Identification and Analysis of Putative Polyhydroxyalkanoate Synthase (PhaC) in Pseudomonas fluorescens.

Pseudomonas fluorescens KLR101 was found to be capable of producing polyhydroxyalkanoate (PHA) using various sugars and fatty acids with carbon numbers ranging from 2 to 6. The PHA granules consisted mainly of a poly(3-hydroxybutyrate) homopolymer and/or poly(3-hydroxybutyrate-co-3-hydroxyvalerate) copolymer. Genomic DNA of P. fluorescens was fractionated and cloned into a lambda library, in which a 5.8-kb fragment that hybridized to a heterologous phaC probe from Ralstonia eutropha was identified. In vivo expression in Klebsiella aerogenes KC2671 (pUMS), restriction mapping, Southern hybridization experiments, and sequencing data revealed that PHA biosynthesis by P. fluorescens relied upon a polypeptide encoded by a 1,683-bp non-operonal ORF, which was preceded by a possible -24/-12 promoter and highly similar to DNA sequences of a gene encoding PHA synthase in the genus Pseudomonas. In vivo expression of the putative PHA synthase gene (phaCPf) in a recombinant Escherichia coli strain was investigated by using glucose and decanoate as substrates. E. coli (phaCPf+, pUMS) grown in medium containing glucose accumulated PHA granules consisting mainly of 3-hydroxybutyrate, whereas only a trace amount of 3-hydroxydecanoate was detected from an E. coli fadR mutant (phaCPf+) grown in medium containing decanoate. In vitro enzymatic assessment experiments showed that 3-hydroxybutyryl-CoA was efficiently used as a substrate of purified PhaCPf, suggesting that the putative PHA synthase of P. fluorescens utilizes mainly short-chain-length PHA precursors as a substrate.

Novosphingobium sediminicola sp. nov. isolated from freshwater sediment.

A yellow-pigmented, Gram-negative, short rod-shaped, non-motile and non-spore-forming bacterial strain, designated HU1-AH51(T), was isolated from freshwater sediment and was characterized using a polyphasic approach, in order to determine its taxonomic position. On the basis of 16S rRNA gene sequence similarity, strain HU1-AH51(T) was shown to belong to the genus Novosphingobium, showing the highest level of sequence similarity with respect to Novosphingobium resinovorum NCIMB 8767(T) (96.0 %), Novosphingobium naphthalenivorans TUT562(T) (96.0 %) and Novosphingobium panipatense SM16(T) (96.0 %). Strain HU1-AH51(T) had a genomic DNA G+C content of 62.6 mol% and Q-10 as the predominant respiratory quinone. Furthermore, the major polyamine component (spermidine) in the cytoplasm and the presence of sphingoglycolipids suggested that strain HU1-AH51(T) belongs to the family Sphingomonadaceae. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain HU1-AH51(T) represents a novel species of the genus Novosphingobium, for which the name Novosphingobium sediminicola sp. nov. is proposed. The type strain is HU1-AH51(T) ( = LMG 24320(T)  = KCTC 22311(T)).

Sphingobium vulgare sp. nov., isolated from freshwater sediment.

A Gram-negative, motile, non-spore-forming bacterial strain, designated HU1-GD12(T), was isolated from freshwater sediment. The strain was characterized by using a polyphasic approach in order to determine its taxonomic position. Comparative analysis of the 16S rRNA gene sequence showed that the isolate constituted a distinct branch within the genus Sphingobium, showing the highest level of sequence similarity with respect to Sphingobium ummariense RL-3(T) (96.2 %). Strain HU1-GD12(T) had a genomic DNA G+C content of 66.8 mol% and Q-10 as the predominant respiratory quinone. Furthermore, the major polyamine component (spermidine) in the cytoplasm and the presence of sphingoglycolipids suggested that strain HU1-GD12(T) belonged to the family Sphingomonadaceae. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain HU1-GD12(T) represents a novel species of the genus Sphingobium, for which the name Sphingobium vulgare sp. nov. is proposed. The type strain is HU1-GD12(T) (=LMG 24321(T)=KCTC 22289(T)).

