Altererythrobacter insulae sp. nov., a lipolytic bacterium isolated from a tidal flat.

A lipolytic, Gram-stain-negative, aerobic, non-motile and coccoid, ovoid or rod-shaped bacterial strain, designated BPTF-M16T, was isolated from tidal flat sediment on the Yellow Sea in the Republic of Korea. Strain BPTF-M16T grew optimally at 30 °C and in the presence of 2.0-3.0 % (w/v) NaCl. A phylogenetic tree of 16S rRNA gene sequences showed that strain BPTF-M16T fell within the clade comprising the type strains of Altererythrobacter species. Strain BPTF-M16T exhibited 16S rRNA gene sequence similarity values of 98.0 and 97.1 % to the type strains of Altererythrobacterishigakiensis and Altererythrobactermarinus, respectively, and of less than 97.0 % to the type strains of the other recognized species. Strain BPTF-M16T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c as the major fatty acid. The major polar lipids detected in strain BPTF-M16T were phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, sphingoglycolipid and one unidentified glycolipid. Mean DNA-DNA relatedness values of strain BPTF-M16T with the type strains of A. ishigakiensis and A. marinus were 22 and 13 %, respectively. The average nucleotide identity value between strain BPTF-M16T and the type strain of A. ishigakiensis was 76.80 %. Differential phenotypic properties, together with the phylogenetic and genetic data, revealed that strain BPTF-M16T is separated from recognized Altererythrobacter species. On the basis of the data presented here, strain BPTF-M16T is considered to represent a novel species of the genus Altererythrobacter, for which the name Altererythrobacter insulae sp. nov. is proposed. The type strain is BPTF-M16T (=KCTC 62421T=KACC 19609T=NBRC 113190T).

Croceicoccus ponticola sp. nov., a lipolytic bacterium isolated from seawater.

A lipolytic, Gram-stain-negative, aerobic, non-motile and coccoid, ovoid or rod-shaped bacterial strain, designated GM-16T, was isolated from seawater around Pohang in the Republic of Korea. Strain GM-16T grew optimally at 30 °C and in the presence of 1.0-2.0 % (w/v) NaCl. The neighbour-joining phylogenetic tree of 16S rRNA gene sequences showed that strain GM-16T fell within the clade comprising the type strains of Croceicoccus species. Strain GM-16T exhibited the highest 16S rRNA gene sequence similarity (97.7 %) to the type strain of Croceicoccus pelagius and sequence similarities of 96.3-96.7 % to the type strains of the other Croceicoccus species. Strain GM-16T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) as major fatty acids. The major polar lipids of strain GM-16T were phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, sphingoglycolipid and one unidentified glycolipid. The DNA G+C content of strain GM-16T was 62.6 mol%. The mean DNA-DNA relatedness value between strain GM-16T and C. pelagius DSM 101479T was 16 %. The average nucleotide identity values between strain GM-16T and the type strains of C.roceicoccus pelagius, C.roceicoccus marinus, C.roceicoccus naphthovorans and C.roceicoccus mobilis were 83.96-84.44 %. The phylogenetic and genetic data and differential phenotypic properties indicated that strain GM-16T is separated from recognized Croceicoccus species. On the basis of the data presented here, strain GM-16T is considered to represent a novel species of the genus Croceicoccus, for which the name Croceicoccus ponticola sp. nov. is proposed. The type strain is GM-16T (=KACC 19611T=KCTC 62423T=NBRC 113192T).

Molecular Insights into Toluene Sensing in the TodS/TodT Signal Transduction System.

TodS is a sensor kinase that responds to various monoaromatic compounds, which either cause an agonistic or antagonistic effect on phosphorylation of its cognate response regulator TodT, and controls tod operon expression in Pseudomonas putida strains. We describe a molecular sensing mechanism of TodS that is activated in response to toluene. The crystal structures of the TodS Per-Arnt-Sim (PAS) 1 sensor domain (residues 43-164) and its complex with toluene (agonist) or 1,2,4-trimethylbenzene (antagonist) show a typical ß2α3ß3 PAS fold structure (residues 45-149), forming a hydrophobic ligand-binding site. A signal transfer region (residues 150-163) located immediately after the canonical PAS fold may be intrinsically flexible and disordered in both apo-PAS1 and antagonist-bound forms and dramatically adapt an α-helix upon toluene binding. This structural change in the signal transfer region is proposed to result in signal transmission to activate the TodS/TodT two-component signal transduction system. Site-directed mutagenesis and ß-galactosidase assays using a P. putida reporter strain system verified the essential residues involved in ligand sensing and signal transfer and suggest that the Phe(46) residue acts as a ligand-specific switch.

