Bacterial community in saline farmland soil on the Tibetan plateau: responding to salinization while resisting extreme environments.

BACKGROUND: Salinization damages the health of soil systems and reduces crop yields. Responses of microbial communities to salinized soils and their functional maintenance under high salt stress are valuable scientific problems. Meanwhile, the microbial community of the salinized soil in the plateau environment is less understood. Here, we applied metagenomics technology to reveal the structure and function of microorganisms in salinized soil of the Tibetan Plateau. RESULTS: The diversity of composition and function of microbial community in saline soil have changed significantly. The abundances of chemoautotrophic and acidophilic bacteria comprising Rhodanobacter, Acidobacterium, Candidatus Nitrosotalea, and Candidatus Koribacter were significantly higher in saline soil. The potential degradation of organic carbon in the saline soil, as well as the production of NO and N2O via denitrification, and the production of sulfate by sulfur oxidation were significantly higher than the non-saline soil. Both types of soils were rich in genes encoding resistance to environmental stresses (i.e., cold, ultraviolet light, and hypoxia in Tibetan Plateau). The resistance of the soil microbial communities to the saline environment is based on the absorption of K+ as the main mechanism, with cross-protection proteins and absorption buffer molecules as auxiliary mechanisms in our study area. Network analysis showed that functional group comprising chemoautotrophic and acidophilic bacteria had significant positive correlations with electrical conductivity and total sulfur, and significant negative correlations with the total organic carbon, pH, and available nitrogen. The soil moisture, pH, and electrical conductivity are likely to affect the bacterial carbon, nitrogen, and sulfur cycles. CONCLUSIONS: These results indicate that the specific environment of the Tibetan Plateau and salinization jointly shape the structure and function of the soil bacterial community, and that the bacterial communities respond to complex and harsh living conditions. In addition, environmental feedback probably exacerbates greenhouse gas emissions and accelerates the reduction in the soil pH. This study will provide insights into the microbial responses to soil salinization and the potential ecological risks in the special plateau environment.

Sediment Microbial Communities and Their Potential Role as Environmental Pollution Indicators in Xuande Atoll, South China Sea.

In this study, 39 sediment samples were collected from Qilian Island, Iltis Bank, and Yongxing Island in Xuande Atoll in the South China Sea (SCS), and the microbial community structures and distribution were analyzed. The microbial community was influenced by both natural environmental factors and human activities. The abundance of genera Vibrio and Pseudoalteromonas, which are associated with pathogenicity and pollutant degradation, were significantly higher in Qilian Island than in Yongxing Island and Iltis Bank, suggesting possible contamination of Qilian Island area through human activities. Pathogenic or typical pollutants-degrading bacteria were found to be negatively correlated with most of the commonly occurring bacterial populations in marine sediment, and these bacteria were more likely to appear in the sediment of deep water layer. This co-occurrence pattern may be due to bacterial adaptation to environmental changes such as depth and contaminations from human activities, including garbage disposal, farming, and oil spills from ships. The findings of this study could help in understanding the potential influences of human activities on the ecosystem at the microbial level.

Sensitivity assessment of denitrifying bacteria against typical antibiotics in groundwater.

The effects of antibiotics on nitrate denitrification in groundwater have acquired growing concern. Denitrification is a microbially mediated process. The effects of antibiotics on denitrification were mainly reflected in denitrifying bacteria. However, little is known about the relationship between antibiotics and denitrifying bacteria. Based on this, both direct antimicrobial susceptibility testing and microbial batch-culture experiments were conducted to assess the influences of typical antibiotics on denitrifying groundwater bacteria, mainly Pseudomonas (46.17%). Denitrifying bacteria, screened from a long-term groundwater denitrification environment, were tested for sensitivity to five typical antibiotics in groundwater: sulfamethoxazole (SMX), erythromycin (ERY), enrofloxacin (ENR), clindamycin (CLI), and tetracycline (TCY). The results showed that the sensitivity of denitrifying bacteria to antibiotics is mainly related to the type and concentration of antibiotics. For antibiotic types, the order of sensitivity by quantitative assessment is ENR > TCY > SMX > ERY > CLI. Fluoroquinolones (FQs) represented by ENR were selected to explore their concentration effects. The influences on denitrifying bacteria were divided into the high concentration effect (500 µg L-1 to 100 mg L-1) and the low concentration effect (100 ng L-1 to 10 µg L-1) with about 100 µg L-1 as a boundary. Exposure to high concentrations had significant inhibitory effects on bacterial growth and exhibited dose dependency, especially for ciprofloxacin (CIP). The low concentration effect was independent of concentration, which may be stimulation or inhibition. The stimulation mainly occurred due to ENR-exposure. For inhibitory effects, Lomefloxacin (LOM) was more effective than other FQs. Especially for inhibition at ng-level exposure, LOM and norfloxacin (NOR) exposures led to the highest and lowest inhibition rates, respectively.

