in 78-ME. Our results provide the context to the co-occurrence of diverse defence mechanisms in the genome of Cycloclasticus sp. 78-ME, which protect the genome of this highly specialized PAH-degrader. This study contributes to the further understanding of complex networks established in petroleum-based microbial communities.
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- 2016
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107. The Deep-Sea Polyextremophile Halobacteroides lacunaris TB21 Rough-Type LPS: Structure and Inhibitory Activity towards Toxic LPS
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Lorenzo, Flaviana Di, primary, Palmigiano, Angelo, additional, Paciello, Ida, additional, Pallach, Mateusz, additional, Garozzo, Domenico, additional, Bernardini, Maria-Lina, additional, Cono, Violetta La, additional, Yakimov, Michail M., additional, Molinaro, Antonio, additional, and Silipo, Alba, additional
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- 2017
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108. Metabolic and evolutionary patterns in the extremely acidophilic archaeon Ferroplasma acidiphilum YT
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Golyshina, Olga V., primary, Tran, Hai, additional, Reva, Oleg N., additional, Lemak, Sofia, additional, Yakunin, Alexander F., additional, Goesmann, Alexander, additional, Nechitaylo, Taras Y., additional, LaCono, Violetta, additional, Smedile, Francesco, additional, Slesarev, Alexei, additional, Rojo, David, additional, Barbas, Coral, additional, Ferrer, Manuel, additional, Yakimov, Michail M., additional, and Golyshin, Peter N., additional
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- 2017
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109. Self‐healing capacity of deep‐sea ecosystems affected by petroleum hydrocarbons
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Scoma, Alberto, primary, Yakimov, Michail M, additional, Daffonchio, Daniele, additional, and Boon, Nico, additional
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- 2017
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110. Activity screening of environmental metagenomic libraries reveals novel carboxylesterase families
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Popovic, Ana, primary, Hai, Tran, additional, Tchigvintsev, Anatoly, additional, Hajighasemi, Mahbod, additional, Nocek, Boguslaw, additional, Khusnutdinova, Anna N., additional, Brown, Greg, additional, Glinos, Julia, additional, Flick, Robert, additional, Skarina, Tatiana, additional, Chernikova, Tatyana N., additional, Yim, Veronica, additional, Brüls, Thomas, additional, Paslier, Denis Le, additional, Yakimov, Michail M., additional, Joachimiak, Andrzej, additional, Ferrer, Manuel, additional, Golyshina, Olga V., additional, Savchenko, Alexei, additional, Golyshin, Peter N., additional, and Yakunin, Alexander F., additional
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- 2017
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111. Discovery of anaerobic lithoheterotrophic haloarchaea, ubiquitous in hypersaline habitats
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Sorokin, Dimitry Y, primary, Messina, Enzo, additional, Smedile, Francesco, additional, Roman, Pawel, additional, Damsté, Jaap S Sinninghe, additional, Ciordia, Sergio, additional, Mena, Maria Carmen, additional, Ferrer, Manuel, additional, Golyshin, Peter N, additional, Kublanov, Ilya V, additional, Samarov, Nazar I, additional, Toshchakov, Stepan V, additional, La Cono, Violetta, additional, and Yakimov, Michail M, additional
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- 2017
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112. Complete genome sequence of 'Halanaeroarchaeum sulfurireducens' M27-SA2, a sulfur-reducing and acetate-oxidizing haloarchaeon from the deep-sea hypersaline anoxic lake Medee
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Messina, Enzo (author), Sorokin, Dimitry Y. (author), Kublanov, Ilya V. (author), Toshchakov, Stepan (author), Lopatina, Anna (author), Arcadi, Erika (author), Smedile, Francesco (author), La Spada, Gina (author), La Cono, Violetta (author), Yakimov, Michail M. (author), Messina, Enzo (author), Sorokin, Dimitry Y. (author), Kublanov, Ilya V. (author), Toshchakov, Stepan (author), Lopatina, Anna (author), Arcadi, Erika (author), Smedile, Francesco (author), La Spada, Gina (author), La Cono, Violetta (author), and Yakimov, Michail M. (author)
- Abstract
Strain M27-SA2 was isolated from the deep-sea salt-saturated anoxic lake Medee, which represents one of the most hostile extreme environments on our planet. On the basis of physiological studies and phylogenetic positioning this extremely halophilic euryarchaeon belongs to a novel genus 'Halanaeroarchaeum' within the family Halobacteriaceae. All members of this genus cultivated so far are strict anaerobes using acetate as the sole carbon and energy source and elemental sulfur as electron acceptor. Here we report the complete genome sequence of the strain M27-SA2 which is composed of a 2,129,244-bp chromosome and a 124,256-bp plasmid. This is the second complete genome sequence within the genus Halanaeroarchaeum. We demonstrate that genome of 'Halanaeroarchaeum sulfurireducens' M27-SA2 harbors complete metabolic pathways for acetate and sulfur catabolism and for de novo biosynthesis of 19 amino acids. The genomic analysis also reveals that 'Halanaeroarchaeum sulfurireducens' M27-SA2 harbors two prophage loci and one CRISPR locus, highly similar to that of Kulunda Steppe (Altai, Russia) isolate 'H. sulfurireducens' HSR2T. The discovery of sulfur-respiring acetate-utilizing haloarchaeon in deep-sea hypersaline anoxic lakes has certain significance for understanding the biogeochemical functioning of these harsh ecosystems, which are incompatible with life for common organisms. Moreover, isolations of Halanaeroarchaeum members from geographically distant salt-saturated sites of different origin suggest a high degree of evolutionary success in their adaptation to this type of extreme biotopes around the world., BT/Environmental Biotechnology
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- 2016
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113. Functional enzyme diversity in a number of extreme and non-extreme environments
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Pozo, Mercedes V. del, Martínez-Martínez, Mónica, Alcaide, María, Bargiela, Rafael, Chernikova, Tatyana, Golyshin, Peter N., Yakimov, Michail M., Mapelli, Francesca, Daffonchio, Daniele, Golyshina, Olga V., Ferrer, Manuel, European Commission, and Ministerio de Economía y Competitividad (España)
- Abstract
Trabajo presentado en el 10th International Congress on Extremophiles, celebrado en San Petesburgo (Rusia) del 07 al 11 de septiembre de 2014., The collaborative projects, MAMBA, MAGICPAH, ULIXES, funded by the EU FP7 program, and the BIO2011- 25012 (funded by Spanish Ministry of Economy and Competitiveness) are focused on using environmental sites around the Planet (including soils, acid mines, superficial and deep seawater, etc.) as resources of novel microbial assemblages, gene sequences and enzyme activities, some of which could have potential scientific and industrial applications. Some of the environments, that included contaminated and concontaminated sites, may be inhabited by extremophiles that contains “extremozymes”. The investigation of their “extremozymes”, and their new functions and protein folds, and the correlation between those characteristics and environmental constraints is of interest for achieving the full understating of extreme ecosystem functioning. Here, using cultivation-independent techniques, and in particular, metagenomics, we have selected and analyzed microbial communities from various extreme and non extreme environments and provided a draft vision into their enzyme properties., The authors gratefully acknowledge the financial support provided by the European Community projects ULIXES (FP7-KBBE-2010-266473), MAGICPAH (FP7-KBBE-2009-245226), and MAMBA (FP7-KBBE-2008-226977). This work was further funded by grant BIO2011-25012 from the Spanish Ministry of Economy and Competitiveness.
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- 2014
114. Living at the Limits: Evidence for Microbial Eukaryotes Thriving under Pressure in Deep Anoxic, Hypersaline Habitats
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Stoeck, Thorsten, Filker, Sabine, Edgcomb, Virginia, Orsi, William, Yakimov, Michail M., Pachiadaki, Maria, Breiner, Hans-Werner, LaCono, Violetta, and Stock, Alexandra
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Article Subject - Abstract
The advent of molecular tools in microbial ecology paved the way to exploit the diversity of microbes in extreme environments. Here, we review these tools as applied in one of the most polyextreme habitats known on our planet, namely, deep hypersaline anoxic basins (DHABs), located at ca. 3000–3500 m depth in the Eastern Mediterranean Sea. Molecular gene signatures amplified from environmental DHAB samples identified a high degree of genetic novelty, as well as distinct communities in the DHABs. Canonical correspondence analyses provided strong evidence that salinity, ion composition, and anoxia were the strongest selection factors shaping protistan community structures, largely preventing cross-colonization among the individual basins. Thus, each investigated basin represents a unique habitat (“isolated islands of evolution”), making DHABs ideal model sites to test evolutionary hypotheses. Fluorescence in situ hybridization assays using specifically designed probes revealed that the obtained genetic signatures indeed originated from indigenous polyextremophiles. Electron microscopy imaging revealed unknown ciliates densely covered with prokaryote ectosymbionts, which may enable adaptations of eukaryotes to DHAB conditions. The research reviewed here significantly advanced our knowledge on polyextremophile eukaryotes, which are excellent models for a number of biological research areas, including ecology, diversity, biotechnology, evolutionary research, physiology, and astrobiology.
