Halomonas cibimaris sp. nov., isolated from jeotgal, a traditional Korean fermented seafood

Two moderately halophilic, facultatively aerobic, motile bacteria with flagella, designated strains 10-C-3^T and 30-C-3, were isolated from jeotgal, a traditional Korean fermented seafood. Cells of the strains were observed to be ovoid-rods showing catalase- and oxidase-positive reactions and production of creamy-pink pigments. Growth of strain 10-C-3^T was observed at 15–35 °C (optimum, 25–30 °C), at pH 5.5–9.0 (optimum, pH 7.0–7.5), and in the presence of 3–15 % (w/v) salts (optimum: 5–10 %). The two strains were found to contain C_18:1 ω7c, C_16:0, summed feature 3 (as defined by the MIDI system, comprising C_16:1 ω7c and/or C_16:1 ω6c), and C_12:0 3-OH as the major cellular fatty acids. The G+C contents of the genomic DNA of strains 10-C-3^T and 30-C-3 were determined to be 63.2 and 63.1 mol%, respectively and the respiratory quinone detected was ubiquinone 9 (Q-9) only. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strains 10-C-3^Tand 30-C-3 formed a distinct phyletic lineage within the genus Halomonas and are most closely related to Halomonas fontilapidosi 5CR^T with 95.2 % of 16S rRNA sequence similarity. Strains 10-C-3^Tand 30-C-3 shared 99.2 % of 16S rRNA gene sequence similarity and their DNA–DNA relatedness value was 96.6 ± 0.9 %. On the basis of phenotypic, chemotaxonomic and molecular features, strains 10-C-3^Tand 30-C-3 represent a novel species of the genus Halomonas, for which the name Halomonas cibimaris sp. nov. is proposed. The type strain is 10-C-3^T (= KACC 14932^T = JCM 16914^T).     

The X-ray crystal structure of 6-deoxy-α-l-sorbofuranose. Conformational analysis of ketohexofuranosides and their comparison with ribofuranosides and arabinofuranosides

The crystal and molecular structure of 6-deoxy-l-sorbose have been determined by the application of multisolution methods and refined to an R-index of 0.063 for 560 reflections, using three-dimensional intensity data collected on a Picker automatic diffractometer. The compound crystallizes in the space group P2₁2₁2₁ with unit-cell dimensions a = 18.470 (10), b = 7.636 (10), and c = 5.371 (8) Å; Z = 4. The molecule occurs as the α-furanose form, which is also the preponderant tautomer in solution. The puckering of the furanoid ring is C-3′-exo-C-4′-endo (₃T⁴) [equivalent to C-2′-exo-C-3′-endo (₂T³) in the numbering for d-ribose], with P and τ_m angles of -6.5 and 42.7° respectively. Conformational analysis of the known ketofuranosides shows that the ₃T⁴ (₂T³ in d-ribose numbering) puckering mode, which is typical of α-nucleosides, is favored, in contrast to the favored ³T₂ or ²T₃ puckering mode for the β-d-ribonucleosides and β-d-arabinonucleosides. The conformational differences among furanoid rings are mainly influenced by the configuration at the anomeric carbon atom. The favored orientation about the C-2′-C-1′ bond (O-5′-C-2′-C-1′-O-1′)of the ketofuranosidesis — gauche. All four hydroxyl groups are involved in donor-acceptor hydrogen bonding, and O-4′-8 appears to be involved in a bifurcated hydrogen bond to O-2′ and O-3′ of neighboring molecules.     

