Expression and characterization of catechol 1,2-dioxygenase from Oceanimonas marisflavi 102-Na3.

The gene of catechol 1, 2-dioxygenase was identified and cloned from the genome of Oceanimonas marisflavi 102-Na3. The protein was expressed in Escherichia coli BL21 (DE3) and purified to homogeneity of a dimer with molecular mass of 69.2 kDa. The enzyme was highly stable in pH 6.0-9.5 and below 45 °C and exhibited the maximum activity at pH 8.0 and 30 °C. Being the first characterized intradiol dioxygenase from marine bacteria Oceanimonas sp., the enzyme showed catalytic activity for catechol, 3-methylcatechol, 4-methylcatechol, 3-chlorocatechol, 4-chlorocatechol and pyrogallol. For catechol, Km and Vmax were 11.2 µM and 13.4 U/mg of protein, respectively. The enzyme also showed resistance to most of the metal ions, surfactants and organic solvents, being a promising biocatalyst for biodegradation of aromatic compounds in complex environments.

Analysis of Zobellella denitrificans ZD1 draft genome: Genes and gene clusters responsible for high polyhydroxybutyrate (PHB) production from glycerol under saline conditions and its CRISPR-Cas system.

Polyhydroxybutyrate (PHB) is biodegradable and renewable and thus considered as a promising alternative to petroleum-based plastics. However, PHB production is costly due to expensive carbon sources for culturing PHB-accumulating microorganisms under sterile conditions. We discovered a hyper PHB-accumulating denitrifying bacterium, Zobellella denitrificans ZD1 (referred as strain ZD1 hereafter) capable of using non-sterile crude glycerol (a waste from biodiesel production) and nitrate to produce high PHB yield under saline conditions. Nevertheless, the underlying genetic mechanisms of PHB production in strain ZD1 have not been elucidated. In this study, we discovered a complete pathway of glycerol conversion to PHB, a novel PHB synthesis gene cluster, a salt-tolerant gene cluster, denitrifying genes, and an assimilatory nitrate reduction gene cluster in the ZD1 genome. Interestingly, the novel PHB synthesis gene cluster was found to be conserved among marine Gammaproteobacteria. Higher levels of PHB accumulation were linked to higher expression levels of the PHB synthesis gene cluster in ZD1 grown with glycerol and nitrate under saline conditions. Additionally, a clustered regularly interspaced short palindromic repeat (CRISPR)-Cas type-I-E antiviral system was found in the ZD1 genome along with a long spacer list, in which most of the spacers belong to either double-stranded DNA viruses or unknown phages. The results of the genome analysis revealed strain ZD1 used the novel PHB gene cluster to produce PHB from non-sterile crude glycerol under saline conditions.

Characteristics of bacterial isolates in Swiss farmed and ornamental fish from a retrospective study from 2000 to 2017.

INTRODUCTION: Aquaculture is a rapidly growing field of food production of high economic importance. Bacterial infections are an important threat to aquaculture growth and also a common problem in ornamental fish. Some pathogenic agents and aquaculture production types are reported to be associated with increased disease. However, a detailed description of bacterial pathogens causing disease in Swiss aquaculture and ornamental pet fish is still missing. In this study we describe 1448 bacterial isolations originating from 1134 diagnostic laboratory submissions from farmed and ornamental fish in Switzerland for the period from 2000 to 2017. A strong seasonality was observed with submissions peaking in spring and summer. Bacterial isolations in fish submitted from organic farms were approximately six times more frequent than in conventional fish farms. Flavobacteriaceae, aeromonads and Yersinia ruckeri were the most common isolates from aquaculture, and motile aeromonads and Vibrio spp. were most often isolated from ornamental fish. The results of this study provide some interesting hypotheses, but further research is needed to better characterize risk factors for bacterial diseases in both aquaculture and aquarium fish in Switzerland.