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- 2014
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115. Promiscuity and extremophily: expanding the pool of substrates available to extremophiles that mineralize aromatic pollutants
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Alcaide, María, Tornés, Jesús, Stogios, Peter J., Xu, Xiaohui, Gertler, Christoph, Di Leo, Rosa, Bargiela, Rafael, Lafraya Aguado, Álvaro, Chernikova, Tatyana, Golyshina, Olga V., Nechitaylo, Taras Y., Plumeier, Iris, Pieper, Dietmar H., Yakimov, Michail M., Savchenko, Alexei, Golyshin, Peter N., Ferrer, Manuel, Ministerio de Economía y Competitividad (España), and European Commission
- Abstract
Trabajo presentado en el 10th International Congress on Extremophiles, celebrado en San Petesburgo (Rusia) del 07 al 11 de septiembre de 2014., Several microorganisms have the ability to gain energy from hydrophobic organic solvents that are highly toxic for the majority of them. When bacteria are confronted with aromatic compounds, cells face an enticing contradiction. Briefly these chemical species can be mineralized, allowing the microorganism to colonize niches refractory to other microbes for which they are toxic. Therefore, once a site is contaminated, the microbial community greatly changed allowing “extremophiles” to develop. Microbial ability to thrive in polluted sites depends upon adaptation of their enzymatic machinery. To note is that enzymes commonly work in complex environments. External factors (substrate diversity, concentration, presence of ions, temperature, pH, protein-protein interactions, etc.), and protein features themselves (modularity, overall structure and single or multiple mutations), exemplified a complex scenario that may influence activity levels and substrate specificity in a way that cannot be derived from community genome and transcript datasets. Accordingly, this stresses the need for further biochemical and structural studies in order to quantify more accurately enzyme activity characteristics as they may have ecological implications. C-C meta-cleavage product (MCP) hydrolases are key enzymes for the complete mineralization of aromatic pollutants. The catalytic mechanism of MCP hydrolases is well-known; still the mechanisms by which promiscuity can be gained in this protein family, in particular the unusual ability to hydrolyze both esters and MCP, is not clearly understood. Herein, we describe six distinct α/β hydrolases obtained by genomic approaches, four of which have the un-precedent characteristic of activity towards multiple substrates. Using crystallography and site-directed mutagenesis we have identified three residues of the binding site (S32, V130 and W144) of one of these proteins that provides a cogent explanation for the unusual selectivity profile (Alcaide et al., 2013). The data suggest that hydrolases with such broad substrate range may persist in microbial communities to much greater extent than previously anticipated, expanding the pool of substrates available to microorganisms that mineralize organic carbon. Hence this type of enzyme may contribute to the global carbon cycling processes and for channeling complex substrates into the common catabolic pathways, including recalcitrant organic pollutants. The results may open up new research avenues into comparative catalysis models, structural and mechanistic studies, as well as expand the ecological implications and biotechnological applications of MCP hydrolases., The authors acknowledge the financial support of the European Community projects MAMBA, MAGICPAH, ULIXES and KILLSPILL and grants CSD2007-00005 and BIO2011-25012 from the Spanish Ministry of Economy and Competitiveness.
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- 2014
116. Challenging Oil Bioremediation at Deep-Sea Hydrostatic Pressure
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Scoma, Alberto, primary, Yakimov, Michail M., additional, and Boon, Nico, additional
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- 2016
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117. In situ grazing experiments apply new technology to gain insights into deep-sea microbial food webs
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Pachiadaki, Maria G., primary, Taylor, Craig, additional, Oikonomou, Andreas, additional, Yakimov, Michail M., additional, Stoeck, Thorsten, additional, and Edgcomb, Virginia, additional
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- 2016
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118. Analysis of defence systems and a conjugative IncP-1 plasmid in the marine polyaromatic hydrocarbons-degrading bacteriumCycloclasticussp. 78-ME
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Yakimov, Michail M., primary, Crisafi, Francesca, additional, Messina, Enzo, additional, Smedile, Francesco, additional, Lopatina, Anna, additional, Denaro, Renata, additional, Pieper, Dietmar H., additional, Golyshin, Peter N., additional, and Giuliano, Laura, additional
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- 2016
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119. Complete genome sequence of ‘Halanaeroarchaeum sulfurireducens’ M27-SA2, a sulfur-reducing and acetate-oxidizing haloarchaeon from the deep-sea hypersaline anoxic lake Medee
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Messina, Enzo, primary, Sorokin, Dimitry Y., additional, Kublanov, Ilya V., additional, Toshchakov, Stepan, additional, Lopatina, Anna, additional, Arcadi, Erika, additional, Smedile, Francesco, additional, La Spada, Gina, additional, La Cono, Violetta, additional, and Yakimov, Michail M., additional
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- 2016
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120. Oil-degrading bacteria from a membrane bioreactor (BF-MBR) system for treatment of saline oily waste: Isolation, identification and characterization of the biotechnological potential
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Cappello, Simone, primary, Volta, Anna, additional, Santisi, Santina, additional, Morici, Claudia, additional, Mancini, Giuseppe, additional, Quatrini, Paola, additional, Genovese, Maria, additional, Yakimov, Michail M., additional, and Torregrossa, Michele, additional
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- 2016
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121. Identification and Characterization of Carboxyl Esterases of Gill Chamber-Associated Microbiota in the Deep-Sea Shrimp Rimicaris exoculata by Using Functional Metagenomics
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Alcaide, Maria, Tchigvintsev, Anatoli, Martinez-martinez, Monica, Popovic, Ana, Reva, Oleg N., Lafraya, Alvaro, Bargiela, Rafael, Nechitaylo, Taras Y., Matesanz, Ruth, Cambon-bonavita, Marie-anne, Jebbar, Mohamed, Yakimov, Michail M., Savchenko, Alexei, Golyshina, Olga V., Yakunin, Alexander F., Golyshin, Peter N., Ferrer, Manuel, Alcaide, Maria, Tchigvintsev, Anatoli, Martinez-martinez, Monica, Popovic, Ana, Reva, Oleg N., Lafraya, Alvaro, Bargiela, Rafael, Nechitaylo, Taras Y., Matesanz, Ruth, Cambon-bonavita, Marie-anne, Jebbar, Mohamed, Yakimov, Michail M., Savchenko, Alexei, Golyshina, Olga V., Yakunin, Alexander F., Golyshin, Peter N., and Ferrer, Manuel
- Abstract
The shrimp Rimicaris exoculata dominates the fauna in deep-sea hydrothermal vent sites along the Mid-Atlantic Ridge (depth, 2,320 m). Here, we identified and biochemically characterized three carboxyl esterases from microbial communities inhabiting the R. exoculata gill that were isolated by naive screens of a gill chamber metagenomic library. These proteins exhibit low to moderate identity to known esterase sequences (<= 52%) and to each other (11.9 to 63.7%) and appear to have originated from unknown species or from genera of Proteobacteria related to Thiothrix/Leucothrix (MGS-RG1/RG2) and to the Rhodobacteraceae group (MGS-RG3). A library of 131 esters and 31 additional esterase/lipase preparations was used to evaluate the activity profiles of these enzymes. All 3 of these enzymes had greater esterase than lipase activity and exhibited specific activities with ester substrates (<= 356 U mg(-1)) in the range of similar enzymes. MGS-RG3 was inhibited by salts and pressure and had a low optimal temperature (30 degrees C), and its substrate profile clustered within a group of low-activity and substrate-restricted marine enzymes. In contrast, MGS-RG1 and MGS-RG2 were most active at 45 to 50 degrees C and were salt activated and barotolerant. They also exhibited wider substrate profiles that were close to those of highly active promiscuous enzymes from a marine hydrothermal vent (MGS-RG2) and from a cold brackish lake (MGS-RG1). The data presented are discussed in the context of promoting the examination of enzyme activities of taxa found in habitats that have been neglected for enzyme prospecting; the enzymes found in these taxa may reflect distinct habitat-specific adaptations and may constitute new sources of rare reaction specificities.
