Undibacter mobilis gen. nov., sp. nov. isolated from an artificial wetland in Okcheon, Korea.

Strain GY_HT was isolated from an artificial wetland in Okcheon, Chungcheongbuk-do Province, Republic of Korea. Strain GY_HT was closely related to Pseudolabrys taiwanensis CC-BB4T based on 16S rRNA gene sequences (94.7 % similarity) and clustered within the family Nitrobacteraceae. Cells of the isolate were Gram-stain-negative, catalase-negative and oxidase-positive, and colonies were white or pale transparent. A flagellum was observed, and the isolate could respire both aerobically and anaerobically. Growth of GY_ HT was observed in the following conditions: 10-45 °C, pH 5-11 and 0-4 % NaCl. The optimal conditions for growth were 25 °C, pH 6.5-7.5 and 0.5-1.5 % NaCl. The major fatty acids were C19 : 0 cyclo ω8c (35.8 %) and summed feature 8 (C18 : 1 ω7c/C18 : 1 ω6c; 27.4 %). The major quinone was found to be ubiquinone-10. Diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylcholine were the major polar lipids. The G+C content of the genome of GY_HT was 63.3 mol%. Based on its phylogenomic, physiological and biochemical attributes, strain GY_HT represents a novel species of a novel genus of the family Nitrobacteraceae. We propose the name as Undibacter mobilis gen. nov., sp. nov. The type strain is GY_HT (=KCTC 62792T=JCM 32856T).

Sphingorhabdus pulchriflava sp. nov., isolated from a river.

A facultatively anaerobic and Gram-stain-negative bacterium, strain GY_GT, was isolated from a river (Daedeock-cheon) in Daejeon, Republic of Korea. The isolate was catalase-positive, oxidase-positive and formed yellow colonies. Strain GY_GT was phylogenetically classified as belonging in the genus Sphingorhabdus. Its closely related strains were Sphingorhabdus wooponensis 03SU3-PT (97.1 % similarity), Sphingorhabdus buctiana T5T (96.9 %), Sphingorhabdus contaminans JC216T (96.5 %), Sphingorhabdus rigui 01SU5-PT (96.5 %) and Sphingorhabdus planktonica G1A_585T (96.3 %) based on 16S rRNA gene sequences. The growth conditions for GY_GT were at 10-45 °C (optimum, 25 °C), pH 6-10 (pH 7) and 0-4% NaCl (0.5-1.5 %). Strain GY_GT could utilize turanose, d-fructose-6-phosphate, glucuronamide, α-keto-glutaric acid and acetoacetic acid. The major fatty acids of strain GY_GT were summed features 8 (C18 : 1 ω7c/C18 : 1 ω6c; 40.6 %) and 3 (C16 : 1 ω6c/C16 : 1 ω7c; 24.7 %). The major quinone required for respiration was Q-10. The polar lipids of strain GY_GT were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and sphingolipid. The G+C content of the genome was 57.7 mol%. The average nucleotide identity and average amino acid identity values between strains GY_GT and S. wooponensis were 71.0 and 72.7 %, respectively. Based on phylogenetic and phenotypic attributes, we suggest that strain GY_GT is a novel species in the genus Sphingorhabdus and propose the name Sphingorhabdus pulchriflava. The type strain is GY_GT (=KCTC 62791T=JCM 32855T).

A Human Antibody That Binds to the Sixth Ig-Like Domain of VCAM-1 Blocks Lung Cancer Cell Migration In Vitro.