The crystal structure of d-glucose 6-(sodium hydrogen-phosphate)

The title compound, when recrystallised from water, is monoclinic, space group P2₁, with a = 5.774(4), b = 7.189(5), c = 12.69(1) Å, β = 106.66(5)°, and Z = 2. The crystal structure was determined from three-dimensional X-ray diffraction data taken on an automatic diffractometer with CuKα, and refined by least-squares techniques to R = 0.034 for 977 reflexions. The pyranose ring adopts the ⁴C₁ conformation. The conformation about the exocyclic C-5-C-6 bond is gauche-trans [the torsion angles O-6-C-6-C-5-O-5 and O-6-C-6-C-5-C-4 are 64.2(8) and ?175.6(7)°, respectively], which is significantly different from the gauche-gauche geometry in d-glucose 6-(barium phosphate). The phosphate ester bond, P-O-6, is 1.584(3) Å. All of the oxygen-bonded hydrogen atoms are involved in intermolecular hydrogen-bonds.     

Genome Sequence of Nitratireductor pacificus Type Strain pht-3B

Nitratireductor pacificus strain pht-3B^T was isolated from a pyrene-degrading consortium enriched from the deep sea sediment of the Pacific Ocean. Here, we present the draft genome of strain pht-3B^T, which contains 4,466,205 bp with a G+C content of 65.51% and contains 4,197 protein-coding genes and 46 tRNA genes.     

Strukturanalyse der methyl-2,3,6-tridesoxy-2-C-[2-hydroxy-1,1-(Äthylendithio)Äthyl]-α-l-threo-hexopyranosid-4-ulo-22,4-pyranose

Methyl 2,3,6-trideoxy-2-C-[2-hydroxy-1,1-(ethylenedithio)ethyl]-α-l-threo-hexopyranosid-4-ulo-2²,4-pyranose (1) crystallizes in a rhombic space group P2₁2₁2₁ with four molecules in the elementary unit. The structure was refined to an R-value of 0.057. The aldopyranose ring adopts a ¹C₄ conformation with an axial side-chain forming a hemiacetal ring to the keto group at C-4. Both six-membered rings connected in the 2,7-dioxabicyclo[3.3.1]nonane system differ only slightly from the ¹C₄ chair conformation. The spirocyclic dithiolane ring adopts a nearly ideal envelope form with a deviation of C-21 from the plane S-1-C-7-S-2-C-22. The dihedral angle O-5-C-1 O-1-C-11 of 59.1° is an agreement with the exo-anomeric effect.     

<Emphasis Type="Italic">Paenibacillus oryzisoli</Emphasis> sp. nov., isolated from the rhizosphere of rice

A novel bacterium, strain 1ZS3-15^T, was isolated from rhizosphere of rice. Its taxonomic position was investigated using a polyphasic approach. The novel strain was observed to be Gram-stain positive, spore-forming, aerobic, motile and rod-shaped. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain 1ZS3-15^T was recovered within the genus Paenibacillus. It is closely related to Paenibacillus pectinilyticus KCTC 13222^T (97.9 % similarity), Paenibacillus frigoriresistens CCTCC AB 2011150^T (96.8 %), Paenibacillus alginolyticus JCM 9068^T (96.4 %) and Paenibacillus chondroitinus DSM 5051^T (95.5 %). The fatty acid profile of strain 1ZS3-15^T, which showed a predominance of anteiso-C_15:0 and iso-C_16:0, supported the allocation of the strain into the genus Paenibacillus. The predominant menaquinone was found to be MK-7. The polar lipids profile of strain 1ZS3-15^T was found to consist of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, one unidentified lipid and two unidentified aminophospholipids. The cell wall peptidoglycan contains meso-diaminopimelic acid. Based on draft genome sequences, the DNA–DNA relatedness between strain 1ZS3-15^T and the closely related species P. pectinilyticus KCTC 13222^T are 24.2 ± 1.0 %, and the Average Nucleotide Identity values between the strains are 78.9 ± 0.1 %, which demonstrated that this isolate represents a new species in the genus Paenibacillus. The DNA G+C content was determined to be 45.3 mol%, which is within the range reported for Paenibacillus species. Characterisation by genotypic, chemotaxonomic and phenotypic analysis indicated that strain 1ZS3-15^T represents a novel species of the genus Paenibacillus, for which the name Paenibacillus oryzisoli sp. nov. is proposed. The type strain is 1ZS3-15^T (= ACCC 19783^T = JCM 30487^T).     

