Tabrizicola oligotrophica sp. nov. and Rhodobacter tardus sp. nov., two new species of bacteria belonging to the family Rhodobacteraceae

Two Gram-stain-negative, aerobic, non-motile bacteria, designated KMS-5^T and CYK-10^T, were isolated from freshwater environments. 16S rRNA gene sequence similarity results indicated that these two novel strains belong to the family Rhodobacteraceae. Strain KMS-5^T is closely related to species within the genus Tabrizicola (96.1-96.8 % sequence similarity) and Cypionkella (96.5-97.0 %). Strain CYK-10^T is closest to Rhodobacter thermarum YIM 73036^T with 96.6 % sequence similarity. Phylogenetic analyses based on 16S rRNA gene sequences and an up-to-date bacterial core gene set showed that strain KMS-5^T is affiliated with species in the genus Tabrizicola and strain CYK-10^T is placed in a distinct clade with Rhodobacter blasticus ATCC 33485^T, Rhodobacter thermarum YIM 73036^T and Rhodobacter flagellatus SYSU G03088^T. These two strains shared common chemotaxonomic features comprising Q-10 as the major quinone, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylcholine as the principal polar lipids, and C_18 : 1  ω7c as the main fatty acid. The average nucleotide identity, average amino acid identity and digital DNA-DNA hybridization values between these two novel isolates and their closest relatives were below the cut-off values of 95-96, 90 and 70 %, respectively, used for species demarcation. The obtained polyphasic taxonomic data suggested that strain KMS-5^T represents a novel species within the genus Tabrizicola, for which the name Tabrizicola oligotrophica sp. nov. is proposed with KMS-5^T (=BCRC 81196^T=LMG 31337^T) as the type strain, and strain CYK-10^T should represent a novel species of the genus Rhodobacter, for which the name Rhodobacter tardus sp. nov. is proposed with CYK-10^T (=BCRC 81191^T=LMG 31336^T) as the type strain.

Flavobacterium ichthyis sp. nov., isolated from a fish pond

Bacterial strain NST-5T, isolated from a fish pond in Taiwan, was characterized using a polyphasic taxonomy approach. Results of phylogenetic analyses based on 16S rRNA gene sequences and coding sequences of 92 protein clusters indicated that strain NST-5T formed a phylogenetic lineage in the genus Flavobacterium . Analysis of 16S rRNA gene sequences showed that strain NST-5T showed the highest similarity to Flavobacterium enshiense DK69T (94.9 %), Flavobacterium ahnfeltiae 10Alg 130T (94.8 %) and Flavobacterium vireti THG-SM1T (94.8 %). Strain NST-5T showed 68.9–72.5% average nucleotide identity and 19.1–23.7% digital DNA–DNA hybridization identity with the type strains of other close related Flavobacterium species. Cells of the strain were Gram-stain-negative, strictly aerobic, motile by gliding, rod-shaped and formed yellow colonies. Optimal growth occurred at 30 °C, pH 7 and with 0.5% NaCl. Strain NST-5T contained iso-C15:0, C15:0 and iso-C16:0 as the predominant fatty acids. The major hydroxyl fatty acids were iso-C16:0 3-OH and iso-C17:0 3-OH. The polar lipid profile consisted of phosphatidylethanolamine, three uncharacterized aminophospholipids, two uncharacterized phospholipids and one uncharacterized aminolipid. The major polyamine was homospermidine. The major isoprenoid quinone was MK-6. The DNA G+C content of the genomic DNA was 35.5 mol%. Differential phenotypic properties, together with the phylogenetic inference, demonstrate that strain NST-5T should be classified as a novel species of the genus Flavobacterium , for which the name Flavobacterium ichthyis sp. nov. is proposed. The type strain is NST-5T (=BCRC 81198T=LMG 31341T).

Sphingomonas crocodyli sp. nov., isolated from a crocodile pond

Strain CCP-7^T, isolated from a freshwater pond in Taiwan, was characterized using a polyphasic taxonomy approach. Phylogenetic analyses based on 16S rRNA gene sequences and coding sequences of 92 protein clusters indicated that strain CCP-7^T formed a phylogenetic lineage in the genus Sphingomonas. Strain CCP-7^T was most closely related to Sphingomonas starnbergensis 382^T and Sphingomonas naphthae DKC-5-1^T with 96.2 % 16S rRNA gene sequence similarity. Strain CCP-7^T showed 65.5-76.7 % average nucleotide identity and 20.2-22.5 % digital DNA-DNA hybridization identity with the strains of other related Sphingomonas species. Cells were Gram-stain-negative, aerobic, motile, rod-shaped and formed light orange-coloured colonies. Optimal growth occurred at 30 °C, pH 6 and in the absence of NaCl. The major fatty acid of strain CCP-7^T was C18 : 1ω7c. The polar lipid profile consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylmonomethylethanolamine, three uncharacterized sphingoglycolipids, two uncharacterized phospholipids and six uncharacterized lipids. The predominant polyamine was homospermidine. The only isoprenoid quinone was Q-10. Genomic DNA G+C content of strain CCP-7^T was 64.5 %. On the basis of phenotypic and genotypic properties and phylogenetic inference, strain CCP-7^T should be classified in a novel species of the genus Sphingomonas, for which the name Sphingomonas crocodyli sp. nov. is proposed. The type strain is CCP-7^T (=BCRC 81096^T=LMG 30311^T=KCTC 62190^T).