Vascular cell adhesion molecule-1 (VCAM-1) is closely associated with tumor progression and metastasis. However, the relevance and role of VCAM-1 in lung cancer have not been clearly elucidated. In this study, we found that VCAM-1 was highly overexpressed in lung cancer tissue compared with that of normal lung tissue, and high VCAM-1 expression correlated with poor survival in lung cancer patients. VCAM-1 knockdown reduced migration of A549 human lung cancer cells into Matrigel, and competitive blocking experiments targeting the Ig-like domain 6 of VCAM-1 (VCAM-1-D6) demonstrated that the VCAM-1-D6 domain was critical for VCAM-1 mediated A549 cell migration into Matrigel. Next, we developed a human monoclonal antibody specific to human and mouse VCAM-1-D6 (VCAM-1-D6 huMab), which was isolated from a human synthetic antibody library using phage display technology. Finally, we showed that VCAM-1-D6 huMab had a nanomolar affinity for VCAM-1-D6 and that it potently suppressed the migration of A549 and NCI-H1299 lung cancer cell lines into Matrigel. Taken together, these results suggest that VCAM-1-D6 is a key domain for regulating VCAM-1-mediated lung cancer invasion and that our newly developed VCAM-1-D6 huMab will be a useful tool for inhibiting VCAM-1-expressing lung cancer cell invasion.

Oxidizing capacity of periodate activated with iron-based bimetallic nanoparticles.

Nanosized zerovalent iron (nFe0) loaded with a secondary metal such as Ni or Cu on its surface was demonstrated to effectively activate periodate (IO4-) and degrade selected organic compounds at neutral pH. The degradation was accompanied by a stoichiometric conversion of IO4- to iodate (IO3-). nFe0 without bimetallic loading led to similar IO4- reduction but no organic degradation, suggesting the production of reactive iodine intermediate only when IO4- is activated by bimetallic nFe0 (e.g., nFe0-Ni and nFe0-Cu). The organic degradation kinetics in the nFe0-Ni(or Cu)/IO4- system was substrate dependent: 4-chlorophenol, phenol, and bisphenol A were effectively degraded, whereas little or no degradation was observed with benzoic acid, carbamazepine, and 2,4,6-trichlorophenol. The substrate specificity, further confirmed by little kinetic inhibition with background organic matter, implies the selective nature of oxidant in the nFe0-Ni(or Cu)/IO4- system. The comparison with the photoactivated IO4- system, in which iodyl radical (IO3•) is a predominant oxidant in the presence of methanol, suggests IO3• also as primary oxidant in the nFe0-Ni(or Cu)/IO4- system.

Biodegradation of biphenyl and 2-chlorobiphenyl by a Pseudomonas sp. KM-04 isolated from PCBs-contaminated coal mine soil.

The biphenyl-degrading strain, Pseudomonas sp. KM-04, was isolated from polychlorinated biphenyls-contaminated soil sample obtained from the vicinity of a former coal mine. We herein report that strain KM-04 can use biphenyl as a sole carbon source, and resting cells convert biphenyl to its corresponding metabolic intermediates. Incubation of KM-04 with autoclaved mining-contaminated soil for 10 days in a slurry system reduced the levels of biphenyl and 2-chlorobiphenyl by 98.5 % and 82.3 %, respectively. Furthermore, treatment of a mine-soil microcosm with strain KM-04 for 15 days in a composting system under laboratory conditions reduced the levels of biphenyl and 2-chlorobiphenyl by 87.1 % and 68.7 %, respectively. These results suggest that KM-04 is a potential candidate for the biological removal of biphenyl and its chlorinated derivatives from polychlorinated biphenyl-contaminated mining areas.

Carbon dioxide-assisted thermochemical conversion of magnetically harvested harmful algae into syngas and metal biochar.

With rising of harmful algae blooming and toxin exposure, practical utilization of harmful algae has been developed. This work aimed to magnetically harvest Microcystis aeruginosa (MA) using iron oxides and investigate the feasibility of algae/iron oxides mixture as feedstock in pyrolytic platform to produce syngas and metal biochar. Carbon dioxide (CO2) was used as a feeding gas to enhance the production efficiency of syngas and also functioned pH controller for better MA harvesting and toxin removal. CO2 support brought multiple benefits: magnetite (Fe3O4) and maghemite (γ-Fe2O3) recovered MA in a relatively short period of time (∼1 min), the recovered biomass generated 34-fold increased carbon monoxide, and metal biochar adsorbed higher amount of toxin from MA (2.8-fold). Pyrolytic utilization of harmful algae supported by CO2 and iron oxides could be one of promising techniques for evolution of metal biochar to remove toxin, while efficiently recover biomass and enhance syngas production.