Improved xylose tolerance and 2,3-butanediol production of Klebsiella pneumoniae by directed evolution of rpoD and the mechanisms revealed by transcriptomics.

BACKGROUND: The biological production of 2,3-butanediol from xylose-rich raw materials from Klebsiella pneumoniae is a low-cost process. RpoD, an encoding gene of the sigma factor, is the key element in global transcription machinery engineering and has been successfully used to improve the fermentation with Escherichia coli. However, whether it can regulate the tolerance in K. pneumoniae remains unclear. RESULTS: In this study, the kpC mutant strain was constructed by altering the expression quantity and genotype of the rpoD gene, and this exhibited high xylose tolerance and 2,3-butanediol production. The xylose tolerance of kpC strain was increased from 75 to 125 g/L, and the yield of 2,3-butanediol increased by 228.5% compared with the parent strain kpG, reaching 38.6 g/L at 62 h. The RNA sequencing results showed an upregulated expression level of 500 genes and downregulated expression level of 174 genes in the kpC mutant strain. The pathway analysis further showed that the differentially expressed genes were mainly related to signal transduction, membrane transport, carbohydrate metabolism, and energy metabolism. The nine most-promising genes were selected based on transcriptome sequencing, and were evaluated for their effects on xylose tolerance. The overexpression of the tktA encoding transketolase, pntA encoding NAD(P) transhydrogenase subunit alpha, and nuoF encoding NADH dehydrogenase subunit F conferred increased xylose consumption and increased 2,3-butanediol production to K. pneumoniae. CONCLUSIONS: These results suggest that the xylose tolerance and 2,3-butanediol production of K. pneumoniae can be greatly improved by the directed evolution of rpoD. By applying transcriptomic analysis, the upregulation of tktA, pntA, and nuoF that were coded are essential for the xylose consumption and 2,3-butanediol production. This study will provide reference for further research on improving the fermentation abilities by means of other organisms.

Nanoporous TiO2-Based Distributed Bragg Reflectors for Near-Infrared Wavelength Applications.

We reported the fabrication and characteristics of distributed Bragg reflectors (DBRs), made of titanium dioxide (TiO2) dense/nanoporous film stacks, operating in the near-infrared wavelength region of 0.8-1.1 µm. To form the nanoporous TiO2 films with a low refractive index (low-n), the oblique angle deposition (OAD) technique was employed at a high incident vapor flux angle of 80 degrees. For the fabricated DBRs consisting of TiO2 dense/nanoporous (high-n/low-n) thin films, the high reflectance band was gradually increased and the stop bandwidth was narrowed with increasing the number of DBR pairs. Particularly, the TiO2 DBR with only 6 pairs exhibited a normalized stop bandwidth (Δλ/λ(c)) of -11.6% at a center wavelength (λ(c)) of 0.96 µm as well as high reflectance values of > 95% over a wide mid-infrared wavelength region of 0.9-1.01 µm (i.e., Δλ = 0.111 µm). Furthermore, the reflectance characteristics were investigated at incident light angles of 20-70 degrees for different polarized lights. For theoretical optical analyses, the reflectance calculations were also performed by a rigorous coupled-wave analysis method, showing a similar tendency to the experimentally measured data.

Broadband high-reflective distributed Bragg reflectors based on amorphous silicon films for semiconductor laser facet coatings.

We fabricated amorphous silicon (a-Si)-based distributed Bragg reflectors (DBRs) consisting of alternating dense/porous films (i.e., pair) for a center wavelength (λ(c)) of 0.96 µm by oblique angle deposition (OAD) technique using an electron-beam evaporation system. The dense (high refractive index, i.e., high-n) and porous (low-n) a-Si films were deposited at two incident vapor flux angles of 0° and 80° in the OAD, respectively. Their optical reflectance characteristics were investigated in the wavelength range of 0.6-1.5 µm, including theoretical comparison using a rigorous coupled-wave analysis method. Above three pairs, the reflectivity (R) of a-Si DBRs was almost saturated at wavelengths around 0.96 µm, exhibiting R values of >97%. For the a-Si DBR with only three pairs, a broad normalized stop bandwidth (Δλ/λ(c)) of ∼22.5% was obtained at wavelengths of ∼0.87-1.085 µm, keeping high R values of >95%. To simply demonstrate the feasibility of device applications, the a-Si DBR with three pairs was coated as a high-reflection layer at the rear facet of GaAs/InGaAs quantum-well laser diodes (LDs) operating at λ=0.96 µm. For the LDs coated with three-pair a-Si DBR, external differential quantum efficiency (η(d)) was nearly doubled compared to the uncoated LDs, indicating the η(d) value of ∼50.6% (i.e., η(d)∼25.5% for the uncoated LDs).