Ferruginibacter alkalilentus gen. nov., sp. nov. and Ferruginibacter lapsinanis sp. nov., novel members of the family 'Chitinophagaceae' in the phylum Bacteroidetes, isolated from freshwater sediment.

Six Gram-negative, non-gliding, rod-shaped bacterial strains isolated from freshwater sediment were subjected to polyphasic analyses to determine their taxonomic positions. Analysis of the 16S rRNA gene sequences of the six strains revealed that they represent two separate genomic species in a new lineage within the phylum Bacteroidetes, related to members of the family 'Chitinophagaceae', in which they were most closely related to members of the genus Terrimonas (93.4-90.5 %). Two of the isolates, HU1-GD23(T) and HU1-HG42(T), had a sequence similarity of 96.2 %, with DNA G+C contents of 39.4 and 38.5 mol%, respectively. They possessed MK-7 as the predominant respiratory quinone and contained high amounts of iso-pentadecanoic acid and 3-hydroxy-iso-heptadecanoic acid in their cell envelopes, properties shared by members of the family 'Chitinophagaceae'. They were well differentiated from other members of the family 'Chitinophagaceae' by additional physiological and biochemical characteristics. In conclusion, strains HU1-GD23(T) (=KCTC 22306(T)=LMG 24312(T)) and HU1-HG42(T) (=KCTC 22305(T)=LMG 24324(T)) are considered to represent two novel species of a novel genus, Ferruginibacter gen. nov., for which the names Ferruginibacter alkalilentus sp. nov. and Ferruginibacter lapsinanis sp. nov., are proposed, respectively.

Burkholderia sediminicola sp. nov., isolated from freshwater sediment.

A Gram-negative, motile and rod-shaped bacterium, designated HU2-65W(T), was isolated from freshwater sediment. The strain possessed ubiquinone 8 as the predominant isoprenoid quinone and contained major amounts of omega7-cis-octadecenoic acid and hexadecanoic acid in its cell envelope, which are properties shared by members of the genus Burkholderia. On the basis of 16S rRNA gene sequence similarity, strain HU2-65W(T) was most closely related to the type strain of Burkholderia xenovorans (98.4 %). The DNA G+C content of strain HU2-65W(T) was 61.2 mol%, and DNA-DNA relatedness values to type strains of closely related species were found to be much lower than 70 %, indicating that the strain represents a separate genomic species within the genus Burkholderia. Strain HU2-65W(T) was also differentiated from other species of the genus by physiological and biochemical characteristics. Consequently, strain HU2-65W(T) is considered to represent a single, novel species of the genus Burkholderia, for which the name Burkholderia sediminicola sp. nov. is proposed, with the type strain HU2-65W(T) (=KCTC 22086(T) =LMG 24238(T)).

Salinicoccus jeotgali sp. nov., isolated from jeotgal, a traditional Korean fermented seafood.

A novel, moderately halophilic, Gram-positive coccus, designated strain S2R53-5(T), was isolated from jeotgal, a traditional Korean fermented seafood. The organism was strictly aerobic, non-motile, non-sporulating and catalase- and oxidase-positive. Strain S2R53-5(T) grew in the presence of 0.5-15 % (w/v) NaCl and at pH 6.5-11.0, with optimum growth at 5 % (w/v) NaCl and pH 7.0. The temperature range for growth was 20.0-30.0 degrees C, with an optimum temperature of 30 degrees C. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain S2R53-5(T) belongs to the family Staphylococcaceae and was most closely related to Salinicoccus roseus DSM 5351(T) (96.8 % gene sequence similarity), Salinicoccus hispanicus DSM 5352(T) (96.1 %), Salinicoccus alkaliphilus T8(T) (95.2 %) and Jeotgalicoccus halotolerans YKJ-101(T) (95.1 %). The genomic DNA G+C content was 47.0 mol%, which is in the range of 46-51 mol% that is characteristic for the genus Salinicoccus. Levels of DNA-DNA relatedness between strain S2R53-5(T) and S. roseus DSM 5351(T), S. hispanicus DSM 5352(T) and S. alkaliphilus KCTC 13928(T) were 32.2, 15.4 and 4.6 %, respectively. Chemotaxonomic data (major menaquinone, MK-6; major fatty acids, iso-C(15 : 0) and anteiso-C(15 : 0); cell-wall murein type, Lys and Gly) and 16S rRNA gene sequence analysis supported the affiliation of strain S2R53-5(T) with the genus Salinicoccus. The combined evidence from the low DNA-DNA relatedness, physiological, biochemical and other genotypic data indicate that strain S2R53-5(T) clearly represents a novel species of the genus Salinicoccus, for which the name Salinicoccus jeotgali sp. nov. is proposed. The type strain is S2R53-5(T) (=KCTC 13030(T)=LMG 23640(T)).

