New insight into the contributions of thermogenic processes and biogenic sources to the generation of organic compounds in hydrothermal fluids.

Experiments on hydrothermal degradation of Pyrococcus abyssi biomass were conducted at elevated pressure (40 MPa) over a 200-450 °C temperature range in sapphire reaction cells. Few organic compounds could be detected in the 200 °C experiment. This lack was attributed to an incomplete degradation of P. abyssi cells. On the contrary, a wide range of soluble organic molecules were generated at temperatures ≥ 350 °C including toluene, styrene, C8-C16 alkyl-benzenes, naphthalene, C11-C16 alkyl-naphthalenes, even carbon number C12-C18 polycyclic aromatic hydrocarbons, C15-C18 alkyl-phenanthrenes and C8:0-C16:0 n-carboxylic acids. The effect of time on the final organic composition of the degraded P. abyssi solutions at 350 °C was also investigated. For that purpose the biomass was exposed for 10, 20, 60, 90, 270 and 720 min at 350 °C. We observed a similar effect of temperature and time on the chemical diversity obtained. In addition, temperature and time increased the degree of alkylation of alkyl-benzenes. This study offers additional evidence that a portion of the aliphatic hydrocarbons present in the fluids from the Rainbow ultramafic-hosted hydrothermal field may be abiogenic whereas a portion of the aromatic hydrocarbons and n-carboxylic acids may have a biogenic origin. We suggest that aromatic hydrocarbons and linear fatty acids at the Rainbow site may be derived directly from thermogenic alteration of material from the sub-seafloor biosphere. Yet we infer that the formation and dissolution of carboxylic acids in hydrothermal fluids may be controlled by other processes than in our experiments.

Geoglobus acetivorans sp. nov., an iron(III)-reducing archaeon from a deep-sea hydrothermal vent.

A hyperthermophilic, anaerobic, dissimilatory Fe(III)-reducing, facultatively chemolithoautotrophic archaeon (strain SBH6(T)) was isolated from a hydrothermal sample collected from the deepest of the known World Ocean hydrothermal fields, Ashadze field (1 degrees 58' 21'' N 4 degrees 51' 47'' W) on the Mid-Atlantic Ridge, at a depth of 4100 m. The strain was enriched using acetate as the electron donor and Fe(III) oxide as the electron acceptor. Cells of strain SBH6(T) were irregular cocci, 0.3-0.5 mum in diameter. The temperature range for growth was 50-85 degrees C, with an optimum at 81 degrees C. The pH range for growth was 5.0-7.5, with an optimum at pH 6.8. Growth of SBH6(T) was observed at NaCl concentrations ranging from 1 to 6 % (w/v) with an optimum at 2.5 % (w/v). The isolate utilized acetate, formate, pyruvate, fumarate, malate, propionate, butyrate, succinate, glycerol, stearate, palmitate, peptone and yeast extract as electron donors for Fe(III) reduction. It was also capable of growth with H(2) as the sole electron donor, CO(2) as a carbon source and Fe(III) as an electron acceptor without the need for organic substances. Fe(III) [in the form of poorly crystalline Fe(III) oxide or Fe(III) citrate] was the only electron acceptor that supported growth. 16S rRNA gene sequence analysis revealed that the closest relative of the isolated organism was Geoglobus ahangari 234(T) (97.0 %). On the basis of its physiological properties and phylogenetic analyses, the isolate is considered to represent a novel species, for which the name Geoglobus acetivorans sp. nov. is proposed. The type strain is SBH6(T) (=DSM 21716(T) =VKM B-2522(T)).

Deferribacter autotrophicus sp. nov., an iron(III)-reducing bacterium from a deep-sea hydrothermal vent.