Salsuginimonas clara gen. nov., sp. nov., a member of the family Pseudoalteromonadaceae isolated from a brackish river

A bacterial strain designated LSN-49^T was isolated from a brackish river in Taiwan and characterized using a polyphasic taxonomy approach. Cells of strain LSN-49^T were Gram-staining-negative, aerobic, poly-β-hydroxybutyrate accumulating, motile by means of a monopolar flagellum, non-spore forming, straight rods and formed shiny and translucent colonies. Growth occurred at 20-40 °C (optimum, 25-30 °C), at pH 6-10 (optimum, pH 7-8) and with 0-3 % (w/v) NaCl [optimum, 0-1 % (w/v)]. The predominant fatty acids were summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c), C17 : 1ω8c and C16 : 0. The polar lipid profile consisted of a mixture of phosphatidylethanolamine (PE), phosphatidylglycerol (PG), phosphatidylcholine, (PC), two uncharacterized aminophospholipids (APL1 and APL2), one uncharacterized glycolipid (GL1), four uncharacterized phospholipids (PL1-PL4) and four uncharacterized lipids (L1-L4). The major polyamine was putrescine. The major isoprenoid quinone was Q-8 and the DNA G+C content was 51.0 mol%. The results of phylogenetic analyses based on 16S rRNA gene sequences indicated that LSN-49^T formed a distinct lineage with respect to closely related genera in the family Pseudoalteromonadaceae. LSN-49^T was most closely related to Pseudoalteromonas, Algicola and Psychrosphaera and showed 89.3-92.1 % sequence similarity with members of the family Pseudoalteromonadaceae with validly published names. On the basis of the genotypic and phenotypic data, LSN-49^T represents a novel genus and species of the family Pseudoalteromonadaceae, for which the name Salsuginimonas clara gen. nov., sp. nov. is proposed. The type strain is LSN-49^T (=BCRC 81005^T=LMG 29726^T=KCTC 52439^T).

Analysis of antibiotic fungicide kasugamycin in irrigation water by high performance liquid chromatography

A high performance liquid chromatographic (HPLC) analysis method with an ultraviolet (UV) detector and an Aqua C18 (250 x 4.6 mm, Phenomenex) column were applied to analyze the antibiotic fungicide kasugamycin in water. An aromatic sulfonic acid spe column (Backerbond, J. T. Backer) was used to remove the interfering materials from irrigation water. A good linear relation existed between the concentration of the fungicide and the peak area, and correlation coefficient of linearity from 0.1 to 10.2 microg/mL was 0.998. The accuracies expressed as the recoveries of kasugamycin from irrigation water ranged from 112.2 to 111.7 %. The precisions expressed as relative standard deviations (RSD) were found to be below 7.0 %. The quantitative detection limit (LOQ) of kasugamycin in irrigation water was set at 2.2 microg/mL which was 2-times higher than the method detection limit (MDL) 1.03 microg/mL. Electrospray ionization-mass (ESI-MS) and fast-atom bombardment-mass (FAB-MS) were applied to compare the ability of identifying the component of the eluent peak from HPLC, and the result indicated that electrospray ionization-mass (ESI-MS) was more sensitive than fast-atom bombardment-mass (FAB-MS) in the detection of kasugamycin. There was no kasugamycin residue detected in irrigation water samples collected from paddyfields at Wufong, indicated that the residues of kasugamycin in water were less than 2.2 microg/mL, and the risk of water contamination was very low.

Extraction of DNA from soil for analysis of bacterial diversity in transgenic and nontransgenic papaya sites

The influence of transgenic crops on the soil diversity of microorganisms is one of the major risk assessments being conducted in Taiwan since 2007, and a reliable soil DNA extraction method for denaturing gradient gel electrophoresis (DGGE) is required. Six soils of different type, organic matter content, cation exchange capacity, and pH were tested, and four previously reported soil DNA extraction methods were applied to these soils. Soil DNA extracts by Zhou's CS method plus QIAquick gel was recommended in our laboratory for DGGE to monitor the microbial diversity in soil. There were some differences on the bacterial diversity based on DGGE patterns at the beginning of planting, and the difference decreased after six months. The results also indicated that clay content (10.8-25.0%) and pH (4.4-6.9) of different soil samples we tested did not affect the DNA extraction efficiencies, but positive correlations were found between the organic matter content (1.2-3.9%) of soils and the DNA yields in Widmer's GS method (r = 0.93, p = 0.005) and the MoBio UC method (r = 0.92, p = 0.007). Coefficient of determinations between organic matter content and DNA yield were higher than those between clay content, CEC, and pH, indicating that organic matter content was more correlated with DNA yield than that clay content, CEC, and pH in our soil samples tested.

Gating as a control element in constrictive binding and guest release by hemicarcerands

Theoretical modeling of the dynamics of complexation and decomplexation of guest molecules by container molecules reveals that gating has a critical influence on the ease of formation and stability of host-guest complexes. Hosts equipped with gates can form very stable complexes with a variety of guests under readily achievable conditions. Gating involves conformational processes of the host molecule that alter the size of the portals through which guest molecules pass. "French door" and "sliding door" mechanisms of gate opening are identified.

Photooxidation of troglitazone, a new antidiabetic drug

Troglitazone (CS-045) is a new oral antidiabetic drug reported to be effective in insulin-resistant diabetes and to show antihypertensive effects. Photooxidation of troglitazone gave the quinone and quinone epoxide as the major final stable products. An intermediate observed by NMR spectroscopy was shown to be the hydroperoxydienone, which is moderately stable at room temperature. The rate constant of singlet oxygen quenching by troglitazone is 2.14 x 10(8) M(-1) s(-1) and the reaction rate constant in acetone-d6 is 8.64 X 10(6) M(-1) s(-1). Only the chroman ring of troglitazone reacts with and quenches singlet oxygen significantly, and its reactivity and products are analogous to those of alpha-tocopherol. The reactivity of CS-45 toward singlet oxygen is much larger than that of the related compounds lacking the chroman ring.