Polynyas, areas of open water surrounded by sea ice, are sites of intense primary production and ecological hotspots in the Antarctic Ocean. This study determined the spatial variation in communities of prokaryotes in a polynya in the Amundsen Sea using 454 pyrosequencing technology, and the results were compared with biotic and abiotic environmental factors. The bacterial abundance was correlated with that of phytoplankton, Phaeocystis spp. and diatoms. A cluster analysis indicated that the bacterial communities in the surface waters of the polynya were distinct from those under the sea ice. Overall, two bacterial clades, Polaribacter (20-64%) and uncultivated Oceanospirillaceae (7-34%), dominated the surface water in the polynya while the Pelagibacter clade was abundant at all depths (7-42%). The archaeal communities were not as diverse as the bacterial communities in the polynya, and marine group I was dominant (> 80%). Canonical correspondence analysis indicated that the oceanographic properties facilitated the development of distinct prokaryotic assemblages in the polynya. This analysis of the diversity and composition of the psychrophilic prokaryotes associated with high phytoplankton production provides new insights into the roles of prokaryotes in biogeochemical cycles in high-latitude polynyas.

This study evaluated the effects of culture conditions, including carbon and nitrogen sources, L-monosodium glutamate (MSG), and initial pH, on gamma-aminobutyric acid (GABA) production by HYE1 isolated from kimchi, a Korean traditional fermented food. HYE1 was screened by the production analysis of GABA and genetic analysis of the glutamate decarboxylase gene, resulting in 14.64 mM GABA after 48 h of cultivation in MRS medium containing 1% (w/v) MSG. In order to increase GABA production by HYE1, the effects of carbon and nitrogen sources on GABA production were preliminarily investigated via one-factor-at-a-time optimization strategy. As the results, 2% maltose and 3% tryptone were determined to produce 17.93 mM GABA in modified MRS medium with 1% (w/v) MSG. In addition, the optimal MSG concentration and initial pH were determined to be 1% and 5.0, respectively, resulting in production of 18.97 mM GABA. Thereafter, response surface methodology (RSM) was applied to determine the optimal conditions of the above four factors. The results indicate that pH was the most significant factor for GABA production. The optimal culture conditions for maximum GABA production were also determined to be 2.14% (w/v) maltose, 4.01% (w/v) tryptone, 2.38% (w/v) MSG, and an initial pH of 4.74. In these conditions, GABA production by HYE1 was predicted to be 21.44 mM using the RSM model. The experiment was performed under these optimized conditions, resulting in GABA production of 18.76 mM. These results show that the predicted and experimental values of GABA production are in good agreement.

DNA stable isotope probing and metagenomic sequencing were used to assess the metabolic potential of iron-reducing bacteria involved in anaerobic aromatic hydrocarbon degradation in oil spill-affected tidal flats. In a microcosm experiment, (13) C-toluene was degraded with the simultaneous reduction of Fe(III)-NTA, which was also verified by quasi-stoichiometric (13) C-CO2 release. The metabolic potential of the dominant member affiliated with the genus Desulfuromonas in the heavy DNA fraction was inferred using assembled scaffolds (designated TF genome, 4.40 Mbp with 58.8 GC mol%), which were obtained by Illumina sequencing. The gene clusters with peripheral pathways for toluene and benzoate conversion possessed the features of strict and facultative anaerobes. In addition to the class II-type benzoyl-CoA reductase (Bam) of strict anaerobes, the class I-type (Bcr) of facultative anaerobes was encoded. Genes related to the utilization of various anaerobic electron acceptors, including iron, nitrate (to ammonia), sulfur and fumarate, were identified. Furthermore, genes encoding terminal oxidases (caa3 , cbb3 and bd) and a diverse array of genes for oxidative stress responses were detected in the TF genome. This metabolic versatility may be an adaptation to the fluctuating availability of electron acceptors and donors in tidal flats.

A putative gene (gadlbhye1) encoding glutamate decarboxylase (GAD) was cloned from Lactobacillus brevis HYE1 isolated from kimchi, a traditional Korean fermented vegetable. The amino acid sequences of GADLbHYE1 showed 48% homology with the GadA family and 99% identity with the GadB family from L. brevis. The cloned GADLbHYE1 was functionally expressed in Escherichia coli using inducible expression vectors. The expressed recombinant GADLbHYE1 was successfully purified by Ni-NTA affinity chromatography, and had a molecular mass of 54 kDa with optimal hydrolysis activity at 55 °C and pH 4.0. Its thermal stability was determined to be higher than that of other GADs from L. brevis, based on its melting temperature (75.18 °C). Kinetic parameters including K and V values for GADLbHYE1 were 4.99 mmol/L and 0.224 mmol/L/min, respectively. In addition, the production of gamma-aminobutyric acid in E. coli BL21 harboring gadlbhye1/pET28a was increased by adding pyridoxine as a cheaper coenzyme.

b Ammonia-oxidizing archaea (AOA) typically predominate over ammonia-oxidizing bacteria in marine sediments. We herein present the draft genome sequence of an ammonia-oxidizing archaeon, "Candidatus Nitrosopumilus sediminis" AR2, which was enriched in culture from a marine sediment obtained off Svalbard, within the Arctic Circle. The typical genes involved in archaeal ammonia oxidation and carbon fixation necessary for chemolithoautotrophic growth were observed. Interestingly, the AR2 genome sequence was revealed to possess, uniquely among cultivated AOA from marine environments, a capability for urea utilization.

