Consulta: creatorFacets:"L'Haridon, Stephane"
Registros recuperados: 12
Data/hora: 09/06/2024 04:40:52

Methanococcoides
Provedor de dados: Institutional Archive of Ifreme (ArchiMer)
Autores: L'Haridon, Stephane; Toffin, Laurent; Roussel, Erwan.
Me.tha.no.coc.co'i.des. Gr. adj. suff. ‐oides similar to; N.L. neut. n. Methanococcoides organism similar to Methanococcus. Euryarchaeota / Methanomicrobia / Methanosarcinales / Methanosarcinaceae / Methanococcoides The genus Methanococcoides comprises four species, Methanococcoides methylutens, Methanococcoides burtonii, Methanococcoides alaskense, and Methanococcoides vulcani. Cells are irregular cocci, 0.5–3 μm in diameter, occurring singly or in pairs, and may be motile. Clumps of cells can also observed. Cells exhibit a blue‐green autofluorescence under UV illumination. The cell wall consists of a very thin protein S‐layer, approximately 10‐nm thick. Susceptible to lysis by hypotonic or detergent shock. Eurypsychrophilic to mesophilic. Strict...
Tipo: Text
Palavras-chave: Anaerobe; Psychrophile; Mesophile; Methyl compound reduction; Marine anoxic sediment; Deep‐sea mud volcano; Cold seeps.
Ano: 2020
URL: https://archimer.ifremer.fr/doc/00614/72595/74852.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

The interplay at the replisome mitigates the impact of oxidative damage on the genetic integrity of hyperthermophilic Archaea
Provedor de dados: Institutional Archive of Ifreme (ArchiMer)
Autores: Killelea, Tom; Palud, Adeline; Akcha, Farida; Lemor, Mélanie; L'Haridon, Stephane; Godfroy, Anne; Henneke, Ghislaine.
8-oxodeoxyguanosine (8-oxodG), a major oxidised base modification, has been investigated to study its impact on DNA replication in hyperthermophilic Archaea. Here we show that 8-oxodG is formed in the genome of growing cells, with elevated levels following exposure to oxidative stress. Functional characterisation of cell-free extracts and the DNA polymerisation enzymes, PolB, PolD, and the p41/p46 complex, alone or in the presence of accessory factors (PCNA and RPA) indicates that translesion synthesis occurs under replicative conditions. One of the major polymerisation effects was stalling, but each of the individual proteins could insert and extend past 8-oxodG with differing efficiencies. The introduction of RPA and PCNA influenced PolB and PolD in...
Tipo: Text
Ano: 2019
URL: https://archimer.ifremer.fr/doc/00502/61372/64989.pdf

