EXAFS study on the cause of enrichment of heavy REEs on bacterial cell surfaces

Rare earth element (REE) pattern is a unique geochemical tracer and has been measured for various natural materials. Among these, the REE distribution pattern between bacteria and water exhibits anomalous enrichment in the heavy REE (HREE) part, which can act as a signature of bacteria-related materials in natural samples. In this study, the REE binding site on the cell surface of a Gram-positive bacterium (Bacillus subtilis) responsible for HREE enrichment has been identified using extended X-ray absorption fine structure (EXAFS) coupled with a study of the variation in REE distribution patterns. The EXAFS data showed that the HREEs form complexes with multiple phosphate site (including phosphoester site) with a larger coordination number (CN) at lower REE-bacteria ratios ([REE]/[bac]), while light and middle REEs form complexes to the phosphate site with a lower CN. The fraction coordinated to carboxylate increased for all REEs with increasing [REE]/[bac] ratio. On the other hand, the enrichment of HREE in the REE distribution patterns of the bacteria was less marked with increasing [REE]/[bac] ratio. This result is consistent with the EXAFS data, because the REE pattern of surface complex with multiple phosphate in a reference material exhibits a monotonous increase for heavier REE, while phosphate surface complex with a low CN and a carboxylate site reach a maximum around Sm and Eu. Based on these results, it is clear that the REE are primarily bound to the phosphate site and subsequently to the carboxylate site on the bacterial cell surface.Regarding the pH dependence in the range (3 < pH < 7), both the EXAFS and REE pattern data indicate that the fraction of REE-carboxylate increased as the pH increases. The results above obtained for B. subtilis were also valid for Escherichia coli, a Gram-negative bacterium, showing that similar phosphate and carboxylate sites are also available in the cell walls of E. coli, or other Gram negative bacteria. In all our results, the variation in REE patterns correlated with the binding site indicated by EXAFS, showing that the REE pattern itself reflects the binding site of the REE at the bacterial surface for various parameters (pH and [REE]/[bac] ratio). Thus, the REE patterns can be used to estimate the binding sites for lower [REE]/[bac] ratios where spectroscopic techniques cannot be applied.The average bond length between the REE and oxygen was compared for various REE sorbed on bacteria, showing that the bond length for HREE (Er to Lu) was much shorter than those extrapolated from the trend between La and Dy, because of the selective binding of the HREE as the multiple phosphate surface complexes. Our results are consistent with the selective enrichment of the HREE at the bacterial cell surfaces, considering that chemical species with a shorter bond length are more stable. Thus, it is clear that the HREE enrichment at the bacterial cell surfaces is caused by the formation of the multiple phosphate surface complexes. Based on these results, it is suggested that materials having such phosphate sites such as bacteria and bacteria-related materials can induce anomalous HREE enrichment in natural systems.     

Iron–bentonite interactions in the Kawasaki bentonite deposit,Zao area,Japan

Greenish veins occurring in brecciated bentonite were found in the Kawasaki bentonite deposit of the Zao region in Miyagi Prefecture, Japan. Their occurrence possibly indicates the interaction of bentonite with Fe-rich hydrothermal solutions. In order to prove the hypothesis and understand the long-term mineralogical and petrographic evolution of bentonite during such interactions, the greenish veins and the surrounding altered bentonite were analyzed using X-ray fluorescence (XRF), scanning electron microscopy (SEM), X-ray diffraction (XRD), electron probe micro-analysis (EPMA), scanning transmission electron microscopy with energy dispersed spectroscopy (STEM-EDS) and micro X-ray absorption near-edge structure (XANES). The greenish veins resulting from hydrothermal solution are composed of mixed-layer minerals consisting of smectite and glauconite (glaucony), pyrite and opal. The occurrences indicate that glaucony and pyrite formed almost simultaneously from hydrothermal solution prior to opal precipitation. The mineral assemblages of the greenish veins and their surroundings indicate that the hydrothermal activity had most likely taken place at a temperature of less than 100 °C and that the pH and Eh conditions of the reacted solution were neutral to alkaline pH and reducing. The unaltered bentonite is composed mainly of Al smectite and opal. These minerals coexist as a mixture within the resolution level of the microprobe analyses. On the other hand, the bentonite in contact with the greenish veins consists of discrete opal grains and dioctahedral Al smectite containing Fe and was altered mineralogically and petrographically by the hydrothermal activity. Both the clay minerals and the opal were formed by dissolution and subsequent precipitation from the interaction of the original bentonite with the hydrothermal solution.     

Evaluation of intrinsic vulnerability to nitrate contamination of groundwater: appropriate fertilizer application management

In agricultural areas, fertilizer application is the main source of nitrate contamination of groundwater. To develop fertilizer management strategies to combat this problem, arable land in Hokkaido, Japan was evaluated using geographic information system techniques for intrinsic groundwater vulnerability to nitrate contamination. The DRASTIC method was modified to adapt it to the Hokkaido environment and used for the evaluation. Of the seven original DRASTIC factors, the depth to water (D), net recharge (R), soil media (S), topography (T), and impact of vadose zone media (I) were selected and used to explain the vertical movement of contaminants to the aquifer. The rating for the net recharge factor was also modified to a dilution factor for contaminants, rather than as a transporter. The frequency of wells with nitrate concentrations exceeding the Japanese environmental standard (10 mg/L) was reasonably explained by vulnerability evaluation results (GLM: logit-link, quasi-binomial distribution, Y = [1 + exp(6.873765 − 0.045988 × X)]⁻¹, p < 0.001). However, in the paddy fields and pastures, vulnerability did not exhibit a clear relationship with the frequency of wells exceeding the standard. This suggests that the modified DRASTIC method is applicable for fertilizer application management in upland fields. In addition, under the ongoing policy for acreage allotment for rice production, this method will be useful for deciding the arrangement of arable land and crop rotation taking into consideration the potential risk of fertilizer-induced nitrate contamination of groundwater.     