INTRODUCTION: L'aquaculture est un secteur de la production alimentaire en pleine croissance et d'une grande importance économique. Les infections bactériennes constituent une menace importante pour la croissance de l'aquaculture mais également un problème courant chez les poissons d'ornement. Certains agents pathogènes et types de production aquacole seraient associés à une plus forte incidence de certaines maladies. Une description complète des agents pathogènes bactériens responsables de maladies chez les poissons d'élevage et d'ornement en Suisse fait cependant défaut. Nous décrivons dans cette étude 1448 isolats bactériens provenant de 1134 soumissions de poissons d'élevage et de poissons d'ornement en Suisse à un laboratoire de diagnostic entre 2000 et 2017. Une forte saisonnalité a été observée au printemps et en été. Les infections bactériennes chez les poissons de fermes biologiques étaient environ six fois plus fréquentes que dans les exploitations conventionnelles. Flavobacteriaceae, Aeromonas spp. et Yersinia ruckeri sont les isolats qui ont été les plus communément isolés des soumissions des piscicultures. Vibrio spp. ainsi que les espèces motiles d'Aeromonas spp. ont été les principaux isolats mis en évidence chez les poissons d'ornement. Les résultats de cette étude fournissent des hypothèses intéressantes, mais des recherches supplémentaires sont nécessaires pour mieux caractériser les facteurs de risque des maladies bactériennes chez les poissons d'aquaculture et d'aquarium en Suisse.

Dongshaea marina gen. nov., sp. nov., a facultatively anaerobic marine bacterium that ferments glucose with gas production.

Two isolates of heterotrophic, facultatively anaerobic, marine bacteria, designated DM1 and DM2T, were recovered from a lagoon sediment sample of Dongsha Island, Taiwan. Cells were Gram-reaction-negative rods. Nearly all of the cells were non-motile and non-flagellated during the late exponential to early stationary phase of growth, while a few of the cells exhibited motility with monotrichous flagellation. The two isolates required NaCl for growth and grew optimally at about 30 °C, 2-3 % NaCl and pH 7-8. They grew aerobically and could achieve anaerobic growth by fermenting d-glucose or other carbohydrates with production of acids and the gases, including CO2 and H2. Ubiquinone Q-8 was the only respiratory quinone. Cellular fatty acids were predominated by C16 : 0, C18 : 1ω7c and C16 : 1ω7c. The major polar lipid was phosphatidylethanolamine. Strains DM1 and DM2T had DNA G+C contents of 52.0 and 51.8 mol%, respectively, as determined by HPLC analysis. Phylogenetic analyses based on 16S rRNA gene sequences clearly indicated that the two isolates formed a distinct genus-level lineage in the family Aeromonadaceae of the class Gammaproteobacteria and was an outgroup with respect to a stable supragenic clade comprising species of the genera Oceanimonas, Oceanisphaera and Zobellella. The phylogenetic data and those from chemotaxonomic, physiological and morphological characterizations support the establishment of a novel species and genus inside the family Aeromonadaceae, for which the name Dongshaea marina gen. nov., sp. nov. is proposed. The type strain is DM2T (=BCRC 81069T=JCM 32096T).

Zobellella endophytica sp. nov., isolated from the roots of Phragmites communis in the Kumtag Desert.

A Gram-negative, aerobic, non-spore-forming, rod-shaped, motile bacterium, named strain 59N8T, was isolated from Phragmites communis roots in the Kumtag Desert. Phylogenetic analysis based on the 16S rRNA gene sequence showed that the isolate belongs to the genus Zobellella within the family Aeromonadaceae. The analysis showed that strain 59N8T was most closely related to Zobellella taiwanensis ZT1T. The average nucleotide identity value with Zobellella taiwanensis ZT1T was 88.2 %, and the digital DNA-DNA hybridization value was 29.7±2.4 %, which was calculated using the Genome-to-Genome Distance Calculator. The G+C content of strain 59N8T was 62.8 mol%. Strain 59N8T grew at 0-5 % (w/v) NaCl (optimum, 0-4 %), pH 6.0-9.0 (optimum, 7.0-8.0) and at 10-45 °C. The major cellular fatty acids were summed feature 8 (C18 : 1ω7c/C18 : 1ω6c), summed feature 3 (C16 : 1ω7c/C16 : 1ω6c) and C16 : 0. The major polar lipids in strain 59N8T were phosphatidylethanolamine and phosphatidylglycerol. Based on the chemotaxonomic, phylogenetic and phenotypic data, strain 59N8T represents a novel species in the genus Zobellella, for which the name Zobellellaendophytica sp. nov. is proposed. The type strain is 59N8T (=ACCC 60074T=KCTC 62456T).

[Isolation and Nitrogen Removal Characteristics of Salt-tolerant Heterotrophic Nitrification and Aerobic Denitrification Bacteria Zobellella sp. B307].