Microbial mediated reaction of dimethylarsinic acid in wetland water and sediments.

The biogeochemical reactions of dimethylarsinic acid (DMAs(V)) were investigated using simulated wetland systems in a laboratory. DMAs(V) was injected into the wetland water, and the As concentrations in the water, plants, and sediments were monitored. Aqueous and solid-phase As speciation was evaluated, and the results revealed that the DMAs(V) was completely transported to the sediments and plants. X-ray absorption spectroscopic measurement of the As in the sediment revealed that approximately 85-95% of As existed as inorganic As species, demonstrating the important role of microorganisms in the biogeochemical reaction of DMAs(V). The influences of microbes were further investigated in smaller batches under aerobic and anaerobic conditions. The microbial batch results showed that DMAs(V) demethylation reduced the total aqueous As concentration, demonstrating that As(V) has higher affinity to wetland sediment than DMAs(V). The redox conditions were also revealed as an important controlling factor of the As reaction and, under anaerobic conditions, we observed the presence of the most toxic form of inorganic As(III) in the aqueous phase. Although this study reports one example from a specific wetland, the important roles of the redox conditions and microbial influences were identified from the comprehensive analysis of As speciation and mass balance.

Biosorption of Uranyl Ions from Aqueous Solution by Parachlorella sp. AA1.

In the present study we investigated the ability of the microalgal strain Parachlorella sp. AA1 to biologically uptake a radionuclide waste material. Batch experiments were conducted to investigate the biosorption of uranyl ions (U(VI)) in the 0.5-50.0 mg/L concentration range by strain AA1. The results showed that AA1 biomass could uptake U(VI). The highest removal efficiency and biosorption capacity (95.6%) occurred within 60 h at an initial U(VI) concentration of 20 mg/L. The optimum pH for biosorption was 9.0 at a temperature of 25 °C. X-ray absorption near edge structure analysis confirmed the presence of U(VI) in pellets of Parachlorella sp. AA1 cells. The biosorption methods investigated here may be useful in the treatment and disposal of nuclides and heavy metals in diverse wastewaters.

Effect of Treating Acid Sulfate Soils with Phosphate Solubilizing Bacteria on Germination and Growth of Tomato (Lycopersicon esculentum L.).

Acid sulfate soils contain sulfide minerals that have adverse environmental effects because they can lead to acidic drainage and prevent the establishment of vegetation. The current study examined the effect of a novel method for the restoration of these soils and the promotion of germination and plant growth. Thus, we isolated two strains of phosphate solubilizing bacteria, Methylobacterium sp. PS and Caballeronia sp. EK, characterized their properties, and examined their effects in promoting the growth of tomato plants (Lycopersicon esculentum L.) in acid sulfate soil. Compared with untreated control soil, treatment of acid sulfate soils with these bacterial strains led to increased seed germination, growth of plants with more leaves, and plants with greater levels of total-adenosine tri-phosphate (tATP). Relative to the untreated control soil, the addition of Caballeronia sp. EK led to a 60% increase in seed germination after 52 days, growth of plants with more than 3 times as many leaves, and a 45.2% increase in tATP after 50 days. This strain has potential for use as a plant biofertilizer that promotes vegetation growth in acid sulfate soils by improving the absorption of phosphorous.

Effects on Pinus densiflora Seedlings as Affected by Different Container Growth Conditions.

