Size resolved characteristics of urban and suburban bacterial bioaerosols in Japan as assessed by 16S rRNA amplicon sequencing.

To study the size-resolved characteristics of airborne bacterial community composition, diversity, and abundance, outdoor aerosol samples were analysed by 16S rRNA gene-targeted quantitative PCR and amplicon sequencing with Illumina MiSeq. The samples were collected using size-resolved samplers between August and October 2016, at a suburban site in Toyama City and an urban site in Yokohama City, Japan. The bacterial communities were found to be dominated by Actinobacteria, Firmicutes, and Proteobacteria. At the genus level, we found a high abundance of human skin-associated bacteria, such as Propionibacterium, Staphylococcus, and Corynebacterium, in the urban site. Whereas, a high abundance of bacteria associated with soil and plants, such as Methylobacterium and Sphingomonas, was observed in the suburban site. Furthermore, our data revealed a shift in the bacterial community structure, diversity, and abundance of total bacteria at a threshold of 1.1-µm diameter. Interestingly, we observed that Legionella spp., the causal agents of legionellosis in humans, were mainly detected in > 2.1 µm coarse particles. Our data indicate that local environmental factors including built environments could influence the outdoor airborne bacterial community at each site. These results provide a basis for understanding the size-resolved properties of bacterial community composition, diversity, and abundance in outdoor aerosol samples and their potential influence on human health.

Airborne Microbial Communities at High-Altitude and Suburban Sites in Toyama, Japan Suggest a New Perspective for Bioprospecting.

Airborne microorganisms, especially those at high altitude, are exposed to hostile conditions, including ultraviolet (UV) radiation, desiccation, and low temperatures. This study was conducted to compare the composition and abundance of airborne microorganisms at a high-altitude site, Mt. Jodo [2,839 m above mean sea level (AMSL)] and a suburban site (23 m AMSL) in Toyama, Japan. To our knowledge, this is the first study to investigate microbial communities in air samples collected simultaneously at two sites in relatively close proximity, from low and high altitude. Air samples were collected over a period of 3 years during 2009-2011. We then examined the bacterial and eukaryotic communities and estimated the abundance of bacteria and fungi with real-time TaqMan PCR. The airborne bacterial and eukaryotic communities differed between high-altitude and suburban sites on each sampling day. Backward trajectory analysis of air masses that arrived at high-altitude and suburban sites on each sampling day displayed almost the same paths. The bacterial communities were dominated by Actinobacteria, Firmicutes, and Proteobacteria, while the eukaryotic communities included Ascomycota, Basidiomycota, and Streptophyta. We also predicted some application of such microbial communities. The airborne bacterial and fungal abundance at the high-altitude site was about two times lower than that at the suburban site. These results showed that each airborne microbial communities have locality even if they are collected close location.

Single field-of-view tomographic imaging of 3D impurity emission distribution in magnetized edge plasma of LHD.

A new tomographic scheme is proposed for reconstructing three dimensional (3D) impurity emission distributions from two dimensional (2D) measurements with a single field-of-view in the magnetized edge plasma in a Large Helical Device (LHD). The 2D image is obtained with a multi-channel fiber array spectrometer, which views the entire region of the edge stochastic magnetic layer of LHD, including divertor plates, divertor legs, the stochastic layer, and the last closed flux surface. The scheme introduces new regularization terms in the Lagrangian function, based on the transport feature in magnetized plasma that the transport parallel to the magnetic field lines is much faster than the transport across the magnetic field, thus assuming smooth distribution in the parallel direction. The scheme is benchmarked with the test data of 3D distribution in the measurement volume, where the effectiveness of the various regularization terms is surveyed and feasibility of the scheme is confirmed. The new scheme is applied to the experimental data in LHD for carbon impurity emissions of C1+ and C3+, where the obtained distributions are discussed taking into account the plasma wall interaction and charge dependence of ionization potentials.

A fast-time-response extreme ultraviolet spectrometer for measurement of impurity line emissions in the Experimental Advanced Superconducting Tokamak.