Kaposi's Sarcoma-Associated Herpesvirus Viral Interferon Regulatory Factor 4 (vIRF4) Perturbs the G1-S Cell Cycle Progression via Deregulation of the cyclin D1 Gene.

Kaposi's sarcoma-associated herpesvirus (KSHV) infection modulates the host cell cycle to create an environment optimal for its viral-DNA replication during the lytic life cycle. We report here that KSHV vIRF4 targets the ß-catenin/CBP cofactor and blocks its occupancy on the cyclin D1 promoter, suppressing the G1-S cell cycle progression and enhancing KSHV replication. This shows that KSHV vIRF4 suppresses host G1-S transition, possibly providing an intracellular milieu favorable for its replication.

Shiga Toxins Activate the NLRP3 Inflammasome Pathway To Promote Both Production of the Proinflammatory Cytokine Interleukin-1ß and Apoptotic Cell Death.

Shiga toxin (Stx)-mediated immune responses, including the production of the proinflammatory cytokines tumor necrosis-α (TNF-α) and interleukin-1ß (IL-1ß), may exacerbate vascular damage and accelerate lethality. However, the immune signaling pathway activated in response to Stx is not well understood. Here, we demonstrate that enzymatically active Stx, which leads to ribotoxic stress, triggers NLRP3 inflammasome-dependent caspase-1 activation and IL-1ß secretion in differentiated macrophage-like THP-1 (D-THP-1) cells. The treatment of cells with a chemical inhibitor of glycosphingolipid biosynthesis, which suppresses the expression of the Stx receptor globotriaosylceramide and subsequent endocytosis of the toxin, substantially blocked activation of the NLRP3 inflammasome and processing of caspase-1 and IL-1ß. Processing and release of both caspase-1 and IL-1ß were significantly reduced or abolished in Stx-intoxicated D-THP-1 cells in which the expression of NLRP3 or ASC was stably knocked down. Furthermore, Stx mediated the activation of caspases involved in apoptosis in an NLRP3- or ASC-dependent manner. In Stx-intoxicated cells, the NLRP3 inflammasome triggered the activation of caspase-8/3, leading to the initiation of apoptosis, in addition to caspase-1-dependent pyroptotic cell death. Taken together, these results suggest that Stxs trigger the NLRP3 inflammasome pathway to release proinflammatory IL-1ß as well as to promote apoptotic cell death.

Structural insights into the regulation of sialic acid catabolism by the Vibrio vulnificus transcriptional repressor NanR.

Pathogenic and commensal bacteria that experience limited nutrient availability in their host have evolved sophisticated systems to catabolize the mucin sugar N-acetylneuraminic acid, thereby facilitating their survival and colonization. The correct function of the associated catabolic machinery is particularly crucial for the pathogenesis of enteropathogenic bacteria during infection, although the molecular mechanisms involved with the regulation of the catabolic machinery are unknown. This study reports the complex structure of NanR, a repressor of the N-acetylneuraminate (nan) genes responsible for N-acetylneuraminic acid catabolism, and its regulatory ligand, N-acetylmannosamine 6-phosphate (ManNAc-6P), in the human pathogenic bacterium Vibrio vulnificus. Structural studies combined with electron microscopic, biochemical, and in vivo analysis demonstrated that NanR forms a dimer in which the two monomers create an arched tunnel-like DNA-binding space, which contains positively charged residues that interact with the nan promoter. The interaction between the NanR dimer and DNA is alleviated by the ManNAc-6P-mediated relocation of residues in the ligand-binding domain of NanR, which subsequently relieves the repressive effect of NanR and induces the transcription of the nan genes. Survival studies in which mice were challenged with a ManNAc-6P-binding-defective mutant strain of V. vulnificus demonstrated that this relocation of NanR residues is critical for V. vulnificus pathogenesis. In summary, this study presents a model of the mechanism that regulates sialic acid catabolism via NanR in V. vulnificus.