Genome Sequence of Thalassospira profundimaris Type Strain WP0211

Thalassospira profundimaris WP0211^T was isolated from a pyrene-degrading consortium, enriched from deep-sea sediment collected from the West Pacific Ocean. Here, we present the draft genome of strain WP0211^T, which contains 4,380,232 bp with a G+C content of 55.19% and contains 4,040 protein-coding genes and 45 tRNAs.     

Description of Aestuariivivens marinum sp. nov., Aestuariivivens sediminis sp. nov. and Aestuariivivens sediminicola sp. nov., three new species isolated from the upper layer of tidal flat sediment

Nine bacterial strains designated MT3-5-12^T, MT3-5-27, MTV1-9, S-DT1-15^T, S-DT1-34, MTV5-3^T, MTV4-17, MTV5-12 and MTV5-13 were isolated from the upper layer (1–5 cm in depth) of tidal flat sediment in Quanzhou Bay, China. The 16S rRNA gene of these strains shared maximum sequence similarities with Aestuariivivens insulae KCTC 42350^T of 94.9–97.1%. Phylogenetic analyses based on 16S rRNA gene sequences and 120 conserved concatenated proteins placed these strains in three novel phylogenetic clades affiliated to the genus Aestuariivivens of the family Flavobacteriaceae. Strains MT3-5-12^T, MT3-5-27 and MTV1-9 were phylogenetically close to A. insulae KCTC 42350^T. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strains MT3-5-12^Tand MTV1-9 and A. insulae KCTC 42350^T were estimated to be 78.5-78.7% and 22.5%, respectively. Strains S-DT1-15^T and S-DT1-34 formed a distinctly separated clade from A. insulae KCTC 42350^T. The ANI and dDDH values between strains S-DT1-15^T and S-DT1-34 and A. insulae KCTC 42350^T were 76.3–76.4% and 20.4–20.5%, respectively. The other four strains MTV5-3^T, MTV4-17, MTV5-12 and MTV5-13, formed a third novel clade, distinctly separated from A. insulae KCTC 42350^T. The ANI and dDDH values between strains MTV5-3^T and MTV4-17 and A. insulae KCTC 42350^T were 74.7% and 19.1–19.2%, respectively. The phylogenetic analyses and whole genomic comparisons, combined with phenotypic and chemotaxonomic features, strongly supported the nine strains could be classified as three novel species within the genus Aestuariivivens, for which the names Aestuariivivens marinum sp. nov. MT3-5-12^T, Aestuariivivens sediminis sp. nov. S-DT1-15^T, and Aestuariivivens sediminicola sp. nov. MTV5-3^T are proposed.     

Oceanospirillum nioense sp. nov., a marine bacterium isolated from sediment sample of Palk bay, India

A novel Gram-negative, spiral shaped, motile bacterium, designated strain NIO-S6^T, was isolated from a sediment sample collected from Off-shore Rameswaram, Tamilnadu, India. Strain NIO-S6^T was found to be positive for oxidase, DNase and lysine decarboxylase activities and negative for catalase, gelatinase, lipase, ornithine decarboxylase, nitrate reductase, aesculinase, amylase and urease activities. The fatty acids were determined to be dominated by C_10:0 3OH, C_16:0, C_16:1 and C_18:1. Strain NIO-S6^T contains Q-8 as the major respiratory quinone. The DNA G+C content of the strain NIO-S6^T was determined to be 49.5 ± 0.6 mol %. Phylogenetic analysis based on 16S rRNA gene sequence of strain NIO-S6^T indicated Oceanospirillum linum and Oceanospirillum maris of the family Oceanospirillaceae (phylum Proteobacteria) are the closest related species with sequence similarities of 98.4 and 97.8 % respectively. Other members of the family showed sequence similarities <96.4 %. However, DNA–DNA hybridization with Oceanospirillum linum LMG 5214^T and Oceanospirillum maris LMG 5213^T showed a relatedness of 31.5 and 46.9 % with respect to strain NIO-S6^T. Based on the phenotypic characteristics and on phylogenetic inference, strain NIO-S6^T is proposed as a novel species of the genus Oceanospirillum as Oceanospirillum nioense sp. nov. and the type strain is NIO-S6^T (=MTCC 11154^T = KCTC 32008^T).     

