Arachidicoccus soli sp. nov., a bacterium isolated from soil.

A Gram-stain-negative, aerobic, non-motile and rod-shaped bacterium, designated KIS59-12T, was isolated from a soil sample collected on Hodo island, Boryeong, Republic of Korea. The strain grew at 10-33 °C, pH 6.0-7.5 and with 0-4 % NaCl (w/v). Results of phylogenetic analysis based on 16S rRNA gene sequences showed that strain KIS59-12T was in the same clade as Arachidicoccus rhizosphaerae Vu-144T and Arachidicoccus ginsenosidivorans Gsoil809T with 97.5 and 97.2 % sequence similarity, respectively. Comparative genome analysis between strain KIS59-12T and A. rhizosphaerae Vu-144T showed that average nucleotide identity value was 69.4 % and the digital DNA-DNA hybridization value was 19.1 %. The major respiratory quinone was menaquinone-7. The major polar lipids were phosphatidylethanolamine and an unknown polar lipid. The predominant cellular fatty acids were iso-C15 : 0, iso-C15 : 1 G and iso-C17 : 0 3-OH, which supported the affiliation of strain KIS59-12T with the genus Arachidicoccus. The major polyamines were homospermidine and putrescine. The genomic DNA G+C content was 36.4 mol%. On the basis of phylogenetic, physiological and chemotaxonomic characteristics, strain KIS59-12T represents a novel species of the genus Arachidicoccus, for which the name Arachidicoccus soli sp. nov. is proposed. The type strain of Arachidicoccus soli is KIS59-12T (=KACC 17340T=NBRC 113161T).

Chitinophaga agri sp. nov., a bacterium isolated from soil of reclaimed land.

A Gram-negative, aerobic, and long rod-shaped bacterium, designated as H33E-04T, was isolated from the soil of reclaimed land, Republic of Korea. The strain grew at a temperature range of 15-40 °C, pH 5.0-10.0, and 0-2% NaCl (w/v). The phylogenetic analysis based on 16S rRNA gene sequences showed that strain H33E-04T was in the same clade with Chitinophaga pinensis DSM 2588T, Chitinophaga filiformis IFO 15056T, and Chitinophaga ginsengisoli Gsoil 052T with 98.4%, 97.9%, and 97.8% sequence similarities, respectively. The de novo genome assembly revealed that the DNA G + C content of the strain was 46.2 mol%. Comparative genome analysis between strain H33E-04T and C. pinensis DSM 2588 T showed that the average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values were 79.9% and 23.4%, respectively. The major respiratory quinone was menaquinone-7 (MK-7) and the predominant cellular fatty acids were iso-C15:0 (31.7%), C16:1 ω5c (31.2%), and iso-C17:0 3-OH (11.8%), supporting the affiliation of strain H33E-04T with the genus Chitinophaga. Based on phylogenetic, physiological, and chemotaxonomic characteristics, strain H33E-04T represents a novel species of the genus Chitinophaga, for which the name Chitinophaga agri sp. nov. is proposed. The type strain of Chitinophaga agri is H33E-04T (= KACC 21303T = NBRC114512T).

Xylophilus rhododendri sp. nov., Isolated from Flower of Royal Azalea, Rhododendron schlippenbachii.

A bacterial strain, designated CJ1-R5T, was isolated from the flower of the royal azalea plant (Rhododendron schlippenbachii) collected in Jeju Island, Republic of Korea. The strain was a Gram-negative, strictly aerobic, motile, rod-shaped bacterium, growing at a temperature range of 4-33 °C (optimum 28-30 °C), pH 5.0-9.0 (optimum pH 7.0-8.0), and 0-1% NaCl (optimum 0%). The 16S rRNA sequence analysis of strain CJ1-R5T revealed the highest sequence similarity (97.9%) with Xylophilus ampelinus ATCC 33914T, and sequence similarities of less than 97.2% with other validly named species. Phylogenetic tree analysis based on the 16S rRNA gene sequences showed that strain CJ1-R5T clustered with Xylophilus ampelinus ATCC 33914T and two uncultured bacterial clones. The only quinone observed in strain CJ1-R5T was ubiquinone-8. The polar lipids observed were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, one unidentified aminophospholipid and two unidentified lipids. The major fatty acids were C16:0, C17:0 cyclo, and summed feature 8 (C18:1 ω7c and/or C18:1 ω6c). The genome size of strain CJ1-R5T was 5.85 Mbp. The genomic G + C content was 68.4 mol%. ANI and dDDH values between strain CJ1-R5T and Xylophilus ampelinus ATCC 33914T were 79.0% and 22.5%, respectively. Based on the polyphasic taxonomic data, strain CJ1-R5T is considered to represent a novel species, for which the name Xylophilus rhododendri sp. nov. is proposed. The type strain is CJ1-R5T (= KACC 21265T = CCTCC AB2020030T).