Genome evolution and adaptation in a long-term experiment with Escherichia coli.

The relationship between rates of genomic evolution and organismal adaptation remains uncertain, despite considerable interest. The feasibility of obtaining genome sequences from experimentally evolving populations offers the opportunity to investigate this relationship with new precision. Here we sequence genomes sampled through 40,000 generations from a laboratory population of Escherichia coli. Although adaptation decelerated sharply, genomic evolution was nearly constant for 20,000 generations. Such clock-like regularity is usually viewed as the signature of neutral evolution, but several lines of evidence indicate that almost all of these mutations were beneficial. This same population later evolved an elevated mutation rate and accumulated hundreds of additional mutations dominated by a neutral signature. Thus, the coupling between genomic and adaptive evolution is complex and can be counterintuitive even in a constant environment. In particular, beneficial substitutions were surprisingly uniform over time, whereas neutral substitutions were highly variable.

Charting microbial phenotypes in multiplex nanoliter batch bioreactors.

High-throughput growth phenotyping is receiving great attention for establishing the genotype-phenotype map of sequenced organisms owing to the ready availability of complete genome sequences. To date, microbial growth phenotypes have been investigated mostly by the conventional method of batch cultivation using test tubes, Erlenmeyer flasks, or the recently available microwell plates. However, the current batch cultivation methods are time- and labor-intensive and often fail to consider sophisticated environmental changes. The implementation of batch cultures at the nanoliter scale has been difficult because of the quick evaporation of the culture medium inside the reactors. Here, we report a microfluidic system that allows independent cell cultures in evaporation-free multiplex nanoliter reactors under different culture conditions to assess the behavior of cells. The design allows three experimental replicates for each of eight culture environments in a single run. We demonstrate the versatility of the device by performing growth curve experiments with Escherichia coli and microbiological assays of antibiotics against the opportunistic pathogen Pseudomonas aeruginosa. Our study highlights that the microfluidic system can effectively replace the traditional batch culture methods with nanoliter volumes of bacterial cultivations, and it may be therefore promising for high-throughput growth phenotyping as well as for single-cell analyses.

Construction and manipulation of a new Kaposi's sarcoma-associated herpesvirus bacterial artificial chromosome clone.

Efficient genetic modification of herpesviruses such as Kaposi's sarcoma-associated herpesvirus (KSHV) has come to rely on bacterial artificial chromosome (BAC) technology. In order to facilitate this approach, we generated a new KSHV BAC clone, called BAC16, derived from the rKSHV.219 virus, which stems from KSHV and Epstein-Barr virus-coinfected JSC1 primary effusion lymphoma (PEL) cells. Restriction enzyme and complete sequencing data demonstrate that the KSHV of JSC1 PEL cells showed a minimal level of sequence variation across the entire viral genome compared to the complete genomic sequence of other KSHV strains. BAC16 not only stably propagated in both Escherichia coli and mammalian cells without apparent genetic rearrangements, but also was capable of robustly producing infectious virions (∼5 × 10(7)/ml). We also demonstrated the utility of BAC16 by generating deletion mutants of either the K3 or K5 genes, whose products are E3 ligases of the membrane-associated RING-CH (MARCH) family. While previous studies have shown that individual expression of either K3 or K5 results in efficient downregulation of the surface expression of major histocompatibility complex class I (MHC-I) molecules, we found that K5, but not K3, was the primary factor critical for the downregulation of MHC-I surface expression during KSHV lytic reactivation or following de novo infection. The data presented here demonstrate the utility of BAC16 for the generation and characterization of KSHV knockout and mutant recombinants and further emphasize the importance of functional analysis of viral genes in the context of the KSHV genome besides the study of individual gene expression.

Gaetbulibacter lutimaris sp. nov., isolated from a tidal flat sediment.