Genome Sequence of Nitratireductor indicus Type Strain C115

Nitratireductor indicus strain C115^T was isolated from a crude-oil-degrading consortium enriched from deep seawater of the Indian Ocean. Here, we present the draft genome of strain C115^T, which contains 4,992,479 bp with a G+C content of 60.8% and contains 4,825 protein-coding genes and 45 tRNA genes.     

Genome Sequence of Legionella tunisiensis Strain LegMT,a New Legionella Species Isolated from Hypersaline Lake Water

Legionella tunisiensis is a gammaproteobacterium from the class Legionellaceae, growing in amoebae. We sequenced the genome from strain LegM^T. It is composed of 3,508,121 bp and contains 4,747 protein-coding genes and 38 RNA genes, including 3 rRNA genes.     

Genome Sequence of Idiomarina xiamenensis Type Strain 10-D-4

Idiomarina xiamenensis strain 10-D-4^T was isolated from an oil-degrading consortium enriched from surface seawater around the Xiamen island. Here, we present the draft genome of strain 10-D-4^T, which contains 2,899,282 bp with a G+C content of 49.48% and contains 2,673 protein-coding genes and 43 tRNA genes.     

Genome Sequence of Galbibacter marinum Type Strain ck-I2-15

Galbibacter marinum strain ck-I2-15^T was isolated from an arsenite-resistant consortium enriched from the deep sea sediment of a hydrothermal vent field on the Southwest Indian Ocean Ridge. Here, we present the draft genome of strain ck-I2-15^T, which contains 3,572,447 bp with a G+C content of 37.04% and contains 3,099 protein-coding genes and 38 tRNA genes.     

<Emphasis Type="Italic">Uliginosibacterium sangjuense</Emphasis> sp. nov., isolated from sediment of the Nakdong River

A Gram-negative, aerobic, motile by flagella, and light yellow bacterium, designated SS1-76^T, was isolated from sediment of the Nakdong River in Sangju-si, Republic of Korea. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the isolate SS1-76^T belongs to the genus Uliginosibacterium of the family Rhodocyclaceae, exhibiting high sequence similarity with the type strains of Uliginosibacterium gangwonense 5YN10-9^T (96.0%) and Uliginosibacterium paludis KBP-13^T (94.9%). Strain SS1-76^T contains ubiquinone-8 as a respiratory quinone and summed feature 3 (C_16:1 ω7c and/or C_16:1 ω6c), C_16:0, and C_14:0 as major fatty acids. The cellular polar lipids are composed of phosphatidylethanolamine, phosphatidylglycerol, and unidentified aminophospholipids. The DNA G+C content was 65.3 mol%. Phenotypic, chemotaxonomic, and phylogenetic evidence clearly indicated that strain SS1-76^T represents a novel species of the genus Uliginosibacterium, for which the name Uliginosibacterium sangjuense sp. nov. is proposed. The type strain is SS1-76^T (= KCTC 52159^T = JCM 31375^T).     

