Consulta: creatorFacets:"Jebbar, Mohamed"
Registros recuperados: 41
Data/hora: 18/06/2024 14:48:46

Complete Genome Sequence of the Hyperthermophilic, Piezophilic, Heterotrophic, and Carboxydotrophic Archaeon Thermococcus barophilus MP
Provedor de dados: Institutional Archive of Ifreme (ArchiMer)
Autores: Vannier, Pauline; Marteinsson, Viggo Thor; Fridjonsson, Olafur Hedinn; Oger, Philippe; Jebbar, Mohamed.
Thermococcus barophilus is a hyperthermophilic, anaerobic, mixed heterotrophic, and carboxydotrophic euryarchaeon isolated from the deep sea hydrothermal vent Snakepit site on the mid-Atlantic ridge at a depth of 3,550 m. T. barophilus is the first true piezophilic, hyperthermophilic archaeon isolated, having an optimal growth at 40 MPa. Here we report the complete genome sequence of strain MP, the type strain of T. barophilus. The genome data reveal a close proximity with Thermococcus sibiricus, another Thermococcus isolated from the deep biosphere and a possible connection to life in the depths.
Tipo: Text
Ano: 2011
URL: http://archimer.ifremer.fr/doc/00031/14185/11865.pdf

DNA extractions from deep subseafloor sediments: Novel cryogenic-mill-based procedure and comparison to existing protocols
Provedor de dados: Institutional Archive of Ifreme (ArchiMer)
Autores: Alain, Karine; Callac, Nolwenn; Ciobanu, Maria Cristina; Reynaud, Yann; Duthoit, Frederique; Jebbar, Mohamed.
Extracting DNA from deep subsurface sediments is challenging given the complexity of sediments types, low bio-masses, resting structures (spores, cysts) frequently encountered in deep sediments, and the potential presence of enzymatic inhibitors. Promising results for cell lysis efficiency were recently obtained by use of a cryogenic mill (Lipp et al., 2008). These findings encouraged us to devise a DNA extraction protocol using this tool. Thirteen procedures involving a combination of grinding in liquid nitrogen (for various durations and beating rates) with different chemical solutions (phenol, chloroform, SDS, sarkosyl, proteinase, GTC), or with use of DNA recovery kits (MagExtractor (R)) were compared. Effective DNA extraction was evaluated in terms of...
Tipo: Text
Palavras-chave: Sediment; DNA extraction; Deep subsurface biosphere.
Ano: 2011
URL: http://archimer.ifremer.fr/doc/00056/16691/14364.pdf

The many ways of coping with pressure
Provedor de dados: Institutional Archive of Ifreme (ArchiMer)
Autores: Oger, Philippe M.; Jebbar, Mohamed.
The current paper reviews strategies employed by microorganisms from the deep biosphere, especially piezophiles (from the greek piezo = to press and philo = love), to cope with high hydrostatic pressure (HHP) prevailing in these biotopes. The aim of this review is not to constitute an exhaustive report of our current knowledge on the physiology of piezophiles, as recent reviews have covered part of this subject in detail (Abe, 2007; Lauro and Bartlett, 2008; Michiels et al., 2008; Simonato et al., 2006). Rather, we illustrate here, via a few chosen examples, where we stand in our understanding of the mechanisms employed by microorganisms from the depths of our planet to cope with HHP. (C) 2010 Institut Pasteur. Published by Elsevier Masson SAS. All rights...
Tipo: Text
Palavras-chave: Adaptation and evolution; Archaea; Deep biosphere; High hydrostatic pressure; Piezophile; Stress response.
Ano: 2010
URL: http://archimer.ifremer.fr/doc/00027/13797/11043.pdf

The Effect of Crowding on Protein Stability, Rigidity, and High Pressure Sensitivity in Whole Cells
Provedor de dados: Institutional Archive of Ifreme (ArchiMer)
Autores: Golub, Maksym; Martinez, Nicolas; Michoud, Gregoire; Ollivier, Jacques; Jebbar, Mohamed; Oger, Philippe; Peters, Judith.
In live cells, high concentrations up to 300–400 mg/mL, as in Eschericia coli (Ellis, R. J. Curr. Opin. Struct. Biol. 2001, 11, 114) are achieved which have effects on their proper functioning. However, in many experiments only individual parts of the cells as proteins or membranes are studied in order to get insight into these specific components and to avoid the high complexity of whole cells, neglecting by the way the influence of crowding. In the present study, we investigated cells of the order of Thermococcales, which are known to live under extreme conditions, in their intact form and after cell lysis to extract the effect of crowding on the molecular dynamics of the proteome and of water molecules. We found that some parameters characterizing the...
Tipo: Text
Ano: 2018
URL: https://archimer.ifremer.fr/doc/00454/56526/58329.pdf

Complete Genome Sequence of the Obligate Piezophilic Hyperthermophilic Archaeon Pyrococcus yayanosii CH1
Provedor de dados: Institutional Archive of Ifreme (ArchiMer)
Autores: Jun, Xu; Liu Lupeng,; Xu Minjuan,; Oger, Philippe; Wang Fengping,; Jebbar, Mohamed; Xiang, Xiao.
Pyrococcus yayanosii CH1 is the first obligate piezophilic hyperthermophilic archaeon isolated from the deep-sea hydrothermal site Ashadze on the mid-Atlantic ridge at a depth of 4,100 m. This organism grows within a temperature range of 80 to 108 degrees C and a hydrostatic pressure range of 20 to 120 MPa, with optima at 98 degrees C and 52 MPa, respectively. Here, we report the complete genome sequence (1,716,817 bp, with a G+C content of 51.6%) of the type strain P. yayanosii CH1(T) (= JCM 16557). This genomic information reveals a systematic view of the piezoadaptation strategy and evolution scenario of metabolic pathways in Thermococcales.
Tipo: Text
Ano: 2011
URL: http://archimer.ifremer.fr/doc/00041/15247/12621.pdf