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- 2015
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122. The ocean sampling day consortium
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Kopf, Anna, Bicak, Mesude, Kottmann, Renzo, Schnetzer, Julia, Kostadinov, Ivaylo, Lehmann, Katja, Fernandez-Guerra, Antonio, Jeanthon, Christian, Rahav, Eyal, Ullrich, Matthias S., Wichels, Antje, Gerdts, Gunnar, Polymenakou, Paraskevi, Kotoulas, Georgios, Siam, Rania, Abdallah, Rehab Z., Sonnenschein, Eva C., Cariou, Thierry, O’Gara, Fergal, Jackson, Stephen, Orlic, Sandi, Steinke, Michael, Busch, Julia, Duarte, Bernardo, Caçador, Isabel, Canning-Clode, Joao, Bobrova, Oleksandra, Marteinsson, Viggo, Reynisson, Eyjolfur, Loureiro, Clara Magalhaes, Luna, Gian Marco, Quero, Grazia Marina, Loscher, Carolin R., Kremp, Anke, DeLorenzo, Marie E., Øvreås, Lise, Tolman, Jennifer, LaRoche, Julie, Penna, Antonella, Frischer, Marc, Davis, Timothy, Katherine, Barker, Meyer, Christopher P., Ramos, Sandra, Magalhaes, Catarina, Jude-Lemeilleur, Florence, Aguirre-Macedo, Ma Leopoldina, Wang, Shiao, Poulton, Nicole, Jones, Scott, Collin, Rachel, Fuhrman, Jed A., Conan, Pascal, Alonso, Cecilia, Stambler, Noga, Goodwin, Kelly, Yakimov, Michail M., Baltar, Federico, Bodrossy, Levente, Van De Kamp, Jodie, Frampton, Dion M. F., Ostrowski, Martin, Van Ruth, Paul, Malthouse, Paul, Claus, Simon, Deneudt, Klaas, Mortelmans, Jonas, Pitois, Sophie, Wallom, David, Salter, Ian, Costa, Rodrigo, Schroeder, Declan C., Kandil, Mahrous M., Amaral, Valentina, Biancalana, Florencia, Santana, Rafael, Pedrotti, Maria Luiza, Yoshida, Takashi, Ogata, Hiroyuki, Ingleton, Tim, Munnik, Kate, Rodriguez-Ezpeleta, Naiara, Berteaux-Lecellier, Veronique, Wecker, Patricia, Cancio, Ibon, Vaulot, Daniel, Bienhold, Christina, Ghazal, Hassan, Chaouni, Bouchra, Essayeh, Soumya, Ettamimi, Sara, Zaid, El Houcine, Boukhatem, Noureddine, Bouali, Abderrahim, Chahboune, Rajaa, Barrijal, Said, Timinouni, Mohammed, El Otmani, Fatima, Bennani, Mohamed, Mea, Marianna, Todorova, Nadezhda, Karamfilov, Ventzislav, ten Hoopen, Petra, Cochrane, Guy R., L’Haridon, Stephane, Bizsel, Kemal Can, Vezzi, Alessandro, Lauro, Federico M., Martin, Patrick, Jensen, Rachelle M., Hinks, Jamie, Gebbels, Susan, Rosselli, Riccardo, De Pascale, Fabio, Schiavon, Riccardo, dos Santos, Antonina, Villar, Emilie, Pesant, Stephane, Cataletto, Bruno, Malfatti, Francesca, Edirisinghe, Ranjith, Herrera Silveira, Jorge A., Barbier, Michele, Turk, Valentina, Tinta, Tinkara, Fuller, Wayne J., Salihoglu, Ilkay, Serakinci, Nedime, Ergoren, Mahmut Cerkez, Bresnan, Eileen, Iriberri, Juan, Fronth Nyhus, Paul Anders, Bente, Edvardsen, Karlsen, Hans Erik, Golyshin, Peter N., Gasol, Josep M., Moncheva, Snejana, Dzhembekova, Nina, Johnson, Zackary, Sinigalliano, Christopher D., Gidley, Maribeth Louise, Zingone, Adriana, Danovaro, Roberto, Tsiamis, Georgios, Clark, Melody S., Costa, Ana Cristina, El Bour, Monia, Martins, Ana M., Collins, R. Eric, Ducluzeau, Anne-Lise, Martinez, Jonathan, Costello, Mark J., Amaral-Zettler, Linda A., Gilbert, Jack A., Davies, Neil, Field, Dawn, Glockner, Frank Oliver, Kopf, Anna, Bicak, Mesude, Kottmann, Renzo, Schnetzer, Julia, Kostadinov, Ivaylo, Lehmann, Katja, Fernandez-Guerra, Antonio, Jeanthon, Christian, Rahav, Eyal, Ullrich, Matthias S., Wichels, Antje, Gerdts, Gunnar, Polymenakou, Paraskevi, Kotoulas, Georgios, Siam, Rania, Abdallah, Rehab Z., Sonnenschein, Eva C., Cariou, Thierry, O’Gara, Fergal, Jackson, Stephen, Orlic, Sandi, Steinke, Michael, Busch, Julia, Duarte, Bernardo, Caçador, Isabel, Canning-Clode, Joao, Bobrova, Oleksandra, Marteinsson, Viggo, Reynisson, Eyjolfur, Loureiro, Clara Magalhaes, Luna, Gian Marco, Quero, Grazia Marina, Loscher, Carolin R., Kremp, Anke, DeLorenzo, Marie E., Øvreås, Lise, Tolman, Jennifer, LaRoche, Julie, Penna, Antonella, Frischer, Marc, Davis, Timothy, Katherine, Barker, Meyer, Christopher P., Ramos, Sandra, Magalhaes, Catarina, Jude-Lemeilleur, Florence, Aguirre-Macedo, Ma Leopoldina, Wang, Shiao, Poulton, Nicole, Jones, Scott, Collin, Rachel, Fuhrman, Jed A., Conan, Pascal, Alonso, Cecilia, Stambler, Noga, Goodwin, Kelly, Yakimov, Michail M., Baltar, Federico, Bodrossy, Levente, Van De Kamp, Jodie, Frampton, Dion M. F., Ostrowski, Martin, Van Ruth, Paul, Malthouse, Paul, Claus, Simon, Deneudt, Klaas, Mortelmans, Jonas, Pitois, Sophie, Wallom, David, Salter, Ian, Costa, Rodrigo, Schroeder, Declan C., Kandil, Mahrous M., Amaral, Valentina, Biancalana, Florencia, Santana, Rafael, Pedrotti, Maria Luiza, Yoshida, Takashi, Ogata, Hiroyuki, Ingleton, Tim, Munnik, Kate, Rodriguez-Ezpeleta, Naiara, Berteaux-Lecellier, Veronique, Wecker, Patricia, Cancio, Ibon, Vaulot, Daniel, Bienhold, Christina, Ghazal, Hassan, Chaouni, Bouchra, Essayeh, Soumya, Ettamimi, Sara, Zaid, El Houcine, Boukhatem, Noureddine, Bouali, Abderrahim, Chahboune, Rajaa, Barrijal, Said, Timinouni, Mohammed, El Otmani, Fatima, Bennani, Mohamed, Mea, Marianna, Todorova, Nadezhda, Karamfilov, Ventzislav, ten Hoopen, Petra, Cochrane, Guy R., L’Haridon, Stephane, Bizsel, Kemal Can, Vezzi, Alessandro, Lauro, Federico M., Martin, Patrick, Jensen, Rachelle M., Hinks, Jamie, Gebbels, Susan, Rosselli, Riccardo, De Pascale, Fabio, Schiavon, Riccardo, dos Santos, Antonina, Villar, Emilie, Pesant, Stephane, Cataletto, Bruno, Malfatti, Francesca, Edirisinghe, Ranjith, Herrera Silveira, Jorge A., Barbier, Michele, Turk, Valentina, Tinta, Tinkara, Fuller, Wayne J., Salihoglu, Ilkay, Serakinci, Nedime, Ergoren, Mahmut Cerkez, Bresnan, Eileen, Iriberri, Juan, Fronth Nyhus, Paul Anders, Bente, Edvardsen, Karlsen, Hans Erik, Golyshin, Peter N., Gasol, Josep M., Moncheva, Snejana, Dzhembekova, Nina, Johnson, Zackary, Sinigalliano, Christopher D., Gidley, Maribeth Louise, Zingone, Adriana, Danovaro, Roberto, Tsiamis, Georgios, Clark, Melody S., Costa, Ana Cristina, El Bour, Monia, Martins, Ana M., Collins, R. Eric, Ducluzeau, Anne-Lise, Martinez, Jonathan, Costello, Mark J., Amaral-Zettler, Linda A., Gilbert, Jack A., Davies, Neil, Field, Dawn, and Glockner, Frank Oliver
- Abstract
© The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in GigaScience 4 (2015): 27, doi:10.1186/s13742-015-0066-5., Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial Biodiversity, Bioinformatics, Biotechnology) project to obtain a snapshot of the marine microbial biodiversity and function of the world’s oceans. It is a simultaneous global mega-sequencing campaign aiming to generate the largest standardized microbial data set in a single day. This will be achievable only through the coordinated efforts of an Ocean Sampling Day Consortium, supportive partnerships and networks between sites. This commentary outlines the establishment, function and aims of the Consortium and describes our vision for a sustainable study of marine microbial communities and their embedded functional traits., This work was supported by the Micro B3 project, which is funded from the European Union’s Seventh Framework Programme (FP7; Joint Call OCEAN.2011‐2: Marine microbial diversity – new insights into marine ecosystems functioning and its biotechnological potential) under the grant agreement no 287589.
