Zeaxanthinibacter aestuarii sp. nov., isolated from estuary sediment and emended description of the genus Zeaxanthinibacter Asker et al. 2007.

A Gram-staining-negative, strictly aerobic and yellow-pigmented bacterium, designated strain S2-22T, was isolated from estuary sediment in South Korea. Cells of strain S2-22T were oxidase- and catalase-positive rods without gliding motility. Growth was observed at 15-43 °C (optimum, 35-37 °C), at pH 5.5-9.0 (optimum, pH 6.5-7.5) and in the presence of 0.0-10.0 % (w/v) NaCl (optimum, 2.0 %). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain S2-22T formed a tight phyletic lineage with Zeaxanthinibacter enoshimensis TD-ZE3T with a high bootstrap value and their 16S rRNA gene sequence similarity was 94.6 %. The respiratory quinone detected was menaquinone 6 (MK-6) only and iso-C15 : 0, iso-C17 : 0 3-OH, summed feature 3 (comprising C16 : 1ω7c/C16 : 1ω6c) and iso-C15 : 1G were the major fatty acids. Phosphatidylethanolamine was identified as the major polar lipid and five unidentified aminolipids, two unidentified phospholipids and three unidentified lipids were also detected as minor polar lipids. The G+C content of the genomic DNA was 45.5 mol%. Based on the phenotypic, chemotaxonomic and molecular features, strain S2-22T clearly represents a novel species of the genus Zeaxanthinibacter, for which the name Zeaxanthinibacter aestuarii sp. nov. is proposed. The type strain is S2-22T (=KACC 18503T=JCM 31155T). An emended description of the genus Zeaxanthinibacter is also proposed.

Complete genome sequence of Sphingorhabdus sp. M41, a versatile hydrocarbon degrader, isolated from crude oil-contaminated costal sediment.

Sphingorhabdus sp. M41, capable of degrading aliphatic and aromatic hydrocarbons, was isolated from crude oil-contaminated costal sediment by an enrichment culture and its complete genome was sequenced. The genome of strain M41 has a chromosome with a size of 3,324,420bp, including 44 tRNAs, 6 rRNAs, and 3118 protein-coding genes. In addition, many potential genes responsible for the biodegradation of aliphatic and aromatic hydrocarbons were identified from the genome. This is the first complete genome of the genus Sphingorhabdus, which will provide insights into the bioremediation of crude oil-contaminated costal sediment by strain M41.

Complete genome of Zhongshania aliphaticivorans SM-2(T), an aliphatic hydrocarbon-degrading bacterium isolated from tidal flat sediment.

Zhongshania aliphaticivorans SM-2(T), a degrader of aliphatic hydrocarbons, is a Gram-negative, rod-shaped, flagellated, facultatively aerobic bacterium. Here, we report the genome sequence of strain SM-2(T), which has a size of 4,204,359bp with 44 tRNAs, 9 rRNAs, and 3664 protein-coding genes. In addition, several genes encoding aliphatic hydrocarbon degraders (alkane 1-monooxygenase, haloalkane dehalogenase, and cytochrome P450) were detected in the genome shedding light on the function of pollutants degradation.

Maribacter lutimaris sp. nov., isolated from marine sediment.

A Gram-staining-negative, moderately halophilic and strictly aerobic bacterium, designated strain KJ4T, was isolated from marine sediment at Gangjin in South Korea. Cells were catalase- and oxidase-positive long rods with gliding motility. Growth of strain KJ4T was observed at 4-37 °C (optimum, 15-25 °C), at pH 6.0-9.0 (optimum, pH 7.0-8.5) and in the presence of 1.0-7.0% (w/v) NaCl (optimum, 2.0-5.0%). Menaquinone 6 (MK-6) was the only isoprenoid quinone detected and iso-C15:0, iso-C17:0 3-OH, iso-C15:1 G and summed feature 3 (comprising C16:1ω7c and/or C16:1ω6c) were the major cellular fatty acids. The polar lipids of strain KJ4T consisted of phosphatidylethanolamine, an unidentified aminophospholipid and five unidentified lipids. The G+C content of the genomic DNA was 38.0 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain KJ4T formed a distinct phylogenetic lineage within the genus Maribacter. Strain KJ4T was most closely related to Maribacter orientalis KMM 3947T with 97.4% 16S rRNA gene sequence similarity. On the basis of phenotypic, chemotaxonomic and molecular features, strain KJ4T clearly represents a novel species of the genus Maribacter, for which the name Maribacter lutimaris sp. nov. is proposed. The type strain is KJ4T (=KACC 16438T=JCM 31154T).