High hydrostatic pressure adaptive strategies in an obligate piezophile Pyrococcus yayanosii
Provedor de dados: Institutional Archive of Ifreme (ArchiMer)
Autores: Michoud, Gregoire; Jebbar, Mohamed.
Pyrococcus yayanosii CH1, as the first and only obligate piezophilic hyperthermophilic microorganism discovered to date, extends the physical and chemical limits of life on Earth. It was isolated from the Ashadze hydrothermal vent at 4,100 m depth. Multi-omics analyses were performed to study the mechanisms used by the cell to cope with high hydrostatic pressure variations. In silico analyses showed that the P. yayanosii genome is highly adapted to its harsh environment, with a loss of aromatic amino acid biosynthesis pathways and the high constitutive expression of the energy metabolism compared with other non-obligate piezophilic Pyrococcus species. Differential proteomics and transcriptomics analyses identified key hydrostatic pressure-responsive genes...
Tipo: Text
Ano: 2016
URL: https://archimer.ifremer.fr/doc/00342/45295/44756.pdf

Physiological features of Halomonas lionensis sp. nov., a novel bacterium isolated from a Mediterranean Sea sediment
Provedor de dados: Institutional Archive of Ifreme (ArchiMer)
Autores: Gaboyer, Frederic; Vandenabeele-trambouze, Odile; Cao, Junwei; Ciobanu, Maria-cristina; Jebbar, Mohamed; Le Romancer, Marc; Alain, Karine.
A novel halophilic bacterium, strain RHS90T, was isolated from marine sediments from the Gulf of Lions, in the Mediterranean Sea. Its metabolic and physiological characteristics were examined under various cultural conditions, including exposure to stressful ones (oligotrophy, high pressure and high concentrations of metals). Based on phylogenetic analysis of the 16S rRNA gene, the strain was found to belong to the genus Halomonas in the class Gammaproteobacteria. Its closest relatives are H. axialensis and H. meridiana (98% similarity). DNA-DNA hybridizations indicated that the novel isolate is genotypically distinct from these species. The DNA G+C content of the strain is 54.4 mol%. The main fatty acids (C18:1ω7c, 2-OH iso-C15:0, C16:0 and/or C19:0 cyclo...
Tipo: Text
Palavras-chave: Halomonas; Taxonomy; Environmental adaptation; Metal tolerance; Poly-beta-hydroxyalkanoate; Compatible.
Ano: 2014
URL: http://archimer.ifremer.fr/doc/00201/31253/29658.pdf

Complete Genome Sequence of Hyperthermophilic Piezophilic Archaeon Palaeococcus pacificus DY20341(T), Isolated from Deep-Sea Hydrothermal Sediments
Provedor de dados: Institutional Archive of Ifreme (ArchiMer)
Autores: Zeng, Xiang; Jebbar, Mohamed; Shao, Zongze.
We report the genome sequence of Palaeococcus pacificus DY20341(T), isolated from a sediment sample collected from eastern Pacific Ocean hydrothermal fields, which is the first report of a complete genome for a Palaeococcus species. The genome sequence will help to better understand differentiation phylogenetic relationships and evolution of several Thermococcales species.
Tipo: Text
Ano: 2015
URL: https://archimer.ifremer.fr/doc/00601/71312/69741.pdf

Identification and Characterization of Carboxyl Esterases of Gill Chamber-Associated Microbiota in the Deep-Sea Shrimp Rimicaris exoculata by Using Functional Metagenomics
Provedor de dados: Institutional Archive of Ifreme (ArchiMer)
Autores: 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.
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 (&lt;= 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...
Tipo: Text
Ano: 2015
URL: http://archimer.ifremer.fr/doc/00256/36721/36438.pdf

Desulfurobacterium indicum sp nov., a thermophilic sulfur-reducing bacterium from the Indian Ocean
Provedor de dados: Institutional Archive of Ifreme (ArchiMer)
Autores: Cao, Junwei; Birien, Tiphaine; Gayet, Nicolas; Huang, Zhaobin; Shao, Zongze; Jebbar, Mohamed; Alain, Karine.
A novel sulfur-reducing bacterium, strain K6013(T), was isolated from a sulfide sample collected at a depth of 2771 m from a high-temperature hydrothermal vent in the Indian Ocean. Cells were Gram-stain-negative, anaerobic, motile rods (0.92.2 x 0.4-0.6 mu m). The strain grew at NaCl concentrations ranging from 1 to 4.5% (w/v) (optimum 2.5 %), at pH 5 to 8 (optimum pH 6), and at temperatures between 40 and 75 degrees C (optimum 65 degrees C). K6013(T) was an obligate chemolithoautotroph, using thiosulfate, sulfur and nitrate as terminal electron acceptors in the presence of H-2 but not sulfate, sulfite nor nitrite. The major cellular fatty acids were C-16 : 0 (17.4 %), C-18 : 1 omega 7c/C-18 : 1 omega 6c (ummed feature 8, 37.91 %), C-18 : 0 (18.29 %) and...
Tipo: Text
Palavras-chave: Desulfurobacterium; Thermophilic; Hydrothermal vent; Chemolithoautotroph; Sulfur-reducer.
Ano: 2017
URL: http://archimer.ifremer.fr/doc/00395/50637/53724.pdf

Pseudodesulfovibrio indicus gen. nov., sp nov., a piezophilic sulfate-reducing bacterium from the Indian Ocean and reclassification of four species of the genus Desulfovibrio
Provedor de dados: Institutional Archive of Ifreme (ArchiMer)
Autores: Cao, Junwei; Gayet, Nicolas; Zeng, Xiang; Shao, Zongze; Jebbar, Mohamed; Alain, Karine.
A novel sulfate-reducing bacterium, strain J2(T), was isolated from a serpentinized peridotite sample from the Indian Ocean. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain J2(T) clustered with the genus Desulfovibrio within the family Desulfovibrionaceae, but it showed low similarity (87.95 %) to the type species Desulfovibrio desulfuricans DSM 642(T). It was most closely related to Desulfovibrio portus MSL79(T) (96.96 %), followed by Desulfovibrio aespoeensis Aspo-2(T) (96.11 %), Desulfovibrio piezophilus C1TLV30(T) (96.04 %) and Desulfovibrio profundus DSM 11384(T) (95.17 %). Other available sequences shared less than 93.33 % 16S rRNA gene sequence similarity. Cells were Gram-staining-negative, anaerobic, motile vibrios (2-6 x...
Tipo: Text
Ano: 2016
URL: http://archimer.ifremer.fr/doc/00359/47018/47131.pdf