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- 2015
123. Bacterial population and biodegradation potential in chronically crude oil-contaminated marine sediments are strongly linked to temperature
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Ministerio de Economía y Competitividad (España), Università degli Studi di Milano, European Commission, Bargiela, Rafael, Mapelli, Francesca, Rojo, David, Chouaia, Bessem, Tornés, Jesús, Borin, Sara, Richter, Michael, Pozo, Mercedes V. del, Cappello, Simone, Gertler, Christoph, Genovese, María, Denaro, Renata, Martínez-Martínez, Mónica, Fodelianakis, Stilianos, Amer, Ranya A., Bigazzi, David, Han, Xifang, Chen, Jianwei, Chernikova, Tatyana, Golyshina, Olga V., Mahjoubi, Mouna, Jaouanil, Atef, Benzha, Fatima, Magagnini, Mirko, Hussein, Emad, Al-Horani, Fuad, Cherifc, Ameur, Blaghen, Mohamed, Abdel-Fattah, Yasser R, Kalogerakis, Nicolas, Barbas, Coral, Malkawi, Hanan I., Golyshin, Peter N., Yakimov, Michail M., Daffonchio, Daniele, Ferrer, Manuel, Ministerio de Economía y Competitividad (España), Università degli Studi di Milano, European Commission, Bargiela, Rafael, Mapelli, Francesca, Rojo, David, Chouaia, Bessem, Tornés, Jesús, Borin, Sara, Richter, Michael, Pozo, Mercedes V. del, Cappello, Simone, Gertler, Christoph, Genovese, María, Denaro, Renata, Martínez-Martínez, Mónica, Fodelianakis, Stilianos, Amer, Ranya A., Bigazzi, David, Han, Xifang, Chen, Jianwei, Chernikova, Tatyana, Golyshina, Olga V., Mahjoubi, Mouna, Jaouanil, Atef, Benzha, Fatima, Magagnini, Mirko, Hussein, Emad, Al-Horani, Fuad, Cherifc, Ameur, Blaghen, Mohamed, Abdel-Fattah, Yasser R, Kalogerakis, Nicolas, Barbas, Coral, Malkawi, Hanan I., Golyshin, Peter N., Yakimov, Michail M., Daffonchio, Daniele, and Ferrer, Manuel
- Abstract
Two of the largest crude oil-polluted areas in the world are the semi-enclosed Mediterranean and Red Seas, but the effect of chronic pollution remains incompletely understood on a large scale. We compared the influence of environmental and geographical constraints and anthropogenic forces (hydrocarbon input) on bacterial communities in eight geographically separated oil-polluted sites along the coastlines of the Mediterranean and Red Seas. The differences in community compositions and their biodegradation potential were primarily associated (Pâ €‰
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- 2015
124. Metaproteomics and metabolomics analyses of chronically petroleum-polluted sites reveal the importance of general anaerobic processes uncoupled with degradation
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European Commission, Ministerio de Economía y Competitividad (España), Bargiela, Rafael, Herbst, Florian‐Alexander, Martínez-Martínez, Mónica, Seifert, Jana, Rojo, David, Cappello, Simone, Genovese, María, Crisafi, Francesca, Denaro, Renata, Chernikova, Tatyana, Barbas, Coral, Bergen, Martin von, Yakimov, Michail M., Ferrer, Manuel, Golyshin, Peter N., European Commission, Ministerio de Economía y Competitividad (España), Bargiela, Rafael, Herbst, Florian‐Alexander, Martínez-Martínez, Mónica, Seifert, Jana, Rojo, David, Cappello, Simone, Genovese, María, Crisafi, Francesca, Denaro, Renata, Chernikova, Tatyana, Barbas, Coral, Bergen, Martin von, Yakimov, Michail M., Ferrer, Manuel, and Golyshin, Peter N.
- Abstract
Crude oil is one of the most important natural assets for humankind, yet it is a major environmental pollutant, notably in marine environments. One of the largest crude oil polluted areas in the word is the semi‐enclosed Mediterranean Sea, in which the metabolic potential of indigenous microbial populations towards the large‐scale chronic pollution is yet to be defined, particularly in anaerobic and micro‐aerophilic sites. Here, we provide an insight into the microbial metabolism in sediments from three chronically polluted marine sites along the coastline of Italy: the Priolo oil terminal/refinery site (near Siracuse, Sicily), harbour of Messina (Sicily) and shipwreck of MT Haven (near Genoa). Using shotgun metaproteomics and community metabolomics approaches, the presence of 651 microbial proteins and 4776 metabolite mass features have been detected in these three environments, revealing a high metabolic heterogeneity between the investigated sites. The proteomes displayed the prevalence of anaerobic metabolisms that were not directly related with petroleum biodegradation, indicating that in the absence of oxygen, biodegradation is significantly suppressed. This suppression was also suggested by examining the metabolome patterns. The proteome analysis further highlighted the metabolic coupling between methylotrophs and sulphate reducers in oxygen‐depleted petroleum‐polluted sediments.
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- 2015
125. Microbial community of the deep-sea brine Lake Kryos seawater-brine interface is active below the chaotropicity limit of life as revealed by recovery of mRNA
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Centre National de la Recherche Scientifique (France), European Commission, Department of Agriculture and Rural Development (Northern Ireland), Yakimov, Michail M., Cono, Violetta la, Spada, G., Bortoluzzi, Stefania, Messina, Enzo, Smedile, Francesco, Arcadi, Erika, Borghini, M., Ferrer, Manuel, Schmitt-Kopplin, Philippe, Hertkorn, Norbert, Cray, J. A., Hallsworth, J. E., Golyshin, Peter N., Giuliano, Laura, Centre National de la Recherche Scientifique (France), European Commission, Department of Agriculture and Rural Development (Northern Ireland), Yakimov, Michail M., Cono, Violetta la, Spada, G., Bortoluzzi, Stefania, Messina, Enzo, Smedile, Francesco, Arcadi, Erika, Borghini, M., Ferrer, Manuel, Schmitt-Kopplin, Philippe, Hertkorn, Norbert, Cray, J. A., Hallsworth, J. E., Golyshin, Peter N., and Giuliano, Laura
- Abstract
Within the complex of deep, hypersaline anoxic lakes (DHALs) of the Mediterranean Ridge, we identified a new, unexplored DHAL and named it ‘Lake Kryos’ after a nearby depression. This lake is filled with magnesium chloride (MgCl2)‐rich, athalassohaline brine (salinity > 470 practical salinity units), presumably formed by the dissolution of Messinian bischofite. Compared with the DHAL Discovery, it contains elevated concentrations of kosmotropic sodium and sulfate ions, which are capable of reducing the net chaotropicily of MgCl2‐rich solutions. The brine of Lake Kryos may therefore be biologically permissive at MgCl2 concentrations previously considered incompatible with life. We characterized the microbiology of the seawater–Kryos brine interface and managed to recover mRNA from the 2.27–3.03 M MgCl2 layer (equivalent to 0.747–0.631 water activity), thereby expanding the established chaotropicity window‐for‐life. The primary bacterial taxa present there were Kebrit Deep Bacteria 1 candidate division and DHAL‐specific group of organisms, distantly related to Desulfohalobium. Two euryarchaeal candidate divisions, Mediterranean Sea Brine Lakes group 1 and halophilic cluster 1, accounted for > 85% of the rRNA‐containing archaeal clones derived from the 2.27–3.03 M MgCl2 layer, but were minority community‐members in the overlying interface‐layers. These findings shed light on the plausibility of life in highly chaotropic environments, geochemical windows for microbial extremophiles, and have implications for habitability elsewhere in the Solar System.
