Ecological and genomic profiling of anaerobic methane-oxidizing archaea in a deep granitic environment.

Recent single-gene-based surveys of deep continental aquifers demonstrated the widespread occurrence of archaea related to Candidatus Methanoperedens nitroreducens (ANME-2d) known to mediate anaerobic oxidation of methane (AOM). However, it is unclear whether ANME-2d mediates AOM in the deep continental biosphere. In this study, we found the dominance of ANME-2d in groundwater enriched in sulfate and methane from a 300-m deep underground borehole in granitic rock. A near-complete genome of one representative species of the ANME-2d obtained from the underground borehole has most of functional genes required for AOM and assimilatory sulfate reduction. The genome of the subsurface ANME-2d is different from those of other members of ANME-2d by lacking functional genes encoding nitrate and nitrite reductases and multiheme cytochromes. In addition, the subsurface ANME-2d genome contains a membrane-bound NiFe hydrogenase gene putatively involved in respiratory H2 oxidation, which is different from those of other methanotrophic archaea. Short-term incubation of microbial cells collected from the granitic groundwater with 13C-labeled methane also demonstrates that AOM is linked to microbial sulfate reduction. Given the prominence of granitic continental crust and sulfate and methane in terrestrial subsurface fluids, we conclude that AOM may be widespread in the deep continental biosphere.

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.

Formation and Geological Sequestration of Uranium Nanoparticles in Deep Granitic Aquifer.

The stimulation of bacterial activities that convert hexavalent uranium, U(VI), to tetravalent uranium, U(IV), appears to be feasible for cost-effective remediation of contaminated aquifers. However, U(VI) reduction typically results in the precipitation of U(IV) particles less than 5 nanometers in diameter, except for environmental conditions enriched with iron. Because these tiny particles are mobile and susceptible to oxidative dissolution after the termination of nutrient injection, in situ bioremediation remains to be impractical. Here we show that U(IV) nanoparticles of coffinite (U(SiO4)1-x(OH)4x) formed in fracture-filling calcium carbonate in a granitic aquifer. In situ U-Pb isotope dating demonstrates that U(IV) nanoparticles have been sequestered in the calcium carbonate for at least 1 million years. As the microbiologically induced precipitation of calcium carbonate in aquifer systems worldwide is extremely common, we anticipate simultaneous stimulation of microbial activities for precipitation reactions of calcium carbonate and U(IV) nanoparticles, which leads to long-term sequestration of uranium and other radionuclides in contaminated aquifers and deep geological repositories.

Deep microbial life in high-quality granitic groundwater from geochemically and geographically distinct underground boreholes.

Deep granitic aquifer is one of the largest, but least understood, microbial habitats. To avoid contamination from the surface biosphere, underground drilling was conducted for 300 m deep granitic rocks at the Mizunami underground research laboratory (URL), Japan. Slightly alkaline groundwater was characterized by low concentrations of dissolved organic matter and sulfate and the presence of > 100 nM H2 . The initial biomass was the highest (∼10(5) cells ml(-1) ) with the dominance of Hydrogenophaga spp., whereas the phylum Nitrospirae became predominant after 3 years with decreasing biomass (∼10(4) cells ml(-1) ). One week incubation of groundwater microbes after 3 years with (13) C-labelled bicarbonate and 1% H2 and subsequent single-cell imaging with nanometer-scale secondary ion mass spectrometry demonstrated that microbial cells were metabolically active. Pyrosequencing of microbial communities in groundwater retrieved at 3-4 years after drilling at the Mizunami URL and at 14 and 25 years after the drilling at the Grimsel Test Site, Switzerland, revealed the occurrence of common Nitrospirae lineages at the geographically distinct sites. As the close relatives of the Nitrospirae lineages were exclusively detected from deep groundwaters and terrestrial hot springs, it suggests that these bacteria are indigenous and potentially adapted to the deep terrestrial subsurface.

Biogeochemical signals from deep microbial life in terrestrial crust.

In contrast to the deep subseafloor biosphere, a volumetrically vast and stable habitat for microbial life in the terrestrial crust remains poorly explored. For the long-term sustainability of a crustal biome, high-energy fluxes derived from hydrothermal circulation and water radiolysis in uranium-enriched rocks are seemingly essential. However, the crustal habitability depending on a low supply of energy is unknown. We present multi-isotopic evidence of microbially mediated sulfate reduction in a granitic aquifer, a representative of the terrestrial crust habitat. Deep meteoric groundwater was collected from underground boreholes drilled into Cretaceous Toki granite (central Japan). A large sulfur isotopic fractionation of 20-60‰ diagnostic to microbial sulfate reduction is associated with the investigated groundwater containing sulfate below 0.2 mM. In contrast, a small carbon isotopic fractionation (<30‰) is not indicative of methanogenesis. Except for 2011, the concentrations of H2 ranged mostly from 1 to 5 nM, which is also consistent with an aquifer where a terminal electron accepting process is dominantly controlled by ongoing sulfate reduction. High isotopic ratios of mantle-derived 3He relative to radiogenic 4He in groundwater and the flux of H2 along adjacent faults suggest that, in addition to low concentrations of organic matter (<70 µM), H2 from deeper sources might partly fuel metabolic activities. Our results demonstrate that the deep biosphere in the terrestrial crust is metabolically active and playing a crucial role in the formation of reducing groundwater even under low-energy fluxes.

Characterization of saline groundwater at Horonobe, Hokkaido, Japan by SEC-UV-ICP-MS: speciation of uranium and iodine.

The saline groundwater collected at a depth of about 500 m in Horonobe, Japan, where an underground research laboratory (URL) has been built, is rich in saline (Na 4900 ppm, Cl 7600 ppm), iodine (42 ppm), and methane gas. We analyzed the colloids and ions of this groundwater mainly by employing a size exclusion chromatography (SEC) coupled on-line to ultraviolet-visible (UV-Vis) detection and inductively coupled plasma mass spectrometry (ICP-MS) technique and focused on the speciation of uranium and iodine, both of which are of particular importance for radioactive waste disposal. For this purpose, the groundwater sample was introduced to SEC columns after being passed through a 0.45 µm filter but without further pretreatment, such as isolation of colloids. The chromatographic profiles obtained with two different SEC columns were compared. This study revealed that uranium present in the groundwater at several tens of ppt was associated with low molecular weight silica species with neutral charge. The silica species were virtually free of metal elements such as Na, K, Mg, Ca, and Al. This study also found that almost all of the iodine in the groundwater was iodide (I(-)). The groundwater contained an unidentified organic colloid that was not a carrier for the radioactive waste-relevant elements Se, Sr, I, Cs, Th, and U.

Phylogenetic characterization of 16S rRNA gene clones from deep-groundwater microorganisms that pass through 0.2-micrometer-pore-size filters.

A total of 247 clones of 16S rRNA genes from microorganisms captured by 0.2- and 0.1-microm-pore-size filters from sedimentary and granite rock aquifers were amplified and yielded 37 operational taxonomic units (OTUs). Fifteen OTUs captured by 0.1-microm-pore-size filters were affiliated with the candidate divisions OD1 and OP11, representing novel lineages. On the other hand, OTUs captured by 0.2-microm-pore-size filters were largely affiliated with Betaproteobacteria.