A Gram-stain-negative, aerobic, non-flagellated, non-gliding, rod-shaped bacterial strain, D1-y4(T), was isolated from a tidal flat sediment of the South Sea in South Korea and subjected to a polyphasic study. Strain D1-y4(T) grew optimally at 25 °C, at pH 7.0-7.5 and in the presence of 2-3 % (w/v) NaCl. Phylogenetic trees based on 16S rRNA gene sequences revealed that strain D1-y4(T) belonged to the genus Gaetbulibacter, joining the type strain of Gaetbulibacter marinus, with which it exhibited 97.8 % similarity. Sequence similarities to Gaetbulibacter saemankumensis SMK-12(T) and Gaetbulibacter aestuarii KYW382(T) were 96.5 and 96.2 %, respectively. Strain D1-y4(T) contained MK-6 as the predominant menaquionone and iso-C15 : 0, iso-C15 : 1 G and anteiso-C15 : 0 as the major fatty acids. The major polar lipids were phosphatidylethanolamine and one unidentified lipid. The DNA G+C content of strain D1-y4(T) was 34.6 mol% and its mean DNA-DNA relatedness value with G. marinus KCTC 23046(T) was 7 %. The phylogenetic and genetic distinctiveness and differential phenotypic properties revealed that strain D1-y4(T) is distinguishable from the three recognized Gaetbulibacter species. On the basis of the data presented here, strain D1-y4(T) is considered to represent a novel species of the genus Gaetbulibacter, for which the name Gaetbulibacter lutimaris sp. nov. is proposed. The type strain is D1-y4(T) ( = KCTC 23716(T)  = CCUG 61504(T)).

Kangiella sediminilitoris sp. nov., isolated from a tidal flat sediment.

A Gram-stain-negative, non-motile, non-spore-forming, rod-shaped bacterial strain, BB-Mw22(T), was isolated from a tidal flat sediment of the South Sea in South Korea. It grew optimally at 30-37 °C, at pH 7.0-7.5 and in the presence of 2-3 % (w/v) NaCl. Phylogenetic trees based on 16S rRNA gene sequences revealed that strain BB-Mw22(T) belonged to the genus Kangiella and the cluster comprising Kangiella species and strain BB-Mw22(T) was clearly separated from other taxa. Strain BB-Mw22(T) exhibited 95.3-98.7 % 16S rRNA gene sequence similarity to the type strains of recognized Kangiella species. Strain BB-Mw22(T) contained Q-8 as the predominant ubiquionone and iso-C15 : 0 and iso-C11 : 0 3-OH as the major fatty acids. The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine and one unidentified aminolipid. The DNA G+C content of strain BB-Mw22(T) was 48.9 mol%, and its mean DNA-DNA hybridization values with Kangiella geojedonensis YCS-5(T), Kangiella japonica JCM 16211(T) and Kangiella taiwanensis JCM 17727(T) were 14-28 %. Phylogenetic and genetic distinctiveness and differential phenotypic properties revealed that strain BB-Mw22(T) is distinguishable from all recognized Kangiella species. On the basis of the data presented, strain BB-Mw22(T) is considered to represent a novel species of the genus Kangiella, for which the name Kangiella sediminilitoris sp. nov. is proposed. The type strain is BB-Mw22(T) ( = KCTC 23892(T)  = CCUG 62217(T)).

Complete genome sequence of the probiotic bacterium Bifidobacterium bifidum strain BGN4.

Bifidobacterium bifidum, a common endosymbiotic inhabitant of the human gut, is considered a prominent probiotic microorganism that may promote health. We completely decrypted the 2.2-Mb genome sequence of B. bifidum BGN4, a strain that had been isolated from the fecal sample of a healthy breast-fed infant, and annotated 1,835 coding sequences.

Crystal structure of the human N-Myc downstream-regulated gene 2 protein provides insight into its role as a tumor suppressor.

Considerable attention has recently been paid to the N-Myc downstream-regulated gene (NDRG) family because of its potential as a tumor suppressor in many human cancers. Primary amino acid sequence information suggests that the NDRG family proteins may belong to the α/ß-hydrolase (ABH) superfamily; however, their functional role has not yet been determined. Here, we present the crystal structures of the human and mouse NDRG2 proteins determined at 2.0 and 1.7 Å resolution, respectively. Both NDRG2 proteins show remarkable structural similarity to the ABH superfamily, despite limited sequence similarity. Structural analysis suggests that NDRG2 is a nonenzymatic member of the ABH superfamily, because it lacks the catalytic signature residues and has an occluded substrate-binding site. Several conserved structural features suggest NDRG may be involved in molecular interactions. Mutagenesis data based on the structural analysis support a crucial role for helix α6 in the suppression of TCF/ß-catenin signaling in the tumorigenesis of human colorectal cancer, via a molecular interaction.