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- 2015
126. Identification and characterization of carboxyl esterases of gill chamber-associated microbiota in the deep-sea shrimp Rimicaris exoculata by using functional metagenomics
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European Commission, Ministerio de Economía y Competitividad (España), Government of Canada, Ontario Genomics Institute, National Institutes of Health (US), Alcaide, María, Tchigvintsev, Anatoli, Martínez-Martínez, Mónica, Popovic, Ana, Reva, Oleg, Lafraya Aguado, Álvaro, Bargiela, Rafael, Nechitaylo, Taras Y., Matesanz, Ruth, Cambon-Bonavita, M. A., Jebbar, M., Yakimov, Michail M., Savchenko, Alexei, Golyshina, Olga V., Yakunin, Alexander F., Golyshin, Peter N., Ferrer, Manuel, European Commission, Ministerio de Economía y Competitividad (España), Government of Canada, Ontario Genomics Institute, National Institutes of Health (US), Alcaide, María, Tchigvintsev, Anatoli, Martínez-Martínez, Mónica, Popovic, Ana, Reva, Oleg, Lafraya Aguado, Álvaro, Bargiela, Rafael, Nechitaylo, Taras Y., Matesanz, Ruth, Cambon-Bonavita, M. A., Jebbar, M., Yakimov, Michail M., Savchenko, Alexei, Golyshina, Olga V., Yakunin, Alexander F., Golyshin, Peter N., and Ferrer, Manuel
- Abstract
The shrimp Rimicaris exoculata dominates the fauna in deep-sea hydrothermal vent sites along the Mid-Atlantic Ridge (depth, 2,320 m). Here, we identified and biochemically characterized three carboxyl esterases from microbial communities inhabiting the R. exoculata gill that were isolated by naive screens of a gill chamber metagenomic library. These proteins exhibit low to moderate identity to known esterase sequences (≤52%) and to each other (11.9 to 63.7%) and appear to have originated from unknown species or from genera of Proteobacteria related to Thiothrix/Leucothrix (MGS-RG1/RG2) and to the Rhodobacteraceae group (MGS-RG3). A library of 131 esters and 31 additional esterase/lipase preparations was used to evaluate the activity profiles of these enzymes. All 3 of these enzymes had greater esterase than lipase activity and exhibited specific activities with ester substrates (≤356 U mg-1) in the range of similar enzymes. MGS-RG3 was inhibited by salts and pressure and had a low optimal temperature (30°C), and its substrate profile clustered within a group of low-activity and substrate-restricted marine enzymes. In contrast, MGS-RG1 and MGS-RG2 were most active at 45 to 50°C and were salt activated and barotolerant. They also exhibited wider substrate profiles that were close to those of highly active promiscuous enzymes from a marine hydrothermal vent (MGS-RG2) and from a cold brackish lake (MGS-RG1). The data presented are discussed in the context of promoting the examination of enzyme activities of taxa found in habitats that have been neglected for enzyme prospecting; the enzymes found in these taxa may reflect distinct habitat-specific adaptations and may constitute new sources of rare reaction specificities.
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- 2015
127. Bioremediation of oil polluted marine sediments: A bio-engineering treatment
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Cappello, Simone, Calogero, Rosario, Santisi, Santina, Genovese, Maria, Denaro, Renata, Genovese, Lucrezia, Giuliano, Laura, Mancini, Giuseppe, Yakimov, Michail M., Cappello, Simone, Calogero, Rosario, Santisi, Santina, Genovese, Maria, Denaro, Renata, Genovese, Lucrezia, Giuliano, Laura, Mancini, Giuseppe, and Yakimov, Michail M.
- Abstract
The fate of hydrocarbon pollutants and the development of oil-degrading indigenous marine bacteria in contaminated sediments are strongly influenced by abiotic factors such as temperature, low oxygen levels, and nutrient availability. In this work, the effects of different biodegradation processes (bioremediation) on oil-polluted anoxic sediments were analyzed. In particular, as a potential bioremediation strategy for polluted sediments, we applied a prototype of the “Modular Slurry System” (MSS), allowing containment of the sediments and their physical-chemical treatment (by air insufflations, temperature regulation, and the use of a slow-release fertilizer). Untreated polluted sediments served as the blank in a non-controlled experiment. During the experimental period (30 days), bacterial density and biochemical oxygen demand were measured and functional genes were identified by screening. Quantitative measurements of pollutants and an eco-toxicological analysis (mortality of Corophium orientale) were carried out at the beginning and end of the experiments. The results demonstrated the high biodegradative capability achieved with the proposed technology and its strong reduction of pollutant concentrations and thus toxicity. [Int Microbiol 2015; 18(2):127-134]Keywords: bioremediation · biostimulation · chronically polluted sediments · oil-degrading bacteria · Corophium orientale (Crustacea, Amphipoda)
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- 2015
128. Contribution of Bicarbonate Assimilation to Carbon Pool Dynamics in the Deep Mediterranean Sea and Cultivation of Actively Nitrifying and CO2-Fixing Bathypelagic Prokaryotic Consortia.
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La Cono, Violetta, Ruggeri, Gioachino, Azzaro, Maurizio, Crisafi, Francesca, Decembrini, Franco, Denaro, Renata, La Spada, Gina, Maimone, Giovanna, Monticelli, Luis S., Smedile, Francesco, Giuliano, Laura, and Yakimov, Michail M.
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NITRIFYING bacteria ,PROKARYOTIC genomes - Abstract
Covering two-thirds of our planet, the global deep ocean plays a central role in supporting life on Earth. Among other processes, this biggest ecosystem buffers the rise of atmospheric CO
2 . Despite carbon sequestration in the deep ocean has been known for a long time, microbial activity in the meso- and bathypelagic realm via the "assimilation of bicarbonate in the dark" (ABD) has only recently been described in more details. Based on recent findings, this process seems primarily the result of chemosynthetic and anaplerotic reactions driven by different groups of deep-sea prokaryoplankton. We quantified bicarbonate assimilation in relation to total prokaryotic abundance, prokaryotic heterotrophic production and respiration in the meso- and bathypelagic Mediterranean Sea. The measured ABD values, ranging from 133 to 370 μg Cm-3 d-1 , were among the highest ones reported worldwide for similar depths, likely due to the elevated temperature of the deepMediterranean Sea (13-14°C also at abyssal depths). Integrated over the dark water column (≥200m depth), bicarbonate assimilation in the deep-sea ranged from 396 to 873mg C m-2 d-1 . This quantity of produced de novo organic carbon amounts to about 85-424% of the phytoplankton primary production and covers up to 62% of deep-sea prokaryotic total carbon demand. Hence, the ABD process in the meso- and bathypelagic Mediterranean Sea might substantially contribute to the inorganic and organic pool and significantly sustain the deep-sea microbial food web. To elucidate the ABD key-players, we established three actively nitrifying and CO2 -fixing prokaryotic enrichments. Consortia were characterized by the co-occurrence of chemolithoautotrophic Thaumarchaeota and chemoheterotrophic proteobacteria. One of the enrichments, originated from Ionian bathypelagic waters (3,000m depth) and supplemented with low concentrations of ammonia, was dominated by the Thaumarchaeota "low-ammonia-concentration" deep-sea ecotype, an enigmatic and ecologically important group of organisms, uncultured until this study. [ABSTRACT FROM AUTHOR]- Published
- 2018
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129. Relationships between Substrate Promiscuity and Chiral Selectivity of Esterases from Phylogenetically and Environmentally Diverse Microorganisms.