A flat-field extreme ultraviolet (EUV) spectrometer working in the 20-500 Å wavelength range with fast time response has been newly developed to measure line emissions from highly ionized tungsten in the Experimental Advanced Superconducting Tokamak (EAST) with a tungsten divertor, while the monitoring of light and medium impurities is also an aim in the present development. A flat-field focal plane for spectral image detection is made by a laminar-type varied-line-spacing concave holographic grating with an angle of incidence of 87°. A back-illuminated charge-coupled device (CCD) with a total size of 26.6 × 6.6 mm(2) and pixel numbers of 1024 × 255 (26 × 26 µm(2)/pixel) is used for recording the focal image of spectral lines. An excellent spectral resolution of Δλ0 = 3-4 pixels, where Δλ0 is defined as full width at the foot position of a spectral line, is obtained at the 80-400 Å wavelength range after careful adjustment of the grating and CCD positions. The high signal readout rate of the CCD can improve the temporal resolution of time-resolved spectra when the CCD is operated in the full vertical binning mode. It is usually operated at 5 ms per frame. If the vertical size of the CCD is reduced with a narrow slit, the time response becomes faster. The high-time response in the spectral measurement therefore makes possible a variety of spectroscopic studies, e.g., impurity behavior in long pulse discharges with edge-localized mode bursts. An absolute intensity calibration of the EUV spectrometer is also carried out with a technique using the EUV bremsstrahlung continuum at 20-150 Å for quantitative data analysis. Thus, the high-time resolution tungsten spectra have been successfully observed with good spectral resolution using the present EUV spectrometer system. Typical tungsten spectra in the EUV wavelength range observed from EAST discharges are presented with absolute intensity and spectral identification.

Space-resolved 3 m normal incidence spectrometer for edge impurity diagnostics in the large helical device.

A space-resolved vacuum ultraviolet (VUV) spectroscopy using a 3 m normal incidence spectrometer has been developed to measure the impurity profile in the edge ergodic layer composed of stochastic magnetic field by which the edge plasma in the large helical device (LHD) is uniquely characterized. It vertically measures the spatial profile of VUV lines emitted from impurities in the wavelength range of 300-3200 Å. The wavelength interval, Δλ, which can be measured in a single discharge, is about 37 Å. A spectral resolution of 0.153 Å, which results from an entrance slit width of the spectrometer of 20 µm, is adopted. The vertical observation range, ΔZ, can be switched by taking a convex mirror in and out, which enables both the edge profile measurement focused on the ergodic layer and the full profile measurement covering an entire vertical size of the LHD plasma, e.g., 165 ≤ ΔZ ≤ 200 mm and 1000 ≤ ΔZ ≤ 1250 mm for the R(ax)=3.6 m configuration, respectively, which shows a slight wavelength dependence. Precise calibrations on the line dispersion, spectral resolution, vertical range of the observable region, and the spatial resolution have been performed with a unique method. As a preliminary result, the ion temperature profile is obtained for CIV at 1548.20 Å in the second order (denoted as 1548.20 × 2 Å) in high-density helium discharges in addition to the emission profile with a time resolution of 100 ms in a multitrack CCD operation mode. The poloidal flow in the ergodic layer based on the Doppler-shift measurement of CIV at 1548.20 × 2 Å is also observed in high-density hydrogen discharges.

Space-resolved 3 m normal incidence spectrometer for edge impurity diagnostics in the large helical device.