Efficient production of polymyxin in the surrogate host Bacillus subtilis by introducing a foreign ectB gene and disrupting the abrB gene.

In our previous study, Bacillus subtilis strain BSK3S, containing a polymyxin biosynthetic gene cluster from Paenibacillus polymyxa, could produce polymyxin only in the presence of exogenously added L-2,4-diaminobutyric acid (Dab). The dependence of polymyxin production on exogenous Dab was removed by introducing an ectB gene encoding the diaminobutyrate synthase of P. polymyxa into BSK3S (resulting in strain BSK4). We found, by observing the complete inhibition of polymyxin synthesis when the spo0A gene was knocked out (strain BSK4-0A), that Spo0A is indispensable for the production of polymyxin. Interestingly, the abrB-spo0A double-knockout mutant, BSK4-0A-rB, and the single abrB mutant, BSK4-rB, showed 1.7- and 2.3-fold increases, respectively, in polymyxin production over that of BSK4. These results coincided with the transcription levels of pmxA in the strains observed by quantitative real-time PCR (qRT-PCR). The AbrB protein was shown to bind directly to the upstream region of pmxA, indicating that AbrB directly inhibits the transcription of polymyxin biosynthetic genes. The BSK4-rB strain, producing high levels of polymyxin, will be useful for the development and production of novel polymyxin derivatives.

Novel metagenome-derived, cold-adapted alkaline phospholipase with superior lipase activity as an intermediate between phospholipase and lipase.

A novel lipolytic enzyme was isolated from a metagenomic library obtained from tidal flat sediments on the Korean west coast. Its putative functional domain, designated MPlaG, showed the highest similarity to phospholipase A from Grimontia hollisae CIP 101886, though it was screened from an emulsified tricaprylin plate. Phylogenetic analysis showed that MPlaG is far from family I.6 lipases, including Staphylococcus hyicus lipase, a unique lipase which can hydrolyze phospholipids, and is more evolutionarily related to the bacterial phospholipase A(1) family. The specific activities of MPlaG against olive oil and phosphatidylcholine were determined to be 2,957 ± 144 and 1,735 ± 147 U mg(-1), respectively, which means that MPlaG is a lipid-preferred phospholipase. Among different synthetic esters, triglycerides, and phosphatidylcholine, purified MPlaG exhibited the highest activity toward p-nitrophenyl palmitate (C(16)), tributyrin (C(4)), and 1,2-dihexanoyl-phosphatidylcholine (C(8)). Finally, MPlaG was identified as a phospholipase A(1) with lipase activity by cleavage of the sn-1 position of OPPC, interfacial activity, and triolein hydrolysis. These findings suggest that MPlaG is the first experimentally characterized phospholipase A(1) with lipase activity obtained from a metagenomic library. Our study provides an opportunity to improve our insight into the evolution of lipases and phospholipases.

Marinomonas hwangdonensis sp. nov., isolated from seawater.

A Gram-negative, motile, rod-shaped bacterial strain, designated HDW-15(T), was isolated from seawater of the Yellow Sea, Korea, and subjected to a polyphasic taxonomic study. Strain HDW-15(T) grew optimally at pH 7.0-8.0, at 25 °C and in the presence of 2 % (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain HDW-15(T) fell within the clade comprising Marinomonas species, joining the type strain of Marinomonas arctica, with which it exhibited highest 16S rRNA gene sequence similarity (97.7 %). The 16S rRNA gene sequence similarity values between strain HDW-15(T) and the type strains of other Marinomonas species were in the range 93.7-97.2 %. Mean DNA-DNA relatedness values between strain HDW-15(T) and the type strains of M. arctica, Marinomonas polaris and Marinomonas pontica were 5.0-9.9 %. The DNA G+C content of the isolate was 48.7 mol%. Strain HDW-15(T) contained Q-8 as the predominant ubiquinone and C(18 : 1)ω7c, summed feature 3 (C(16 : 1)ω7c and/or iso-C(15 : 0) 2-OH) and C(16 : 0) as the major fatty acids. The major polar lipids found in strain HDW-15(T) were phosphatidylglycerol and phosphatidylethanolamine. Differential phenotypic properties, together with phylogenetic and genetic distinctiveness, showed that strain HDW-15(T) can be differentiated from other Marinomonas species. On the basis of the data presented, strain HDW-15(T) is considered to represent a novel species of the genus Marinomonas, for which the name Marinomonas hwangdonensis sp. nov. is proposed. The type strain is HDW-15(T) (= KCTC 23661(T) = CCUG 61321(T)).

