Anaerobic methane-oxidizing activity in a deep underground borehole dominantly colonized by Ca. Methanoperedenaceae.

The family Ca. Methanoperedenaceae archaea mediates the anaerobic oxidation of methane (AOM) in different terrestrial environments. Using a newly developed high-pressure laboratory incubation system, we investigated 214- and 249-m deep groundwater samples at Horonobe Underground Research Laboratory, Japan, where the high and low abundances of Ca. Methanoperedenaceae archaea have been shown by genome-resolved metagenomics, respectively. The groundwater samples amended with 13 C-labelled methane and amorphous Fe(III) were incubated at a pressure of 1.6 MPa. After 3-7 days of incubation, the AOM rate was 45.8 ± 19.8 nM/day in 214-m groundwater. However, almost no activity was detected from 249-m groundwater. Based on the results from 16S rRNA gene analysis, the abundance of Ca. Methanoperedenaceae archaea was high in the 214-m deep groundwater sample, whereas Ca. Methanoperedenaceae archaea was undetected in the 249-m deep groundwater sample. These results support the in situ AOM activity of Ca. Methanoperedenaceae archaea in the 214-m deep subsurface borehole interval. Although the presence of Fe-bearing phyllosilicates was demonstrated in the 214-m deep groundwater, it needs to be determined whether Ca. Methanoperedenaceae archaea use the Fe-bearing phyllosilicates as in situ electron acceptors by high-pressure incubation amended with the Fe-bearing phyllosilicates.

Sorption of Cs+ and Eu3+ ions onto sedimentary rock in the presence of gamma-irradiated humic acid.

The influence of humic acid (HA) and its radiological degradation on the sorption of Cs+ and Eu3+ by sedimentary rock (obtained from the Horonobe Underground Research Laboratory in Japan) was investigated to understand the sorption process of metal ions and humic substances. Aldrich HA solution was gamma-irradiated assuming a strong radiation from a highly radioactive waste to be disposed of in deep geological formations. Batch sorption experiments were performed to evaluate the effect of gamma-irradiated HA on the sorption of Cs+ and Eu3+ ions. The addition of non-irradiated HA weakened the Eu sorption because of the lower sorption of the negatively charged Eu-HA complexes compared with free Eu ions. The sorption of Cs ions was barely affected by the presence of HA and its gamma irradiation. The concentration ratio of metal complexed and non-complexed species in the solid and liquid phases was evaluated by sequential filtration and chemical equilibrium calculations. The ratios were low in both phases for Cs and supported the minimal contribution of HA to Cs sorption. However, the concentration ratio for Eu3+ in the liquid phase was high, indicating that the complexing ability of HA to Eu3+ was higher than that of HA to Cs+.

Deep groundwater physicochemical components affecting actinide migration.

To better understand the migration behavior of actinides in deep groundwater (GW), the interactions between doped tracers and deep GW components were investigated. La, Sm, Ho, and U tracers (10 or 100 ppb) were doped into sedimentary rock GW samples collected from 250 to 350 m deep boreholes in the experimental gallery of the Horonobe Underground Research Laboratory (URL), Hokkaido, Japan. To evaluate the effect of GW composition on the chemical speciation of actinides, the same tracers were doped into crystalline rock GW samples collected from 300 to 500 m deep boreholes in the experimental gallery at the Mizunami URL, Gifu Prefecture, Japan. Each GW sample was sequentially filtered through a micro-pore filter (0.2 µm) and ultrafilters with a 10 kDa nominal molecular weight limit. Next, the filtrate solutions were analyzed using inductively coupled plasma-mass spectrometry to determine the concentration of tracers retained in solution during each filtration step, and the used filters were analyzed using time-of-flight secondary ion mass spectrometry element mapping and X-ray absorption fine structure spectroscopy to determine the chemical species of the tracers trapped on each filter. It was determined that lanthanide migration was controlled by the amount of phosphates in the Horonobe GW. Therefore, it was expected that the solubility of minor actinides (MAs), which exhibit a similar chemical behavior to that of lanthanides, would be controlled by the formation of phosphates in sedimentary rock GW. Moreover, the data on the Mizunami GW indicated that a fraction of lanthanides and MAs formed hydroxides and/or hydroxocarbonates.

Desulfovibrio subterraneus sp. nov., a mesophilic sulfate-reducing deltaproteobacterium isolated from a deep siliceous mudstone formation.

A novel mesophilic sulfate-reducing bacterium, strain HN2T, was isolated from groundwater sampled from the subsurface siliceous mudstone of the Wakkanai Formation located in Horonobe, Hokkaido, Japan. The bacterium was Gram-negative and vibrio-shaped, and its motility was conferred by a single polar flagellum. Cells had desulfoviridin. Catalase and oxidase activities were not detected. It grew in the temperature range of 25-40 °C (optimum, 35 °C) and pH range of 6.3-8.1 (optimum, pH 7.2-7.6). It used sulfate, thiosulfate, dimethyl sulfoxide, anthraquinone-2,6-disulfonate, Fe3+, and manganese oxide, but not elemental sulfur, nitrite, nitrate, or fumarate as electron acceptors. The strain showed weak growth with sulfite as the electron acceptor. Fermentative growth with pyruvate, lactate and cysteine was observed in the absence of sulfate, but not with malate or fumarate. NaCl was not required, but the strain tolerated up to 40 g l-1. Strain HN2T did not require vitamins. The major cellular fatty acids were iso-C15 : 0 (23.8 %), C18 : 1 ω9t (18.4 %), C18 : 0 (15.0 %), C16 : 0 (14.5 %), and anteiso-C17 :0 (10.1 %). The major respiratory quinone was menaquinone MK-6(H2). The G+C content of the genomic DNA was 56.7 mol%. Based on 16S rRNA gene sequence analysis, the closest phylogenetic relative of strain HN2T is Desulfovibrio psychrotolerans JS1T (97.0 %). Digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values of the strains HN2T and D. psychrotolerans JS1T were 22.2 and 79.8 %, respectively. Based on the phenotypic and molecular genetic evidence, we propose a novel species, D. subterraneus sp. nov. with the type strain HN2T (=DSM 101010T=NBRC 112213T).

