Phenylobacterium ferrooxidans sp. nov., isolated from a sub-surface geothermal aquifer in Iceland.

A novel bacterial strain, HK31-G, was isolated from a subsurface geothermal aquifer (Hellisheidi, SW-Iceland) and was characterized using a polyphasic taxonomic approach. Phylogenetic analysis of 16S rRNA gene along with phylogenomic position indicated that the novel strain belongs to the genus Phenylobacterium. Cells are motile Gram-negative thin rods.

Evolutionary and functional insights into the Ski2-like helicase family in Archaea: a comparison of Thermococcales ASH-Ski2 and Hel308 activities.

RNA helicases perform essential housekeeping and regulatory functions in all domains of life by binding and unwinding RNA molecules. The Ski2-like proteins are primordial helicases that play an active role in eukaryotic RNA homeostasis pathways, with multiple homologs having specialized functions. The significance of the expansion and diversity of Ski2-like proteins in Archaea, the third domain of life, has not yet been established.

Processing of matched and mismatched rNMPs in DNA by archaeal ribonucleotide excision repair.

Ribonucleoside monophosphates (rNMPs) are the main non-canonical nucleotides in genomic DNA, and their incorporation can occur as mismatches or matches . To counteract the mutagenic potential of rNMPs in DNA, all organisms evolved ribonucleotide excision repair (RER), a mechanism initiated by type 2 RNase H. Here, we describe the reconstitution of matched and mismatched rNMP repair using archaeal RER enzymes.

The secretome of Thermococcus barophilus in the presence of carbohydrates and the potential role of the TrmBL4 regulator.

Global transcriptional regulators are crucial for supporting rapid adaptive responses in changing environments. In Thermococcales, the TrmB sugar-sensing regulator family is well represented but knowledge of the functional role/s of each of its members is limited. In this study, we examined the link between TrmBL4 and the degree of protein secretion in different sugar environments in the hyperthermophilic Archaeon Thermococcus barophilus.

Genome analysis of a new sulphur disproportionating species strain F29 and comparative genomics of sulfur-disproportionating bacteria from marine hydrothermal vents.

This paper reports on the genome analysis of strain F29 representing a new species of the genus . This strain, isolated from the Lucky Strike hydrothermal vent field on the Mid-Atlantic Ridge, is able to grow by disproportionation of S with CO as a carbon source. Strain F29 possesses a genome of 2,345,565 bp, with a G+C content of 58.

Genetic Potential of , an Obligate Sulfur-Disproportionating Thermophilic Microorganism.

The biochemical pathways of anaerobic sulfur disproportionation are only partially deciphered, and the mechanisms involved in the first step of S-disproportionation remain unknown. Here, we present the results of sequencing and analysis of the complete genome of strain Sh68, one of two strains isolated to date known to grow exclusively by anaerobic disproportionation of inorganic sulfur compounds. Sh68 is a motile, thermophilic, anaerobic, chemolithoautotrophic microorganism isolated from a hydrothermal pond at Uzon caldera, Kamchatka, Russia.

The Piezo-Hyperthermophilic Archaeon Regulates Its Energy Efficiency System to Cope With Large Hydrostatic Pressure Variations.

Deep-sea ecosystems share a common physical parameter, namely high hydrostatic pressure (HHP). Some of the microorganisms isolated at great depths have a high physiological plasticity to face pressure variations. The adaptive strategies by which deep-sea microorganisms cope with HHP variations remain to be elucidated, especially considering the extent of their biotopes on Earth.

Physiological and Genomic Characterization of a Hyperthermophilic Archaeon sp. nov. Isolated From a Deep-Sea Hydrothermal Vent Warrants the Reclassification of the Genus .

Hyperthermophilic archaea of the genus are the subject of many fundamental and biotechnological researches. Despite their significance, the class is currently represented by only eight species obtained as axenic cultures and taxonomically characterized. Here, we report the isolation and characterization of a new species of from a deep-sea hydrothermal vent (Mid-Atlantic Ridge, TAG) for which the name sp.

sp. nov., a novel extreme thermophilic and piezophilic sulfur-reducing archaeon isolated from a deep-sea hydrothermal chimney.

A novel extreme thermophilic and piezophilic chemoorganoheterotrophic archaeon, strain EXT12c, was isolated from a hydrothermal chimney sample collected at a depth of 2496 m at the East Pacific Rise 9° N. Cells were strictly anaerobic, motile cocci. The strain grew at NaCl concentrations ranging from 1 to 5 % (w/v; optimum, 2.

Genome analysis of Thermosulfuriphilus ammonigenes ST65, an anaerobic thermophilic chemolithoautotrophic bacterium isolated from a deep-sea hydrothermal vent.