The Genome of the Moderate Halophile Amycolicicoccus subflavus DQS3-9A1T Reveals Four Alkane Hydroxylation Systems and Provides Some Clues on the Genetic Basis for Its Adaptation to a Petroleum Environment

The moderate halophile Amycolicicoccus subflavus DQS3-9A1^T is the type strain of a novel species in the recently described novel genus Amycolicicoccus, which was isolated from oil mud precipitated from oil produced water. The complete genome of A. subflavus DQS3-9A1^T has been sequenced and is characteristic of harboring the genes for adaption to the harsh petroleum environment with salinity, high osmotic pressure, and poor nutrient levels. Firstly, it characteristically contains four types of alkane hydroxylases, including the integral-membrane non-heme iron monooxygenase (AlkB) and cytochrome P450 CYP153, a long-chain alkane monooxygenase (LadA) and propane monooxygenase. It also accommodates complete pathways for the response to osmotic pressure. Physiological tests proved that the strain could grow on n-alkanes ranging from C10 to C36 and propane as the sole carbon sources, with the differential induction of four kinds of alkane hydroxylase coding genes. In addition, the strain could grow in 1–12% NaCl with the putative genes responsible for osmotic stresses induced as expected. These results reveal the effective adaptation of the strain DQS3-9A1^T to harsh oil environment and provide a genome platform to investigate the global regulation of different alkane metabolisms in bacteria that are crucially important for petroleum degradation. To our knowledge, this is the first report to describe the co-existence of such four types of alkane hydroxylases in a bacterial strain.     

Lysinibacillus chungkukjangi sp. nov., isolated from Chungkukjang, Korean fermented soybean food

One bacterial strain 2RL3-2^T was isolated from Chungkukjang, a traditional Korean fermented food made from soybeans, and determined to be a Gram-positive, aerobic, spore-forming rod. Growth of the novel strain was optimal at 30°C and pH 7.0. The 16S rRNA gene of strain 2RL3-2^T showed the highest level of sequence similarity to Lysinibacillus sinduriensis BLB-1^T (99.0%), Lysinibacillus massiliensis 4400831^T (97.1%), Lysinibacillus xylanilyticus XDB9^T (97.0%), and Lysinibacillus odysseyi 34hs-1^T (96.8%). Phylogenetic analysis showed that strain 2RL3-2^T formed a robust cluster with L. sinduriensis BLB-1^T, L. massiliensis 4400831^T, and L. odyssey 34hs-1^T. The major fatty acids were anteiso-C15:0 (47.3%), iso-C_16:0 (16.3%), and anteiso-C_17:0 (11.3%), and the only menaquinone was MK-7. Diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylethanolamine were the major polar lipids, along with an unknown phospholipid and two unknown lipids. The peptidoglycan type was A4α, with an interpeptide bridge of l-Lys-d-Asp. DNA-DNA hybridization values between strain 2RL3-2^T and closely related Lysinibacillus species were below 43±4%. Therefore, based on phenotypic, chemotaxonomic, and phylogenetic characteristics, it was determined that strain 2RL3-2^T represents a novel species of the genus Lysinibacillus, for which the name Lysinibacillus chungkukjangi sp. nov. is proposed. The type strain is 2RL3-2^T (=KACC 16626^T =NBRC 108948^T).     

Two new Polyangium species,P. aurulentum sp. nov. and P. jinanense sp. nov., isolated from a soil sample

Polyangium belongs to Polyangiaceae family of Myxococcales, a taxonomic group well-known for their extraordinary social lifestyle and diverse novel gene clusters of secondary metabolites. A yellow-golden strain, designated SDU3-1^T, and two rose pink strains, designated SDU13 and SDU14^T, were isolated from a soil sample. These three strains were aerobic, mesophilic, not salt-tolerant and were able to prey on living microorganisms. SDU13 and SDU14^T formed solitary sporangioles under starvation conditions, while SDU3-1^T had no fruiting body structures. They showed 95.9–97.0% (SDU3-1^T) or 98.7–98.9% (SDU13 and SDU14^T) 16S rRNA gene similarity with the type strains of Polyangium, but were phylogenetically separate from them based on the 16S rRNA gene and genome sequences. Their genomes were 12.3 Mbp (SDU3-1^T), 13.9 Mbp (SDU13) and 13.8 Mbp (SDU14^T) with the G + C content range of 68.3–69.4 mol%. The average nucleotide identity and DNA-DNA hybridization analyses of genomes further indicated that these three strains belonged to two new species in Polyangium. Their major fatty acids were C_18:1ω9c, C_16:0 and C_18:0. The polyphasic taxonomic characterization suggest that the three strains represent two novel species in the genus Polyangium, for which the names Polyangium aurulentum sp. nov. and Polyangium jinanense sp. nov. are proposed, and the type strains are SDU3-1^T (=CGMCC 1.16875^T = KCTC 72136^T) and SDU14^T (=CCTCC AB 2021123^T = KCTC 82625^T), respectively.     