Genome-wide transcriptional responses of Alteromonas naphthalenivorans SN2 to contaminated seawater and marine tidal flat sediment.

A genome-wide transcriptional analysis of Alteromonas naphthalenivorans SN2 was performed to investigate its ecophysiological behavior in contaminated tidal flats and seawater. The experimental design mimicked these habitats that either added naphthalene or pyruvate; tidal flat-naphthalene (TF-N), tidal flat-pyruvate (TF-P), seawater-naphthalene (SW-N), and seawater-pyruvate (SW-P). The transcriptional profiles clustered by habitat (TF-N/TF-P and SW-N/SW-P), rather than carbon source, suggesting that the former may exert a greater influence on genome-wide expression in strain SN2 than the latter. Metabolic mapping of cDNA reads from strain SN2 based on KEGG pathway showed that metabolic and regulatory genes associated with energy metabolism, translation, and cell motility were highly expressed in all four test conditions, probably highlighting the copiotrophic properties of strain SN2 as an opportunistic marine r-strategist. Differential gene expression analysis revealed that strain SN2 displayed specific cellular responses to environmental variables (tidal flat, seawater, naphthalene, and pyruvate) and exhibited certain ecological fitness traits -- its notable PAH degradation capability in seasonally cold tidal flat might be reflected in elevated expression of stress response and chaperone proteins, while fast growth in nitrogen-deficient and aerobic seawater probably correlated with high expression of glutamine synthetase, enzymes utilizing nitrite/nitrate, and those involved in the removal of reactive oxygen species.

Arenimonas aestuarii sp. nov., isolated from estuary sediment.

A novel species of the genus Arenimonas, represented by strain S2-21T, was isolated from an estuary of Asan in South Korea. Cells of strain S2-21T were Gram-stain-negative, aerobic, non-motile rods that were oxidase- and catalase-positive. Growth of strain S2-21T was observed at 15-40 °C (optimum, 25-30 °C), at pH 7.0-8.0 (optimum, pH 7.0) and in the presence of 0-2.0 % (w/v) NaCl (optimum, 0 %). The major cellular fatty acids were iso-C15 : 0, C11 : 0 3-OH, iso-C16 : 0, summed feature 9 (comprising iso-C17 : 1ω9c and/or C16 : 0 10-methyl), anteiso-C17 : 0 and iso-C11 : 0. The only respiratory quinone detected was ubiquinone-8 (Q-8) and the major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylmethylethanol and two unknown phospholipids. The G+C content of the genomic DNA was 62.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain S2-21T formed a tight phyletic lineage with Arenimonas donghaensis HO3-R19T within the genus Arenimonas. Strain S2-21T was related most closely to A. donghaensis HO3-R19T at 98.1 % 16S rRNA gene sequence similarity and the mean DNA-DNA relatedness value between strain S2-21T and the type strain of A. donghaensis was 23.6 ± 2.2 %. On the basis of phenotypic, chemotaxonomic and molecular features, strain S2-21T is considered to represent a novel species of the genus Arenimonas, for which the name Arenimonas aestuarii sp. nov. is proposed. The type strain is S2-21T ( = KACC 18504T = JCM 31129T).

Confluentimicrobium naphthalenivorans sp. nov., a naphthalene-degrading bacterium isolated from sea-tidal-flat sediment, and emended description of the genus Confluentimicrobium Park et al. 2015.