Transfer of Chryseobacterium meningosepticum and Chryseobacterium miricola to Elizabethkingia gen. nov. as Elizabethkingia meningoseptica comb. nov. and Elizabethkingia miricola comb. nov.

The taxonomic positions of six strains (including the type strain) of Chryseobacterium meningosepticum (King 1959) Vandamme et al. 1994 and the type strain of Chryseobacterium miricola Li et al. 2004 were re-evaluated by using a polyphasic taxonomic approach. Phylogenetic analysis, based on 16S rRNA gene sequencing, showed that the strains represent a separate lineage from the type strains of the Chryseobacterium-Bergeyella-Riemerella branch within the family Flavobacteriaceae (90.7-93.9 % similarities), which was supported by phenotypic differences. Combined phylogenetic and phenotypic data showed that C. meningosepticum and C. miricola should be transferred to a new genus, Elizabethkingia gen. nov., with the names Elizabethkingia meningoseptica comb. nov. (type strain, ATCC 13253(T) = NCTC 10016(T) = LMG 12279(T) = CCUG 214(T)) and Elizabethkingia miricola comb. nov. (type strain, DSM 14571(T) = JCM 11413(T) = GTC 862(T)) proposed.

Kaistella koreensis gen. nov., sp. nov., a novel member of the Chryseobacterium-Bergeyella-Riemerella branch.

Gram-negative, non-spore-forming, rod-shaped, yellow-pigmented bacteria isolated from a freshwater stream in Korea were investigated to determine their taxonomic position. Complete 16S rRNA gene sequence analysis indicated that the organisms should be placed in the Chryseobacterium-Bergeyella-Riemerella branch in the family Flavobacteriaceae. Phylogenetically, the strains were most closely related to Chryseobacterium balustinum ATCC 33487(T) and Chryseobacterium scophthalmum LMG 13028(T) (94.3 and 94.1 % 16S rRNA gene sequence similarity, respectively) and they clustered on a separate well-supported branch. The strains contained menaquinone MK-6 as the predominant respiratory quinone and showed higher G+C contents (41.7 mol%) than other species in the Chryseobacterium-Bergeyella-Riemerella branch and i-C(15 : 0) as a major fatty acid (47-52 %). The phylogenetic distances from any species with validly published names and their phenotypic properties confirmed that the strains constitute a separate species in a new genus, for which the name Kaistella koreensis gen. nov., sp. nov. is proposed (type strain Chj707(T)=KCTC 12107(T)=IAM 15050(T)).

Odorous swine wastewater treatment by purple non-sulfur bacteria, Rhodopseudomonas palustris, isolated from eutrophicated ponds.

Three strains of phototrophic, purple, non-sulfur bacteria, isolated from eutrophic ponds, were used to treat odorous swine wastewater. One isolate, Rhodopseudomonas palustris, when cultured in swine wastewater without supplementation for 7 d, removed odorous organic acids (170 mg l(-1)), COD (10,000 mg l(-1)) and phosphate (180 mg l(-1)).