Inverted tetrahedron-pyramidal micropatterned polymer films for boosting light output power in flip-chip light-emitting diodes.

We report the improved light output power in gallium nitride-based green flip-chip light-emitting diodes (FCLEDs) employed with inverted tetrahedron-pyramidal micropatterned polydimethylsiloxane (ITPM PDMS) films as an encapsulation and protection layer. The micropatterns are transferred into the surface of PDMS films from the sapphire substrate master molds with two-dimensional periodic hexagonal TPM arrays by a soft imprint lithography method. The ITPM PDMS film laminated on the sapphire dramatically enhances the diffuse transmittance (T(D)) in a wavelength (λ) range of 400-650 nm, exhibiting the larger T(D) value of ~53% at λ = 525 nm, (cf., T(D) ~1% for planar sapphire). By introducing the ITPM PDMS film on the outer surface of sapphire in FCLEDs, the light output power is enhanced, indicating the increment percentage of ~11.1% at 500 mA of injection current compared to the reference FCLED without the ITPM PDMS film, together with better electroluminescence intensity and far-field radiation pattern.

Tunable distributed Bragg reflectors with wide-angle and broadband high-reflectivity using nanoporous/dense titanium dioxide film stacks for visible wavelength applications.

Highly-tolerant distributed Bragg reflectors (DBRs) based on the same materials consisting of nanoporous/dense titanium dioxide (TiO2) film pair structures with wide-angle and broadband highly-reflective properties at visible wavelengths are reported. For a high refractive index contrast, the two dense and nanoporous TiO2 film stacks are alternatingly deposited on silicon (Si) substrates by a oblique angle deposition (OAD) method at two vapor flux angles (θα) of 0 and 80° for high and low refractive indices, respectively. For the TiO2 DBRs at a center wavelength (λ(c)) of 540 nm, the maximum level in reflectance (R) band is increased with increasing the number of pairs, exhibiting high R values of > 90% for 5 pairs, and the normalized stop bandwidth (∆λ/λ(c)) of ~17.8% is obtained. At λ(c) = 540 nm, the patterned TiO2 DBR with 5 pairs shows an uniform relative reflectivity over a whole surface of 3 inch-sized Si wafer and a large-scalable fabrication capability with any features. The angle-dependent reflectance characteristics of TiO2 DBR at λ(c) = 540 nm are also studied at incident angles (θ(inc)) of 20-70° for p-, s-, and non-polarized lights in the wavelength region of 350-750 nm, yielding high R values of > 70.4% at θ(inc) values of 20-70° for non-polarized light. By adjusting the λ(c)/4 thicknesses of nanoporous and dense films, for λ(c) = 450, 540, and 680 nm, tunable broadband TiO2 DBRs with high R values of > 90% at wavelengths of 400-800 nm are realized.

Rapid characterization of chemical constituents and rats metabolites of the traditional Chinese patent medicine Gegen-Qinlian-Wan by UHPLC/DAD/qTOF-MS.

Gegen-Qinlian-Wan (GQW) is a popular traditional Chinese patent medicine for the treatment of diarrhea. It is composed of four herbal medicines, Puerariae Radix, Scutellariae Radix, Coptidis Rhizoma, and Glycyrrhizae Radix. In this study, a rapid and sensitive method based on ultra high-performance liquid chromatography coupled with diode-array detection and quadrupole time-of-flight mass spectrometry (UHPLC-DAD-qTOF-MS) was established to characterize the chemical constituents and rats metabolites of GQW. Samples were separated on an Agilent Zorbax Eclipse Plus-C(18) column (100 mm × 2.1 mm, 1.8 µm) by gradient elution using acetonitrile and water containing 0.1% formic acid as the mobile phase. On the basis of UV and qTOF high-accuracy mass spectral analysis, a total of 62 compounds were identified or tentatively characterized from GQW, including 42 flavonoids, 8 alkaloids, 6 triterpenoids, 3 phenylethanoid glycosides, and 3 other types. Among them, 27 compounds were confirmed by comparing with reference standards. Furthermore, metabolites in rats plasma and urine after oral administration of GQW were also analyzed. A total of 42 compounds were identified, including 29 prototypes and 13 metabolites through metabolic pathways of demethylation, methylation, hydrolysis, sulfate conjugation, and glucuronide conjugation. Glucuronidated flavonoids were the main constituents in the plasma, and were then transformed into aglycones and excreted from urine. This is the first systematic study on the chemical constituents and metabolic profiling of GQW.