The Association of Perioperative Serum Lactate Levels with Postoperative Delirium in Elderly Trauma Patients.

BACKGROUND: Several studies have shown the utility of lactate level as a predictor of early outcomes in trauma patients. We conducted this study to evaluate the association of perioperative serum lactate levels with postoperative delirium (POD) in elderly trauma patients. MATERIALS AND METHODS: This study included 466 elderly trauma patients with measurements of serum lactate levels on admission and 1 h after surgery. The associations of POD with serum lactate levels (on admission and 1 h after surgery) and lactate clearance were analyzed using Kendall's correlation. Perioperative serum lactate levels and lactate clearance as predictors of POD were evaluated using univariate and multivariable analyses. RESULTS: The incidence of POD in the present study was 38.1%. Serum lactate levels on admission and at 1 h after surgery were significantly higher in major trauma than in minor trauma. In univariate analysis of perioperative serum lactate levels and lactate clearance as predictors of POD, the odds ratio (OR) for serum lactate level on admission was 4.19 (P < 0.01, 2.91 < 95% confidence interval (CI) < 6.02) and that 1 h after surgery was 3.83 (P < 0.01, 2.79 < 95% CI < 5.25); however, the OR for serum change of lactate level was 0.99 ((P < 0.09, 0.99 < 95% CI < 1.00). In multivariable analysis for predictors of POD, the OR for serum lactate level on admission was 2.40 (P < 0.09, 0.87 < 95% CI < 6.7), that for serum lactate 1 h after surgery was 2.83 (P=0.01, 1.28 < 95% CI < 6.24), that for ICU admission was 3.01 (P=0.01, 2.09 < 95% CI < 6.03), and that for ISS was 1.47 (P < 0.01, 1.27 < 95% CI < 3.70). CONCLUSIONS: Taking together the results of univariate and multivariable analyses, serum lactate level 1 h after surgery may be used as a prediction model of POD development in elderly trauma patients.

Chryseolinea soli sp. nov., isolated from soil.

A yellow-colored bacterium with gliding motility, strain KIS68-18T, was isolated from a soil sample at Bijin Island in Tongyeong city, Republic of Korea. The cells were strictly aerobic, Gram-staining-negative, non-spore-forming, and rod-shaped. The strain grew at the range of 10-35°C (optimum, 25-30°C), pH 5.5-8.0 (optimum, 6.0-7.5), and 0-0.5% (w/v) NaCl. A phylogenetic analysis based on 16S rRNA gene sequences revealed that strain KIS68-18T was closely related to Chryseolinea serpens DSM 24574T (98.9%) and had low sequence similarities (below 92.6%) with other members of the family 'Cytophagaceae' in the phylum Bacteroidetes. The major respiratory quinone system was MK-7 and the predominant cellular fatty acids were C16:1ω5c (38.8%), iso-C15:0 (18.5%), and summed feature 3 (C16:1ω7c and/or C16:1ω6c, 10.6%). The polar lipids consisted of phosphatidylethanolamine, one unidentified phospholipid, three unidentified aminophospholipids, two unidentified aminolipids, and five unidentified lipids. The DNA G + C content was 50.9%. Based on the phylogenetic, physiological, and chemotaxonomic data, stain KIS68-18T represents a novel species of the genus Chryseolinea, for which the name Chryseolinea soli sp. nov. is proposed. The type strain of Chryseolinea soli is KIS68-18T (= KACC 17327T = NBRC 113100T).

Siphonobacter intestinalis sp. nov., a bacterium isolated from the feces of Pseudorhynchus japonicus.