Les Biotechnologies Marines dans le Grand Ouest
Provedor de dados: Institutional Archive of Ifreme (ArchiMer)
Autores: Boyen, Catherine; Jaouen, Pascal; Blanchard, Gilbert; Compere, Chantal; Dufour, Alain; Durand, Patrick; Guerard, Fabienne; Hallouin, Florence; Jebbar, Mohamed; Le Blay, Gwenaelle; Le Deit, Hervé; Le Seyec, Jocelyne; Monks, Brian; Portal-sellin, Rachel; Probert, Ian; Pruvost, Jeremy.
Marine (= blue) biotechnology, i.e. the utilization of marine bio-resources as a target or source of biotechnological applications, is a field with massive potential for innovation and economic growth. In a context of rapid climate change and increasing pressure on natural resources, renewed interest in marine biotechnology has been promoted by application of recent methodological and technological advances, notably in bioprocessing and in the various –omics domains, to the study of marine biodiversity. Marine biological resources potentially represent a sustainable raw material for exploitation in diverse fields, including nutrition, health, agriculture, aquaculture, energy, environment, and cosmetics. Marine biotechnology is now recognized as a...
Tipo: Text
Ano: 2015
URL: http://archimer.ifremer.fr/doc/00273/38460/36860.pdf

Complete genome sequence and whole-genome phylogeny of Kosmotoga pacifica type strain SLHLJ1T from an East Pacific hydrothermal sediment
Provedor de dados: Institutional Archive of Ifreme (ArchiMer)
Autores: Jiang, Lijing; L'Haridon, Stephane; Jebbar, Mohamed; Xu, Hongxiu; Alain, Karine; Shao, Zongze.
Kosmotoga pacifica strain SLHLJ1T is a thermophilic chemoorganoheterotrophic bacterium isolated from a deep-sea hydrothermal sediment. It belongs to the physiologically homogeneous Thermotogaceae family. Here, we describe the phenotypic features of K. pacifica together with its genome sequence and annotation. The chromosome has 2,169,170 bp, organized in one contig. A total of 1897 candidate protein-encoding genes and 177 RNA genes were identified. The 16S rRNA gene sequence of this strain is distantly related to sequences of some relatives classified in the same genus (K. olearia 7.02% and K. shengliensis 7.83%), with dissimilarity percentages close to the threshold generally described for genus delineation. Nevertheless, the percentage of conserved...
Tipo: Text
Palavras-chave: Marine; Hydrothermal vent; Thermotogales; Chemoorganoheterotroph; Thermophile.
Ano: 2017
URL: http://archimer.ifremer.fr/doc/00371/48191/48324.pdf

Genomic Insights into the Carbon and Energy Metabolism of a Thermophilic Deep-Sea Bacterium Deferribacter autotrophicus Revealed New Metabolic Traits in the Phylum Deferribacteres
Provedor de dados: Institutional Archive of Ifreme (ArchiMer)
Autores: Slobodkin, Alexander; Slobodkina, Galina; Allioux, Maxime; Alain, Karine; Jebbar, Mohamed; Shadrin, Valerian; Kublanov, Ilya; Toshchakov, Stepan; Bonch-osmolovskaya, Elizaveta.
nformation on the biochemical pathways of carbon and energy metabolism in representatives of the deep lineage bacterial phylum Deferribacteres are scarce. Here, we report the results of the sequencing and analysis of the high-quality draft genome of the thermophilic chemolithoautotrophic anaerobe Deferribacter autotrophicus. Genomic data suggest that CO2 assimilation is carried out by recently proposed reversible tricarboxylic acid cycle (“roTCA cycle”). The predicted genomic ability of D. autotrophicus to grow due to the oxidation of carbon monoxide was experimentally proven. CO oxidation was coupled with the reduction of nitrate to ammonium. Utilization of CO most likely involves anaerobic [Ni, Fe]-containing CO dehydrogenase. This is the first evidence...
Tipo: Text
Palavras-chave: Autotrophic; Thermophile; RoTCA cycle; CO oxidation; Fe(III)-reduction; Nitrate reduction.
Ano: 2019
URL: https://archimer.ifremer.fr/doc/00589/70078/68051.pdf

Restoration of the di-myo-inositol-phosphate pathway in the piezo-hyperthermophilic archaeon Thermococcus barophilus
Provedor de dados: Institutional Archive of Ifreme (ArchiMer)
Autores: Cario, Anais; Mizgier, Alex; Thiel, Axel; Jebbar, Mohamed; Oger, Phil M.
Most Thermococcales accumulate di-myo-inositol-phosphate (DIP) as an organic solute as a response to heat stress. We have studied the accumulation of this osmolyte in the high-hydrostatic pressure adapted hyperthermophile Thermococcus barophilus. We found no accumulation of DIP under any of the stress conditions tested, although this archaeon harbors the 3 DIP synthesis genes. Lack of synthesis is due to the lack of expression of TERMP_01135 coding for the second step of DIP synthesis. In contrast to other species, the T. barophilus synthesis operon is interrupted by a four gene locus, in reverse orientation. Restoring an operon like structure at the DIP locus restored DIP synthesis, but did not have an impact on growth characteristics, suggesting that...
Tipo: Text
Palavras-chave: High hydrostatic pressure; Heat stress; Di-myo-inositol-phosphate; Thermococcus barophilus.
Ano: 2015
URL: http://archimer.ifremer.fr/doc/00270/38113/37216.pdf