Thermosulfuriphilus ammonigenes ST65 is an anaerobic thermophilic bacterium isolated from a deep-sea hydrothermal vent chimney. T. ammonigenes is an obligate chemolithoautotroph utilizing elemental sulfur as an electron donor and nitrate as an electron acceptor with sulfate and ammonium formation.

Methanohalophilus profundi sp. nov., a methylotrophic halophilic piezophilic methanogen isolated from a deep hypersaline anoxic basin.

A novel anaerobic methylotrophic halophilic methanogen strain SLHTYRO was isolated from a deep hypersaline anoxic basin called "Tyro" located in the Eastern Mediterranean Sea. Cells of SLHTYRO were motile cocci. The strain SLHTYRO grew between 12 and 37 °C (optimum 30 °C), at pH between 6.

Genomic Characterization and Environmental Distribution of a Thermophilic Anaerobe SH388 Involved in Disproportionation of Sulfur Compounds in Shallow Sea Hydrothermal Vents.

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. SH388 is an anaerobic thermophilic bacterium isolated from a shallow sea hydrothermal vent.

Complete genome sequence of Thermosulfurimonas marina SU872, an anaerobic thermophilic chemolithoautotrophic bacterium isolated from a shallow marine hydrothermal vent.

Thermosulfurimonas marina strain SU872 is a thermophilic, anaerobic, chemolithoautotrophic bacterium, isolated from a shallow-sea hydrothermal vent in the Pacific Ocean near Kunashir Island, that is able to grow by disproportionation of inorganic sulfur compounds and dissimilatory nitrate reduction to ammonium. Here we report the complete genome sequence of strain SU872, which presents one circular chromosome of 1,763,258 bp with a mean G + C content of 58.9 mol%.

Complete genome sequence of Methanofervidicoccus sp. A16, a thermophilic methanogen isolated from Mid Cayman Rise hydrothermal vent.

Methanofervidicoccus sp. A16 is a novel thermophilic and obligate hydrogenotrophic methanogen isolated from a deep-sea hydrothermal vent chimney sample at the Mid Cayman spreading center, Caribbean Sea. Here we report the complete genome of strain A16, which has one circular chromosome of 1,485,358 bp with a mean G+C content of 35.

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.

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.

Experimental and Simulation Efforts in the Astrobiological Exploration of Exooceans.

The icy satellites of Jupiter and Saturn are perhaps the most promising places in the Solar System regarding habitability. However, the potential habitable environments are hidden underneath km-thick ice shells. The discovery of Enceladus' plume by the Cassini mission has provided vital clues in our understanding of the processes occurring within the interior of exooceans.

Genomic Insights into the Carbon and Energy Metabolism of a Thermophilic Deep-Sea Bacterium Revealed New Metabolic Traits in the Phylum .

Information on the biochemical pathways of carbon and energy metabolism in representatives of the deep lineage bacterial phylum are scarce. Here, we report the results of the sequencing and analysis of the high-quality draft genome of the thermophilic chemolithoautotrophic anaerobe . Genomic data suggest that CO assimilation is carried out by recently proposed reversible tricarboxylic acid cycle ("roTCA cycle").

Chemosynthetic ectosymbionts associated with a shallow-water marine nematode.

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.

Electroactive Bacteria Associated With Stainless Steel Ennoblement in Seawater.

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.

The Effect of Crowding on Protein Stability, Rigidity, and High Pressure Sensitivity in Whole Cells.

In live cells, high concentrations up to 300-400 mg/mL, as in Eschericia coli (Ellis, R. J. Curr.

Development of an Effective 6-Methylpurine Counterselection Marker for Genetic Manipulation in Thermococcus barophilus.

A gene disruption system for was developed using simvastatin (HMG-CoA reductase encoding gene) for positive selection and 5-Fluoroorotic acid (5-FOA), a 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 (<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 , consistently correlated with the gene (encoding a hypoxanthine-guanine phosphoribosyl-transferase).

Complete Genome Sequence of the Halophilic Methylotrophic Methanogen Archaeon Strain FDF-1.

We report here the complete genome sequence (2.08 Mb) of strain FDF-1, 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 , , and are three different species within the family.

Arsenobetaine: an ecophysiologically important organoarsenical confers cytoprotection against osmotic stress and growth temperature extremes.

Arsenic, a highly cytotoxic and cancerogenic metalloid, is brought into the biosphere through geochemical sources and anthropogenic activities. A global biogeochemical arsenic biotransformation cycle exists in which inorganic arsenic species are transformed into organoarsenicals, which are subsequently mineralized again into inorganic arsenic compounds. Microorganisms contribute to this biotransformation process greatly and one of the organoarsenicals synthesized and degraded in this cycle is arsenobetaine.

Draft Genome Sequence of Type Strain 306, an Alphaproteobacterium Isolated from Mediterranean Sea Sediments.

strain 306 is an alphaproteobacterium isolated from Mediterranean Sea sediments. It belongs to the genus , 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.