The ocean sampling day consortium
Provedor de dados: Institutional Archive of Ifreme (ArchiMer)
Autores: Kopf, Anna; Bicak, Mesude; Kottmann, Renzo; Schnetzer, Julia; Kostadinov, Ivaylo; Lehmann, Katja; Fernandez-guerra, Antonio; Jeanthon, Christian; Rahav, Eyal; Ullrich, Matthias; Wichels, Antje; Gerdts, Gunnar; Polymenakou, Paraskevi; Kotoulas, Giorgos; Siam, Rania; Abdallah, Rehab Z.; Sonnenschein, Eva C.; Cariou, Thierry; O'Gara, Fergal; Jackson, Stephen; Orlic, Sandi; Steinke, Michael; Busch, Julia; Duarte, Bernardo; Cacador, Isabel; Canning-clode, Joao; Bobrova, Oleksandra; Marteinsson, Viggo; Reynisson, Eyjolfur; Loureiro, Clara Magalhaes; Luna, Gian Marco; Quero, Grazia Marina; Loescher, Carolin R.; Kremp, Anke; Delorenzo, Marie E.; Ovreas, Lise; Tolman, Jennifer; Laroche, Julie; Penna, Antonella; Frischer, Marc; Davis, Timothy; Katherine, Barker; Meyer, Christopher P.; Ramos, Sandra; Magalhaes, Catarina; Jude-lemeilleur, Florence; Leopoldina Aguirre-macedo, Ma; Wang, Shiao; Poulton, Nicole; Jones, Scott; Collin, Rachel; Fuhrman, Jed A.; Conan, Pascal; Alonso, Cecilia; Stambler, Noga; Goodwin, Kelly; Yakimov, Michael 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; 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; Silveira, Jorge A. Herrera; Barbier, Michele; Turk, Valentina; Tinta, Tinkara; Fuller, Wayne J.; Salihoglu, Ilkay; Serakinci, Nedime; Ergoren, Mahmut Cerkez; Bresnan, Eileen; Iriberri, Juan; Nyhus, Paul Anders Fronth; Bente, Edvardsen; Karlsen, Hans Erik; Golyshin, Peter N.; Gasol, Josep M.; Moncheva, Snejana; Dzhembekova, Nina; Johnson, Zackary; Sinigalliano, Christopher David; Gidley, Maribeth Louise; Zingone, Adriana; Danovaro, Roberto; Tsiamis, George; 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; Gloeckner, Frank Oliver.
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.
Tipo: Text
Palavras-chave: Ocean sampling day; OSD; Biodiversity; Genomics; Health Index; Bacteria; Microorganism; Metagenomics; Marine; Micro B3; Standards.
Ano: 2015
URL: https://archimer.ifremer.fr/doc/00371/48262/48647.pdf

Methanogenic activity and diversity in the centre of the Amsterdam Mud Volcano, Eastern Mediterranean Sea
Provedor de dados: Institutional Archive of Ifreme (ArchiMer)
Autores: Lazar, Cassandre; Parkes, R. John; Cragg, Barry A.; L'Haridon, Stephane; Toffin, Laurent.
Marine mud volcanoes are geological structures emitting large amounts of methane from their active centres. The Amsterdam mud volcano (AMV), located in the Anaximander Mountains south of Turkey, is characterized by intense active methane seepage produced in part by methanogens. To date, information about the diversity or the metabolic pathways used by the methanogens in active centres of marine mud volcanoes is limited. 14C-radiotracer measurements showed that methylamines/methanol, H2/CO2 and acetate were used for methanogenesis in the AMV. Methylotrophic methanogenesis was measured all along the sediment core, Methanosarcinales affiliated sequences were detected using archaeal 16S PCR-DGGE and mcrA gene libraries, and enrichments of methanogens showed...
Tipo: Text
Palavras-chave: Methanogenesis; McrA; Archaea.
Ano: 2012
URL: http://archimer.ifremer.fr/doc/00087/19795/17538.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

Etude de la diversité microbienne des bassins hypersalés anoxiques profonds de la Mer Méditerranée orientale
Provedor de dados: Institutional Archive of Ifreme (ArchiMer)
Autores: L'Haridon, Stephane.
 Since 1983, the existence of Deep Hypersaline anoxic basins (DHABs) has been revealed in the Eastern Mediterranean basin. These basins which represent extremes environments (anoxic, hypersalty, dark, high hydrostatic pressure)  have  been  under  investigation  and  increasing  interest  the  last  fifteen  years.  The  molecular  approaches revealed  the  presence  of  active  and  uncultivated  microbial  communities  in  the  DHABs  with  two  main  metabolic processes  such  as  methanogenesis  and  sulphate-reduction.  Until  now,  no  representative  strain  of  the  different uncultivated lineages thriving in the DHABs (ex : lineages MSBL, Mediteranean Sea Brine Lake) or involved in the two processes  have  been  yet  cultivated.  The  main ...
Tipo: Text
Palavras-chave: DHABs; Environnement extrême; Methanohalophilus; Pression hydrostatique; Génome.; DHABs; Extreme environnement; Methanohalophilus; Hydrostatic pressure; Genome.
Ano: 2017
URL: https://archimer.ifremer.fr/doc/00609/72136/70888.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