Functional Screening of Hydrolytic Activities Reveals an Extremely Thermostable Cellulase from a Deep-Sea Archaeon
Provedor de dados: Institutional Archive of Ifreme (ArchiMer)
Autores: Leis, Benedikt; Heinze, Simon; Angelov, Angel; Pham, Vu Thuy Trang; Thürmer, Andrea; Jebbar, Mohamed; Golyshin, Peter N.; Streit, Wolfgang R.; Daniel, Rolf; Liebl, Wolfgang.
Extreme habitats serve as a source of enzymes that are active under extreme conditions and are candidates for industrial applications. In this work, six large-insert mixed genomic libraries were screened for hydrolase activities in a broad temperature range (8–70°C). Among a variety of hydrolytic activities, one fosmid clone, derived from a library of pooled isolates of hyperthermophilic archaea from deep sea vents, displayed hydrolytic activity on carboxymethyl cellulose substrate plates at 70°C but not at lower temperatures. Sequence analysis of the fosmid insert revealed a gene encoding a novel glycoside hydrolase family 12 (GHF12) endo-1,4-β-glucanase, termed Cel12E. The enzyme shares 45% sequence identity with a protein from the archaeon Thermococcus...
Tipo: Text
Palavras-chave: Functional screenings; Extreme thermostable protein; Archaeal endoglucanase; Enzymatic characterization.
Ano: 2015
URL: https://archimer.ifremer.fr/doc/00601/71319/69744.pdf

Abiotic stress protection by ecologically abundant dimethylsulfoniopropionate and its natural and synthetic derivatives: insights from   B   acillus subtilis
Provedor de dados: Institutional Archive of Ifreme (ArchiMer)
Autores: Broy, Sebastian; Chen, Chiliang; Hoffmann, Tamara; Brock, Nelson L.; Nau-wagner, Gabriele; Jebbar, Mohamed; Smits, Sander H. J.; Dickschat, Jeroen S.; Bremer, Erhard.
Dimethylsulfoniopropionate (DMSP) is an abundant osmolyte and anti-stress compound produced primarily in marine ecosystems. After its release into the environment, microorganisms can exploit DMSP as a source of sulfur and carbon, or accumulate it as an osmoprotectant. However, import systems for this ecophysiologically important compatible solute, and its stress-protective properties for microorganisms that do not produce it are insufficiently understood. Here we address these questions using a well-characterized set of Bacillus subtilis mutants to chemically profile the influence of DMSP import on stress resistance, the osmostress-adaptive proline pool and on osmotically controlled gene expression. We included in this study the naturally occurring...
Tipo: Text
Ano: 2015
URL: https://archimer.ifremer.fr/doc/00242/35302/33910.pdf

Microorganisms persist at record depths in the subseafloor of the Canterbury Basin
Provedor de dados: Institutional Archive of Ifreme (ArchiMer)
Autores: Ciobanu, Maria Cristina; Burgaud, Gaetan; Dufresne, Alexis; Breuker, Anja; Redou, Vanessa; Ben Maamar, Sarah; Gaboyer, Frederic; Vandenabeele-trambouze, Odile; Lipp, Julius Sebastian; Schippers, Axel; Vandenkoornhuyse, Philippe; Barbier, Georges; Jebbar, Mohamed; Godfroy, Anne; Alain, Karine.
The subsurface realm is colonized by microbial communities to depths of &gt;1000 meters below the seafloor (m.b.sf.), but little is known about overall diversity and microbial distribution patterns at the most profound depths. Here we show that not only Bacteria and Archaea but also Eukarya occur at record depths in the subseafloor of the Canterbury Basin. Shifts in microbial community composition along a core of nearly 2 km reflect vertical taxa zonation influenced by sediment depth. Representatives of some microbial taxa were also cultivated using methods mimicking in situ conditions. These results suggest that diverse microorganisms persist down to 1922 m.b.sf. in the seafloor of the Canterbury Basin and extend the previously known depth limits of...
Tipo: Text
Palavras-chave: Deep biosphere; Subsurface life; Eukaryote; Record depth.
Ano: 2014
URL: http://archimer.ifremer.fr/doc/00201/31243/29895.pdf

Thermococcus piezophilus sp. nov., a novel hyperthermophilic and piezophilic archaeon with a broad pressure range for growth, isolated from a deepest hydrothermal vent at the Mid-Cayman Rise
Provedor de dados: Institutional Archive of Ifreme (ArchiMer)
Autores: Dalmasso, Cecile; Oger, Philippe; Selva, Gwendoline; Courtine, Damien; L'Haridon, Stephane; Garlaschelli, Alexandre; Roussel, Erwan; Miyazaki, Junichi; Reveillaud, Julie; Jebbar, Mohamed; Takai, Ken; Maignien, Lois; Alain, Karine.
A novel strictly anaerobic, hyperthermophilic archaeon, designated strain CDGST, was isolated from a deep-sea hydrothermal vent in the Cayman Trough at 4964 m water depth. The novel isolate is obligate anaerobe and grows chemoorganoheterotrophically with stimulation of growth by sulphur containing compounds. Its growth is optimal at 75 °C, pH 6.0 and under a pressure of 50 MPa. It possesses the broadest hydrostatic pressure range for growth that has ever been described for a microorganism. Its genomic DNA G + C content is 51.11 mol%. The novel isolate belongs to the genus Thermococcus. Phylogenetic analyses indicated that it is most closely related to Thermococcus barossii DSM17882T based on its 16S rRNA gene sequence, and to ‘Thermococcus onnurineus’ NA1...
Tipo: Text
Palavras-chave: Thermococcus; Piezophile; Hydrothermal vent; Cayman Trough.
Ano: 2016
URL: http://archimer.ifremer.fr/doc/00348/45949/45655.pdf

Draft Genome of   Halomonas lionensis   RHS90   T   , a Stress-Tolerant Gammaproteobacterium Isolated from Mediterranean Sea Sediments
Provedor de dados: Institutional Archive of Ifreme (ArchiMer)
Autores: Gaboyer, Frédéric; Maignien, Loïs; Jebbar, Mohamed; Alain, Karine.
Members of the genus Halomonas are physiologically versatile and harbor ecological adaptations enabling the colonization of contrasted environments. We present here the draft genome of Halomonas lionensis RHS90T, isolated from Mediterranean Sea sediments. Numerous genes related to stress tolerance, DNA repair, or external signal-sensing systems were predicted, which could represent selective advantages of this marine bacterium.
Tipo: Text
Ano: 2017
URL: https://archimer.ifremer.fr/doc/00388/49906/50477.pdf