Strain 63MJ-2T was isolated from the feces of broad-winged katydid (Pseudorhynchus japonicus) collected in Korea. The 16S rRNA gene sequence of this strain showed the highest sequence similarity with that of Siphonobacter aquaeclarae P2T (96.1%) and had low similarities (below 86.3%) with those of other members of family 'Flexibacteraceae'. The strain 63MJ-2T is a strictly aerobic, Gram-stain-negative, non-motile, rod-shaped bacterium. The strain grew at 4-35°C (optimum, 25-30°C), pH of 5.0-9.0 (optimum, 6.0-7.0), and 0-2.0% (optimum, 1.0-2.0) (w/v) NaCl. The DNA G+C content of strain 63MJ-2T was 43.5 mol%. The major fatty acids were C16:1 ω5c (42.5%), iso-C17:0 3-OH (18.7%), and summed feature 3 (iso-C15:0 2-OH and/or C16:1 ω7c, 18.0%). The major menaquinone was MK-7 and polar lipids were phosphatidylethanolamine, six unknown aminolipids, and five unknown lipids. Based on the evidence from our polyphasic taxonomic study, we conclude that strain 63MJ-2T should be classified as a novel species of the genus Siphonobacter, and propose the name Siphonobacter intestinalis sp. nov. The type strain is 63MJ-2T (=KACC 18663T =NBRC 111883T).

Sphingomonas parvus sp. nov. isolated from a ginseng-cultivated soil.

Strain GP20-2(T) was isolated from a soil cultivated with ginseng in Korea. The 16S rRNA gene sequence of this strain showed the highest sequence similarity with Sphingomonas daechungensis CH15-11(T) (96.7%) and Sphingomonas sediminicola Dae 20(T) (96.2%) among the type strains. The strain GP20-2(T) was a strictly aerobic, Gram-negative, non-motile, rod-shaped bacterium that formed very tiny colonies, less than 0.3 mm in diameter after 10 days on R2A agar. The strain grew at 10-35-C (optimum, 35-C), at a pH of 5.0-8.0 (optimum, pH 6.0), and in the absence of NaCl. The DNA G+C content of strain GP20-2(T) was 67.2 mol%. It contained ubiquinone Q-10 as the major isoprenoid quinone, and summed feature 8 (C18:1ω6c and/or C18:1ω7c, 49.8%) and C16:0 (17.0%) as the major fatty acids. On the basis of evidence from our polyphasic taxonomic study, we concluded that strain GP20-2(T) should be classified as a novel species of the genus Sphingomonas, for which the name Sphingomonas parvus sp. nov. is proposed. The type strain is GP20-2(T) (=KACC 12865(T) =DSM 100456(T)).

Mucilaginibacter ginsengisoli sp. nov., isolated from a ginseng-cultivated soil.

A dark-pink-coloured bacterial strain, B4Y-8T, was isolated from a soil cultivated with ginseng. The 16S rRNA gene sequence of this strain showed highest similarity with Mucilaginibacter litoreus BR-18T (96.8 %), Mucilaginibacter lutimaris BR-3T (96.6 %) and Mucilaginibacter defluvii A5T (96.2 %) among the type strains of species of the genus Mucilaginibacter. Strain B4Y-8T was a strictly aerobic, Gram-stain-negative, non-motile, short-rod-shaped bacterium producing a large amount of extracellular polymeric substance. The strain grew at 10-35 °C (optimum, 25 °C), at pH 3.0-11.0 (optimum, pH 7.0) and in the presence of 0-1 % (w/v) NaCl (optimum, 0 %). The DNA G+C content of strain B4Y-8T was 49.0 mol%. It contained menaquinone 7 (MK-7) as the major isoprenoid quinone, and summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c) and iso-C15 : 0 as the major fatty acids. On the basis of evidence from the present polyphasic taxonomic study, strain B4Y-8T should be classified as representing a novel species of the genus Mucilaginibacter, for which the name Mucilaginibacter ginsengisoli sp. nov. is proposed. The type strain is B4Y-8T ( = KACC 18152T = JCM 30759T).

Complete Genome Sequence of Bacillus amyloliquefaciens subsp. plantarum CC178, a Phyllosphere Bacterium Antagonistic to Plant Pathogenic Fungi.

Bacillus amyloliquefaciens subsp. plantarum strain CC178 is a phyllosphere bacterium with antagonistic activity against a wide range of plant fungal pathogens. The genome of strain CC178 is 3,916,828 bp in size and harbors 3,972 genes. Six giant gene clusters are dedicated to the nonribosomal synthesis of antimicrobial polypeptides and polyketides.

Paenibacillus cucumis sp. nov. isolated from greenhouse soil.