The purpose of this study was to determine the effects that different container conditions have on Pinus densiflora seedling growth. Under greenhouse cultivation, there were no statistical differences observed in plant height and the number of branches; however, significant differences in root collar diameter and root status were observed. In control container growth conditions, the roots grew in an abnormal spiral shape, while in negative phototropism container growth conditions the roots grew in a vertical shape. In outdoor cultivation, seedlings in various container growth conditions showed significant differences. The seedlings that were grown in negative phototropism container growth conditions showed the greatest increases in height, number of branches, root collar diameter, and root growth. This study determined that seedling roots in negative phototropism container growth conditions grew vertically, thus displaying successful rooting when they were transplanted outdoors. This resulted in favorable measurements in height, number of branches, root collar diameter, and root growth.

Synthesis of nickel/biochar composite from pyrolysis of Microcystis aeruginosa and its practical use for syngas production.

This study proposes a sustainable waste-to-energy/biochar platform using a toxic microalgal biomass waste. In particular, CO2-feeding pyrolysis of Microcystis aeruginosa (M. aeruginosa) waste was investigated, focusing on the analysis of gaseous pyrolysates and properties of biochar with a construction of mass balance. Also, the catalytic capability of biochar produced from M. aeruginosa was explored to reinforce the mechanistic impact of CO2 on the pyrolysis process within the overall process level. Ni impregnated biochar composite was further synthesized and used as a catalyst to promote syngas formation in the CO2-feeding pyrolysis process of M. aeruginosa.

The human gut archaeome: identification of diverse haloarchaea in Korean subjects.

BACKGROUND: Archaea are one of the least-studied members of the gut-dwelling autochthonous microbiota. Few studies have reported the dominance of methanogens in the archaeal microbiome (archaeome) of the human gut, although limited information regarding the diversity and abundance of other archaeal phylotypes is available. RESULTS: We surveyed the archaeome of faecal samples collected from 897 East Asian subjects living in South Korea. In total, 42.47% faecal samples were positive for archaeal colonisation; these were subsequently subjected to archaeal 16S rRNA gene deep sequencing and real-time quantitative polymerase chain reaction-based abundance estimation. The mean archaeal relative abundance was 10.24 ± 4.58% of the total bacterial and archaeal abundance. We observed extensive colonisation of haloarchaea (95.54%) in the archaea-positive faecal samples, with 9.63% mean relative abundance in archaeal communities. Haloarchaea were relatively more abundant than methanogens in some samples. The presence of haloarchaea was also verified by fluorescence in situ hybridisation analysis. Owing to large inter-individual variations, we categorised the human gut archaeome into four archaeal enterotypes. CONCLUSIONS: The study demonstrated that the human gut archaeome is indigenous, responsive, and functional, expanding our understanding of the archaeal signature in the gut of human individuals. Video Abstract.

Bioremediation of PCDD/Fs-contaminated municipal solid waste incinerator fly ash by a potent microbial biocatalyst.

Removal of polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/Fs) from fly ash poses a serious problem. In the study presented here, we used a microbial biocatalyst which is a mixture of 4 bacterial and 5 fungal dioxin-degrading strains. The ability of this biocatalyst to bioremediate PCDD/Fs from contaminated municipal solid waste incinerator (MSWI) fly ash was examined by solid-state fermentation under laboratory conditions. Treatment of MSWI fly ash with the microbial biocatalyst for 21 days resulted in a 68.7% reduction in total toxic PCDD/Fs. Further analyses revealed that the microbial biocatalyst also removed 66.8% of the 2,3,7,8-substituted congeners from the fly ash. During the treatment period, the presence of the individual strains composing the microbial biocatalyst was monitored by the amplification of strain-specific DNA sequences followed by denaturing gradient gel electrophoresis (DGGE). This analysis showed that all of the bacterial and fungal strains composing this dioxin-degrading microbial mixture maintained under the dioxin treatment conditions. These results demonstrate that this microbial biocatalyst could potentially be used in the bioremediation of PCDD/Fs from contaminated fly ash.