"Ménage à trois": a selfish genetic element uses a virus to propagate within Thermotogales
Provedor de dados: Institutional Archive of Ifreme (ArchiMer)
Autores: Lossouarn, Julien; Nesbo, Camilla L.; Mercier, Coraline; Zhaxybayeva, Olga; Johnson, Milo S.; Charchuck, Rhianna; Farasin, Julien; Bienvenu, Nadege; Baudoux, Anne-claire; Michoud, Gregoire; Jebbar, Mohamed; Geslin, Claire.
Prokaryotic viruses play a major role in the microbial ecology and evolution. However, the virosphere associated with deep-sea hydrothermal ecosystems remains largely unexplored. Numerous instances of lateral gene transfer have contributed to the complex and incongruent evolutionary history of Thermotogales, an order well represented in deep-sea hydrothermal vents. The presence of clustered regularly interspaced short palindromic repeats (CRISPR) loci has been reported in all Thermotogales genomes, suggesting that these bacteria have been exposed to viral infections that could have mediated gene exchange. In this study, we isolated and characterized the first virus infecting bacteria from the order Thermotogales, Marinitoga piezophila virus 1 (MPV1). The...
Tipo: Text
Ano: 2015
URL: http://archimer.ifremer.fr/doc/00254/36483/36732.pdf

Kosmotoga pacifica sp. nov., a thermophilic chemoorganoheterotrophic bacterium isolated from an East Pacific hydrothermal sediment
Provedor de dados: Institutional Archive of Ifreme (ArchiMer)
Autores: L'Haridon, Stephane; Jiang, Lijing; Alain, Karine; Chalopin, Morgane; Rouxel, Ouafae; Beauverger, Mikael; Xu, Hongxiu; Shao, Zongze; Jebbar, Mohamed.
A novel strictly anaerobic thermophilic heterotrophic bacterium, strain SLHLJ1T, was isolated from a Pacific hydrothermal sediment. Cells were Gram-negative coccobacilli (approximately 1.0 × 0.6 μm) with a toga. It grew at temperatures between 33 and 78 °C (optimum 70 °C). Elemental sulphur and l-cystine stimulated its growth. It contained C16:0, C16:1 ω11c, C18:0 and C18:1 ω9c as major fatty acids (&gt;5 %), 3 phospholipids and 2 glycolipids as polar lipids. Its DNA G+C content was 43.7 mol%. Phylogenetic analyses based on 16S rRNA gene sequences placed strain SLHLJ1T within the family Thermotogaceae. The novel isolate was most closely related to Kosmotoga arenicorallina (97.93 % 16S rRNA gene sequence similarity), K. olearia (92.43 %) and K. shengliensis...
Tipo: Text
Palavras-chave: Thermotogales; Kosmotoga; Kosmotoga pacifica; Hydrothermal sediment.
Ano: 2014
URL: http://archimer.ifremer.fr/doc/00171/28204/26509.pdf

Microbial Diversity and Biosignatures: An Icy Moons Perspective
Provedor de dados: Institutional Archive of Ifreme (ArchiMer)
Autores: Jebbar, Mohamed; Hickman-lewis, Keyron; Cavalazzi, Barbara; Taubner, Ruth-sophie; Rittmann, Simon K.-m. R.; Antunes, Andre.
The icy moons of the outer Solar System harbor potentially habitable environments for life, however, compared to the terrestrial biosphere, these environments are characterized by extremes in temperature, pressure, pH, and other physico-chemical conditions. Therefore, the search for life on these icy worlds is anchored on the study of terrestrial extreme environments (termed “analogue sites”), which harbor microorganisms at the frontiers of polyextremophily. These so-called extremophiles have been found in areas previously considered sterile: hot springs, hydrothermal vents, acidic or alkaline lakes, hypersaline environments, deep sea sediments, glaciers, and arid areas, amongst others. Such model systems and communities in extreme terrestrial environments...
Tipo: Text
Palavras-chave: Extremophiles; Prokaryotes; Metabolism; Diversity; Adaptation; Space explorat.
Ano: 2020
URL: https://archimer.ifremer.fr/doc/00606/71771/70275.pdf

Genome Sequence of the Piezophilic, Mesophilic Sulfate-Reducing Bacterium Desulfovibrio indicus J2(T)
Provedor de dados: Institutional Archive of Ifreme (ArchiMer)
Autores: Cao, Junwei; Maignien, Lois; Shao, Zongze; Alain, Karine; Jebbar, Mohamed.
The complete genome sequence of Desulfovibrio indicus J2(T), a member of the family Desulfovibrionaceae, consists of 3,966,573-bp in one contig and encodes 3,461 predicted genes, 5 noncoding RNAs, 3 rRNAs operons, and 52 tRNA-encoding genes. The genome is consistent with a heterotrophic, anaerobic lifestyle including the sulfate reduction pathway.
Tipo: Text
Ano: 2016
URL: https://archimer.ifremer.fr/doc/00601/71311/69740.pdf

High protein flexibility and reduced hydration water dynamics are key pressure adaptive strategies in prokaryotes
Provedor de dados: Institutional Archive of Ifreme (ArchiMer)
Autores: Martinez, N.; Michoud, Gregoire; Cario, A.; Ollivier, J.; Franzetti, B.; Jebbar, Mohamed; Oger, P.; Peters, J.
Water and protein dynamics on a nanometer scale were measured by quasi-elastic neutron scattering in the piezophile archaeon Thermococcus barophilus and the closely related pressure-sensitive Thermococcus kodakarensis, at 0.1 and 40 MPa. We show that cells of the pressure sensitive organism exhibit higher intrinsic stability. Both the hydration water dynamics and the fast protein and lipid dynamics are reduced under pressure. In contrast, the proteome of T. barophilus is more pressure sensitive than that of T. kodakarensis. The diffusion coefficient of hydration water is reduced, while the fast protein and lipid dynamics are slightly enhanced with increasing pressure. These findings show that the coupling between hydration water and cellular constituents...
Tipo: Text
Ano: 2016
URL: https://archimer.ifremer.fr/doc/00350/46083/45742.pdf