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Coscolín, Cristina, Martínez-Martínez, Mónica, Chow, Jennifer, Bargiela, Rafael, García-Moyano, Antonio, Bjerga, Gro E. K., Bollinger, Alexander, Stokke, Runar, Steen, Ida H., Golyshina, Olga V., Yakimov, Michail M., Jaeger, Karl-Erich, Yakunin, Alexander F., Streit, Wolfgang R., Golyshin, Peter N., and Ferrer, Manuel
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BIOCHEMICAL substrates ,CHIRALITY - Abstract
Substrate specificity and selectivity of a biocatalyst are determined by the protein sequence and structure of its active site. Finding versatile biocatalysts acting against multiple substrates while at the same time being chiral selective is of interest for the pharmaceutical and chemical industry. However, the relationships between these two properties in naturalmicrobial enzymes remain underexplored. Here, we performed an experimental analysis of substrate promiscuity and chiral selectivity in a set of 145 purified esterases fromphylogenetically and environmentally diversemicroorganisms, which were assayed against 96 diverse esters, 20 of which were enantiomers. Our results revealed a negative correlation between substrate promiscuity and chiral selectivity in the evaluated enzymes. Esterases displaying prominent substrate promiscuity and large catalytic environments are characterized by low chiral selectivity, a feature that has limited commercial value. Although a low level of substrate promiscuity does not guarantee high chiral selectivity, the probability that esterases with smaller active sites possess chiral selectivity factors of interest for industry (>25) is significantly higher than for promiscuous enzymes. Together, the present study unambiguously demonstrates that promiscuous and selective esterases appear to be rare in nature and that substrate promiscuity can be used as an indicator of the chiral selectivity level of esterases, and vice versa. [ABSTRACT FROM AUTHOR]
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- 2018
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130. Intrinsic bioremediation potential of a chronically polluted marine coastal area
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Catania, Valentina, primary, Santisi, Santina, additional, Signa, Geraldina, additional, Vizzini, Salvatrice, additional, Mazzola, Antonio, additional, Cappello, Simone, additional, Yakimov, Michail M., additional, and Quatrini, Paola, additional
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- 2015
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131. Alcanivoraceae fam. nov.
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Golyshin, Peter N., primary, Harayama, Shigeaki, additional, Timmis, Kenneth N., additional, and Yakimov, Michail M., additional
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- 2015
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132. Alcanivorax
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Golyshin, Peter N., primary, Harayama, Shigeaki, additional, Timmis, Kenneth N., additional, and Yakimov, Michail M., additional
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- 2015
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133. Metaproteomics and metabolomics analyses of chronically petroleum‐polluted sites reveal the importance of general anaerobic processes uncoupled with degradation
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Bargiela, Rafael, primary, Herbst, Florian‐Alexander, additional, Martínez‐Martínez, Mónica, additional, Seifert, Jana, additional, Rojo, David, additional, Cappello, Simone, additional, Genovese, María, additional, Crisafi, Francesca, additional, Denaro, Renata, additional, Chernikova, Tatyana N., additional, Barbas, Coral, additional, Bergen, Martin, additional, Yakimov, Michail M., additional, Ferrer, Manuel, additional, and Golyshin, Peter N., additional
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- 2015
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134. Hydrostatic pressure effects membrane and storage lipid compositions of the piezotolerant hydrocarbon-degrading Marinobacter hydrocarbonoclasticus strain #5
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Grossi, Vincent, Yakimov, Michail M., Al Ali, Badr, Tapilatu, Yosmina, CUNY, Philippe, Goutx, Madeleine, La Cono, Violetta, Giuliano, Laura, TAMBURINI, Christian, PaleoEnvironnements et PaleobioSphere (PEPS), Institut national des sciences de l'Univers (INSU - CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Insitute for Coastal Marine Environment, Consiglio Nazionale delle Ricerche (CNR), Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines (LMGEM), Centre National de la Recherche Scientifique (CNRS)-Université de la Méditerranée - Aix-Marseille 2, Mediterranean Science Commission, Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), Université de la Méditerranée - Aix-Marseille 2-Centre National de la Recherche Scientifique (CNRS), European Science Foundation : MIDDLE 06-EuroDEEP-FP-004, CNRS-INSU : BIOHYDEX EC2CO, and National Council of Research (CNR)
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[SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere ,DEEP-SEA BACTERIUM ,TRIACYLGLYCEROL BIOSYNTHESIS ,MARINE-SEDIMENTS ,GROWTH TEMPERATURE ,MEDITERRANEAN SEA ,BIODEGRADATION ,FATTY-ACIDS ,WAX ESTER ,PROKARYOTES ,BAROPHILIC BACTERIA ,ComputingMilieux_MISCELLANEOUS - Abstract
International audience; A new piezotolerant alkane-degrading bacterium (Marinobacter hydrocarbonoclasticus strain #5) was isolated from deep (3475 m) Mediterranean seawater and grown at atmospheric pressure (0.1 MPa) and at 35 MPa with hexadecane as sole source of carbon and energy. Modification of the hydrostatic pressure influenced neither the growth rate nor the amount of degraded hexadecane 90%) during 13 days of incubation. However, the lipid composition of the cells sharply differed under both pressure conditions. At 0.1 MPa, M. hydrocarbonoclasticus #5 biosynthesized large amounts 62% of the total cellular lipids) of hexadecane-derived wax esters (WEs), which accumulated in the cells under the form of individual lipid bodies. Intracellular WEs were also synthesized at 35 MPa, but their proportion was half that at 0.1 MPa. This lower WE content at high pressure was balanced by an increase in the total cellular phospholipid content. The chemical composition of WEs formed under both pressure conditions also strongly differed. Saturated WEs were preferentially formed at 0.1 MPa whereas diunsaturated WEs dominated at 35 MPa. This increase of the unsaturation ratio of WEs resembled the one classically observed for bacterial membrane lipid homeostasis. Remarkably, the unsaturation ratio of membrane fatty acids of M. hydrocarbonoclasticus grown at 35 MPa was only slightly higher than at 0.1 MPa. Overall, the results suggest that intracellular WEs and phospholipids play complementary roles in the physiological adaptation of strain #5 to different hydrostatic pressures.
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- 2010
135. Bacterial population and biodegradation potential in chronically crude oil-contaminated marine sediments are strongly linked to temperature
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Bargiela, Rafael, primary, Mapelli, Francesca, additional, Rojo, David, additional, Chouaia, Bessem, additional, Tornés, Jesús, additional, Borin, Sara, additional, Richter, Michael, additional, Del Pozo, Mercedes V., additional, Cappello, Simone, additional, Gertler, Christoph, additional, Genovese, María, additional, Denaro, Renata, additional, Martínez-Martínez, Mónica, additional, Fodelianakis, Stilianos, additional, Amer, Ranya A., additional, Bigazzi, David, additional, Han, Xifang, additional, Chen, Jianwei, additional, Chernikova, Tatyana N., additional, Golyshina, Olga V., additional, Mahjoubi, Mouna, additional, Jaouanil, Atef, additional, Benzha, Fatima, additional, Magagnini, Mirko, additional, Hussein, Emad, additional, Al-Horani, Fuad, additional, Cherif, Ameur, additional, Blaghen, Mohamed, additional, Abdel-Fattah, Yasser R., additional, Kalogerakis, Nicolas, additional, Barbas, Coral, additional, Malkawi, Hanan I., additional, Golyshin, Peter N., additional, Yakimov, Michail M., additional, Daffonchio, Daniele, additional, and Ferrer, Manuel, additional
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- 2015
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136. Biodegradation of crude oil by individual bacterial strains and a mixed bacterial consortium
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Santisi, Santina, primary, Cappello, Simone, additional, Catalfamo, Maurizio, additional, Mancini, Giuseppe, additional, Hassanshahian, Mehdi, additional, Genovese, Lucrezia, additional, Giuliano, Laura, additional, and Yakimov, Michail M., additional
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- 2015
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137. Elemental sulfur and acetate can support life of a novel strictly anaerobic haloarchaeon
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Sorokin, Dimitry Y, primary, Kublanov, Ilya V, additional, Gavrilov, Sergei N, additional, Rojo, David, additional, Roman, Pawel, additional, Golyshin, Peter N, additional, Slepak, Vladlen Z, additional, Smedile, Francesco, additional, Ferrer, Manuel, additional, Messina, Enzo, additional, La Cono, Violetta, additional, and Yakimov, Michail M, additional
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- 2015
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138. Identification and Characterization of Carboxyl Esterases of Gill Chamber-Associated Microbiota in the Deep-Sea Shrimp Rimicaris exoculata by Using Functional Metagenomics
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Alcaide, María, primary, Tchigvintsev, Anatoli, additional, Martínez-Martínez, Mónica, additional, Popovic, Ana, additional, Reva, Oleg N., additional, Lafraya, Álvaro, additional, Bargiela, Rafael, additional, Nechitaylo, Taras Y., additional, Matesanz, Ruth, additional, Cambon-Bonavita, Marie-Anne, additional, Jebbar, Mohamed, additional, Yakimov, Michail M., additional, Savchenko, Alexei, additional, Golyshina, Olga V., additional, Yakunin, Alexander F., additional, Golyshin, Peter N., additional, and Ferrer, Manuel, additional
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- 2015
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139. Comparison of Niskin vs. in situ approaches for analysis of gene expression in deep Mediterranean Sea water samples
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Edgcomb, Virginia P., Taylor, Craig D., Pachiadaki, Maria G., Honjo, Susumu, Engstrom, Ivory B., Yakimov, Michail M., Edgcomb, Virginia P., Taylor, Craig D., Pachiadaki, Maria G., Honjo, Susumu, Engstrom, Ivory B., and Yakimov, Michail M.