A space-resolved vacuum ultraviolet (VUV) spectroscopy using a 3 m normal incidence spectrometer has been developed to measure the impurity profile in the edge ergodic layer composed of stochastic magnetic field by which the edge plasma in the large helical device (LHD) is uniquely characterized. It vertically measures the spatial profile of VUV lines emitted from impurities in the wavelength range of 300-3200 Å. The wavelength interval, Δλ, which can be measured in a single discharge, is about 37 Å. A spectral resolution of 0.153 Å, which results from an entrance slit width of the spectrometer of 20 µm, is adopted. The vertical observation range, ΔZ, can be switched by taking a convex mirror in and out, which enables both the edge profile measurement focused on the ergodic layer and the full profile measurement covering an entire vertical size of the LHD plasma, e.g., 165 ≤ ΔZ ≤ 200 mm and 1000 ≤ ΔZ ≤ 1250 mm for the R(ax)=3.6 m configuration, respectively, which shows a slight wavelength dependence. Precise calibrations on the line dispersion, spectral resolution, vertical range of the observable region, and the spatial resolution have been performed with a unique method. As a preliminary result, the ion temperature profile is obtained for CIV at 1548.20 Å in the second order (denoted as 1548.20 × 2 Å) in high-density helium discharges in addition to the emission profile with a time resolution of 100 ms in a multitrack CCD operation mode. The poloidal flow in the ergodic layer based on the Doppler-shift measurement of CIV at 1548.20 × 2 Å is also observed in high-density hydrogen discharges.

Space-resolved extreme ultraviolet spectroscopy free of high-energy neutral particle noise in wavelength range of 10-130 Å on the large helical device.

A flat-field space-resolved extreme ultraviolet (EUV) spectrometer system working in wavelength range of 10-130 Å has been constructed in the Large Helical Device (LHD) for profile measurements of bremsstrahlung continuum and line emissions of heavy impurities in the central column of plasmas, which are aimed at studies on Zeff and impurity transport, respectively. Until now, a large amount of spike noise caused by neutral particles with high energies (≤180 keV) originating in neutral beam injection has been observed in EUV spectroscopy on LHD. The new system has been developed with an aim to delete such a spike noise from the signal by installing a thin filter which can block the high-energy neutral particles entering the EUV spectrometer. Three filters of 11 µm thick beryllium (Be), 3.3 µm thick polypropylene (PP), and 0.5 µm thick polyethylene terephthalate (PET: polyester) have been examined to eliminate the spike noise. Although the 11 µm Be and 3.3 µm PP filters can fully delete the spike noise in wavelength range of λ ≤ 20 Å, the signal intensity is also reduced. The 0.5 µm PET filter, on the other hand, can maintain sufficient signal intensity for the measurement and the spike noise remained in the signal is acceptable. As a result, the bremsstrahlung profile is successfully measured without noise at 20 Å even in low-density discharges, e.g., 2.9 × 10(13) cm(-3), when the 0.5 µm PET filter is used. The iron n = 3-2 Lα transition array consisting of FeXVII to FeXXIV is also excellently observed with their radial profiles in wavelength range of 10-18 Å. Each transition in the Lα array can be accurately identified with its radial profile. As a typical example of the method a spectral line at 17.62 Å is identified as FeXVIII transition. Results on absolute intensity calibration of the spectrometer system, pulse height and noise count analyses of the spike noise between holographic and ruled gratings and wavelength response of the used filters are also presented with performance of the present spectrometer system.

Absolute sensitivity calibration of vacuum and extreme ultraviolet spectrometer systems and Z(eff) measurement based on bremsstrahlung continuum in HL-2A tokamak.

A grazing-incidence flat-field extreme ultraviolet (EUV) spectrometer has been newly developed in HL-2A tokamak. Typical spectral lines are observed from intrinsic impurities of carbon, oxygen, iron, and extrinsic impurity of helium in the wavelength range of 20 Å-500 Å. Bremsstrahlung continuum is measured at different electron densities of HL-2A discharges to calibrate absolute sensitivity of the EUV spectrometer system and to measure effective ionic charge, Z(eff). The sensitivity of a vacuum ultraviolet (VUV) spectrometer system is also absolutely calibrated in overlapped wavelength range of 300 Å-500 Å by comparing the intensity between VUV and EUV line emissions.

Effect of high-energy neutral particles on extreme ultraviolet spectroscopy in large helical device.

Spectra measured by an extreme ultraviolet (EUV) spectrometer frequently suffer large spike noise when Large Helical Device is operated in low-density range (≤ 3 × 10(13) cm(-3)) with neutral beam injection (NBI). The spike noise completely disappears in electron cyclotron heating discharges. In order to examine the effect of NBI, a carbon filter with thickness of 150 nm was installed in the EUV spectrometer. As a result, the spike noise was reduced by an order of magnitude. It is experimentally verified that the spike noise is caused by escaping high-energy neutral particles resulting from the circulating high-energy hydrogen ions borne from NBI.