Antioxidant flavonoids from Epimedium wushanense.

Two new flavonoids, wushanicaritin (1) and wushankaempferol (2), along with 24 known flavonoids were isolated from the whole herb of Epimedium wushanense T.S. Ying (Berberidaceae). On the basis of NMR and ESI-MS spectroscopic analysis, structures of compounds 1 and 2 were elucidated as 8-γ-hydroxy-γ,γ-dimethylpropyl-3,5,7-trihydroxy-4'- methoxyflavone and kaempferol 3-O-α-l-[2,3-di-O-ß-D-(6-E-p-coumaroyl) glucopyranosyl]-rhamnopyranosyl-7-O-α-L-rhamnopyranoside, respectively. DPPH radical scavenging activity tests indicated that 1 (IC(50) 35.3 µM) exhibited antioxidant activity comparable to Vitamin C (IC(50) 32.0 µM), while 2 (IC(50) 443.7 µM) showed weak activity.

Qualitative and quantitative analyses of Epimedium wushanense by high-performance liquid chromatography coupled with diode array detection and electrospray ionization tandem mass spectrometry.

A new HPLC-DAD-ESI-MS(n) method was developed for rapid separation, characterization and quantitation of flavonoids in Epimedium wushanense, a popular Chinese herbal medicine. For qualitative identification, a total of 37 compounds were characterized from the underground and aerial parts of E. wushanense. Among them, 28 compounds were prenylated flavonoids, and 23 were confirmed by comparing with reference standards. For quantitative analysis, 12 major flavonoids including kaempferol glycosides, desmethylicaritin glycosides, and icaritin glycosides were simultaneously determined by HPLC/UV. Samples were separated on a Waters Symmetry C(18) column at 35 °C eluted with a gradient three-component mobile phase of acetonitrile, methanol, and water containing 0.03% v/v formic acid. All the flavonoids showed good linearity (r(2) ≥0.9997). The recoveries varied from 92.6 to 106.1% at three concentration levels. This method was applied to the determination of 20 samples of different geographical sources, harvesting time, and plant parts. Contents of the predominant flavonoid, epimedin C, ranged from 1.4 to 5.1% in aerial parts and 1.0 to 2.8% in underground parts. The methods established in this paper were simple and reliable and could be used for the quality control of E. wushanense.

HPLC-DAD-MS(n) analysis and HPLC quantitation of chemical constituents in Xian-ling-gu-bao capsules.

In this study, a systematic method was established for the global quality control of Xian-ling-gu-bao capsules (XLGB), a popular six-herb Traditional Chinese Patent Medicine (TCPM) for the treatment of osteoporosis. Both qualitative and quantitative analyses were conducted. In qualitative analysis part, a fast and sensitive method based on high-performance liquid chromatography coupled with diode-array detection and electrospray ionization tandem mass spectrometry (HPLC-DAD-MS(n)) was established for rapid separation and sensitive identification. Samples were separated on a Waters Symmetry C(18) column (250mm×4.6mm, 5µm) by gradient elution using acetonitrile (A) and water-formic acid (B; 0.03%, v/v) as mobile phase at a flow rate of 1.0ml/min. Based on the mass spectra, UV spectra and retention time, 47 compounds were identified or tentatively characterized, including 27 flavonols (all from Epimedii Herba, the major component herb), 4 coumarins, 3 flavonones, 1 chalcone, 3 isoflavones, 1 coumestrol, 3 triterpenoid saponins, 1 iridoid, 3 steroidal saponins, and 1 phenolic acid. Among them, 18 compounds were confirmed by comparing with reference standards. In quantitative analysis part, 10 major compounds in 18 batches of XLGB were simultaneously determined by HPLC/UV detected at 270nm. The method was validated with respect to intra- and inter-day precision, repeatability and stability, with RSD less than 1.0%, 1.5%, 2.9% and 1.8%, respectively. All the 10 analytes showed good linearity in wide linear ranges (r(2)=0.9999), and their average recoveries varied between 97.8% and 104.9%.