A heterotrophic nitrification and aerobic denitrification strain, B307, was isolated from the sediment of Jiaozhou Bay. The strain was identified by 16S rRNA sequence analysis, and its optimization condition and salt-tolerance characteristics were studied by single factor experiment. The denitrification effect in single or mixed nitrogen sources was investigated under optimum conditions. The results allowed the strain to be identified as Zobellella sp., based on 16S rRNA sequence analysis. The best carbon source was sodium succinate, and the optimum C/N was 5, the optimal initial pH was 9, and the optimal temperature was 35-40℃ respectively. After 12 hours, the NH4+-N and the NO3--N removal efficiencies were 98.35% and 99.75% in a mixed nitrogen source system. The removal efficiencies for NH4+-N and NO3--N were 97.67% and 94.39% within 24 hours when salinity was 75 g·L-1. The strain has highly efficient heterotrophic nitrification-aerobic denitrification ability and strong salt tolerance, which demonstrated that the strain has potential for extensive application for nitrogen removal in high salt wastewater.

Oceanimonas marisflavi sp. nov., a polycyclic aromatic hydrocarbon-degrading marine bacterium.

A Gram-stain-negative, strictly aerobic, motile and rod-shaped bacterial strain, designated 102-Na3T, was isolated from sediment of Sinduri beach in Taean, Republic of Korea. Strain 102-Na3T grew optimally at 28-37 °C, at pH 7.0-11.0 and in the presence of 1-3 % (w/v) NaCl, but NaCl was not an absolute requirement for growth. The neighbour-joining phylogenetic tree based on 16S rRNA gene sequences showed that strain 102-Na3T joined the clade comprising the type strains of Oceanimonasspecies. Strain 102-Na3T exhibited 16S rRNA gene sequence similarity values of 98.8, 98.3 and 98.0 % to the type strains of Oceanimonas doudoroffii MBIC1298T, Oceanimonas baumannii GB6T and Oceanimonas smirnovii 31-13T, respectively. Strain 102-Na3T contained summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c), summed feature 8 (comprising C18 : 1ω7c and/or C18 : 1ω6c), C16 : 0 and C12 : 0 as major fatty acids. The major quinone was ubiquinone-8. The polar lipids were composed of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and two unidentified amino lipids. The DNA G+C content was 56.8 mol%. Strain 102-Na3T exhibited DNA-DNA relatedness values of 25.7, 21.7 and 14.8 % to the type strains of O. doudoroffii, O. baumannii and O. smirnovii, respectively. Differential phenotypic properties, together with its phylogenetic and genetic distinctiveness, revealed that strain 102-Na3T is separated from recognized species of the genus Oceanimonas. On the basis of the data presented, strain 102-Na3T (=KCTC 62271T=JCM 32358T=DSM 106032T) is considered the type strain of a novel species of the genus Oceanimonas, for which the name Oceanimonas marisflavi sp. nov. is proposed.

Zobellella maritima sp. nov., a polycyclic aromatic hydrocarbon-degrading bacterium, isolated from beach sediment.

A novel Gram-stain-negative, motile, rod-shaped bacterium, designated strain 102-Py4T, was isolated from Sinduri beach sediment in Taean, Republic of Korea. Cells were aerobic, oxidase-positive and catalase-positive. The isolate grew optimally with 1-3 % (w/v) NaCl, but NaCl is not an absolute requirement for growth. 16S rRNA gene sequence analysis revealed that strain 102-Py4T clustered together with Zobellella aerophila and fell within the clade formed by recognized species of the genus Zobellella. Its closest phylogenetic neighbours were Z. aerophila JC2671T (98.1 % 16S rRNA gene sequence similarity), Zobellella denitrificans ZD1T (96.4 %) and Zobellella taiwanensis ZT1T (96.0 %). The major fatty acids were summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c), C12 : 0, summed feature 8 (comprising C18 : 1ω7c and/or C18 : 1ω6c) and C16 : 0. The polar lipids were phosphatidylethanolamine, phosphatidylglycerol and two unidentified amino lipids. The DNA G+C content was 62.1 mol%. The DNA-DNA relatedness value between strain 102-Py4T and Z. aerophila JC2671T was 12.4±1.3 %. The phenotypic properties of 102-Py4T demonstrated that this strain could be distinguished from other Zobellella species. On the basis of the data presented, strain 102-Py4T (=KCTC 62272T=JCM 32359T=DSM 106043T) is considered to represent a novel species of the genus Zobellella, for which the name Zobellella maritima sp. nov. is proposed.

