Winogradskyella damuponensis sp. nov., isolated from seawater.

A novel bacterium, designated F081-2(T), isolated from seawater from Damupo beach in Pohang, Korea, was investigated using a polyphasic taxonomic approach. Cells were yellow-pigmented, strictly aerobic, motile by gliding, Gram-negative-staining and rod-shaped. The temperature, pH and NaCl ranges for growth were 4-35 °C, pH 5.5-9.5 and 1.0-5.0 %, respectively. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain F081-2(T) belonged to a distinct lineage in the genus Winogradskyella of the family Flavobacteriaceae, sharing 93.7-98.1 % similarity with recognized members of the genus. Low levels of DNA-DNA relatedness values were found between strain F081-2(T) and Winogradskyella eximia KCTC 12219(T) (61.1 %), Winogradskyella thalassocola KCTC 12221(T) (47.0 %), Winogradskyella echinorum KCTC 22026(T) (39.3 %), Winogradskyella rapida CCUG 56098(T) (34.3 %) and Winogradskyella arenosi JCM 17633(T) (33.4 %). The major cellular fatty acids were iso-C(15 : 0) (25.3 %), iso-C(15 : 1) G (14.6 %), iso-C(17 : 0) 3-OH (9.3 %), anteiso-C(15 : 0) (7.8 %) and iso-C(15 : 0) 3-OH (7.6 %). The polar lipid profile was composed of phosphatidylethanolamine, one unidentified aminolipid, one unidentified phospholipid, one unidentified aminophospholipid and six unidentified lipids. The major respiratory quinone was menaquinone-6 and the DNA G+C content of the strain was 32.3 mol%. On the basis of phenotypic, phylogenetic and genotypic data, strain F081-2(T) represents a novel species within the genus Winogradskyella, for which the name Winogradskyella damuponensis sp. nov. is proposed. The type strain is F081-2(T) (=KCTC 23552(T) = JCM 17633(T)).

Sagittula marina sp. nov., isolated from seawater and emended description of the genus Sagittula.

A novel bacterium, designated strain F028-2(T), was isolated from seawater at Damupo beach in Pohang, Korea, and investigated in a taxonomic study using a polyphasic approach. This novel strain was strictly aerobic, non-motile, Gram-stain-negative and rod-shaped, and occasionally formed aggregates. The temperature, pH and NaCl ranges for growth were 4-30 °C, pH 6.5-9.0 and 1-7% (w/v), respectively. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain F028-2(T) formed a lineage within the family Rhodobacteraceae of the class Alphaproteobacteria, and was closely related to members of the genera Sagittula and Antarctobacter with 96.3-96.4% sequence similarities. The polar lipid profile of strain F028-2(T) comprised diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, two unidentified aminolipids, one unidentified phospholipid and six unidentified lipids. The predominant cellular fatty acids were C18:1ω7c and C12:1 3-OH. The genomic DNA G+C content of strain F028-2(T) was 61.6 mol% and the major respiratory quinone was Q-10. Based on phenotypic, phylogenetic and genotypic data, strain F028-2(T) is considered to represent a novel species in the genus Sagittula, for which the name Sagittula marina sp. nov. is proposed. The type strain is F028-2(T) (=KCTC 23543(T)=JCM 17627(T)). An emended description of the genus Sagittula is also proposed.

Psychroserpens damuponensis sp. nov., isolated from seawater.

A novel bacterium, designated strain F051-1(T), isolated from a seawater sample collected from the coast at Damupo beach in Pohang, Korea, was investigated in a polyphasic taxonomic study. Cells were yellow-pigmented, strictly aerobic, Gram-staining-negative and rod-shaped. The temperature, pH and NaCl ranges for growth were 4-30 °C, pH 6.0-9.0 and 1.0-6.0 % (w/v), respectively. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain F051-1(T) belongs to the genus Psychroserpens in the family Flavobacteriaceae. Its closest relatives were Psychroserpens burtonensis ACAM 188(T) (96.8 % 16S rRNA gene sequence similarity) and Psychroserpens mesophilus KOPRI 13649(T) (95.7 %). The major cellular fatty acids were iso-C(15 : 0), iso-C(15 : 1) G and anteiso-C(15 : 0). The polar lipid profile consisted of a mixture of phosphatidylethanolamine, two unidentified aminolipids, one unidentified phospholipid and eight unidentified lipids. The major respiratory quinone was menaquinone-6 and the genomic DNA G+C content of the strain was 33.5 mol%. On the basis of phenotypic, phylogenetic and genotypic data, strain F051-1(T) represents a novel species within the genus Psychroserpens, for which the name Psychroserpens damuponensis sp. nov. is proposed. The type strain is F051-1(T) ( = KCTC 23539(T)  = JCM 17632(T)).

