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.

Contrasting life-history responses to climate variability in eastern and western North Pacific sardine populations.

Massive populations of sardines inhabit both the western and eastern boundaries of the world's subtropical ocean basins, supporting both commercial fisheries and populations of marine predators. Sardine populations in western and eastern boundary current systems have responded oppositely to decadal scale anomalies in ocean temperature, but the mechanism for differing variability has remained unclear. Here, based on otolith microstructure and high-resolution stable isotope analyses, we show that habitat temperature, early life growth rates, energy expenditure, metabolically optimal temperature, and, most importantly, the relationship between growth rate and temperature are remarkably different between the two subpopulations in the western and eastern North Pacific. Varying metabolic responses to environmental changes partly explain the contrasting growth responses. Consistent differences in the life-history traits are observed between subpopulations in the western and eastern boundary current systems around South Africa. These growth and survival characteristics can facilitate the contrasting responses of sardine populations to climate change.

Extracting daily isotopic records on fish otolith (Trachurus japonicus) by combining micro-milling and micro-scale isotopic analysis (MICAL-CF-IRMS).

RATIONALE: The recent progress in micro-scale isotopic analytical techniques for otoliths has enabled the reconstruction of the experienced water temperature history of fish in every few days resolution using the stable oxygen isotope ratio (δ18 O) of otoliths. We aimed to improve those techniques and extract the daily δ18 O records of otoliths formed during the juvenile period. METHODS: Growth rings were formed daily in fish otoliths. We precisely distinguished the daily rings in otoliths of Japanese jack mackerel Trachurus japonicus, and milled them along daily growth rings using a high-spatial resolution micromilling system (Geomill326). Then, we determined the stable carbon and oxygen (δ13 C, δ18 O) isotopic compositions using a high-precision micro-scale isotopic analytical system (MICAL3c with IsoPrime 100). RESULTS: We successfully milled each daily ring with width ranging from 14.0 to 62.9 µm (average 27.0 µm) during the high growth period (30-70 days after hatching), and determined the isotopic compositions of otolith aragonite. CONCLUSIONS: Our improved micro-scale analytical method is the first to determine the daily δ18 O history of fish otoliths. By using our method together with the δ18 O - water temperature equation, the daily history of experienced water temperature can be elucidated. Our high-resolution milling and analytical technique can also be applied to high-resolution isotope analysis for stalactites, clams, and corals.

Advanced approach to analyzing calcareous protists for present and past pelagic ecology: Comprehensive analysis of 3D-morphology, stable isotopes, and genes of planktic foraminifers.

Marine protists play an important role in oceanic ecosystems and biogeochemical cycles. However, the difficulties in culturing pelagic protists indicate that their ecology and behavior remain poorly understood; phylogeographic studies based on single-cell genetic analyses have often shown that they are highly divergent at the biological species level, with variable geographic distributions. This indicates that their ecology could be complex. On the other hand, the biomineral (calcareous) shells of planktic foraminifers are widely used in geochemical analyses to estimate marine paleoenvironmental characteristics (i.e., temperature), because the shell chemical composition reflects ambient seawater conditions. Among the pelagic protists, planktic foraminifers are ideal study candidates to develop a combined approach of genetic, morphological, and geochemical methods, thus reflecting environmental and ecological characteristics. The present study precisely tested whether the DNA extraction process physically and chemically affects the shells of the planktic foraminifer Globigerinoides ruber. We used a nondestructive method for analyzing physical changes (micro-focus X-ray computed tomography (MXCT) scanning) to compare specimens at the pre- and post-DNA extraction stages. Our results demonstrate that DNA extraction has no significant effect on shell density and thickness. We measured stable carbon and oxygen isotopes on the shell of each individual in a negative control or one of two DNA-extracted groups and detected no significant differences in isotopic values among the three groups. Moreover, we evaluated isotopic variations at the biological species level with regard to their ecological characteristics such as depth habitat, life stages, and symbionts. Thus, our examination of the physiochemical effects on biomineral shells through DNA extraction shows that morphological and isotopic analyses of foraminifers can be combined with genetic analysis. These analytical methods are applicable to other shell-forming protists and microorganisms. In this study, we developed a powerful analytical tool for use in ecological and environmental studies of modern and past oceans.

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.

Grain-scale stable carbon and oxygen isotopic variations of the international reference calcite, IAEA-603.