Indigenous Knowledge on Soil Classification of Ethnic Groups in Luang Prabang Province of the Lao PDR

Introduction Traditional agriculture based on indigenous knowledge (IK) has been practiced in many areas for centuries. Such practices are often the basis of very sustainable technologies, which are potentially suitable for developmental programs. Polthanee (2001) reported that such farmer practices have been repeatedly found to be valid, rational and usually suited to the local environmental conditions. Moreover, with increased under- standing of agro-ecosystems, professionals in agricultura…     

Incessant excitation of the Earth's free oscillations: global comparison of superconducting gravimeter records

Records of superconducting gravimeters (SGs) at Canberra (Australia), Esashi (Japan), Metsähovi (Finland) and Syowa Stations (Antarctica) were analyzed to search for further evidence of background free oscillations of the Earth. Spectrograms for 1-year period and averaged power spectra for seismically quiet periods were obtained for each of the stations. Anomalous features of the oscillations observed at Syowa Station, such as an apparent seasonal variation and a high intensity at frequencies between 3 and 4 mHz, were absent at the other SG stations. Among the SG stations used in this study, the background free oscillations were detected most consistently and distinctly at Canberra, where the noise level was comparable to that at the IDA quietest station, while that at Syowa Station was close to the critical limit for detecting the oscillations. The background free oscillations provide a good reference to evaluate the noise level in the milliHertz band.     

Supercooled drizzle formed by condensation–coalescence in the mid-winter season of the Canadian Arctic

Supercooled drizzle (freezing drizzle) was observed at Inuvik, N.W.T., Canada (68°22′N, 133°42′W) on December 20, 21 and 27, 1995. Meteorological conditions in which the supercooled drizzle could form under low temperatures (colder than −20°C) in the mid-winter season of the Canadian Arctic were examined from the sounding data and data measured by a passive microwave radiometer at ground level. The following results were obtained. (1) Supercooled drizzle fell to the ground with ice pellets and frozen drops on snow crystals. (2) The maximum size of supercooled drizzle particles increased as the depth of cloud layer saturated with respect to water increased. (3) Because a layer of air temperature higher than 0°C was not detected from the sounding data at Inuvik, melting of snow particles was impossible. It was concluded, therefore, that supercooled drizzle was formed by the condensation–coalescence process below freezing temperature.     

Open boundary value problems in ocean dynamics by finite elements

This paper presents recent results of application of the finite element models to wave overtopping and wave run-up problems in ocean dynamics. Open boundaries are prescribed as natural boundary condition obtained from the continuity equation of the Galerkin finite element formulation. The numerical results are, in general, reasonably good agreements with the histrical field data.     

An atomic level study of rhenium and radiogenic osmium in molybdenite

Local atomic structures of Re and radiogenic Os in molybdenite from the Onganja mine, Namibia, were examined using X-ray absorption fine structure (XAFS). Rhenium L_III-edge X-ray absorption near-edge structure (XANES) and extended X-ray absorption fine structure (EXAFS) show that the oxidation state of Re, the interatomic distances between Re and the neighboring atoms, and the coordination number of Re to S are very similar to those of Mo in molybdenite. The results confirm that Re is present as Re(IV) in the Mo site in molybdenite.Measurement of L_III-edge XANES and EXAFS of a minor concentration (8.55 ppm) of radiogenic Os was accomplished in fluorescence mode by removing the interfering X-rays from Re and other elements using a crystal analyzer system. The data indicate that the oxidation state of radiogenic Os is Os(III) and Os(IV) and clearly different from Os(II) in natural sulfide minerals, such as OsS₂ (erlichmanite). XANES data also suggest that radiogenic Os does not form a secondary Os phase, such as OsS₂ or Os metal, in molybdenite.EXAFS of radiogenic Os was successfully simulated assuming that Os is present in the Mo site in molybdenite. The data are consistent with the XANES data; Os does not form Os phases in molybdenite. The EXAFS simulation showed that the interatomic distance between Os and S is 2.27 Å, which is 0.12 Å smaller than the distances of Re-S and Mo-S (2.39 Å) in molybdenite. Similar valences and ionic sizes of Re and Mo in molybdenite support the fact that large amounts of Re can be incorporated into the Mo site as has been observed in previous studies, whereas the different properties of Os compared to Mo and Re suggested here support much lower abundance of common Os in molybdenite. This makes molybdenite an ideal mineral for the Re-Os geochronometer as shown in many studies. However, the shorter distance between radiogenic Os and S compared to those of Re-S and Mo-S in molybdenite suggests that the radiogenic Os has a smaller ionic size than Re(IV) and Mo(IV). Furthermore, Os may be partly present as Os(III). Smaller and lower charge Os can diffuse faster than larger and higher charge Re in molybdenite at a given set of conditions. Hence, our study provides an atomic-level explanation for the high mobility of Os compared to Re, which has been suggested by earlier workers using laser ablation ICP-MS.