Oceanisphaera avium sp. nov., isolated from the gut of the cinereous vulture, Aegypius monachus.

A Gram-stain-negative, aerobic, catalase- and oxidase-positive, rod-shaped, flagellated bacterial strain, designated AMac2203T, was isolated from the gut of the cinereous vulture, Aegypiusmonachus, collected from the Seoul Grand Park Zoo, Republic of Korea. Strain AMac2203T grew optimally at 15-25 °C, pH 7-8 and in the presence of 3-5 % (w/v) NaCl. Phylogenetic analysis revealed 97.4-97.9 % and 96.9-97.3 % sequence similarities of the 16S rRNA genes to its counterparts in Oceanisphaera profunda SM1222T and Oceanisphaera ostreae T-w6T, respectively. The predominant fatty acids (>10 %) of strain AMac2203T were summed feature 3 (C16 : 0ω7c and/or C16 : 1ω6c, 33.6 %), summed feature 8 (C18 : 1ω7c, 24.5 %) and C16 : 0 (19.9 %). The primary isoprenoid quinone was ubiquinone-8. Polar lipids included phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, an unidentified amino lipid and an unidentified lipid. Based on complete genome sequencing of strain AMac2203T and the closest related type strain, O. profunda, the OrthoANI value is 77.5 %, which is below the 95 % cut-off for species demarcation. The genomic DNA G+C content of strain AMac2203T is 47.1 mol%. Thus, strain AMac2203T represents a novel species candidate of the genus Oceanisphaera. We propose the name Oceanisphaeraavium sp. nov., with strain AMac2203T (=KCTC 62118T=JCM 32207T) as the type strain.

Analysis of bacterial FAMEs using gas chromatography - vacuum ultraviolet spectroscopy for the identification and discrimination of bacteria.

The identification of microorganisms is very important in different fields and alternative methods are necessary for a rapid and simple identification. The use of fatty acids for bacterial identification is gaining attention as phenotypic characteristics are reflective of the genotype and are more easily analyzed. In this work, gas chromatography-vacuum ultraviolet spectroscopy (GC-VUV) was used to determine bacteria fatty acid methyl esters (FAMEs), to identify and discriminate different environmental bacteria based on their fatty acid profile. Microorganisms were grown in agar and their fatty acids extracted, saponified, and esterified before analysis. Unique FAME profiles were obtained for each microorganism mainly composed of branched, cyclopropane, hydroxy, saturated, and unsaturated fatty acid methyl esters. S. maltophilia showed a higher diversity of fatty acids while Bacillus species showed higher complexity in terms of branched-chain FAMEs, with several iso and anteiso forms. 12 different bacteria genera and 15 species were successfully differentiated based on their fatty acid profiles after performing PCA and cluster analysis. Some difficult to differentiate species, such as Bacillus sp., which are genetically very similar, were differentiated with the developed method.

Oceanisphaera marina sp. nov., isolated from a deep-sea seamount.

A Gram-stain-negative, rod-shaped, strictly aerobic, motile bacterial strain, designated YM319T, was isolated from a seamount near the Yap Trench in the tropical western Pacific. Phylogenetic analysis based on 16S rRNA gene sequence showed that strain YM319T was related to the genus Oceanisphaera and had highest 16S rRNA gene sequence similarities with the type strains Oceanisphaera profunda SM1222T (97.4 %), Oceanisphaera sediminis TW92T (97.3 %) and Oceanisphaera ostreae T-w6T (97.1 %). The predominant cellular fatty acids were summed feature 3 (composed of iso-C15 : 0 2-OH and/or C16 : 1 ω7c), C16 : 0 and C18 : 1ω7c. Strain YM319T had Q-8 as the predominant ubiquinone. The polar lipid profile contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, one unidentified phospholipid and four unidentified lipids. The genomic DNA G+C content of strain YM319T was 54.8 mol%. On the basis of the evidence presented in this study, strain YM319T represents a novel species of the genus Oceanisphaera, for which we propose the name Oceanisphaera marina sp. nov. (type strain YM319T=KACC 18564T=CGMCC 1.15923T).

Reclassification of Aeromonas sharmana to a new genus as Pseudaeromonas sharmana gen. nov., comb. nov., and description of Pseudaeromonas pectinilytica sp. nov. isolated from a freshwater stream.