RATIONALE: The new international reference material IAEA-603 (calcite) for stable carbon and oxygen isotopes (δ13 C and δ18 O values) was released in 2016 to replace the previous reference material, NBS19 (exhausted). We examined the grain-scale isotopic variations in IAEA-603 for application to microscale isotopic analysis of carbonate samples. METHODS: Individual grains of IAEA-603 were analyzed with an IsoPrime100 isotope ratio mass spectrometer with a customized continuous-flow gas preparation system (MICAL3c). The individual grains of IAEA-603 were observed by optical and scanning electron microscopy, and their observational characteristics (grain color and size) were compared with their stable isotope compositions. RESULTS: Translucent grains (main component of IAEA-603; grain weight, 4-132 µg) had homogeneous isotopic ratios, comparable with the grain-scale isotopic homogeneity of NBS 19. Their average δ13 C and δ18 O values were the same as the recommended values determined by the IAEA. Opaque (whitish) grains (1-2 per 100 grains; grain weight, 8-63 µg) were significantly more depleted in 13 C and 18 O than the translucent grains. CONCLUSIONS: Low-abundance opaque grains (1-2 grains out of 100 grains) have lower δ13 C and δ18 O values, suggesting that these grains should be eliminated when using IAEA-603 for single-grain (microscale) isotope analysis.

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.

Stable hydrogen isotopic analysis of nanomolar molecular hydrogen by automatic multi-step gas chromatographic separation.

We have developed a new automated analytical system that employs a continuous flow isotope ratio mass spectrometer to determine the stable hydrogen isotopic composition (δD) of nanomolar quantities of molecular hydrogen (H(2)) in an air sample. This method improves previous methods to attain simpler and lower-cost analyses, especially by avoiding the use of expensive or special devices, such as a Toepler pump, a cryogenic refrigerator, and a special evacuation system to keep the temperature of a coolant under reduced pressure. Instead, the system allows H(2) purification from the air matrix via automatic multi-step gas chromatographic separation using the coolants of both liquid nitrogen (77 K) and liquid nitrogen + ethanol (158 K) under 1 atm pressure. The analytical precision of the δD determination using the developed method was better than 4‰ for >5 nmol injections (250 mL STP for 500 ppbv air sample) and better than 15‰ for 1 nmol injections, regardless of the δD value, within 1 h for one sample analysis. Using the developed system, the δD values of H(2) can be quantified for atmospheric samples as well as samples of representative sources and sinks including those containing small quantities of H(2) , such as H(2) in soil pores or aqueous environments, for which there is currently little δD data available. As an example of such trace H(2) analyses, we report here the isotope fractionations during H(2) uptake by soils in a static chamber. The δD values of H(2) in these H(2)-depleted environments can be useful in constraining the budgets of atmospheric H(2) by applying an isotope mass balance model.

Geomicrobiological properties of ultra-deep granitic groundwater from the Mizunami Underground Research Laboratory (MIU), central Japan.

Although deep subterranean crystalline rocks are known to harbor microbial ecosystems, geochemical factors that constrain the biomass, diversity, and metabolic activities of microorganisms remain to be clearly defined. To better understand the geochemical and microbiological relationships, we characterized granitic groundwater collected from a 1,148- to 1,169-m-deep borehole interval at the Mizunami Underground Research Laboratory site, Japan, in 2005 and 2008. Geochemical analyses of the groundwater samples indicated that major electron acceptors, such as NO(3)(-) and SO(4)(2-), were not abundant, while dissolved organic carbon (not including organic acids), CH(4) and H(2), was moderately rich in the groundwater sample collected in 2008. The total number of acridine orange-stained cells in groundwater samples collected in 2005 and 2008 were 1.1 x 10(4) and 5.2 x 10(4) cells/mL, respectively. In 2005 and 2008, the most common phylotypes determined by 16S rRNA gene sequence analysis were both related to Thauera spp., the cultivated members of which can utilize minor electron donors, such as aromatic and aliphatic hydrocarbons. After a 3-5-week incubation period with potential electron donors (organic acids or CH(4) + H(2)) and with/without electron acceptors (O(2) or NO(3)(-)), dominant microbial populations shifted to Brevundimonas spp. These geomicrobiological results suggest that deep granitic groundwater has been stably colonized by Thauera spp. probably owing to the limitation of O(2), NO(3)(-), and organic acids.