A Proposed Method to Estimate In Situ Dissolved Gas Concentrations in Gas-Saturated Groundwater.

Gas-saturated groundwater forms bubbles when brought to atmospheric pressure, preventing precise determination of its in situ dissolved gas concentrations. To overcome this problem, a modeling approach called the atmospheric sampling method is suggested here to recover the in situ dissolved gas concentrations of groundwater collected ex situ under atmospheric conditions at the Horonobe Underground Research Laboratory, Japan. The results from this method were compared with results measured at the same locations using two special techniques, the sealed sampler and pre-evacuated vial methods, that have been developed to collect groundwater under its in situ conditions. In gas-saturated groundwater cases, dissolved methane and inorganic carbon concentrations derived using the atmospheric sampling method were mostly within ±4 and ±10%, respectively, of values from the sealed sampler and pre-evacuated vial methods. In gas-unsaturated groundwater, however, the atmospheric sampling method overestimated the in situ dissolved methane concentrations, because the groundwater pressure at which bubbles appear (Pcritical ) was overestimated. The atmospheric sampling method is recommended for use where gas-saturated groundwater can be collected only ex situ under atmospheric conditions.

Potential for microbial H2 and metal transformations associated with novel bacteria and archaea in deep terrestrial subsurface sediments.

Geological sequestration in deep underground repositories is the prevailing proposed route for radioactive waste disposal. After the disposal of radioactive waste in the subsurface, H2 may be produced by corrosion of steel and, ultimately, radionuclides will be exposed to the surrounding environment. To evaluate the potential for microbial activities to impact disposal systems, we explored the microbial community structure and metabolic functions of a sediment-hosted ecosystem at the Horonobe Underground Research Laboratory, Hokkaido, Japan. Overall, we found that the ecosystem hosted organisms from diverse lineages, including many from the phyla that lack isolated representatives. The majority of organisms can metabolize H2, often via oxidative [NiFe] hydrogenases or electron-bifurcating [FeFe] hydrogenases that enable ferredoxin-based pathways, including the ion motive Rnf complex. Many organisms implicated in H2 metabolism are also predicted to catalyze carbon, nitrogen, iron and sulfur transformations. Notably, iron-based metabolism is predicted in a novel lineage of Actinobacteria and in a putative methane-oxidizing ANME-2d archaeon. We infer an ecological model that links microorganisms to sediment-derived resources and predict potential impacts of microbial activity on H2 consumption and retardation of radionuclide migration.

Interaction of rare earth elements and components of the Horonobe deep groundwater.

To better understand the migration behavior of minor actinides in deep groundwater, the interactions between doped rare earth elements (REEs) and components of Horonobe deep groundwater were investigated. Approximately 10 ppb of the REEs, i.e. Y, La, Ce, Pr, Nd, Sm, Eu, Gd, Tb, Dy, Er, Tm, and Yb were doped into a groundwater sample collected from a packed section in a borehole drilled at 140 m depth in the experiment drift of Horonobe Underground Research Laboratory in Hokkaido, Japan. The groundwater sample was sequentially filtered with a 0.2 µm pore filter, and 10 kDa, 3 kDa and 1 kDa nominal molecular weight limit (NMWL) ultrafilters with conditions kept inert. Next, the filtrate solutions were analyzed with inductively coupled plasma mass spectrometry (ICP-MS) to determine the concentrations of the REEs retained in solution at each filtration step, while the used filters were analyzed through neutron activation analysis (NAA) and TOF-SIMS element mapping to determine the amounts and chemical species of the trapped fractions of REEs on each filter. A strong relationship between the ratios of REEs retained in the filtrate solutions and the ionic radii of the associated REEs was observed; i.e. smaller REEs occur in larger proportions dissolved in the solution phase under the conditions of the Horonobe groundwater. The NAA and TOF-SIMS analyses revealed that portions of the REEs were trapped by the 0.2 µm pore filter as REE phosphates, which correspond to the species predicted to be predominant by chemical equilibrium calculations for the conditions of the Horonobe groundwater. Additionally, small portions of colloidal REEs were trapped by the 10 kDa and 3 kDa NMWL ultrafilters. These results suggest that phosphate anions play an important role in the chemical behavior of REEs in saline (seawater-based) groundwater, which may be useful for predicting the migration behavior of trivalent actinides released from radioactive waste repositories in the far future.

[A case with late-onset MELAS with hallucination and delusion].

We report a 53-year-old male patient with late onset mitochondrial myopathy, encephalopathy, lactic acidosis and stroke-like episodes(MELAS) with hallucination and delusion. The patient manifested various neurological symptoms including perceptive deafness, muscle weakness of limbs with loss of consciousness, sensory abnormalities in hands, feet and a face, abnormal sense of taste, tremor, palsy of upward eye movement and weak deep tendon reflexes prior to the psychotic episode. He was diagnosed as MELAS, because of high serum lactic acid and pyruvic acid, and the point mutation in the mitochondrial DNA 3243. SPECT imaging showed decreased perfusion in occipital cortex and thalamus. These SPECT changes improved after disappearing visual hallucination. Hallucination might be caused by delirium due to stroke-like episode. Dysfunction in the occipital cortex and thalamus might be involved with this perfusion change.