Radial profile measurement of electron temperature in edge stochastic magnetic field layer of LHD using intensity ratio of extreme ultraviolet line emissions.

Vertical profile of neon line emissions in 30-650 Å wavelength range has been observed in horizontally elongated plasma cross section of Large Helical Device (LHD). Intensity ratio between the neon line emissions is studied to measure the radial profile of electron temperature in the edge stochastic magnetic field layer of LHD. The edge temperature profile successfully obtained from the line ratio of NeVIII 2s-3p to 2p-3s transitions is compared with the simulation based on three-dimensional edge transport code. The result shows a reasonably good agreement with the edge temperature profile analyzed from atomic data and analysis structure code. The electron temperature at last closed flux surface measured from the intensity ratio is also in good agreement with that measured from Thomson scattering.

Two-dimensional measurement of edge impurity emissions using space-resolved extreme ultraviolet spectrometer in Large Helical Device.

A space-resolved extreme ultraviolet (EUV) spectrometer working in wavelength range of 50-500 Å has been developed to measure two-dimensional distribution of impurity spectral lines emitted from edge plasma of Large Helical Device (LHD), in which the magnetic field is formed by stochastic magnetic field with three-dimensional structure called ergodic layer. The two-dimensional measurement of edge impurity line emissions is carried out by scanning horizontally the observation chord of the space-resolved EUV spectrometer during single LHD discharge. Images of CIV (312.4 Å) and HeII (303.78 Å) are presented as the first result. The results are compared with ones calculated from the edge chord length in the ergodic layer of LHD plasma.

Absolute intensity calibration of flat-field space-resolved extreme ultraviolet spectrometer using radial profiles of visible and extreme ultraviolet bremsstrahlung continuum emitted from high-density plasmas in Large Helical Device.

A precise absolute intensity calibration of a flat-field space-resolved extreme ultraviolet (EUV) spectrometer working in wavelength range of 60-400 Å is carried out using a new calibration technique based on radial profile measurement of the bremsstrahlung continuum in Large Helical Device. A peaked vertical profile of the EUV bremsstrahlung continuum has been successfully observed in high-density plasmas (n(e) ≥ 10(14) cm(-3)) with hydrogen ice pellet injection. The absolute calibration can be done by comparing the EUV bremsstrahlung profile with the visible bremsstrahlung profile of which the absolute value has been already calibrated using a standard lamp. The line-integrated profile of measured visible bremsstrahlung continuum is firstly converted into the local emissivity profile by considering a magnetic surface distortion due to the plasma pressure, and the local emissivity profile of EUV bremsstrahlung is secondly calculated by taking into account the electron temperature profile and free-free gaunt factor. The line-integrated profile of the EUV bremsstrahlung continuum is finally calculated from the local emissivity profile in order to compare with measured EUV bremsstrahlung profile. The absolute intensity calibration can be done by comparing measured and calculated EUV bremsstrahlung profiles. The calibration factor is thus obtained as a function of wavelength with excellent accuracy. It is also found in the profile analysis that the grating reflectivity of EUV emissions is constant along the direction perpendicular to the wavelength dispersion. Uncertainties on the calibration factor determined with the present method are discussed including charge-coupled device operation modes.

Z(eff) measurement using extreme ultraviolet bremsstrahlung emission in LHD.