Interaction of Sb(III) with iron sulfide under anoxic conditions: Similarities and differences compared to As(III) interactions.

This study examined the reaction mechanism of arsenite, As(III), and antimonite, Sb(III), with iron sulfide and compared their pH-dependent reaction behaviors under strictly anoxic environments. The comparison of Sb(III) with As(III), based on their chemical similarity, may provide useful insight into understanding the geochemical behavior of the less studied Sb(III). The pH-dependent batch sorption studies revealed that As(III) and Sb(III) displayed similar removal trends with pH in terms of the removal efficiency. However, the aqueous As(III) species transformed to thioarsenite species, while aqueous Sb(III) species remained inert under the highly sulfidic anoxic system. An X-ray absorption spectroscopy study demonstrated the reaction of As(III) and Sb(III) at acidic pH was closely related to the precipitation of sulfide minerals As2S3 and Sb2S3, respectively, as a consequence of the reaction with sulfide produced through mackinawite dissolution. Meanwhile, the removal at basic pH was inferred as a surface reaction, possibly through surface complexation, surface-precipitation, or both. In this study, the pH-dependent Sb(III) uptake mechanisms proved to be similar to the corresponding mechanisms for As(III) uptake, with mackinawite demonstrating a superior capacity to scavenge Sb(III) in ferrous and sulfide-rich reducing environments.

Effect of heavy metals on the biodegradation of dibenzofuran in liquid medium.

The effect of heavy metals on the degradation of dibenzofuran by Sphingomonas wittichii RW1 was determined in liquid cultures. The results showed that 10mg/L cadmium, mercury and copper not only affected the growth of RW1 with dibenzofuran but also the ability of resting cells to degrade this compound. Growth and degradation were strongly inhibited by mercury, even at 1mg/L, while the inhibitory effect of cadmium and copper at the same concentration or at 5mg/L were negligible. In contrast, arsenic and lead did not affect degradation or growth, even at very high concentrations of 100mg/L. Subsequent analyses additionally revealed that concentrations of arsenic and lead remained unchanged following incubation, while those of cadmium, mercury and copper decreased significantly.

Arsenic uptake and speciation in Arabidopsis thaliana under hydroponic conditions.

Arsenic (As) uptake and species in Arabidopsis thaliana were evaluated under hydroponic conditions. Plant nutrient solutions were treated with arsenite [As(III)] or arsenate [As(V)], and aqueous As speciation was conducted using a solid phase extraction (SPE) cartridge. Arabidopsis reduced As(V) to As(III) in the nutrient solution, possibly due to root exudates such as organic acids or the efflux of As(III) from plant roots after in vivo reduction of As(V) to As(III). Arsenic uptake by Arabidopsis was associated with increased levels of Ca and Fe, and decreased levels of K in plant tissues. Arsenic in Arabidopsis mainly occurred as As(III), which was coordinated with oxygen and sulfur based on XANES and EXAFS results. The existence of As(III)O and As(III)S in EXAFS indicates partial biotransformation of As(III)O to a sulfur-coordinated form because of limited amount of glutathione in plants. Further understanding the mechanism of As biotransformation in Arabidopsis may help to develop measures that can mitigate As toxicity via genetic engineering.

Biosequestration of copper by bacteria isolated from an abandoned mine by using microbially induced calcite precipitation.

Abandoned mine sites are frequently polluted with high concentrations of heavy metals. In this study, 25 calcite-forming bacteria were newly isolated from the soil of an abandoned metal mine in Korea. Based on their urease activity, calcite production, and resistance to copper toxicity, four isolates were selected and further identified by 16S rRNA gene sequencing. Among the isolates, Sporosarcina soli B-22 was selected for subsequent copper biosequestration studies, using the sand impermeability test by production of calcite and extracellular polymeric substance. High removal rates (61.8%) of copper were obtained when the sand samples were analyzed using an inductively coupled plasma-optical emission spectrometer following 72 h of incubation. Scanning electron microscopy showed that the copper carbonate precipitates had a diameter of approximately 5-10 µm. X-ray diffraction further confirmed the presence of copper carbonate and calcium carbonate crystals.