Strain CO 4-7(T) was isolated from greenhouse soil used for cultivation of cucumbers in Korea. The 16S rRNA gene sequence of strain CO 4-7(T) showed the highest sequence similarity with Paenibacillus contaminans CKOBP-6(T) (94.2%) among the type strains. Strain CO 4-7(T) was a strictly aerobic, Gram-staining-positive, endospore-forming, and motile rodshaped bacterium. Strain CO 4-7(T) grew at 10-45°C (optimum, 30°C), at pH 6.0-7.5 (optimum, pH 6.5) and in the presence of 0-5% NaCl (optimum, 0.5%). The DNA G+C content of strain CO 4-7(T) was 48.5 mol%. It contained MK-7 as the major isoprenoid quinone and anteiso-C15:0 (51.8%), C16:0 (12.7%), and iso-C16:0 (8.6%) as the major fatty acids. The cell wall contained meso-diaminopimelic acid. Based on evidence from our polyphasic taxonomic study, it was concluded that strain CO 4-7T should be classified as a novel species of the genus Paenibacillus, for which, the name Paenibacillus cucumis sp. nov. is proposed. The type strain is CO 4-7(T) (=KACC 17444(T)=JCM 19515(T)).

Niabella terrae sp. nov. isolated from greenhouse soil.

An orange-colored bacterial strain, ICM 1-15(T), was isolated from greenhouse soil. The 16S rRNA gene sequence of this strain showed the highest sequence similarity with Niabella ginsengisoli GR10-1(T) (95.2%) and Niabella yanshanensis CCBAU 05354(T) (95.0%) among the type strains. The strain ICM 1-15(T) was a strictly aerobic, Gram-negative, non-spore-forming, non-motile, flexirubin pigment-producing, short rod-shaped bacterium. The strain grew at 15-35°C (optimum, 25°C), at a pH of 5.0-8.5 (optimum, pH 6.5), and in the presence of 0-3% NaCl (optimum, 1%). The DNA G+C content of strain ICM 1-15(T) was 43.6 mol%. It contained MK-7 as the major isoprenoid quinone and iso-C15:0 (38.9%), iso-C15:1 G (20.3%), and iso-C17:0 3-OH (12.9%) as the major fatty acids. On the basis of evidence from our polyphasic taxonomic study, we concluded that strain ICM 1-15(T) should be classified within a novel species of the genus Niabella, for which the name Niabella terrae sp. nov. is proposed. The type strain is ICM 1-15(T) (=KACC 17443(T) =JCM 19502(T)).

Zobellella aerophila sp. nov., isolated from seashore sand, and emended description of the genus Zobellella.

A strictly aerobic, nitrate-reducing, motile, rod-shaped member of the class Gammaproteobacteria, designated strain JC2671(T), was isolated from a seashore sand sample from Dokdo, Korea. The isolate reduced nitrate to nitrite, but not to nitrogen, and required NaCl for growth. 16S rRNA gene sequence analysis indicated that the isolate belonged to the genus Zobellella within the order Alteromonadales with sequence similarities of 96.0-97.6 % to strains of Zobellella species with validly published names. However, in DNA-DNA hybridization studies, a low genomic relatedness (43 %) between strain JC2671(T) and the type strain of Zobellella denitrificans indicated that the isolate represented a novel genomic species. The polar lipid pattern (phosphatidylethanolamine and phosphatidylglycerol), predominant cellular fatty acids [C(16 : 0), summed feature 3 (C(16 : 1)ω6c and/or C(16 : 1)ω7c) and summed feature 8 (C(18 : 1)ω6c and/or C(18 : 1)ω7c)] and the DNA G+C content (59 mol%) of the novel strain were consistent with its assignment to the genus Zobellella. In contrast, a number of phenotypic characteristics, namely a requirement of NaCl for growth, the inability to grow under facultatively anaerobic conditions, the absence of nitrite reduction and differences in carbohydrate utilization and enzymic activities, clearly distinguished the novel isolate from other species of the genus Zobellella. Data from this polyphasic study indicate that strain JC2671(T) represents a novel species in the genus Zobellella, for which the name Zobellella aerophila sp. nov. is proposed. The type strain is JC2671(T) ( = KACC 15081(T)  = JCM 17110(T)). The description of the genus Zobellella has been emended accordingly.

Substrate specificity and structural characteristics of the novel Rieske nonheme iron aromatic ring-hydroxylating oxygenases NidAB and NidA3B3 from Mycobacterium vanbaalenii PYR-1.