Grain-scale heterogeneities in the stable carbon and oxygen isotopic compositions of the international standard calcite materials (NBS 19, NBS 18, IAEA-CO-1, and IAEA-CO-8).

We determined grain-scale heterogeneities (from 6 to 88 microg) in the stable carbon and oxygen isotopic compositions (delta(13)C and delta(18)O) of the international standard calcite materials (NBS 19, NBS 18, IAEA-CO-1, and IAEA-CO-8) using a continuous-flow isotope ratio mass spectrometry (CF-IRMS) system that realizes a simultaneous determination of the delta(13)C and the delta(18)O values with standard deviations (S.D.) of less than 0.05 per thousand for CO(2) gas. Based on the S.D. of the delta(13)C and delta(18)O values determined for CO(2) gases evolved from the different grains of the same calcite material, we found that NBS 19, IAEA-CO-1, and IEAE-CO-8 were homogeneous for delta(13)C (less than 0.10 per thousand S.D.), and that only NBS 19 was homogeneous for delta(18)O (less than 0.14 per thousand S.D.). On the level of single grains, we found that both IAEA-CO-1 and IAEA-CO-8 were heterogeneous for delta(18)O (1.46 per thousand and 0.76 per thousand S.D., respectively), and that NBS 18 was heterogeneous for both delta(13)C and delta(18)O (0.34 per thousand and 0.54 per thousand S.D., respectively). Closer inspection of NBS 18 grains revealed that the highly deviated isotopic compositions were limited to the colored grains. By excluding such colored grains, we could also obtain the homogeneous delta(13)C and delta(18)O values (less than 0.18 per thousand and less than 0.16 per thousand S.D., respectively) for NBS 18. We conclude that NBS 19, IAEA-CO-1, or pure grains in NBS 18 are suitable to be used as the standard reference material for delta(13)C, and that either NBS 19 or pure grains in NBS 18 are suitable to be used as the reference material for delta(18)O during the grain-scale isotopic analyses of calcite.

Determination of the 15N/14N, 17O/16O, and 18O/16O ratios of nitrous oxide by using continuous-flow isotope-ratio mass spectrometry.

We developed a rapid, sensitive, and automated analytical system to determine the delta15N, delta18O, and Delta17O values of nitrous oxide (N2O) simultaneously in nanomolar quantities for a single batch of samples by continuous-flow isotope-ratio mass spectrometry (CF-IRMS) without any cumbersome and time-consuming pretreatments. The analytical system consisted of a vacuum line to extract and purify N2O, a gas chromatograph for further purification of N2O, an optional thermal furnace to decompose N2O to O2, and a CF-IRMS system. We also used pneumatic valves and pneumatic actuators in the system so that we could operate it automatically with timing software on a personal computer. The analytical precision was better than 0.12 per thousand for delta15N with >4 nmol N2O injections, 0.25 per thousand for delta18O with >4 nmol N2O injections, and 0.20 per thousand for Delta17O with >20 nmol N2O injections for a single measurement. We were also easily able to improve the precision (standard errors) to better than 0.05 per thousand for delta15N, 0.10 per thousand for delta18O, and 0.10 per thousand for Delta17O through multiple analyses with more than four repetitions with 190 nmol samples using the automated analytical system. Using the system, the delta15N, delta18O, and Delta17O values of N2O can be quantified not only for atmospheric samples, but also for other gas or liquid samples with low N2O content, such as soil gas or natural water. Here, we showed the first ever Delta17O measurements of soil N2O.

Stable carbon and oxygen isotopic determination of sub-microgram quantities of CaCO3 to analyze individual foraminiferal shells.

We have developed an analytical system to determine stable isotopic compositions (delta13C and delta18O) of sub-microgram quantities of CaCO3 for the purpose of analyzing individual foraminiferal shells, using continuous-flow isotope ratio mass spectrometry (CF-IRMS). The system consists of a micro-volume CaCO3 decomposition tube, stainless steel CO2 purification vacuum line with a quantity-regulating unit, helium-purged CO2 purification line, gas chromatograph, and a CF-IRMS system. By using this system, we can determine stable carbon and oxygen isotopic compositions as low as 0.2 microg of CaCO3, with standard deviations of +/-0.10 per thousand for delta13C and +/-0.18 per thousand for delta18O within a 4-h reaction time and 30-min analysis period.