Preparation of Calcined Zirconia-Carbon Composite from Metal Organic Frameworks and Its Application to Adsorption of Crystal Violet and Salicylic Acid.

Zirconia-carbon (ZC) composites were prepared via calcination of Zr-based metal organic frameworks, UiO-66 and amino-functionalized UiO-66, under N2 atmosphere. The prepared composites were characterized using a series of instrumental analyses. The surface area of the ZC composites increased with the increase of calcination temperature, with the formation of a graphite oxide phase observed at 900 °C. The composites were used for adsorptive removal of a dye (crystal violet, CV) and a pharmaceutical and personal care product (salicylic acid, SA). The increase of the calcination temperature resulted in enhanced adsorption capability of the composites toward CV. The composite calcined at 900 °C exhibited a maximum uptake of 243 mg·g-1, which was much greater than that by a commercial activated carbon. The composite was also effective in SA adsorption (102 mg·g-1), and N-functionalization of the composite further enhanced its adsorption capability (109 mg·g-1). CV adsorption was weakly influenced by solution pH, but was more dependent on the surface area and pore volume of the ZC composite. Meanwhile, SA adsorption showed strong pH dependence, which implies an active role of electrostatic interactions in the adsorption process. Base-base repulsion and hydrogen bonding are also suggested to influence the adsorption of CV and SA, especially for the N-functionalized composite.

Biological removal of polychlorinated dibenzo-p-dioxins from incinerator fly ash by Sphingomonas wittichii RW1.

The ability of Sphingomonas wittichii strain RW1 to remove polychlorinated dibenzo-p-dioxins (PCDDs) from fly ash was investigated. All experiments were carried out in a slurry-phase system. Preliminary studies with resting cells of strain RW1 in a model fly ash system showed the complete removal of dibenzofuran (DF) and 81% of dibenzo-p-dioxin (DD). Incubation of real fly ash collected from municipal waste incinerators with strain RW1 for 15 days resulted in a 75.5% reduction in toxic PCDDs. When the same experiment was carried out using dead strain RW1 cells a 20.2% reduction in toxic PCDDs was observed, indicating that adsorption onto biomass was an important factor in dioxin elimination. Further analyses revealed that live strain RW1 cells removed 83.8% of the 2,3,7,8-substituted congeners from the fly ash, while dead cells removed 32.1% of the same congeners. To enhance the removal efficiency of toxic PCDDs, the effects of adding surfactant, repeated inoculation, and pre-adaptation of cultures were also studied. The removal of toxic PCDDs was enhanced by up to 10.3% upon repeated inoculation of the strain RW1, but was not much affected by the addition of surfactant. The present results suggest that S. wittichii strain RW1 is a potential candidate for the industrial removal of PCDDs from incinerator fly ash.

Is the biotransformation of chlorinated dibenzo-p-dioxins by Sphingomonas wittichii RW1 governed by thermodynamic factors?

Density functional theory (DFT) calculations were used to explore the relationship between the biotransformation of dibenzo-p-dioxin and selected chlorinated derivatives by resting cells of Sphingomonas wittichii RW1 and measuring the thermodynamic properties of the biotransformation substrates. Sphingomonas wittichii RW1 can aerobically catabolize dibenzo-p-dioxin as well as 2,7-dichloro-, 1,2,3-trichloro-, 1,2,3,4-tetrachloro-, and 1,2,3,4,7,8-hexachlorodibenzo-p-dioxin; however, neither the 2,3,7-trichloro- nor the 1,2,3,7,8-pentachlorodibenzo-p-dioxin was transformed to its corresponding metabolic intermediate. The experimental biotransformation rates established were apparently governed by the selected thermodynamic properties of the substrates tested.