A thermophilic, anaerobic, chemolithoautotrophic bacterium (designated strain SL50(T)) was isolated from a hydrothermal sample collected at the Mid-Atlantic Ridge from the deepest of the known World ocean hydrothermal fields, Ashadze field (1 degrees 58' 21'' N 4 degrees 51' 47'' W) at a depth of 4100 m. Cells of strain SL50(T) were motile, straight to bent rods with one polar flagellum, 0.5-0.6 mum in width and 3.0-3.5 mum in length. The temperature range for growth was 25-75 degrees C, with an optimum at 60 degrees C. The pH range for growth was 5.0-7.5, with an optimum at pH 6.5. Growth of strain SL50(T) was observed at NaCl concentrations ranging from 1.0 to 6.0 % (w/v) with an optimum at 2.5 % (w/v). The generation time under optimal growth conditions for strain SL50(T) was 60 min. Strain SL50(T) used molecular hydrogen, acetate, lactate, succinate, pyruvate and complex proteinaceous compounds as electron donors, and Fe(III), Mn(IV), nitrate or elemental sulfur as electron acceptors. The G+C content of the DNA of strain SL50(T) was 28.7 mol%. 16S rRNA gene sequence analysis revealed that the closest relative of strain SL50(T) was Deferribacter abyssi JR(T) (95.5 % similarity). On the basis of its physiological properties and phylogenetic analyses, the isolate is considered to represent a novel species, for which the name Deferribacter autotrophicus sp. nov. is proposed. The type strain is SL50(T) (=DSM 21529(T)=VKPM B-10097(T)). Deferribacter autotrophicus sp. nov. is the first described deep-sea bacterium capable of chemolithoautotrophic growth using molecular hydrogen as an electron donor and ferric iron as electron acceptor and CO(2) as the carbon source.

Cloning, expression, and characterization of DNA polymerase I from the hyperthermophilic archaea Thermococcus fumicolans.

The DNA polymerase I gene of a newly described deep-sea hydrothermal vent Archaea species, Thermococcus fumicolans, from IFREMERS's collection of hyperthermophiles has been cloned in Escherichia coli. As in Thermococcus litoralis, the gene is split by two intervening sequences (IVS) encoding inteins inserted in sites A and C of family B DNA polymerases. The entire DNA polymerase gene, containing both inteins, was expressed at 30 degrees C in E. coli strain BL21(DE3)pLysS using the pARHS2 expression vector. The native polypeptide precursor of 170kDa was obtained, and intein splicing as well as ligation of the three exteins was observed in vitro after heat exposure. The recombinant enzyme was purified and some of its activities were characterized: polymerization, thermostability, exonuclease activities, and fidelity.

Pyrococcus glycovorans sp. nov., a hyperthermophilic archaeon isolated from the East Pacific Rise.

A hyperthermophilic archaeon, strain AL585T, was isolated from a deep-sea hydrothermal vent located on the East Pacific Rise at latitude 13 degrees N and a depth of 2650 m. The isolate was a strictly anaerobic coccus with a mean cell diameter of 1 micron. The optimum temperature, pH and concentration of sea salt for growth were 95 degrees C, 7.5 and 30 g l-1. Under these conditions, the doubling time and cell yield were 0.5 h and 5 x 10(8) cells ml-1. Strain AL585T grew preferentially in media containing complex proteinaceous carbon sources, glucose and elemental sulfur. The G + C content of the DNA was 47 mol%. Sequencing of the 16S rDNA gene showed that strain AL585T belonged to the genus Pyrococcus and was probably a new species. This was confirmed by total DNA hybridization. Consequently, this strain is described as a new species, Pyrococcus glycovorans sp. nov.

Thermococcus hydrothermalis sp. nov., a new hyperthermophilic archaeon isolated from a deep-sea hydrothermal vent.

An extremely thermophilic archaeon, strain AL662T, was isolated from a deep-sea hydrothermal vent located on the East Pacific Rise at a latitude of 21 degrees N. This strain is a strictly anaerobic coccus, and its cells range from 0.8 to 2 microns in diameter. The optimum temperature, pH, and Sea Salt concentration for growth are 85 degrees C, 6, and 20 to 40 g/liter, respectively. Strain AL662T grows preferentially on proteolysis products, on a mixture of 20 amino acids, and on maltose in the presence of elemental sulfur. The membrane lipids consist of di- and tetraether glycerol lipids. The DNA G+C content is 58 mol%. Sequencing of the 16S rRNA gene showed that strain AL662T belongs to the genus Thermococcus. On the basis of hybridization results, we propose that this strain should be placed in a new species, Thermococcus hydrothermalis.

A putative SOS repair gene (dinF-like) in a hyperthermophilic archaeon.

The hyperthermophilic archaeon, Pyrococcus (strain IFREMER AL585), contains an ORF that encodes a polypeptide with a high similarity to the Escherichia coli dinF (DNA damage-inducible) gene product. The conservation of this protein between Archaea and Bacteria suggests that a SOS repair system might operate in Archaea.