Arthrobacter pokkalii sp nov,a Novel Plant Associated Actinobacterium with Plant Beneficial Properties,Isolated from Saline Tolerant Pokkali Rice,Kerala, India

A novel yellow colony-forming bacterium, strain P3B162^T was isolated from the pokkali rice rhizosphere from Kerala, India, as part of a project study aimed at isolating plant growth beneficial rhizobacteria from saline tolerant pokkali rice and functionally evaluate their abilities to promote plant growth under saline conditions. The novel strain P3B162^T possesses plant growth beneficial traits such as positive growth on 1-aminocyclopropane-1-carboxylic acid (ACC), production of indole acetic acid (IAA) and siderophore. In addition, it also showed important phenotypic characters such as ability to form biofilm and utilization of various components of plant root exudates (sugars, amino acids and organic acids), clearly indicating its lifestyle as a plant rhizosphere associated bacterium. Taxonomically, the novel strain P3B162^T was affiliated to the genus Arthrobacter based on the collective results of phenotypic, genotypic and chemotaxonomic analyses. Moreover, molecular analysis using 16S rRNA gene showed Arthrobacter globiformis NBRC 12137^T, Arthrobacter pascens DSM 20545^T and Arthrobacter liuii DSXY973^T as the closely related phylogenetic neighbours, showing more than 98% 16S rRNA similarity values, whereas the recA gene analysis displayed Arthrobacter liuii JCM 19864^T as the nearest neighbour with 94.7% sequence similarity and only 91.7% to Arthrobacter globiformis LMG 3813^T and 88.7% to Arthrobacter pascens LMG 16255^T. However, the DNA-DNA hybridization values between strain P3B162^T, Arthrobacter globiformis LMG 3813^T, Arthrobacter pascens LMG 16255^T and Arthrobacter liuii JCM 19864^T was below 50%. In addition, the novel strain P3B162^T can be distinguished from its closely related type strains by several phenotypic characters such as colony pigment, tolerance to NaCl, motility, reduction of nitrate, hydrolysis of DNA, acid from sucrose, cell wall sugars and cell wall peptidoglycan structure. In conclusion, the combined results of this study support the classification of strain P3B162^T as a novel Arthrobacter species and we propose Arthrobacter pokkalii sp.nov.as its name. The type strain is P3B162^T (= KCTC 29498^T = MTCC 12358^T).     

Genome Sequence of Afipia birgiae,a Rare Bacterium Associated with Amoebae

Afipia birgiae is an alphaproteobacterium from the family Bradyrhizobiaceae, growing in amoebae, and a potential human pathogen. We sequenced the genome of type strain 34632^T. It is composed of 5,325,467 bp and contains 5,160 protein-coding genes and 53 RNA genes, including 3 rRNA genes.     

Genome Sequence of Thalassospira xiamenensis Type Strain M-5

Thalassospira xiamenensis M-5^T was isolated from the surface water of a waste oil pool at the oil storage dock in the city of Xiamen, Fujian Province, China. Here, we present the draft genome of strain M-5^T, which contains 4,705,237 bp with a G+C content of 54.65% and contains 4,343 protein-coding genes and 46 tRNA genes.