Shewanella algicola sp. nov., a marine bacterium isolated from brown algae.

A Gram-stain-negative, aerobic, rod-shaped bacterium motile by means of a single polar flagella, strain ST-6T, was isolated from a brown alga (Sargassum thunbergii) collected in Jeju, Republic of Korea. Strain ST-6T was psychrotolerant, growing at 4-30 °C (optimum 20 °C). Phylogenetic analysis based on 16S rRNA and gyrB gene sequences revealed that strain ST-6T belonged to a distinct lineage in the genus Shewanella. Strain ST-6T was related most closely to Shewanella basaltis J83T, S. gaetbuli TF-27T, S. arctica IT12T, S. vesiculosa M7T and S. aestuarii SC18T, showing 96-97 % and 85-70 % 16S rRNA and gyrB gene sequences similarities, respectively. DNA-DNA relatedness values between strain ST-6T and the type strains of two species of the genus Shewanella were <22.6 %. The major cellular fatty acids (>5 %) were summed feature 3 (comprising C16:1ω7c and/ or iso-C15:0 2-OH), C16:0, iso-C13:0 and C17:1ω8c. The DNA G+C content of strain ST-6Twas 42.4 mol%, and the predominant isoprenoid quinones were menaquinone MK-7 and ubiquinones Q-7 and Q-8. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain ST-6T is considered to represent a novel species of the genus Shewanella, for which the name Shewanella algicola sp. nov. is proposed. The type strain is ST-6T (= KCTC 23253T = JCM 31091T).

Winogradskyella eckloniae sp. nov., a marine bacterium isolated from the brown alga Ecklonia cava.

A novel bacterial strain, designated EC29(T), was isolated from the brown alga Ecklonia cava collected on Jeju Island, Republic of Korea. Cells of strain EC29(T) were Gram-stain-negative, aerobic, rod-shaped and motile by gliding. Growth was observed at 10-30 °C (optimum, 20-25 °C), at pH 6.0-9.5 (optimum, pH 7.5) and in the presence of 1-5% (w/v) NaCl. Phylogenetic analyses based on the 16S rRNA gene sequence revealed that the strain belonged to the genus Winogradskyella. Strain EC29(T) exhibited the highest 16S rRNA gene sequence similarities, of 96.5-97.8%, to the type strains of Winogradskyella pulchriflava EM106(T), Winogradskyella echinorum KMM 6211(T) and Winogradskyella ulvae KMM 6390(T). Strain EC29(T) exhibited < 27% DNA-DNA relatedness with Winogradskyella pulchriflava EM106(T) and Winogradskyella echinorum KMM 6211(T). The predominant fatty acids of strain EC29(T) were iso-C15 : 0, iso-C15 : 1 G, C15 : 0, iso-C17 : 0 3-OH, iso-C15 : 0 3-OH and anteiso-C15 : 0. The DNA G+C content was 31.1 mol% and the major respiratory quinone was menaquinone-6 (MK-6). Based on a polyphasic study, strain EC29(T) is considered to represent a novel species of the genus Winogradskyella, for which the name Winogradskyella eckloniae sp. nov. is proposed. The type strain is EC29(T) ( = KCTC 32172(T) = JCM 18703(T)).

Erythrobacter jejuensis sp. nov., isolated from seawater.

A Gram-staining-negative, yellow-pigmented, non-motile, strictly aerobic, rod-shaped bacterium, designated strain CNU001(T), was isolated from seawater collected on the coast of Jeju Island, South Korea, and subjected to a polyphasic taxonomic study. The temperature, pH and NaCl ranges for growth were 10-30 °C, pH 6.0-10.0 and 2.0-5.0 %, respectively. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain CNU001(T) belonged to the genus Erythrobacter in the family Erythrobacteraceae, with Erythrobacter longus DSM 6997(T) (96.6 % sequence similarity), Erythrobacter gaetbuli SW-161(T) (96.3 %), Erythrobacter vulgaris 022 2-10(T) (96.2 %), Erythrobacter nanhaisediminis T30(T) (96.1 %) and other members of the genus Erythrobacter (<96.0 %) identified as the novel strain's closest relatives. The major cellular fatty acids were C18 : 1ω7c and C17 : 1ω6c. The polar lipids were found to be diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phosphatidylglycerol, one sphingoglycolipid, one unidentified aminolipid and six other unidentified lipids. The major respiratory quinone was ubiquinone-10 (UQ-10) and the genomic DNA G+C content of the novel strain was 58.9 mol%. On the basis of phenotypic, phylogenetic and genotypic data, strain CNU001(T) represents a novel species within the genus Erythrobacter, for which the name Erythrobacter jejuensis sp. nov. is proposed. The type strain is CNU001(T) ( = KCTC 23090(T)  = JCM 16677(T)).