Genetic Manipulations of the Hyperthermophilic Piezophilic Archaeon Thermococcus barophilus
Provedor de dados: Institutional Archive of Ifreme (ArchiMer)
Autores: Thiel, Axel; Michoud, Gregoire; Moalic, Yann; Flament, Didier; Jebbar, Mohamed.
In this study, we developed a gene disruption system for Thermococcus barophilus using simvastatin for positive selection and 5-fluoroorotic acid (5-FOA) for negative selection or counterselection to obtain markerless deletion mutants using single-and double-crossover events. Disruption plasmids carrying flanking regions of each targeted gene were constructed and introduced by transformation into wild-type T. barophilus MP cells. Initially, a pyrF deletion mutant was obtained as a starting point for the construction of further markerless mutants. A deletion of the hisB gene was also constructed in the UBOCC-3256 (Delta pyrF) background, generating a strain (UBOCC-3260) that was auxotrophic for histidine. A functional pyrF or hisB allele from T. barophilus...
Tipo: Text
Ano: 2014
URL: http://archimer.ifremer.fr/doc/00187/29818/28263.pdf

Genomic Characterization and Environmental Distribution of a Thermophilic Anaerobe Dissulfurirhabdus thermomarina SH388T Involved in Disproportionation of Sulfur Compounds in Shallow Sea Hydrothermal Vents
Provedor de dados: Institutional Archive of Ifreme (ArchiMer)
Autores: Allioux, Maxime; Yvenou, Steven; Slobodkina, Galina; Slobodkin, Alexander; Shao, Zongze; Jebbar, Mohamed; Alain, Karine.
Marine hydrothermal systems are characterized by a pronounced biogeochemical sulfur cycle with the participation of sulfur-oxidizing, sulfate-reducing and sulfur-disproportionating microorganisms. The diversity and metabolism of sulfur disproportionators are studied to a much lesser extent compared with other microbial groups. Dissulfurirhabdus thermomarina SH388T is an anaerobic thermophilic bacterium isolated from a shallow sea hydrothermal vent. D. thermomarina is an obligate chemolithoautotroph able to grow by the disproportionation of sulfite and elemental sulfur. Here, we present the results of the sequencing and analysis of the high-quality draft genome of strain SH388T. The genome consists of a one circular chromosome of 2,461,642 base pairs, has a...
Tipo: Text
Palavras-chave: Genome annotation; Dissulfurirhabdus; Shallow sea hydrothermal vents; Inorganic sulfur compound disproportionation.
Ano: 2020
URL: https://archimer.ifremer.fr/doc/00651/76270/77245.pdf

Deep sea, the last great unexplored Earth frontier harboring the largest unknown and untapped remote microbial diversity on our planet
Provedor de dados: Institutional Archive of Ifreme (ArchiMer)
Autores: Jebbar, Mohamed.
Tipo: Text
Ano: 2015
URL: http://archimer.ifremer.fr/doc/00277/38850/37389.pdf

Development of an Effective 6-Methylpurine Counterselection Marker for Genetic Manipulation in Thermococcus barophilus
Provedor de dados: Institutional Archive of Ifreme (ArchiMer)
Autores: Birien, Tiphaine; Thiel, Axel; Henneke, Ghislaine; Flament, Didier; Moalic, Yann; Jebbar, Mohamed.
A gene disruption system for Thermococcus barophilus was developed using simvastatin (HMG-CoA reductase encoding gene) for positive selection and 5-Fluoroorotic acid (5-FOA), a pyrF gene for negative selection. Multiple gene mutants were constructed with this system, which offers the possibility of complementation in trans, but produces many false positives (&lt;80%). To significantly reduce the rate of false positives, we used another counterselective marker, 6-methylpurine (6-MP), a toxic analog of adenine developed in Thermococcus kodakarensis, consistently correlated with the TK0664 gene (encoding a hypoxanthine-guanine phosphoribosyl-transferase). We thus replaced pyrF by TK0664 on our suicide vector and tested T. barophilus strain sensitivity to 6-MP...
Tipo: Text
Palavras-chave: Archaea; Piezophiles; Hyperthermophiles; Genetics; Gene deletion; Deep sea; Hydrothermal vents.
Ano: 2018
URL: https://archimer.ifremer.fr/doc/00425/53679/54523.pdf

Molecular chaperone accumulation as a function of stress evidences adaptation to high hydrostatic pressure in the piezophilic archaeon Thermococcus barophilus
Provedor de dados: Institutional Archive of Ifreme (ArchiMer)
Autores: Cario, Anaïs; Jebbar, Mohamed; Thiel, Axel; Kervarec, Nelly; Oger, Phil M.
The accumulation of mannosyl-glycerate (MG), the salinity stress response osmolyte of Thermococcales, was investigated as a function of hydrostatic pressure in Thermococcus barophilus strain MP, a hyperthermophilic, piezophilic archaeon isolated from the Snake Pit site (MAR), which grows optimally at 40 MPa. Strain MP accumulated MG primarily in response to salinity stress, but in contrast to other Thermococcales, MG was also accumulated in response to thermal stress. MG accumulation peaked for combined stresses. The accumulation of MG was drastically increased under sub-optimal hydrostatic pressure conditions, demonstrating that low pressure is perceived as a stress in this piezophile, and that the proteome of T. barophilus is low-pressure sensitive. MG...
Tipo: Text
Ano: 2016
URL: http://archimer.ifremer.fr/doc/00345/45570/45178.pdf

Pyrococcus CH1, an obligate piezophilic hyperthermophile: extending the upper pressure-temperature limits for life
Provedor de dados: Institutional Archive of Ifreme (ArchiMer)
Autores: Zeng, Xiang; Birrien, Jean-louis; Fouquet, Yves; Cherkashov, Georgy; Jebbar, Mohamed; Querellou, Joel; Oger, Philippe; Cambon-bonavita, Marie-anne; Xiao, Xiang; Prieur, Daniel.
A novel hydrothermal site was discovered in March 2007, on the mid-Atlantic ridge during the cruise 'Serpentine'. At a depth of 4100 m, the site 'Ashadze' is the deepest vent field known so far. Smoker samples were collected with the ROV 'Victor 6000' and processed in the laboratory for the enrichment of anaerobic heterotrophic microorganisms under high-temperature and high-hydrostatic pressure conditions. Strain CH1 was successfully isolated and assigned to the genus Pyrococcus, within the Euryarchaeota lineage within the Archaea domain. This organism grows within a temperature range of 80 to 108 degrees C and a pressure range of 20 to 120 MPa, with optima for 98 degrees C and 52 MPa respectively. Pyrococcus CH1 represents the first obligate piezophilic...
Tipo: Text
Palavras-chave: Thermococcales; Extremophile; Deep sea hydrothermal vent; High hydrostatic pressure; Archaea.
Ano: 2009
URL: http://archimer.ifremer.fr/doc/2009/publication-6812.pdf