- Abstract
Author Posting. © The Author(s), 2014. This is the author's version of the work. It is posted here by permission of Elsevier for personal use, not for redistribution. The definitive version was published in Deep Sea Research Part II: Topical Studies in Oceanography 129 (2016): 213-222, doi:10.1016/j.dsr2.2014.10.020., Obtaining an accurate picture of microbial processes occurring in situ is essential for our understanding of marine biogeochemical cycles of global importance. Water samples are typically collected at depth and returned to the sea surface for processing and downstream experiments. Metatranscriptome analysis is one powerful approach for investigating metabolic activities of microorganisms in their habitat and which can be informative for determining responses of microbiota to disturbances such as the Deepwater Horizon oil spill. For studies of microbial processes occurring in the deep sea, however, sample handling, pressure, and other changes during sample recovery can subject microorganisms to physiological changes that alter the expression profile of labile messenger RNA. Here we report a comparison of gene expression profiles for whole microbial communities in a bathypelagic water column sample collected in the Eastern Mediterranean Sea using Niskin bottle sample collection and a new water column sampler for studies of marine microbial ecology, the Microbial Sampler – In Situ Incubation Device (MS-SID). For some taxa, gene expression profiles from samples collected and preserved 33 in situ were significantly different from potentially more stressful Niskin sampling and 34 preservation on deck. Some categories of transcribed genes also appear to be affected by sample 35 handling more than others. This suggests that for future studies of marine microbial ecology, 36 particularly targeting deep sea samples, an in situ sample collection and preservation approach 37 should be considered., This research was funded by NSF OCE-1061774 to VE and CT, NSF DBI-0424599 to CT and NSF OCE-0849578 to VE and colleague J. Bernhard. Cruise participation was partially supported by Deutsche Forschungsgemeinschaft (DFG) grant STO414/10-1 to T. Stoeck.
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- 2014
140. Heterotrophic bicarbonate assimilation is the main process of de novo organic carbon synthesis in hadal zone of the Hellenic Trench, the deepest part of Mediterranean Sea
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Consiglio Nazionale delle Ricerche, European Commission, Ministerio de Economía y Competitividad (España), Yakimov, Michail M., Cono, Violetta la, Smedile, Francesco, Crisafi, Francesca, Arcadi, Erika, Leonardi, Marcella, Decembrini, Franco, Catalfamo, Maurizio, Bargiela, Rafael, Ferrer, Manuel, Golyshin, Peter N., Giuliano, Laura, Consiglio Nazionale delle Ricerche, European Commission, Ministerio de Economía y Competitividad (España), Yakimov, Michail M., Cono, Violetta la, Smedile, Francesco, Crisafi, Francesca, Arcadi, Erika, Leonardi, Marcella, Decembrini, Franco, Catalfamo, Maurizio, Bargiela, Rafael, Ferrer, Manuel, Golyshin, Peter N., and Giuliano, Laura
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Ammonium‐oxidizing chemoautotrophic members of Thaumarchaea are proposed to be the key players in the assimilation of bicarbonate in the dark (ABD). However, this process may also involve heterotrophic metabolic pathways, such as fixation of carbon dioxide (CO2) via various anaplerotic reactions. We collected samples from the depth of 4900 m at the Matapan‐Vavilov Deep (MVD) station (Hellenic Trench, Eastern Mediterranean) and used the multiphasic approach to study the ABD mediators in this deep‐sea ecosystem. At this depth, our analysis indicated the occurrence of actively CO2‐fixing heterotrophic microbial assemblages dominated by Gammaproteobacteria with virtually no Thaumarchaea present. [14C]‐bicarbonate incorporation experiments combined with shotgun [14C]‐proteomic analysis identified a series of proteins of gammaproteobacterial origin. More than quarter of them were closely related with Alteromonas macleodii ‘deep ecotype’ AltDE, the predominant organism in the microbial community of MVD. The present study demonstrated that in the aphotic/hadal zone of the Mediterranean Sea, the assimilation of bicarbonate is associated with both chemolithoauto‐ and heterotrophic ABD. In some deep‐sea areas, the latter may predominantly contribute to the de novo synthesis of organic carbon which points at the important and yet underestimated role heterotrophic bacterial populations can play the in global carbon cycle/sink in the ocean interior.
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- 2014
141. Functional enzyme diversity in a number of extreme and non-extreme environments
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European Commission, Ministerio de Economía y Competitividad (España), Pozo, Mercedes V. del, Martínez-Martínez, Mónica, Alcaide, María, Bargiela, Rafael, Chernikova, Tatyana, Golyshin, Peter N., Yakimov, Michail M., Mapelli, Francesca, Daffonchio, Daniele, Golyshina, Olga V., Ferrer, Manuel, European Commission, Ministerio de Economía y Competitividad (España), Pozo, Mercedes V. del, Martínez-Martínez, Mónica, Alcaide, María, Bargiela, Rafael, Chernikova, Tatyana, Golyshin, Peter N., Yakimov, Michail M., Mapelli, Francesca, Daffonchio, Daniele, Golyshina, Olga V., and Ferrer, Manuel
- Abstract
The collaborative projects, MAMBA, MAGICPAH, ULIXES, funded by the EU FP7 program, and the BIO2011- 25012 (funded by Spanish Ministry of Economy and Competitiveness) are focused on using environmental sites around the Planet (including soils, acid mines, superficial and deep seawater, etc.) as resources of novel microbial assemblages, gene sequences and enzyme activities, some of which could have potential scientific and industrial applications. Some of the environments, that included contaminated and concontaminated sites, may be inhabited by extremophiles that contains “extremozymes”. The investigation of their “extremozymes”, and their new functions and protein folds, and the correlation between those characteristics and environmental constraints is of interest for achieving the full understating of extreme ecosystem functioning. Here, using cultivation-independent techniques, and in particular, metagenomics, we have selected and analyzed microbial communities from various extreme and non extreme environments and provided a draft vision into their enzyme properties.
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- 2014
142. Alcanivorax borkumensis produces an extracellular siderophore in iron-limitation condition maintaining the hydrocarbon-degradation efficiency
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European Commission, Denaro, Renata, Crisafi, Francesca, Russo, D., Genovese, María, Messina, Enzo, Genovese, L., Carbone, M., Ciavatta, M. L., Ferrer, Manuel, Golyshin, Peter N., Yakimov, Michail M., European Commission, Denaro, Renata, Crisafi, Francesca, Russo, D., Genovese, María, Messina, Enzo, Genovese, L., Carbone, M., Ciavatta, M. L., Ferrer, Manuel, Golyshin, Peter N., and Yakimov, Michail M.