Lysinibacillus jejuensis sp. nov., isolated from swinery waste.

A Gram-positive, endospore-forming, rod-shaped bacterium, designated strain N2-5(T), was isolated from swinery waste collected in Jeju, Republic of Korea. A phylogenetic analysis based on 16S rRNA gene sequences demonstrated that strain N2-5(T) formed a phyletic group within the phylum Firmicutes with less than 97.0% similarities to members of the genus Lysinibacillus, its nearest phylogenetic neighbors. The highest levels of sequence similarity to the isolate were observed against Lysinibacillus xylanilyticus XDB9(T) (96.8%), Lysinibacillus macroides LMG 18474(T) (95.6%), and Lysinibacillus parviboronicapiens BAM-582(T) (95.6%). The organism grew optimally at 30°C and pH 7 and in the presence of 1-3% (w/v) NaCl. Strain N2-5(T) was chemotaxonomically characterized by possessing menaquinone-7 (MK-7) as the major menaquinone, and iso-C15:0 (54.9%), iso-C17:1 ω10c (12.0%), and C16:1 ω7c alcohol (11.8%) as the predominant fatty acids. The genomic DNA G+C content of the novel strain was 43.3 mol% and the cell-wall peptidoglycan was type A4α. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylethanolamine. Based on its phenotypic properties and phylogenetic data, strain N2-5(T) (=DSM 28310(T) =KCTC13837(T)) represents a novel species in the genus Lysinibacillus, for which the name Lysinibacillus jejuensis sp. nov. is proposed.

Winogradskyella jejuensis sp. nov., a marine bacterium isolated from a brown alga Carpopeltis affinis.

A Gram-negative, orange-pigmented, rod-shaped bacterium, designated strain CP32(T) was isolated from a brown alga Carpopeltis affinis collected on the coast of Jeju Island, Republic of Korea. The isolate grew at 10-37°C (optimum 25°C) and at pH 6.5-9.5 (optimum pH 7.0). The 16S rRNA gene sequence of the isolate showed much similarity with the type strains of recognized species of the genus Winogradskyella (94.0-96.6%). The most closely related species were Winogradskyella echinorum KMM 6211(T), Winogradskyella ulvae KMM 6390(T), Winogradskyella thalassocola KMM 3907(T), Winogradskyella poriferorum UST030701-295(T), and Winogradskyella eximia KMM 3944(T). The major respiratory quinone was menaquinone-6 (MK-6) and the predominant cellular fatty acids were iso-C(15:1) G (24.8%), iso-C(15:0) (23.4%), and iso-C(17:0) 3-OH (11.6 %). The DNA G+C content was 33.3 mol%. The polar lipid profile was composed of phosphatidylethanolamine, two aminolipids, and five unknown lipids. On the basis of phenotypic features, and the result of 16S rRNA gene sequence analysis, strain CP32(T) (=KCTC 23835(T) =JCM 18454(T)) represents a novel species of the genus Winogradskyella, for which the name Winogradskyella jejuensis sp. nov. is proposed.

Spongiibacterium flavum gen. nov., sp. nov., a member of the family Flavobacteriaceae isolated from the marine sponge Halichondria oshoro, and emended descriptions of the genera Croceitalea and Flagellimonas.

A gram-negative, strictly aerobic, non-flagellated, non-gliding, oxidase- and catalase-positive, yellow-pigmented rod, designated A11(T), was isolated from a marine sponge, Halichondria oshoro, collected on the coastline of Jeju Island, Republic of Korea. Phylogenetic analysis based on nearly complete 16S rRNA gene sequences revealed that strain A11(T) was a member of the family Flavobacteriaceae. Its closest relatives were members of the genera Muricauda, Flagellimonas and Croceitalea (94.4-94.8 % 16S rRNA gene sequence similarity). The only polar lipid detected in strain A11(T) was phosphatidylethanolamine. The dominant fatty acids were iso-C(15 : 0) (30.4 %), iso-C(15 : 1) G (26.7 %), iso-C(17 : 0) 3-OH (12.4 %) and iso-C(15 : 0) 3-OH (7.3 %). The DNA G+C content of strain A11(T) was 41.7 mol% and its major respiratory quinone was MK-6. On the basis of combined data from phenotypic and phylogenetic analyses, strain A11(T) represents a novel genus and species within the family Flavobacteriaceae, for which the name Spongiibacterium flavum gen. nov., sp. nov. is proposed. The type strain of the type species is A11(T) ( = KCTC 22665(T) = DSM 22638(T)). Emended descriptions of the genera Croceitalea and Flagellimonas are also given.