Deep Sea Microbes Probed by Incoherent Neutron Scattering Under High Hydrostatic Pressure
Provedor de dados: Institutional Archive of Ifreme (ArchiMer)
Autores: Peters, Judith; Martinez, Nicolas; Michoud, Gregoire; Carlo, Anais; Franzetti, Bruno; Oger, Philippe; Jebbar, Mohamed.
The majority of the biosphere is a high pressure environment. Around 70% of the marine biosphere lies at depths below 1000 m, i.e. at pressures of 100 bars or higher. To survive in these environments, deep-biosphere organisms have adapted to life at high pressure. In vitro studies showed that the activity of certain proteins originating from deep-sea organisms is less affected by high pressure than that of enzymes from surface organisms [1-3]. However, the genetic and structural bases for this increased pressure resistance are still unknown. Elastic incoherent neutron scattering studies, which provide access to information about molecular dynamics, constitute a very promising approach to decipher the structural adaptation in proteins living under high...
Tipo: Text
Palavras-chave: Neutron Scattering; Molecular Dynamics; High Pressure; Deep Sea Microbes.
Ano: 2014
URL: http://archimer.ifremer.fr/doc/00251/36186/34725.pdf

Combined Whole-Cell High-Throughput Functional Screening for Identification of New Nicotinamidases/Pyrazinamidases in Metagenomic/Polygenomic Libraries
Provedor de dados: Institutional Archive of Ifreme (ArchiMer)
Autores: Zapata-perez, Ruben; Garcia-saura, Antonio G.; Jebbar, Mohamed; Golyshin, Peter N.; Sanchez-ferrer, Alvaro.
Nicotinamidases catalyze the hydrolysis of the amide bond in nicotinamide (NAM) to produce ammonia and nicotinic acid (NA). These enzymes are an essential component of the NAD(+) salvage pathway and are implicated in the viability of several pathogenic organisms. Its absence in humans makes them a promising drug target. In addition, although they are key analytical biocatalysts for screening modulators in relevant biomedical enzymes, such as sirtuins and poly-ADP-ribosyltransferases, no commercial sources are available. Surprisingly, the finding of an affordable source of nicotinamidase from metagenomic libraries is hindered by the absence of a suitable and fast screening method. In this manuscript, we describe the development of two new whole-cell methods...
Tipo: Text
Palavras-chave: Amidohydrolases; Nicotinamidase; Functional screening; Metagenome; Library; High-throughput screening assays.
Ano: 2016
URL: http://archimer.ifremer.fr/doc/00362/47269/47232.pdf

Complete Genome Sequence of the Hyperthermophilic Piezophilic Archaeon   Pyrococcus kukulkanii   NCB100 Isolated from the Rebecca’s Roost Hydrothermal Vent in the Guaymas Basin
Provedor de dados: Institutional Archive of Ifreme (ArchiMer)
Autores: Oger, Philippe M.; Callac, Nolwenn; Oger-desfeux, Christine; Hughes, Sandrine; Gillet, Benjamin; Jebbar, Mohamed; Godfroy, Anne.
Members of the order Thermococcales are common inhabitants of high-temperature hydrothermal vent systems (black smokers) that are represented in clone libraries mostly by isolates from the Thermococcus genus. We report the complete sequence of a novel species from the Pyrococcus genus, P. kukulkanii strain NCB100, which has been isolated from a flange fragment of the Rebecca’s Roost hydrothermal vent system in the Guaymas Basin.
Tipo: Text
Ano: 2017
URL: https://archimer.ifremer.fr/doc/00476/58798/61335.pdf

The gill chamber epibiosis of deep-sea shrimp Rimicaris exoculata: an in-depth metagenomic investigation and discovery of Zetaproteobacteria
Provedor de dados: Institutional Archive of Ifreme (ArchiMer)
Autores: Jan, Cyrielle; Petersen, Jillian M.; Werner, Johannes; Teeling, Hanno; Huang, Sixing; Gloeckner, Frank Oliver; Golyshina, Olga V.; Dubilier, Nicole; Golyshin, Peter N.; Jebbar, Mohamed; Cambon-bonavita, Marie-anne.
The gill chamber of deep-sea hydrothermal vent shrimp Rimicaris exoculata hosts a dense community of epibiotic bacteria dominated by filamentous Epsilonproteobacteria and Gammaproteobacteria. Using metagenomics on shrimp from the Rainbow hydrothermal vent field, we showed that both epibiont groups have the potential to grow autotrophically and oxidize reduced sulfur compounds or hydrogen with oxygen or nitrate. For carbon fixation, the Epsilonproteobacteria use the reductive tricarboxylic acid cycle, whereas the Gammaproteobacteria use the Calvin–Benson–Bassham cycle. Only the epsilonproteobacterial epibionts had the genes necessary for producing ammonium. This ability likely minimizes direct competition between epibionts and also broadens the spectrum of...
Tipo: Text
Ano: 2014
URL: http://archimer.ifremer.fr/doc/00177/28874/28622.pdf

Complete Genome Sequence of the Halophilic Methylotrophic Methanogen Archaeon     Methanohalophilus portucalensis     Strain FDF-1     T
Provedor de dados: Institutional Archive of Ifreme (ArchiMer)
Autores: L'Haridon, Stephane; Corre, Erwan; Guan, Yue; Vinu, Manikandan; La Cono, Violetta; Yakimov, Michail; Stingl, Ulrich; Toffin, Laurent; Jebbar, Mohamed.
We report here the complete genome sequence (2.08 Mb) of Methanohalophilus portucalensis strain FDF-1T, a halophilic methylotrophic methanogen isolated from the sediment of a saltern in Figeria da Foz, Portugal. The average nucleotide identity and DNA-DNA hybridization analyses show that Methanohalophilus mahii, M. halophilus, and M. portucalensis are three different species within the Methanosarcinaceae family.
Tipo: Text
Ano: 2018
URL: https://archimer.ifremer.fr/doc/00420/53138/54102.pdf