Radial profile measurement of Z(eff) using visible bremsstrahlung (5300 Å) in the Large Helical Device (LHD) has often encountered difficulties because the intensity profile was largely deformed by the nonuniform visible bremsstrahlung emissions from the edge ergodic layer surrounding the core plasma. A space-resolved flat-field extreme ultraviolet (EUV) spectrometer has been newly adopted to measure the Z(eff) profile using the EUV bremsstrahlung continuum in the wavelength range of 70-75 Å. The EUV bremsstrahlung intensity profiles have been measured and checked for all the magnetic configurations with totally different magnetic field structures in the ergodic layer of LHD. It is found that the nonuniform bremsstrahlung emission from the thick ergodic layer can be entirely eliminated by use of the EUV emission with relatively high photon energy of 170 eV. As a result, the Z(eff) profile can be successfully measured for most of discharges regardless of magnetic field structures of the ergodic layer. The Z(eff) profiles measured in the EUV range are compared with those measured in the visible range at a magnetic configuration with the thinnest ergodic layer thickness. The result verifies that the use of the EUV bremsstrahlung continuum is an alternative way for the Z(eff) measurement in toroidal plasmas with nonuniform bremsstrahlung emissions at the edge. Typical results from the EUV bremsstrahlung measurement are presented showing a fairly flat Z(eff) profile with error bars of ±14%.

Space-resolved extreme ultraviolet spectrometer for impurity emission profile measurement in Large Helical Device.

A space-resolved extreme ultraviolet (EUV) spectrometer working in 60-400 A range has been developed to observe impurity emission profiles in core and edge plasmas of Large Helical Device (LHD). A flat focus is made for plane surface detector by using a varied line spacing holographic grating with an angle of incidence of 87 degrees. An excellent spectral resolution of 0.22 A at 200 A is then obtained after careful adjustment of the optical components. In the profile measurement of the LHD plasmas, the toroidal resolution is important as well as the radial resolution because the magnetic surfaces of LHD quickly change when the observation chord is tilted at a slightly different toroidal location. Horizontal dispersion is therefore selected for the present spectrometer. As a result, the toroidal resolution of 75 mm is achieved at the plasma position. An enough radial resolution of 10 mm is also obtained at spatial-resolution slit width of 0.2 mm. In order to measure the full radial profile of LHD plasmas the spectrometer is placed at a distance of approximately 9200 mm away from the plasma center and a backilluminated charge-coupled device with a size of 6.6x26.6 mm(2) is set vertical to the horizontal dispersion. Half of the LHD plasma, i.e., approximately 50 cm, can be measured along the vertical direction at horizontally elongated plasma cross section. A full vertical profile can be obtained by changing the vertical angle of the EUV spectrometer. As an example the full vertical profile of edge C IV (312.4 A) emission is presented. A wavelength interval of 35-65 A can be simultaneously observed, which varies according to the wavelength to be measured. A local emission profile of Fe XX (132.67 A) is also presented after Abel inversion as a typical example of the core EUV emission. Finally, the EUV spectrometer is absolutely calibrated using EUV bremsstrahlung continuum profile in comparison with absolute values of visible bremsstrahlung continuum profile because the bremsstrahlung continuum can be easily detected in high-density discharges of LHD.

Fast ion charge exchange spectroscopy measurement using a radially injected neutral beam on the large helical device.

An experimental technique to investigate fast ion confinement based on charge exchange spectroscopy of H(alpha)-light was applied to evaluate the confinement property of perpendicular fast ions in large helical device (LHD). Sensitivities of the H(alpha) spectra to the pitch angles of injected neutral beams (NBs) and these to the angle between the sight line of the measurement and NB injection path are examined. The energy dependence of the charge exchange cross section significantly affects the observed spectra since the driving NB is injected perpendicular to the magnetic field lines in the geometry of LHD. The measured spectra are compared to the spectra of GNET simulation results and the simulated spectra agreed well with the experimental measurement when we take into account the contribution of halo neutrals. Although it is difficult to obtain the fast ion distribution functions directly, this technique provides useful experimental data in benchmarking simulation codes.

Spectroscopic evaluation of three different gratings used for a flat-field extreme ultraviolet spectrometer to monitor Delta n=1 transitions from medium-Z impurities in 10-30 A.