- Abstract
Obligate marine hydrocarbonoclastic bacteria possess genetic and physiological features to use hydrocarbons as sole source of carbon and to compete for the uptake of nutrients in usually nutrient-depleted marine habitats. In the present work we have studied the siderophore-based iron uptake systems in Alcanivorax borkumensis SK2 and their functioning during biodegradation of an aliphatic hydrocarbon, tetradecane, under iron limitation conditions. The antiSMASH analysis of SK2 genome revealed the presence of two different putative operons of siderophore synthetases. Search for the predicted core structures indicated that one siderophore is clearly affiliated to the family of complex oligopeptidic siderophores possessing an Orn-Ser-Orn carboxyl motif whereas the second one is likely to belong to the family of SA (salicylic acid)–based siderophores. Analyzing the supernatant of SK2 culture, an extracellular siderophore was identified and its structure was resolved. Thus, along with the recently described membrane-associated amphiphilic tetrapeptidic siderophore amphibactin, strain SK2 additionally produces an extracellular type of iron-chelating molecule with structural similarity to pseudomonins. Comparative Q-PCR analysis of siderophore synthetases demonstrated their significant up-regulation in iron-depleted medium. Different expression patterns were recorded for two operons during the early and late exponential phases of growth, suggesting a different function of these two siderophores under iron-depleted conditions.
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- 2014
143. Halorhabdus tiamatea: Proteogenomics and glycosidase activity measurements identify the first cultivated euryarchaeon from a deep-sea anoxic brine lake as potential polysaccharide degrader
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European Commission, Ministerio de Economía y Competitividad (España), Max Planck Society, Werner, Johannes, Ferrer, Manuel, Michel, Gurvan, Mann, Alexander J., Huang, Sixing, Juárez, Silvia, Ciordia, Sergio, Albar, Juan Pablo, Alcaide, María, Cono, Violetta la, Yakimov, Michail M., Antunes, Andrés, Taborda, Marco, Costa, Milton S. da, Hai, Tran, Glöckner, Frank Oliver, Golyshina, Olga V., Golyshin, Peter N., Teeling, Hanno, European Commission, Ministerio de Economía y Competitividad (España), Max Planck Society, Werner, Johannes, Ferrer, Manuel, Michel, Gurvan, Mann, Alexander J., Huang, Sixing, Juárez, Silvia, Ciordia, Sergio, Albar, Juan Pablo, Alcaide, María, Cono, Violetta la, Yakimov, Michail M., Antunes, Andrés, Taborda, Marco, Costa, Milton S. da, Hai, Tran, Glöckner, Frank Oliver, Golyshina, Olga V., Golyshin, Peter N., and Teeling, Hanno
- Abstract
Summary: Euryarchaea from the genus Halorhabdus have been found in hypersaline habitats worldwide, yet are represented by only two isolates: Halorhabdus utahensisAX-2T from the shallow Great Salt Lake of Utah, and Halorhabdus tiamateaSARL4BT from the Shaban deep-sea hypersaline anoxic lake (DHAL) in the Red Sea. We sequenced the H.tiamatea genome to elucidate its niche adaptations. Among sequenced archaea, H.tiamatea features the highest number of glycoside hydrolases, the majority of which were expressed in proteome experiments. Annotations and glycosidase activity measurements suggested an adaptation towards recalcitrant algal and plant-derived hemicelluloses. Glycosidase activities were higher at 2% than at 0% or 5% oxygen, supporting a preference for low-oxygen conditions. Likewise, proteomics indicated quinone-mediated electron transport at 2% oxygen, but a notable stress response at 5% oxygen. Halorhabdus tiamatea furthermore encodes proteins characteristic for thermophiles and light-dependent enzymes (e.g. bacteriorhodopsin), suggesting that H.tiamatea evolution was mostly not governed by a cold, dark, anoxic deep-sea habitat. Using enrichment and metagenomics, we could demonstrate presence of similar glycoside hydrolase-rich Halorhabdus members in the Mediterranean DHAL Medee, which supports that Halorhabdus species can occupy a distinct niche as polysaccharide degraders in hypersaline environments.
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- 2014
144. Quick stimulation of Alcanivorax sp. by bioemulsificant EPS2003 on microcosm oil spill simulation
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Cappello, Simone, primary, Genovese, Maria, additional, Denaro, Renata, additional, Santisi, Santina, additional, Volta, Anna, additional, Bonsignore, Martina, additional, Mancini, Giuseppe, additional, Giuliano, Laura, additional, Genovese, Lucrezia, additional, and Yakimov, Michail M., additional
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- 2014
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145. The Deep-Sea Polyextremophile Halobacteroides lacunaris TB21 Rough-Type LPS: Structure and Inhibitory Activity towards Toxic LPS.
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Di Lorenzo, Flaviana, Palmigiano, Angelo, Paciello, Ida, Pallach, Mateusz, Garozzo, Domenico, Bernardini, Maria-Lina, La Cono, Violetta, Yakimov, Michail M., Molinaro, Antonio, and Silipo, Alba
- Abstract
The structural characterization of the lipopolysaccharide (LPS) from extremophiles has important implications in several biomedical and therapeutic applications. The polyextremophile Gram-negative bacterium Halobacteroides lacunaris TB21, isolated from one of the most extreme habitats on our planet, the deep-sea hypersaline anoxic basin Thetis, represents a fascinating microorganism to investigate in terms of its LPS component. Here we report the elucidation of the full structure of the R-type LPS isolated from H. lacunaris TB21 that was attained through a multi-technique approach comprising chemical analyses, NMR spectroscopy, and Matrix-Assisted Laser Desorption Ionization (MALDI) mass spectrometry. Furthermore, cellular immunology studies were executed on the pure R-LPS revealing a very interesting effect on human innate immunity as an inhibitor of the toxic Escherichia coli LPS. [ABSTRACT FROM AUTHOR]
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- 2017
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146. Multiplication of microbes below 0.690 water activity: implications for terrestrial and extraterrestrial life
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Stevenson, Andrew, primary, Burkhardt, Jürgen, additional, Cockell, Charles S., additional, Cray, Jonathan A., additional, Dijksterhuis, Jan, additional, Fox‐Powell, Mark, additional, Kee, Terence P., additional, Kminek, Gerhard, additional, McGenity, Terry J., additional, Timmis, Kenneth N., additional, Timson, David J., additional, Voytek, Mary A., additional, Westall, Frances, additional, Yakimov, Michail M., additional, and Hallsworth, John E., additional
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- 2014
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147. The environment shapes microbial enzymes: five cold-active and salt-resistant carboxylesterases from marine metagenomes
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Tchigvintsev, Anatoli, primary, Tran, Hai, additional, Popovic, Ana, additional, Kovacic, Filip, additional, Brown, Greg, additional, Flick, Robert, additional, Hajighasemi, Mahbod, additional, Egorova, Olga, additional, Somody, Joseph C., additional, Tchigvintsev, Dmitri, additional, Khusnutdinova, Anna, additional, Chernikova, Tatyana N., additional, Golyshina, Olga V., additional, Yakimov, Michail M., additional, Savchenko, Alexei, additional, Golyshin, Peter N., additional, Jaeger, Karl-Erich, additional, and Yakunin, Alexander F., additional
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- 2014
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148. Using Real-time PCR to assess changes in the crude oil degrading microbial community in contaminated seawater mesocosms
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Hassanshahian, Mehdi, primary, Yakimov, Michail M., additional, Denaro, Renata, additional, Genovese, Maria, additional, and Cappello, Simone, additional
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- 2014
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149. Heterotrophic bicarbonate assimilation is the main process ofde novoorganic carbon synthesis in hadal zone of the Hellenic Trench, the deepest part of Mediterranean Sea
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Yakimov, Michail M., primary, La Cono, Violetta, additional, Smedile, Francesco, additional, Crisafi, Francesca, additional, Arcadi, Erika, additional, Leonardi, Marcella, additional, Decembrini, Franco, additional, Catalfamo, Maurizio, additional, Bargiela, Rafael, additional, Ferrer, Manuel, additional, Golyshin, Peter N., additional, and Giuliano, Laura, additional
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- 2014
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150. Unveiling microbial activities along the halocline of Thetis, a deep-sea hypersaline anoxic basin
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Pachiadaki, Maria G, primary, Yakimov, Michail M, additional, LaCono, Violetta, additional, Leadbetter, Edward, additional, and Edgcomb, Virginia, additional
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- 2014
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