The Rieske nonheme iron aromatic ring-hydroxylating oxygenases (RHOs) NidAB and NidA3B3 from Mycobacterium vanbaalenii PYR-1 have been implicated in the initial oxidation of high-molecular-weight (HMW) polycyclic aromatic hydrocarbons (PAHs), forming cis-dihydrodiols. To clarify how these two RHOs are functionally different with respect to the degradation of HMW PAHs, we investigated their substrate specificities to 13 representative aromatic substrates (toluene, m-xylene, phthalate, biphenyl, naphthalene, phenanthrene, anthracene, fluoranthene, pyrene, benz[a]anthracene, benzo[a]pyrene, carbazole, and dibenzothiophene) by enzyme reconstitution studies of Escherichia coli. Both Nid systems were identified to be compatible with type V electron transport chain (ETC) components, consisting of a [3Fe-4S]-type ferredoxin and a glutathione reductase (GR)-type reductase. Metabolite profiles indicated that the Nid systems oxidize a wide range of aromatic hydrocarbon compounds, producing various isomeric dihydrodiol and phenolic compounds. NidAB and NidA3B3 showed the highest conversion rates for pyrene and fluoranthene, respectively, with high product regiospecificity, whereas other aromatic substrates were converted at relatively low regiospecificity. Structural characteristics of the active sites of the Nid systems were investigated and compared to those of other RHOs. The NidAB and NidA3B3 systems showed the largest substrate-binding pockets in the active sites, which satisfies spatial requirements for accepting HMW PAHs. Spatially conserved aromatic amino acids, Phe-Phe-Phe, in the substrate-binding pockets of the Nid systems appeared to play an important role in keeping aromatic substrates within the reactive distance from the iron atom, which allows each oxygen to attack the neighboring carbons.

Terrabacter aerolatus sp. nov., isolated from an air sample.

A Gram-positive, strictly aerobic, motile, rod- or coccoid-shaped bacterium, strain 5516J-36(T), was isolated from an air sample from Jeju region, Korea, and its taxonomic position was investigated by a polyphasic approach. The organism grew optimally at 30 degrees C and pH 7.0-8.0. Comparative 16S rRNA gene sequencing studies demonstrated that this strain was highly related phylogenetically to Terrabacter terrae PPLB(T) and Terrabacter tumescens DSM 20308(T), showing 98.9 % sequence similarity to both strains. However, the DNA-DNA reassociation values between 5516J-36(T) and the type strains of Terrabacter terrae and Terrabacter tumescens were low (51 and 48 %, respectively). The peptidoglycan type was A3gamma, the predominant menaquinone was MK-8(H(4)), the polar lipids were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylinositol and an unidentified phosphoglycolipid and the whole-cell sugars were glucose, ribose, rhamnose, xylose and galactose. Mycolic acids were absent. The major fatty acids (>5 % of total fatty acids) were iso-C(15 : 0), iso-C(16 : 0), iso-C(14 : 0), iso-C(17 : 0) and anteiso-C(15 : 0). The DNA G+C content was 71.7 mol%. On the basis of the above data, it is proposed that strain 5516J-36(T) represents a novel species, Terrabacter aerolatus sp. nov. The type strain of Terrabacter aerolatus is 5516J-36(T) (=KACC 20556(T) =DSM 18562(T)).

Kribbella solani sp. nov. and Kribbella jejuensis sp. nov., isolated from potato tuber and soil in Jeju, Korea.

Two actinomycete strains, DSA1T and HD9T, were isolated from a potato tuber and soil from a potato-cultivating field in Jeju, Korea, respectively. A comprehensive 16S rDNA analysis revealed that the isolates belong to the genus Kribbella and share 97.7-98.6% sequence similarity to Kribbella species. The strains also contained typical chemotaxonomic markers of the genus Kribbella: ll-diaminopimelic acid, alanine, glycine and glutamic acid in the cell wall peptidoglycan; mannose, glucose, galactose and ribose as whole cell sugars; diphosphatidylglycerol, phosphatidylcholine and phosphatidylinositol as characteristic phospholipids; and the major menaquinone MK-9 (H4). DNA-DNA hybridization experiments showed that the isolates represented two distinct genomic species. A number of phenotypic properties can be used to differentiate the two isolates from Kribbella species. On the basis of polyphasic evidence, two novel species are proposed: Kribbella solani sp. nov. for strain DSA1T (=KACC 20196T=JCM 12205T) and Kribbella jejuensis sp. nov. for strain HD9T (=KACC 20266T=JCM 12204T).