Thermococcus henrietii 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 EXT12cT, 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, 2.0%), from pH 6.0 to 7.5 (optimum, pH 6.5-7.0), at temperatures between 60 and 95 °C (optimum, 80-85 °C), and at pressures from 0.1 to at least 50 MPa (optimum, 30 MPa). Strain EXT12cT grew chemoorganoheterotrophically on complex proteinaceous substrates. Its growth was highly stimulated by the presence of elemental sulphur or l-cystine, which were reduced to hydrogen sulfide. The DNA G+C content was 54.58 mol%. Phylogenetic analyses based on 16S rRNA gene sequences and concatenated ribosomal protein sequences showed that strain EXT12cT falls into the genus Thermococcus and is most closely related to Thermococcus nautili strain 30-1T. Overall genome relatedness index analyses (average nucleotide identity scores and in silico DNA-DNA hybridizations) showed a sufficient genomic distance between the new genome and the ones of the Thermococcus type strains for the delineation of a new species. On the basis of genotypic and phenotypic data, strain EXT12cT is considered to represent a novel species, for which the name Thermococcus henrietii sp. nov. is proposed, with the type strain EXT12cT (=UBOCC M-2417T=DSM 111004T).

Thermococcus camini sp. nov., a hyperthermophilic and piezophilic archaeon isolated from a deep-sea hydrothermal vent at the Mid-Atlantic Ridge.

A coccoid-shaped, strictly anaerobic, hyperthermophilic and piezophilic organoheterotrophic archaeon, strain Iri35cT, was isolated from a hydrothermal chimney rock sample collected at a depth of 2300 m at the Mid-Atlantic Ridge (Rainbow vent field). Cells of strain Iri35cT grew at NaCl concentrations ranging from 1-5 % (w/v) (optimum 2.0 %), from pH 5.0 to 9.0 (optimum 7.0-7.5), at temperatures between 50 and 90 °C (optimum 75-80 °C) and at pressures from 0.1 to at least 50 MPa (optimum: 10-30 MPa). The novel isolate grew on complex organic substrates, such as yeast extract, tryptone, peptone or beef extract, preferentially in the presence of elemental sulphur or l-cystine; however, these molecules were not necessary for growth. Its genomic DNA G+C content was 54.63 mol%. The genome has been annotated and the metabolic predictions are in accordance with the metabolic characteristics of the strain and of Thermococcales in general. Phylogenetic analyses based on 16S rRNA gene sequences and concatenated ribosomal protein sequences showed that strain Iri35cT belongs to the genus Thermococcus, and is closer to the species T. celericrescens and T. siculi. Average nucleotide identity scores and in silico DNA-DNA hybridization values between the genome of strain Iri35cT and the genomes of the type species of the genus Thermococcus were below the species delineation threshold. Therefore, and considering the phenotypic data presented, strain Iri35cT is suggested to represent a novel species, for which the name Thermococcus camini sp. nov. is proposed, with the type strain Iri35cT (=UBOCC M-2026T=DSM 111003T).

Combined Study of Titanium Dioxide Nanoparticle Transport and Toxicity on Microbial Nitrifying Communities under Single and Repeated Exposures in Soil Columns.

Soils are exposed to nanoparticles (NPs) as a result of their increasing use in many commercial products. Adverse effects of NPs on soil microorganisms have been reported in several ecotoxicological studies using microcosms. Although repeated exposures are more likely to occur in soils, most of these previous studies were performed as a single exposure to NPs. Contrary to single contamination, the study of multiple NP contaminations in soils requires the use of specialized setups. Using a soil column experiment, we compared the influence of single and repeated exposures (one, two, or three exposures that resulted in the same final concentration applied) on the transport of titanium dioxide (TiO2) NPs through soil and the effect of these different exposure scenarios on the abundance and activity of soil nitrifying microbial communities after a 2 month incubation. The transport of TiO2 NPs was very limited under both single and repeated exposures and was highest for the lowest concentration injected during the first application. Significant decreases in nitrification activity and ammonia-oxidizing archaea and bacteria populations were observed only for the repeated exposure scenario (three TiO2 NP contaminations). These results suggest that, under repeated exposures, the transport of TiO2 NPs to deep soil layers and groundwater is limited and that a chronic contamination is more harmful for the soil microbiological functioning than a single exposure.

Role of macropore flow in the transport of Escherichia coli cells in undisturbed cores of a brown leached soil.

The objective of this work was to evaluate the transport of Escherichia coli cells in undisturbed cores of a brown leached soil collected at La Côte St André (France). Two undisturbed soil cores subjected to repeated injections of bacterial cells and/or bromide tracer were used to investigate the effect of soil hydrodynamics and ionic strength on cell mobility. Under the tested experimental conditions, E. coli cells were shown to be transported at the water velocity (retardation factor close to 1) and their retention appeared almost insensitive to water flow and ionic strength variations, both factors being known to control bacterial transport in model saturated porous media. In contrast, E. coli breakthrough curves evolved significantly along with the repetition of the cell injections in each soil core, with a progressive acceleration of their transport. The evolution of E. coli cells BTCs was shown to be due to the evolution of the structure of soil hydraulic pathways caused by the repeated water infiltrations and drainage as may occur in the field. This evolution was demonstrated through mercury intrusion porosimetry (MIP) performed on soil aggregates before and after the repeated infiltrations of bacteria. MIP revealed a progressive and important reduction of the soil aggregate porosity, n, that decreased from approximately 0.5 to 0.3, along with a decrease of the soil percolating step from 27 to 2 µm. From this result a clear compaction of soil aggregates was evidenced that concerned preferentially the pores larger than 2 µm equivalent diameter, i.e. those allowing bacterial cell passage. Since no significant reduction of the global soil volume was observed at the core scale, this aggregate compaction was accompanied by macropore formation that became progressively the preferential hydraulic pathway in the soil cores, leading to transiently bi-modal bacterial BTCs. The evolution of the soil pore structure induced a modification of the main hydrodynamic processes, evolving from a matrix-dominant transfer of water and bacteria to a macropore-dominant transfer. This work points out the importance of using undisturbed natural soils to evaluate the mobility of bacteria in the field, since the evolving hydrodynamic properties of soils appeared to dominate most physicochemical factors.