Archaeal Populations in Hypersaline Sediments Underlying Orange Microbial Mats in the Napoli Mud Volcano
Provedor de dados: Institutional Archive of Ifreme (ArchiMer)
Autores: Lazar, Cassandre Sara; L'Haridon, Stephane; Pignet, Patricia; Toffin, Laurent.
Microbial mats in marine cold seeps are known to be associated with ascending sulfide- and methane-rich fluids. Hence, they could be visible indicators of anaerobic oxidation of methane (AOM) and methane cycling processes in underlying sediments. The Napoli mud volcano is situated in the Olimpi Area that lies on saline deposits; from there, brine fluids migrate upward to the seafloor. Sediments associated with a brine pool and microbial orange mats of the Napoli mud volcano were recovered during the Medeco cruise. Based on analysis of RNA-derived sequences, the "active" archaeal community was composed of many uncultured lineages, such as rice cluster V or marine benthic group D. Function methyl coenzyme M reductase (mcrA) genes were affiliated with the...
Tipo: Text
Ano: 2011
URL: http://archimer.ifremer.fr/doc/00035/14589/12126.pdf

Intrinsic properties of the two replicative DNA polymerases of Pyrococcus abyssi in replicating abasic sites: possible role in DNA damage tolerance?
Provedor de dados: Institutional Archive of Ifreme (ArchiMer)
Autores: Palud, Adeline; Villani, Giuseppe; L'Haridon, Stephane; Querellou, Joel; Raffin, Jean-paul; Henneke, Ghislaine.
Spontaneous and induced abasic sites in hyperthermophiles DNA have long been suspected to occur at high frequency. Here, Pyrococcus abyssi was used as an attractive model to analyse the impact of such lesions onto the maintenance of genome integrity. We demonstrated that endogenous AP sites persist at a slightly higher level in P. abyssi genome compared with Escherichia coli. Then, the two replicative DNA polymerases, PabpolB and PabpolD, were characterized in presence of DNA containing abasic sites. Both Pabpols had abortive DNA synthesis upon encountering AP sites. Under running start conditions, PabpolB could incorporate in front of the damage and even replicate to the full-length oligonucleotides containing a specific AP site, but only when present at...
Tipo: Text
Ano: 2008
URL: http://archimer.ifremer.fr/doc/2008/publication-6113.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

Profundibacter amoris gen. nov., sp. nov., a new member of the Roseobacter clade isolated from Loki’s Castle Vent Field on the Arctic Mid-Ocean Ridge.
Provedor de dados: Institutional Archive of Ifreme (ArchiMer)
Autores: Le Moine Bauer, Sven; Sjøberg, Andreas Gilje; L'Haridon, Stephane; Stokke, Runar; Roalkvam, Irene; Steen, Ida Helene; Dahle, Håkon.
A bacterial strain, designated BAR1T, was isolated from a microbial mat growing on the surface of a barite chimney at the Loki’s Castle Vent Field, at a depth of 2216 m. Cells of strain BAR1T were rod-shaped, Gram-reaction-negative and grew on marine broth 2216 at 10–37 °C (optimum 27–35 °C), pH 5.5–8.0 (optimum pH 6.5–7.5) and 0.5–5.0 % NaCl (optimum 2 %). The DNA G+C content was 57.38 mol%. The membrane-associated major ubiquinone was Q-10, the fatty acid profile was dominated by C18 : 1ω7c (91 %), and the polar lipids detected were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, one unidentified aminolipid, one unidentified lipid and one unidentified phospholipid. Phylogenetic analyses based on 16S rRNA gene sequences showed that...
Tipo: Text
Palavras-chave: Roseobacter; Alphaproteobacteria; Piezophilic; Isolate; Deep-sea; Hydrothermal vent.
Ano: 2019
URL: https://archimer.ifremer.fr/doc/00482/59323/62117.pdf