A novel mesophilic, methylotrophic, methanogenic archaeon, designated strain EK1(T), was enriched and isolated from wetland sediment. Phylogenetic analysis showed that strain EK1(T) was affiliated with the genus Methanomethylovorans within the family Methanosarcinaceae, and shared the highest 16S rRNA and methyl-coenzyme M reductase alpha-subunit gene sequence similarity with the type strain of Methanomethylovorans hollandica (98.8 and 92.6 %, respectively). The cells of strain EK1(T) were observed to be Gram-negative, non-motile and irregular cocci that did not lyse in 0.1 % (w/v) sodium dodecyl sulfate. Methanol, mono-, di- and trimethylamine, dimethyl sulfide and methanethiol were found to be used as catabolic and methanogenic substrates, whereas H2/CO2, formate, 2-propanol and acetate were not. Growth was observed at 25-40 °C (optimum, 37 °C), at pH 5.5-7.5 (optimum, pH 6.0-6.5) and in the presence of 0-0.1 M NaCl (optimum, 0 M). Growth and methane production rates were stimulated in the presence of H2/CO2 although methane production and growth yields were not significantly affected; acetate, formate, 2-propanol and CO/CO2/N2 did not affect methane production. CoCl2 (0.6-2.0 μM) and FeCl2 (25 mg/l) stimulated growth, while yeast extract and peptone did not. The DNA-DNA hybridization experiment revealed a relatedness of <20 % between EK1(T) and the type strains of the genus Methanomethylovorans. The DNA G+C content of strain EK1(T) was determined to be 39.2 mol%. Based on the polyphasic taxonomic study, strain EK1(T) represents a novel species belonging to the genus Methanomethylovorans, for which the name Methanomethylovorans uponensis sp. nov. is proposed. The type strain is strain EK1(T)(=NBRC 109636(T) = KCTC 4119(T) = JCM 19217(T)).

A Gram-reaction-negative, non-motile, aerobic bacterium, designated HJ50T , was isolated from deep seawater of the East Sea, South Korea. Cells were ovoid to rod-shaped (0.5-0.8¾1.3-3.0 mm), often with unequal ends, suggesting a budding mode of reproduction. The strain had an absolute requirement for sea salts and tolerated up to 20 % (w/v) sea salts. T and the type strains of Roseovarius species were grown on MA at 30 u C for 3 days.Morphology and cell size were determined by phasecontrast microscopy (Nikon 80i). Gram staining was performed with BD Gram stain kits according to the instructions of the manufacturer and by the non-staining method as described by Buck (1982). Flagellation was examined by transmission electron microscopy using cells grown on MA at 30 u C. A Formvar-coated grid was floated on a droplet of sample on Parafilm for 1 min to permit adsorption of the specimen. The grid was then transferred onto a drop of negative stain (1 % phosphotungstic acid) for 30 s, blotted with filter paper and then air-dried. The

Alluvial aquifers are one of the mainwater resources in many countries. Iron reduction in alluvial aquifers is often a major anaerobic process involved in bioremediation or causing problems, including the release of As trapped in Fe(III) oxide. We investigated the distribution of potential iron-reducing bacteria (IRB) in riverine alluvial aquifers (B1, B3, and B6 sites) at the Mankyeong River, Republic of Korea. Inactive iron reduction zones, the diversity and abundance of IRB can be examined using a clone library and quantitative PCR analysis of 16S rRNA genes. Geobacter spp. are potential IRB in the iron-reducing zone at the B6 (9 m) site, where high Fe(II) and arsenic (As) concentrations were observed. At the B3 (16 m) site, where low iron reduction activity was predicted, a dominant clone (10.6%) was 99% identical in 16S rRNA gene sequence with Rhodoferax ferrireducens. Although a major clone belonging to Clostridium spp. was found, possible IRB candidates could not be unambiguously determined at the B1 (18 m) site. Acanonical correspondence analysis demonstrated that, among potential IRB, only the Geobacteraceae were well correlated with Fe(II) and As concentrations. Our results indicate high environmental heterogeneity, and thus high spatial variability, in thedistribution of potential IRB in the riverine alluvial aquifersnear the Mankyeong River.