Aquimarina spongiae sp. nov., isolated from marine sponge Halichondria oshoro.

A Gram-stain-negative, yellow-pigmented, rod-shaped, strictly aerobic, non-flagellated, non-gliding and oxidase- and catalase-positive bacterium, designated A6(T), was isolated from a marine sponge, Halichondria oshoro, collected on the coast of Jeju Island, South Korea. Phylogenetic analysis based on the nearly complete 16S rRNA gene sequence revealed that strain A6(T) was a member of the family Flavobacteriaceae. The closest relatives were Aquimarina intermedia LMG 23204(T), A. latercula ATCC 23177(T), A. brevivitae SMK-19(T) and A. muelleri KMM 6020(T), with which strain A6(T) shared 95.7, 95.1, 94.7 and 94.6 % 16S rRNA gene sequence similarity, respectively. The dominant fatty acids of strain A6(T) were iso-C(15 : 0) (32.2 %), iso-C(17 : 0) 3-OH (20.0 %), iso-C(15 : 0) 3-OH (12.3 %), iso-C(15 : 1) G (7.2 %) and summed feature 3 (comprising iso-C(15 : 0) 2-OH and/or C(16 : 1)ω7c; 6.8 %). The DNA G+C content of strain A6(T) was 36.0 mol% and the major respiratory quinone was MK-6. On the basis of combined phenotypic and phylogenetic analyses, strain A6(T) represents a novel species of the genus Aquimarina, for which the name Aquimarina spongiae sp. nov. is proposed. The type strain is A6(T) (=KCTC 22663(T) =DSM 22623(T)).

Formosa spongicola sp. nov., isolated from the marine sponge Hymeniacidon flavia.

A Gram-negative, yellow-pigmented, rod-shaped, strictly aerobic, non-flagellated, oxidase- and catalase-positive, marine bacterium, designated A2(T), was isolated from a marine sponge, Hymeniacidon flavia, collected from the coast of Jeju Island, South Korea. Phylogenetic analysis based on nearly complete 16S rRNA gene sequences revealed that strain A2(T) was a member of the family Flavobacteriaceae. Its closest relatives were Formosa agariphila KMM 3901(T) and Formosa algae KMM 3553(T) (96.99 and 96.98 % 16S rRNA gene sequence similarity, respectively). DNA-DNA relatedness between strain A2(T) and F. agariphila KMM 3901(T) and F. algae KMM 3553(T) was 14.1 and 26.8 %, respectively. The dominant fatty acids (>5 %) of strain A2(T) were iso-C(15 : 0) (33.9 %), iso-C(17 : 0) 3-OH (20.8 %), iso-C(15 : 1) G (10.5 %) and iso-C(15 : 0) 3-OH (6.1 %). The DNA G+C content of strain A2(T) was 36.0 mol% and the major respiratory quinone was MK-6. On the basis of phenotypic and phylogenetic analysis, strain A2(T) represents a novel species of the genus Formosa, for which the name Formosa spongicola sp. nov. is proposed. The type strain is A2(T) (=KCTC 22662(T) =DSM 22637(T)).

Winogradskyella lutea sp. nov., isolated from seawater, and emended description of the genus Winogradskyella.

A novel gram-negative, orange-pigmented, rod-shaped, strictly aerobic, gliding, oxidase- and catalase-positive bacterial strain, A73(T), was isolated from seawater collected off Jeju, South Korea. 16S rRNA gene sequence similarity between A73(T) and type strains of Winogradskyella species with validly published names ranged from 94.1 to 96.2 %. The dominant fatty acids of strain A73(T) were iso-C(15 : 1) G (19.1 %), iso-C(15 : 0) (13.3 %), iso-C(17 : 0) 3-OH (10.0 %) and iso-C(15 : 0) 3-OH (7.2 %). The DNA G+C content of strain A73(T) was 36.0 mol% and its major respiratory quinone was MK-6. On the basis of combined data from phenotypic and phylogenetic analyses, strain A73(T) represents a novel species of the genus Winogradskyella, for which the name Winogradskyella lutea sp. nov. is proposed. The type strain is A73(T) ( = KCTC 23237(T)  = DSM 22624(T)). An emended description of the genus Winogradskyella is also provided.

Aquimarina litoralis sp. nov., isolated from a coastal seawater.