Erythrobacter marinus sp. nov., isolated from seawater.

A Gram-negative, non-motile, ovoid to rod-shaped bacterium, designated strain HWDM-33(T), was isolated from seawater of the Yellow Sea, Korea, and was subjected to a polyphasic taxonomic study. Strain HWDM-33(T) grew optimally at pH 7-8, at 25 °C and in the presence of 2-3 % (w/v) NaCl. Neighbour-joining, maximum-likelihood and maximum-parsimony phylogenetic trees based on 16S rRNA gene sequences showed that strain HWDM-33(T) clustered with Erythrobacter gangjinensis K7-2(T), with which it shared 96.9 % sequence similarity. Strain HWDM-33(T) exhibited 94.2-95.8 % 16S rRNA gene sequence similarity to the type strains of other recognized species of the genus Erythrobacter. Strain HWDM-33(T) contained Q-10 as the predominant ubiquinone and C(18 : 1)ω7c, C(17:1)ω6c, and C(16:1)ω7c and/or iso-C(15 : 0) 2-OH as the major fatty acids. The major polar lipids were sphingoglycolipid, phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine and an unidentified lipid. The DNA G+C content of strain HWDM-33(T) was 66.1 mol%. Differential phenotypic properties and phylogenetic distinctiveness demonstrated that strain HWDM-33(T) was separate from E. gangjinensis and other recognized species of the genus Erythrobacter. On the basis of the data presented here, strain HWDM-33(T) represents a novel species of the genus Erythrobacter, for which the name Erythrobacter marinus sp. nov. is proposed. The type strain is HWDM-33(T) (= KCTC 23554(T) = CCUG 60528(T)).

Winogradskyella aquimaris sp. nov., isolated from seawater.

A Gram-negative, non-flagellated, motile by gliding, aerobic rod, designated DPG-24(T), was isolated from seawater of Geoje Island in the South Sea, Korea. Strain DPG-24(T) grew optimally at 30-37 °C, at pH 7.0-7.5 and with 2% (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain DPG-24(T) belonged to the genus Winogradskyella and clustered with Winogradskyella poriferorum UST030701-295(T) and Winogradskyella exilis 022-2-26(T). Strain DPG-24(T) exhibited 97.6 and 95.8% 16S rRNA gene sequence similarities with W. poriferorum UST030701-295(T) and W. exilis 022-2-26(T), respectively, and 92.4-95.7% with other members of the genus Winogradskyella. Strain DPG-24(T) contained MK-6 as the predominant menaquinone and iso-C(15:1) G, iso-C(15:0) and iso-C(17:0) 3-OH as the major fatty acids. The major polar lipids were phosphatidylethanolamine, one unidentified lipid, one unidentified aminolipid and one unidentified phospholipid. The DNA G+C content was 36.7 mol%. DNA-DNA relatedness between the isolate and W. poriferorum JCM 12885(T) was 10.8%. The differential phenotypic properties and phylogenetic and genetic distinctiveness enabled strain DPG-24(T) to be differentiated from recognized members of the genus Winogradskyella. On the basis of the data presented, strain DPG-24(T) is considered to represent a novel species of the genus Winogradskyella, for which the name Winogradskyella aquimaris sp. nov. is proposed; the type strain is DPG-24(T) ( = KCTC 23502(T)  = CCUG 60798(T)).