A Gram-reaction-negative, rod-shaped, facultatively anaerobic, motile bacterium, designated strain AR1T, was isolated from a freshwater stream in Jeonju, South Korea. Strain AR1T showed highest 16S rRNA gene sequence similarity (96.83 %) and also formed a separate clade with Aeromonas sharmana GPTSA-6T in the phylogenetic tree reconstructed among the members of the family Aeromonadaceae. Major cellular fatty acids are summed feature 3 (C16 : 1ω7c/C16 : 1ω6c) and C16: 0. Diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol are the predominant polar lipids. The genomic DNA G+C content was found to be 54.7 mol%. However, earlier studies on 16S rRNA gene, gyrB, rpoD and universal target region of cpn60 sequences of the members of the genus Aeromonas recommended the transfer of Aeromonas sharmana to a new genus. Hence, based on the comparative polyphasic data obtained during the present study and also on the previous recommendations, it is proposed that Aeromonas sharmana be transferred to a novel genus as Pseudaeromonas sharmana gen. nov., comb. nov. with strain GPTSA-6T (=DSM 17445T=MTCC 7090T=CIP 109378T=CCUG 54939T) as the type strain of the type species of the genus. Also, it is proposed that strain AR1T be designated as a representative of a novel species of this new genus, namely Pseudaeromonas pectinilytica sp. nov. The type strain is AR1T (=KCTC 42754T=JCM 31503T).

Oceanisphaera aquimarina sp. nov., Isolated from Oil-Contaminated Sediment of Ocean Coastal Area from South Korea.

Strain S33(T) was isolated from oil-contaminated sediment of Tae-an coastal region of South Korea. Cells are aerobic, motile, Gram staining-negative, and coccoid shaped. Strain S33(T) grew optimally at the temperature of 25 °C (range of 4-40 °C), pH 6.0 (range of pH 6.0-10.0), and in the presence of 1 % (w/v) NaCl (range of 0-10 %). Ubiquinone-8 was the predominant respiratory quinone. C16:0, summed feature 3 (comprising C16:1ω7c/C16:1ω6c) and C18:1ω7c were the major fatty acids. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, and diphosphatidylglycerol. Strain S33(T) showed the ability to degrade benzene, toluene, and ethylbenzene after 3 days incubation. 16S rRNA gene sequence analysis showed that the strain S33(T) was most closely related to Oceanisphaera sediminis TW92(T) (97.3 %), Oceanisphaera profunda SM1222(T) (97.2 %), and Oceanisphaera ostreae T-w6(T) (97.1 %) and <97 % with other members of the genus Oceanisphaera. The genomic DNA G+C mol% content of strain S33(T) was 51.0 mol%. Based on distinct phenotypic, genotypic, and phylogenetic analysis, strain S33(T) was proposed to represent a novel species in the genus Oceanisphaera as Oceanisphaera aquimarina sp. nov. (= KEMB 1002-058(T) = JCM 30 794(T)).

A novel heterotrophic nitrifying and aerobic denitrifying bacterium, Zobellella taiwanensis DN-7, can remove high-strength ammonium.

A novel heterotrophic bacterium capable of heterotrophic nitrification and aerobic denitrification was isolated from ammonium contaminated landfill leachate and physiochemical and phylogenetically identified as Zobellella taiwanensis DN-7. DN-7 converted nitrate, nitrate, and ammonium to N2 as the primary end product. Single factor experiments suggested that the optimal conditions for ammonium removal were trisodium citrate as carbon source, C/N ratio 8, pH 8.0-10.0, salinity less than 3 %, temperature 30 °C, and rotation speed more than 150 rpm. Specifically, DN-7 could remove 1000.0 and 2000.0 mg/L NH4 (+)-N completely within 96 and 216 h, with maximum removal rates of 19.6 and 17.3 mg L(-1) h(-1), respectively. These results demonstrated that DN-7 is a promising candidate for application of high-strength ammonium wastewater treatments.

Oceanisphaera psychrotolerans sp. nov., isolated from coastal sediment samples.