A Gram-staining-negative, aerobic and moderately halophilic bacterium, designated strain NS6T, was isolated from sea-tidal-flat sediment of the South Sea in Korea. Cells were motile rods with a single flagellum showing positive catalase and oxidase activities. Strain NS6T grew at 15-40 °C (optimum, 30 °C), at pH 6.0-9.0 (optimum, pH 7.0-7.5) and in the presence of 1-5 % (w/v) NaCl (optimum, 2 %). Ubiquinone-10 was identified as the only isoprenoid quinone and summed feature 8 (comprising C18 : 1ω7c/ω6c), C19 : 0 cyclo ω8c, C16 : 0 and C10 : 0 3-OH were the major fatty acids. Strain NS6T contained phosphatidylglycerol, sulfoquinovosyldiacylglycerol, an unidentified amino lipid and an unidentified lipid as the major polar lipids. An unidentified phospholipid and three unidentified lipids were also detected as the minor polar lipids. The G+C content of the genomic DNA was 64.5 mol%. Strain NS6T was most closely related to Confluentimicrobium lipolyticum SSK1-4T with a 96.8 % 16S rRNA gene sequence similarity, and the phylogenetic analysis based on 16S rRNA gene sequences showed that strain NS6T formed a tight phylogenetic lineage with C. lipolyticum SSK1-4T. The physiological, chemotaxonomic and phylogenetic properties suggest that strain NS6T represents a novel species of the genus Confluentimicrobium, for which the name Confluentimicrobium naphthalenivorans sp. nov. is proposed. The type strain is NS6T ( = KCTC 18418T = JCM 30828T). An emended description of the genus Confluentimicrobium is also proposed.

Aliiglaciecola aliphaticivorans sp. nov., an aliphatic hydrocarbon-degrading bacterium, isolated from a sea-tidal flat and emended description of the genus Aliiglaciecola Jean et al. 2013.

A Gram-stain-negative heterotrophic bacterium, designated GSD6(T), capable of growth on aliphatic hydrocarbons as a sole carbon and energy source, was isolated from sea-tidal flat sediment of the Yellow Sea, South Korea. Cells were facultatively aerobic, catalase- and oxidase-positive, motile rods with a single polar flagellum. Growth of strain GSD6(T) was observed at 4-37 °C (optimum 30 °C), at pH 5.5-9.0 (optimum pH 6.5-7.5) and in the presence of 1-9% (w/v) NaCl (optimum 2%). Strain GSD6(T) contained ubiquinone-8 (Q-8) as the sole isoprenoid quinone and summed feature 3 (comprising C16 : 1ω7c and/or iso-C15 : 0 2-OH), C16 : 0, C18 : 1ω7c, C17  : 0 10-methyl and C17 : 1ω8c as the major fatty acids. Phosphatidylethanolamine and phosphatidylglycerol were identified as the major polar lipids. The G+C content of the genomic DNA was 44.6 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain GSD6(T) formed a phylogenetic lineage with members of the genus Aliiglaciecola . Strain GSD6(T) was most closely related to Aliiglaciecola lipolytica E3(T) with a 16S rRNA gene sequence similarity of 97.4%, but their DNA-DNA hybridization value was 39.1 ± 7.1%. On the basis of phenotypic, chemotaxonomic and molecular features, strain GSD6(T) represents a novel species of the genus Aliiglaciecola , for which the name Aliiglaciecola aliphaticivorans sp. nov. is proposed. The type strain is GSD6(T) ( =KACC 18129(T) =JCM 30133(T)). An emended description of the genus Aliiglaciecola is also proposed.

Treadmill exercise improves spatial learning ability by enhancing brain-derived neurotrophic factor expression in the attention-deficit/hyperactivity disorder rats.

Attention-deficit/hyperactivity disorder (ADHD) patients show learning difficulty and impulsiveness. Exercise is known to improve learning ability and memory function. In the present study, we investigated the duration-dependence of the effect of treadmill exercise on spatial learning ability in relation with brain-derived neurotrophic factor (BDNF) expression in ADHD rats. For this study, radial 8-arm maze test and western blot for BDNF and tyrosine kinase B (TrkB) were performed. Spontaneous hypertensive rats were used as the ADHD rats and Wistar-Kyoto rats were used as the control rats. The rats in the exercise groups were forced to run on a treadmill for 10 min, 30 min, and 60 min once a day for 28 consecutive days. ADHD rats displayed impairment of spatial learning ability, in contrast treadmill exercise ameliorated impairment of spatial learning ability. Treadmill exercise for 30 min per day showed most potent ameliorating effect on impairment of spatial learning ability. BDNF and TrkB expressions in the hippocampus were decreased in the ADHD rats, in contrast treadmill exercise enhanced BDNF and TrkB expressions. Treadmill exercise for 30 min and for 60 min per day showed enhancing effects on BDNF and TrkB expressions. Treadmill exercise alleviated deficits in the spatial learning ability through enhancing BDNF and TrkB expressions in the ADHD rats. Treadmill exercise for 30 min per day can be considered as the most effective therapeutic modality for the ADHD symptoms.