A strictly aerobic, red-pigmented, non-motile, catalase- and oxidase-positive, Gram-staining-negative bacterium, designated strain CNURIC011(T), was isolated from seawater off the coast of Jeju Island in Korea. A phylogenetic analysis based on 16S rRNA gene sequences showed that strain CNURIC011(T) belongs to the genus Aquimarina in the family Flavobacteriaceae. 16S rRNA gene sequence analysis revealed that the close relatives of the novel strain are Aquimarina latercula ATCC 23177(T), Aquimarina marcrocephali JAMB N27(T), Aquimarina intermedia KMM 6258(T), Aquimarina muelleri KMM 6020(T), and Aquimarina brevivitae SMK-19(T), with sequence similarities of 97.6, 96.6, 96.0, 95.6, and 94.2%, respectively. DNA-DNA hybridization revealed that the level of relatedness between strain CNURIC011(T) and Aquimarina latercula ATCC 23177(T) (=KCTC 2912(T)) was 4.9%. The DNA G+C content was 35.8 mol% and the major respiratory quinone was MK-6. The major fatty acids were iso-C(15:0) (14.9%), C(15:0) (13.9%), iso-C(17:0) 3-OH (12.6%), iso-C(15:1) G (7.3%), and iso-C(17:1) omega9c (7.2%). On the basis of phenotypic, phylogenetic, and genotypic data, strain CNURIC011(T) represents a novel species within the genus Aquimarina, for which the name Aquimarina litoralis sp. nov. is proposed. The type strain is CNURIC011(T) (=KCTC 22614(T) =JCM 15974(T)).

Gaetbulibacter jejuensis sp. nov., isolated from seawater.

A novel marine bacterium, designated strain CNURIC014(T) was isolated from coastal seawater of Jeju Island in Korea. Strain CNURIC014(T) formed yellow colonies on marine agar 2216 and the cells were Gram-negative, non-motile, strictly aerobic, rod-shaped. The temperature, pH and NaCl ranges for growth were 15-37 degrees C, pH 6.0-9.0 and 1.0-7.0% NaCl. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain CNURIC014(T) was most closely related to Gaetbulibacter marinus and Gaetbulibacter saemankumensis, with a sequence similarity of 95.1% and 94.6%, respectively. The DNA G+C content of the strain was 33.1 mol% and the major respiratory quinone was menaquinone-6. The major cellular fatty acids were iso-C(15:1) (22.8%), iso-C(15:0) (18.8%), summed feature 3 (iso-C(15:0) 2-OH/C(16:1) omega 7c, 12.9%) and iso-C(17:0) 3-OH (11.5%). On the basis of phenotypic, phylogenetic, and genotypic data, strain CNURIC014(T) represents a novel species within the genus Geatbulibacter, for which the name Gaetbulibacter jejuensis sp. nov. is proposed. The type strain is CNURIC014(T)(=KCTC 22615(T) =JCM 15976(T)).

Hyunsoonleella jejuensis gen. nov., sp. nov., a novel member of the family Flavobacteriaceae isolated from seawater.

A novel marine, Gram-staining-negative, yellow-pigmented, rod-shaped bacterial strain, designated CNU004(T), was isolated from a seawater sample collected on the coastline of Jeju Island, South Korea. The strain was strictly aerobic, non-flagellated, non-gliding and oxidase- and catalase-positive. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain CNU004(T) belongs to a distinct lineage in the family Flavobacteriaceae. Strain CNU004(T) exhibited levels of 16S rRNA gene sequence similarity of 93.8-93.9 % to its nearest phylogenetic neighbours, members of the genera Gaetbulibacter, Yeosuana and Algibacter. The new isolate required sea salts or artificial seawater for growth. The optimum ranges of temperature and pH for growth were 30-35 degrees C and pH 7.0-8.0. The DNA G+C content of strain CNU004(T) was 37.7 mol%. The major fatty acids were iso-C(15 : 0), iso-C(15 : 1) G, iso-C(17 : 0) 3-OH and iso-C(15 : 0) 3-OH. Menaquinone-6 was the major respiratory quinone. Zeaxanthin was the major carotenoid pigment produced, and flexirubin-type pigments were not produced. Strain CNU004(T) was able to degrade starch and agar. Based on its phenotypic and genotypic characteristics and on the phylogenetic evidence presented, strain CNU004(T) is considered to represent a novel species of a new genus in the family Flavobacteriaceae, for which the name Hyunsoonleella jejuensis gen. nov., sp. nov. is proposed. The type strain of Hyunsoonleella jejuensis sp. nov. is CNU004(T) (=KCTC 22242(T) =DSM 21035(T)).

Cloning and characterization of monofunctional catalase from photosynthetic bacterium Rhodospirillum rubrum S1.