Spectral characteristics of varied line spacing 2400 grooves/mm gratings used for a flat-field extreme ultraviolet spectrometer have been evaluated to monitor Delta n=1 (n=2-3) transitions from medium-Z impurities in 10-30 A, where many spectral lines from metallic impurities closely exist. For this purpose emission spectra of the Delta n=1 transitions from partially L-shell-ionized Ti and Fe have been measured in large helical device. At first, a ruled and a holographic grating were utilized for the comparative study. Both gratings suppressed higher order light effectively but spectral sensitivity was much higher for the holographic grating. The ruled grating, however, attained better spectral resolution (0.083 A at 18.97 A) in the 10-100 A range compared to that (0.130 A) of the holographic grating. After that a recently developed new holographic grating with different laminar shapes and line spacings has attempted to improve the spectral resolution. As a result, it has considerably improved the spectral resolution in the 10-30 A range, i.e., approximately 0.090 A. However, it is found that the experimentally obtained spectral resolution is quit poor compared to the computationally simulated one, suggesting a technical difficulty in manufacturing exactly the varied line spacing of the holographic grating at such a short wavelength range.

Characteristics of an absolutely calibrated flat-field extreme ultraviolet spectrometer in the 10-130 A range for fusion plasma diagnostics.

A flat-field extreme ultraviolet (EUV) spectrometer with a nominal 2400 grooves/mm aberration-corrected ruled grating has been developed to analyze the emission spectrum in the wavelength range of 10 to 130 A from large helical device (LHD) plasmas. Spectral properties such as resolution, sensitivity, contribution of higher-order light, and background stray light have been studied using emission spectra mainly from intrinsic impurities, e.g., C and Fe. It is found that the spectrometer well resolves closely existing spectral lines of highly ionized medium- and high-Z impurities even in a very short wavelength range such as 10 to 20 A. As a result, it allows one to study the charge state distribution of elements in high-temperature fusion plasma. The ruled grating was then replaced by a laminar type holographic grating for the comparative study. The spectral resolution for the ruled grating (Dlambda approximately 0.08 A at 33.73 A) is clearly better than the holographic grating (Dlambda approximately 0.13 A at 33.73 A). Both gratings well suppress the higher-order light, e.g., the second-order light is only less than 11% of the first-order light for C vi(33.73 A). Relative sensitivity calibration with the wavelength has been done using bremsstrahlung continuum from the LHD plasmas. Absolute intensity calibration has been done by comparing the spectral intensities directly with the absolutely calibrated 1200 grooves/mm EUV spectrometer in the overlapping range of 90-120 A due to the absence of a good branching pair in 10-130 A. As a typical result on the present spectrometer well-resolved n=2-3 full transition arrays from Ne- to Li-like ions are measured for Fe and Ti and wavelengths of the spectral array are tabulated for each charge state. Spectroscopic comparison is also made between the 1200 grooves/mm and 2400 grooves/mm gratings in a range of 50-130 A.

Spectroscopic comparison between 1200 grooves/mm ruled and holographic gratings of a flat-field spectrometer and its absolute sensitivity calibration using bremsstrahlung continuum.

A flat-field extreme ultraviolet (EUV) spectrometer with a varied line spacing groove grating (1200 grooves/mm at grating center) has been developed to study the emission spectra from highly ionized medium Z impurities in large helical device (LHD). It covers a wavelength range of 50-500 A using a mechanically ruled grating, which was later replaced by a newly developed laminar-type holographic grating for comparative studies. Differences in spectral resolution, intensities of higher order spectra, and sensitivities of the spectrometer were studied between the two gratings by observing the emission spectra of LHD plasmas. Although the achieved resolution was alike between them, i.e., deltalambda approximately 0.24 A at 200 A, the holographic grating was much superior in suppressing the higher order light than the ruled grating. The relative sensitivity between the two gratings was evaluated using continuum radiation from LHD plasmas. As a result, it was found that the holographic grating has a flat response in the full wavelength range, but the sensitivity of the ruled grating drops sharply below 200 A. A new technique for the absolute calibration of the EUV holographic grating spectrometer was tried by combining the continuum radiation with a branching ratio of C IV lines (3p-3s: 5800 A/3p-2s: 312 A), and an accurate absolute sensitivity has been successfully obtained.