A novel aerobic, Gram-staining-negative bacterium, designated strain LAM-WHM-ZC(T), was isolated from coastal sediment samples from the Bohai Sea, near Yantai, China. Cells of LAM-WHM-ZC(T) were non-motile, short-rod- or coccoid-shaped. The temperature and pH ranges for growth were 4-40 °C (optimum: 20-33 °C) and pH 5-9 (optimum: pH 7.5). The strain did not require NaCl for growth but tolerated up to 10% NaCl (w/v). The major fatty acids of strain LAM-WHM-ZC(T) were summed feature 3, C12 : 0, C16 : 0, summed feature 2 and summed feature 8. The predominant respiratory quinone was ubiquinone Q-8. The main polar lipids were diphosphatidyglycerol, phosphatigylethanolamine, phosphatidyglycerol, one phospholipid and four unidentified glycolipids. The DNA G+C content was 59.3 mol% as determined by the melting temperature (Tm) method. Analysis of the 16S rRNA gene sequence indicated that the isolate represented a member of the genus Oceanisphaera and was closely related to Oceanisphaera arctica KCTC 23013(T), Oceanisphaera litoralis DSM 15406(T), Oceanisphaera sediminis KACC 15117(T) and Oceanisphaera donghaensis KCTC 12522(T) with 97.7%, 97.1%, 96.6% and 96.6% sequence similarity, respectively. The DNA-DNA hybridization values between strain LAM-WHM-ZC(T) and the four reference strains were 47.4 ± 2.8%, 33.5 ± 2.2%, 28.4 ± 1.8% and 13.7 ± 0.8%, respectively. Based on its phenotypic and genotypic properties, strain LAM-WHM-ZC(T) is suggested to represent a novel species of the genus Oceanisphaera, for which the name Oceanisphaera psychrotolerans sp. nov. is proposed. The type strain is LAM-WHM-ZC(T) ( = ACCC 06516(T) = JCM 30466(T)).

Oceanisphaera profunda sp. nov., a marine bacterium isolated from deep-sea sediment, and emended description of the genus Oceanisphaera.

A Gram-stain-negative, aerobic, oxidase- and catalase-positive, flagellated, rod-shaped bacterial strain, designated SM1222(T), was isolated from the deep-sea sediment of the South China Sea. The strain grew at 4-35 °C and with 0.5-8 % NaCl (w/v). Phylogenetic analysis based on the 16S rRNA gene sequences revealed that strain SM1222(T) was affiliated with the genus Oceanisphaera in the class Gammaproteobacteria. It shared the highest sequence similarity with the type strain of Oceanisphaera ostreae (96.8 %) and 95.4-96.6 % sequence similarities with type strains of other species of the genus Oceanisphaera with validly published names. Strain SM1222(T) contained summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH), C18 : 1ω7c, C16 : 0, C12 : 0 and summed feature 2 (C14 : 0 3-OH and/or iso-C16 : 1 I) as the major fatty acids and ubiquinone Q-8 as the predominant respiratory quinone. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The genomic DNA G+C content of strain SM1222(T) was 51.5 mol%. On the basis of the evidence presented in this study, strain SM1222(T) represents a novel species of the genus Oceanisphaera, for which the name Oceanisphaera profunda sp. nov. is proposed. The type strain of Oceanisphaera profunda is SM1222(T) ( = CCTCC AB 2013241(T) = KCTC 32510(T)). An emended description of the genus Oceanisphaera Romanenko et al. 2003 emend. Choi et al. 2011 is also proposed.

Discrepancies in identification of Vibrio cholerae strains as members of Aeromonadaceae and Enterobacteriaceae by automated microbial identification system.

AIMS: Incidental observation of a discrepancy in identification of Vibrio cholerae prompted a study to understand the ability of an automated microbial identification system to identify this important pathogen. METHODS AND RESULTS: Twenty clinical isolates of V. cholerae showing difference in genetic profiles by random amplified polymorphic DNA (RAPD) fingerprinting, serologically confirmed as O1, and showing presence of ctxA and tcpA genes in PCR were subjected to analysis by Vitek 2 Compact automated identification system for identification. Vitek 2 Compact detected 10 of 20 isolates correctly, whereas the remaining 10 were identified as various members of Aeromonadaceae and Enterobacteriaceae. CONCLUSIONS: Our results indicate that Vitek 2 Compact automated microbial system does not always identify V. cholerae strains correctly. SIGNIFICANCE AND IMPACT OF STUDY: These observations should create awareness among end users about possible misidentifications by automated systems and encourage simultaneous use of serology and/or PCR for correct identification at least for V. cholerae, which is one of the most important enteric pathogens.