In this study, an approx. 2.5-kb gene fragment including the catalase gene from Rhodospirillum rubrum S1 was cloned and characterized. The determination of the complete nucleotide sequence revealed that the cloned DNA fragment was organized into three open reading frames, designated as ORF1, catalase, and ORF3 in that order. The catalase gene consisted of 1,455 nucleotides and 484 amino acids, including the initiation and stop codons, and was located 326 bp upstream in the opposite direction of ORF1. The catalase was overproduced in Escherichia coli UM255, a catalase-deficient mutant, and then purified for the biochemical characterization of the enzyme. The purified catalase had an estimated molecular mass of 189 kDa, consisting of four identical subunits of 61 kDa. The enzyme exhibited activity over a broad pH range from pH 5.0 to pH 11.0 and temperature range from 20 degrees C to 60 degrees C. The catalase activity was inhibited by 3-amino-1,2,4-triazole, cyanide, azide, and hydroxylamine. The enzyme's K(m) value and V(max) of the catalase for H2O2 were 21.8 mM and 39,960 U/mg, respectively. Spectrophotometric analysis revealed that the ratio of A406 to A280 for the catalase was 0.97, indicating the presence of a ferric component. The absorption spectrum of catalase-4 exhibited a Soret band at 406 nm, which is typical of a heme-containing catalase. Treatment of the enzyme with dithionite did not alter the spectral shape and revealed no peroxidase activity. The combined results of the gene sequence and biochemical characterization proved that the catalase cloned from strain S1in this study was a typical monofunctional catalase, which differed from the other types of catalases found in strain S1.

Purification and characterization of a catalase from photosynthetic bacterium Rhodospirillum rubrum S1 grown under anaerobic conditions.

The photosynthetic bacterium, Rhodospirillum rubrum S1, when grown under anaerobic conditions, generated three different types of catalases. In this study, we purified and characterized the highest molecular weight catalase from the three catalases. The total specific catalase activity of the crude cell extracts was 88 U/mg. After the completion of the final purification step, the specific activity of the purified catalase was 1,256 U/mg. The purified catalase evidenced an estimated molecular mass of 318 kDa, consisting of four identical subunits, each of 79 kDa. The purified enzyme exhibited an apparent Km value of 30.4 mM and a Vmax of 2,564 U against hydrogen peroxide. The enzyme also exhibited a broad optimal pH (5.0-9.0), and remained stable over a broad temperature range (20 degrees C-60 degrees C). It maintained 90% activity against organic solvents (ethanol/chloroform) known hydroperoxidase inhibitors, and exhibited no detectable peroxidase activity. The catalase activity of the purified enzyme was reduced to 19% of full activity as the result of the administration of 10 mM 3-amino-1,2,4-triazole, a heme-containing catalase inhibitor. Sodium cyanide, sodium azide, and hydroxylamine, all of which are known heme protein inhibitors, inhibited catalase activity by 50% at concentrations of 11.5 microM, 0.52 microM, and 0.11 microM, respectively. In accordance with these findings, the enzyme was identified as a type of monofunctional catalase.

Evaluation of carbazole degradation by Pseudomonas rhodesiae strain KK1 isolated from soil contaminated with coal tar.

In this study, strain KK1 isolated from coal tar-contaminated soil was found to be able to mineralize carbazole as a sole source of carbon by radiorespirometric analysis. KK1 cells pregrown on phenanthrene were able to mineralize carbazole much more rapidly than cells pregrown on naphthalene, suggesting a possible close linkage between the pathways for carbazole and phenanthrene catabolism. Also, Rieske-type iron sulfur center sequence of dioxygenase from KK1 was analyzed to evaluate carbazole catabolism by KK1. A gene cloned out from KK1 using a universal dioxygenase primer set was found a dioxygenase for initial catabolism of carbazole based on deduced amino acid sequences. Northern hybridization using the putative carbazole dixoygenase gene fragment as a probe provided the information that catabolism of carbazole might be greatly activated in phenanthrene-grown cells. Analysis of PLFAs extracted from KK1 cells exposed to carbazole revealed that lipids 10:0 3OH, 17:0 cyclo, and 18:0 were representatives produced or significantly increased in response to carbazole. Strain KK1 was identified as Pseudomonas species with 94% confidence when BIOLOG system was applied, as Pseudomonas sp. with over 90% confidence by total cellular compositions of fatty acid, and as Pseudomonas rhodesiae with 99% confidence by 16S rRNA sequence. Accordingly, strain KK1 was identified as Pseudomonas rhodesiae based on combination of the data, and designated Pseudomonas rhodesiae KK1. The phylogenetic tree based on 16S rRNA suggested that strain KK1 was far away in the phylogenetic distance from the strains that can degrade carbazole.