Complete Genome Sequence of   Methanohalophilus halophilus   DSM 3094   T   , Isolated from a Cyanobacterial Mat and Bottom Deposits at Hamelin Pool, Shark Bay, Northwestern Australia
Provedor de dados: Institutional Archive of Ifreme (ArchiMer)
Autores: L’haridon, Stéphane; Corre, Erwan; Guan, Yue; Vinu, Manikandan; La Cono, Violetta; Yakimov, Mickail; Stingl, Ulrich; Toffin, Laurent; Jebbar, Mohamed.
The complete genome sequence of Methanohalophilus halophilus DSM 3094T, a member of the Methanosarcinaceae family and the Methanosarcianales order, consists of 2,022,959 bp in one contig and contains 2,137 predicted genes. The genome is consistent with a halophilic methylotrophic anaerobic lifestyle, including the methylotrophic and CO2-H2 methanogensis pathways.
Tipo: Text
Ano: 2017
URL: https://archimer.ifremer.fr/doc/00372/48351/48523.pdf

Electroactive Bacteria Associated With Stainless Steel Ennoblement in Seawater
Provedor de dados: Institutional Archive of Ifreme (ArchiMer)
Autores: Trigodet, Florian; Larche, Nicolas; Morrison, Hilary G.; Jebbar, Mohamed; Thierry, Dominique; Maignien, Lois.
Microorganisms can increase the open-circuit potential of stainless steel immersed in seawater of several hundred millivolts in a phenomenon called ennoblement. It raises the chance of corrosion as the open-circuit potential may go over the pitting corrosion potential. Despite the large impact of the ennoblement, no unifying mechanisms have been described as responsible for the phenomenon. Here we show that the strict electrotroph bacterium "Candidatus Tenderia electrophaga" is detected as an ennoblement biomarker and is only present at temperatures at which we observe ennoblement. This bacterium was previously enriched in biocathode systems. Our results suggest that "Candidatus Tenderia electrophaga," and its previously described extracellular electron...
Tipo: Text
Palavras-chave: Ennoblement; Electroactive bacteria; Stainless steel; Microbial ecology; 16S rRNA gene.
Ano: 2019
URL: https://archimer.ifremer.fr/doc/00482/59371/62144.pdf

RNA processing machineries in Archaea: the 5′-3′ exoribonuclease aRNase J of the β-CASP family is engaged specifically with the helicase ASH-Ski2 and the 3′-5′ exoribonucleolytic RNA exosome machinery
Provedor de dados: Institutional Archive of Ifreme (ArchiMer)
Autores: Phung, Duy Khanh; Etienne, Clarisse; Batista, Manon; Langendijk-genevaux, Petra; Moalic, Yann; Laurent, Sebastien; Liuu, Sophie; Morales, Violette; Jebbar, Mohamed; Fichant, Gwennaele; Bouvier, Marie; Flament, Didier; Clouet-d’orval, Béatrice.
A network of RNA helicases, endoribonucleases and exoribonucleases regulates the quantity and quality of cellular RNAs. To date, mechanistic studies focussed on bacterial and eukaryal systems due to the challenge of identifying the main drivers of RNA decay and processing in Archaea. Here, our data support that aRNase J, a 5′-3′ exoribonuclease of the β-CASP family conserved in Euryarchaeota, engages specifically with a Ski2-like helicase and the RNA exosome to potentially exert control over RNA surveillance, at the vicinity of the ribosome. Proteomic landscapes and direct protein–protein interaction analyses, strengthened by comprehensive phylogenomic studies demonstrated that aRNase J interplay with ASH-Ski2 and a cap exosome subunit. Finally,...
Tipo: Text
Ano: 2020
URL: https://archimer.ifremer.fr/doc/00610/72250/71056.pdf

Draft Genome Sequence of Phaeobacter leonis Type Strain 306, an Alphaproteobacterium Isolated from Mediterranean Sea Sediments
Provedor de dados: Institutional Archive of Ifreme (ArchiMer)
Autores: Gaboyer, Frédéric; Malgnien, Loïs; Jebbar, Mohamed; Alain, Karine.
Phaeobacter leonis strain 306T is an alphaproteobacterium isolated from Mediterranean Sea sediments. It belongs to the genus Phaeobacter, which was recently proposed and is still poorly characterized. In an effort to better understand the fundamental aspects of the microbiology of this genus, we present here the 4.82-Mb draft genome sequence of Phaeobacter leonis strain 306T.
Tipo: Text
Ano: 2017
URL: https://archimer.ifremer.fr/doc/00390/50186/50809.pdf

Chemosynthetic ectosymbionts associated with a shallow-water marine nematode
Provedor de dados: Institutional Archive of Ifreme (ArchiMer)
Autores: Bellec, Laure; Cambon Bonavita, Marie-anne; Hourdez, Stéphane; Jebbar, Mohamed; Tasiemski, Aurélie; Durand, Lucile; Gayet, Nicolas; Zeppilli, Daniela.
Prokaryotes and free-living nematodes are both very abundant and co-occur in marine environments, but little is known about their possible association. Our objective was to characterize the microbiome of a neglected but ecologically important group of free-living benthic nematodes of the Oncholaimidae family. We used a multi-approach study based on microscopic observations (Scanning Electron Microscopy and Fluorescence In Situ Hybridization) coupled with an assessment of molecular diversity using metabarcoding based on the 16S rRNA gene. All investigated free-living marine nematode specimens harboured distinct microbial communities (from the surrounding water and sediment and through the seasons) with ectosymbiosis seemed more abundant during summer....
Tipo: Text
Ano: 2019
URL: https://archimer.ifremer.fr/doc/00494/60614/64098.pdf