Complete genome sequence of Oceanimonas sp. GK1, a halotolerant bacterium from Gavkhouni Wetland in Iran.

Oceanimonas sp. GK1 (IBRC-M 10197) is a marine halotolerant gammaproteobacterium which was characterized as producing large amounts of poly-ß-hydroxybutyrate. Here we present the whole-genome sequence of Oceanimonas sp. GK1, which consists of a single circular chromosome of 3,514,537 bp and two plasmids 8,462 and 4,245 bp in length.

Oceanisphaera arctica sp. nov., isolated from Arctic marine sediment, and emended description of the genus Oceanisphaera.

A novel Gram-staining-negative, coccoid, non-motile bacterium, designated strain V1-41(T), was isolated from a sample of marine sediment collected, at a depth of 200 m, from Kongsfjorden (an inlet on the west coast of Spitsbergen, an island that forms part of the Svalbard archipelago in the Arctic Ocean). The strain formed cream-brown colonies on marine agar. Cells of the novel strain were positive in tests for catalase, oxidase, lysine decarboxylase and ornithine decarboxylase activities but negative for gelatinase and lipase activities. They hydrolysed aesculin, starch and urea, but not casein or DNA. Most of the cellular fatty acids were medium-chain and saturated (37.1%) or long-chain and unsaturated (27.8%), with C(12:0) (37.1%), C(18:1)ω7c, and summed features 2 (19.3%) and 3 (24.1%) predominating. The major respiratory quinone was Q-8. The polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, two unidentified aminophospholipids, four unidentified phospholipids and one other unidentified lipid. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the novel strain's closest known relatives were Oceanisphaera litoralis DSM 15406(T) (98.5% sequence similarity) and Oceanisphaera donghaensis BL1(T) (98.3%). In DNA-DNA hybridizations, however, the levels of relatedness between strain V1-41(T) and O. litoralis DSM 15406(T) and between the novel strain and O. donghaensis DSM 17589(T) were found to be only 19% and 29%, respectively. Based on these low levels of similarity at the DNA-DNA level and the phenotypic and chemotaxonomic differences from O. litoralis DSM 15406(T) and O. donghaensis DSM 17589(T), strain V1-41(T) represents a novel species of the genus Oceanisphaera for which the name Oceanisphaera arctica sp. nov. is proposed. The type strain is V1-41(T) ( = CCUG 58690(T) = KCTC 23013(T) = NBRC 106171(T)).

Oceanisphaera sediminis sp. nov., isolated from marine sediment.

Two strains, designated TW92(T) and TW93, were isolated from marine sediment collected from the south coast of Korea. Cells of both strains were Gram-staining-negative, coccus-shaped, aerobic, motile and catalase- and oxidase-positive. Strain TW92(T) grew optimally in the presence of 2 % (w/v) NaCl (range 1-5%) while strain TW93 grew optimally in the presence of 1% (w/v) NaCl (range 0-12%), and both strains had an optimal growth temperature of 30 °C (range 4-37 °C). Strains TW92(T) and TW93 had the same optimum pH (pH 7), but differed in their ability to grow at pH 10. Phylogenetic analysis based on 16S rRNA gene sequence similarity showed that strains TW92(T) and TW93 were most closely related to Oceanisphaera donghaensis BL1(T), with 98.8% and 98.7% similarity, respectively. Pairwise similarity between the 16S rRNA gene sequences of strains TW92(T) and TW93 was 99.9%. The major fatty acids of both strains were summed features 3 (comprising C(16:1)ω7c/iso-C(15) 2-OH), C(16:0) and C(18:1)ω7c. Both strains possessed the ubiquinone Q-8 as the predominant respiratory quinone and phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol as the polar lipids. The genomic DNA G+C contents of strains TW92(T) and TW93 were 58.5 and 59.6 mol%, respectively. Genomic relatedness values based on DNA-DNA hybridization of strains TW92(T) and TW93 with related species were below 47% and 31%, respectively. DNA-DNA hybridization values between strains TW92(T) and TW93 were above 85%. On the basis of a taxonomic study using polyphasic analysis, it is proposed that the two isolates represent a novel species, Oceanisphaera sediminis sp. nov., with strain TW92(T) (=KACC 15117(T)=JCM 17329(T)) as the type strain and strain TW93 (=KACC 15118=JCM 17330) as an additional strain.