Genome sequence of the unclassified marine Gammaproteobacterium BDW918.

The unclassified marine gammaproteobacterium BDW918, which utilizes volatile fatty acids but not most common carbohydrates and amino acids, was isolated from Dokdo seawater in South Korea. Here we present a draft genome of the strain BDW918, which encodes many putative genes related to fatty acid metabolism and aromatic hydrocarbon degradation.

Postechiella marina gen. nov., sp. nov., isolated from seawater.

A Gram-staining-negative, strictly aerobic, non-motile, yellow-pigmented bacterium, designated strain M091(T), was isolated from seawater at Damupo beach in Pohang, Republic of Korea, and investigated using a polyphasic taxonomic approach. The novel strain grew optimally at 25 °C, pH 7.0-8.0, and in the presence of 3% (w/v) NaCl. In a phylogenetic analysis based on 16S rRNA gene sequences, strain M091(T) formed a lineage within the family Flavobacteriaceae that was distinct from the most closely related genera of Flaviramulus (95.1% sequence similarity), Algibacter (94.9-93.9%), Mariniflexile (94.8-94.2%), Winogradskyella (94.8-93.2%), Lacinutrix (94.7-93.8%) and Tamlana (94.7-92.9%). The polar lipid profile of the novel strain comprised phosphatidylethanolamine, two unidentified aminolipids, one unidentified phospholipid and seven unidentified lipids. The predominant cellular fatty acids were iso-C(15:0) (20.5%), iso-C(17:0) 3-OH (15.4%), iso-C(15:0) 3-OH (12.4%), C(15:0) (10.9%) and iso-C(15:1) G (9.9%). The genomic DNA G+C content of strain M091(T) was 34.4 mol% and the major respiratory quinone was MK-6. Based on phenotypic and genotypic data, strain M091(T) represents a new genus and novel species in the family Flavobacteriaceae, for which the name Postechiella marina gen. nov., sp. nov. is proposed. The type strain of the type species is M091(T) (=KCTC 23537(T)=JCM 17630(T)).

Cloning, expression, purification, crystallization and X-ray crystallographic analysis of glucuronic acid dehydrogenase from Chromohalobacter salexigens.

Glucuronic acid dehydrogenase (GluUADH), the product of the Csal-2474 gene from the halophilic bacterium Chromohalobacter salexigens DSM 3043, is an enzyme with potential use in the conversion of glucuronic acid in seaweed biomass to fuels and chemicals. GluUADH is an enzyme that catalyzes the oxidation of glucuronic acid (GluUA) and galacturonic acid (GalUA) and has a preference for NAD(+) rather than NADP(+) as a cofactor. Recombinant GluUADH was crystallized in the presence of 0.2 M calcium acetate, 0.1 M Tris-HCl pH 7.0 and 20% PEG 3000 at 295 K. X-ray diffraction data were collected to a maximum resolution of 2.1 Å. The GluUADH crystal belonged to space group P6(3), with unit-cell parameters a = b = 122.58, c = 150.49 Å, γ = 120°. With one molecule per asymmetric unit, the crystal volume per unit protein weight (V(M)) is 2.78 Å(3) Da(-1). The structure was solved by the single anomalous dispersion method and structure refinement is in progress.

Aerobic denitrification of Pseudomonas putida AD-21 at different C/N ratios.

An aerobic denitrifier was newly isolated from soil and its denitrification activity under different C/N (carbon/nitrogen) ratios was investigated. The isolate was identified as Pseudomonas putida AD-21 by biochemical studies and 16s rDNA sequencing analysis. P. putida AD-21 tolerated oxygen levels of 5.0-6.0 mg/l. An (15)NH(4)/(14)NO(3) analysis indicated that the nitrogen of NH(4) was preferentially assimilated into the cell mass and that the nitrate removed could be considered an indication of bacterial denitrification efficiency. Increasing the C/N ratio increased the nitrate removal rates, whereas nitrogen assimilation into the cell mass was not affected. The optimal C/N ratio was 8 with a maximum nitrate removal rate of 254.6 mg/l/h and a nitrate removal efficiency of 95.9%. The results suggest that P. putida AD-21 may be a good candidate for aerobic wastewater treatment.