Reclassification of the three species of the genus Krokinobacter into the genus Dokdonia as Dokdonia genika comb. nov., Dokdonia diaphoros comb. nov. and Dokdonia eikasta comb. nov., and emended description of the genus Dokdonia Yoon et al. 2005.

The genera Dokdonia and Krokinobacter, members of the family Flavobacteriaceae in the phylum Bacteroidetes, were found to be phylogenetically closely related from the result of 16S rRNA gene sequence analysis. Dokdonia donghaensis DSW-1(T) exhibited 16S rRNA gene sequence similarity values of 99.3, 98.1 and 98.1% to Krokinobacter genikus Cos-13(T), Krokinobacter diaphorus MSKK-32(T) and Krokinobacter eikastus PMA-26(T), respectively. A taxonomic study of D. donghaensis DSW-1(T), K. genikus CIP 108744(T), K. diaphorus CIP 108745(T) and K. eikastus CIP 108743(T) was conducted using a polyphasic approach. The major fatty acids (>10% of the total fatty acids) in the four strains were iso-C(15:0), iso-C(15:1) G and iso-C(17:0) 3-OH, and their overall fatty acid profiles were essentially similar. The predominant menaquinone found in the type strains of the three species of the genus Krokinobacter was MK-6, in line with the genus Dokdonia. The polar lipid profiles of the type strains of the three species of the genus Krokinobacter were similar to that of D. donghaensis DSW-1(T) in that phosphatidylethanolamine, one unidentified aminolipid and one unidentified lipid were the major polar lipids. In addition, one unidentified aminophospholipid was also present as a major polar lipid in K. diaphorus CIP 108745(T) and K. eikastus CIP 108743(T). D. donghaensis DSW-1(T) was distinguishable from K. genikus CIP 108744(T), K. diaphorus CIP 108745(T) and K. eikastus CIP 108743(T) by genetic relatedness and differential phenotypic properties. On the basis of these data, it is proposed that K. genikus, K. diaphorus and K. eikastus be reclassified into the genus Dokdonia as Dokdonia genika comb. nov. (type strain is Cos-13(T) = NBRC 100811(T) = CIP 108744(T)), Dokdonia diaphoros comb. nov. (type strain is MSKK-32(T) = NBRC 100817(T) = CIP 108745(T)), and Dokdonia eikasta comb. nov. (type strain is PMA-26(T) = NBRC 100814(T) = CIP 108743(T)), respectively. An emended description of the genus Dokdonia is also presented.

Salinimicrobium gaetbulicola sp. nov., isolated from tidal flat sediment.

A Gram-stain-negative, aerobic, non-flagellated, non-gliding and short rod- or rod-shaped bacterial strain, designated BB-My20(T), was isolated from tidal flat sediment taken from the southern coast of Korea. Strain BB-My20(T) grew optimally at 37 °C, at pH 7.0-7.5 and in the presence of 2 % (w/v) NaCl. A phylogenetic tree based on 16S rRNA gene sequences showed that strain BB-My20(T) fell within the clade comprising Salinimicrobium species, joining Salinimicrobium catena HY1(T), with which it had a 16S rRNA gene sequence similarity value of 97.4 %. It exhibited 95.4-96.9 % sequence similarity to the type strains of other members of the genus Salinimicrobium. Strain BB-My20(T) contained MK-6 as the predominant menaquinone and iso-C(15 : 0), anteiso-C(15 : 0) and iso-C(17 : 0) 3-OH as the major fatty acids. The major polar lipids detected in strain BB-My20(T) and S. catena JCM 14015(T) were phosphatidylethanolamine and one unidentified lipid. The DNA G+C content of strain BB-My20(T) was 45.1 mol% and its mean DNA-DNA relatedness value with S. catena JCM 14015(T) was 4.5 %. Differential phenotypic properties, together with its phylogenetic and genetic distinctiveness, revealed that strain BB-My20(T) can be distinguished from the four recognized species of the genus Salinimicrobium. On the basis of the data presented, strain BB-My20(T) is considered to represent a novel species of the genus Salinimicrobium, for which the name Salinimicrobium gaetbulicola sp. nov. is proposed; the type strain is BB-My20(T) ( = KCTC 23579(T) = CCUG 60898(T)).