Showing papers by "Masayuki Miyazaki published in 2013"

Methylomarinum vadi gen. nov., sp. nov., a methanotroph isolated from two distinct marine environments.

Abstract: Two aerobic methane-oxidizing bacterial strains were isolated from distinct marine environments in Japan Strains IT-4T and T2-1 were Gram-stain-negative, aerobic, motile, plump short rods or oval-shaped bacteria with a single polar flagellum and type I intracytoplasmic membranes They were obligate methanotrophs that grew only on methane or methanol Each strain possessed the particulate methane monooxygenase (pMMO) The ribulose monophosphate pathway was operative for carbon assimilation The strains grew best at 37 °C, and did not grow at 45 °C NaCl was required for growth within a concentration range of 1–8 % (w/v) The major phospholipid fatty acids were C16 : 0, C16 : 1ω7c, and C16 : 1ω5t The major isoprenoid quinone was MQ-8 The DNA G+C content was 509–517 mol% The 16S rRNA gene sequences of the strains showed 994 % similarity to each other, and DNA–DNA hybridization analysis indicated that the strains were representatives of the same species The 16S rRNA gene sequences were highly similar to some marine environmental sequences (940–977 % similarity), but did not show similarities more than 94 % with sequences of members of other related genera, such as Methylomicrobium , Methylobacter , Methylomonas and Methylosarcina Phylogenies based on 16S rRNA gene sequences and deduced partial PmoA sequences, and the physiological and chemotaxonomic characteristics revealed that strains IT-4T and T2-1 represent a novel species of a new genus in the family Methylococcaceae , for which the name Methylomarinum vadi gen nov, sp nov is proposed The type strain is IT-4T ( = JCM 13665T = DSM 18976T)

Surugamides A–E, Cyclic Octapeptides with Four d-Amino Acid Residues, from a Marine Streptomyces sp.: LC–MS-Aided Inspection of Partial Hydrolysates for the Distinction of d- and l-Amino Acid Residues in the Sequence

Abstract: Surugamides A–E (1–5), cyclic octapeptides with four d-amino acid residues, were isolated from the broth of marine-derived Streptomyces sp. Their planar structures were determined by analyses of spectroscopic data, and the absolute configuration of constituent amino acid residues was determined by the Marfey’s method. Differentiation of d-Ile and l-Ile in the sequence was established by chiral analysis of fragment peptides obtained from the partial hydrolysate, whose identification was conducted by LC–MS/MS.

Isolation and Characterization of a Thermophilic, Obligately Anaerobic and Heterotrophic Marine Chloroflexi Bacterium from a Chloroflexi-dominated Microbial Community Associated with a Japanese Shallow Hydrothermal System, and Proposal for Thermomarinilinea lacunofontalis gen. nov., sp. nov.

Abstract: A novel marine thermophilic and heterotrophic Anaerolineae bacterium in the phylum Chloroflexi, strain SW7 T , was isolated from an in situ colonization system deployed in the main hydrothermal vent of the Taketomi submarine hot spring field located on the southern part of Yaeyama Archipelago, Japan. The microbial community associated with the hydrothermal vent was predominated by thermophilic heterotrophs such as Thermococcaceae and Anaerolineae, and the next dominant population was thermophilic sulfur oxidizers. Both aerobic and anaerobic hydrogenotrophs including methanogens were detected as minor populations. During the culture-dependent viable count analysis in this study, an Anaerolineae strain SW7 T was isolated from an enrichment culture at a high dilution rate. Strain SW7 T was an obligately anaerobic heterotroph that grew with fermentation and had non-motile thin rods 3.5–16.5 µm in length and 0.2 µm in width constituting multicellular filaments. Growth was observed between 37–65°C (optimum 60°C), pH 5.5–7.3 (optimum pH 6.0), and 0.5–3.5% (w/v) NaCl concentration (optimum 1.0%). Based on the physiological and phylogenetic features of a new isolate, we propose a new species representing a novel genus Thermomarinilinea: the type strain of Thermomarinilinea lacunofontalis sp. nov., is SW7 T (=JCM15506 T =KCTC5908 T ).

Sunxiuqinia faeciviva sp. nov., a facultatively anaerobic organoheterotroph of the Bacteroidetes isolated from deep subseafloor sediment.

Abstract: A facultatively anaerobic organoheterotroph, designated JAM-BA0302T, was isolated from a deep subseafloor sediment at a depth of 247.1 m below the seafloor off the Shimokita Peninsula of Japan in the north-western Pacific Ocean (Site C9001 , water depth 1180 m). Cells of strain JAM-BA0302T showed gliding motility and were thin, long rods with peritrichous fimbriae-like structures. Growth occurred at 4–37 °C (optimum 30 °C; doubling time 8 h), at pH 5.4–8.3 (optimum pH 7.5) and with 5–60 g NaCl l−1 (optimum 20–25 g l−1). The isolate utilized proteinaceous substrates such as yeast extract, tryptone, casein and Casamino acids with O2 respiration or fermentation. Strain JAM-BA0302T was a piezotolerant bacterium that could grow at pressures as high as 25 MPa under aerobic conditions and 10 MPa under anaerobic conditions. The G+C content of the genomic DNA was 43.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain JAM-BA0302T was most closely related to yet-undescribed strains recently isolated from various marine sedimentary environments (>99.6 % 16S rRNA gene sequence similarity) and was moderately related to Sunxiuqinia elliptica DQHS-4T, isolated from a sea cucumber farm sediment (95.5 % 16S rRNA gene sequence similarity) within the Bacteroidetes . The phylogenetic analysis suggested that the isolate should belong to the genus Sunxiuqinia . However, low DNA–DNA relatedness (<11 %) and many physiological and molecular properties differentiated the isolate from those previously described. We propose here a novel species of the genus Sunxiuqinia , with the name Sunxiuqinia faeciviva sp. nov. The type strain is JAM-BA0302T ( = JCM 15547T = NCIMB 14481T).

Synthesis of poly- and oligo(hydroxyalkanoate)s by deep-sea bacteria, Colwellia spp., Moritella spp., and Shewanella spp

Abstract: This is the first report on synthesis of poly(hydroxyalkanoate)s (PHAs) by various deep-sea bacteria (4 types of Colwellia spp., 11 types of Moritella spp., and 18 types of Shewanella spp.) from glucose, fructose, gluconate, or from one of the several plant oils as the sole source of carbon. The overall results provide important and basic information regarding the production of PHAs by deep-sea bacteria and on the diversity of PHA synthase enzymes in nature.

Loktanella cinnabarina sp. nov., isolated from a deep subseafloor sediment, and emended description of the genus Loktanella.

Abstract: A Gram-stain-negative, aerobic, heterotrophic and salt-tolerant bacterium, designated strain LL-001T, was isolated from a deep subseafloor sediment in Japanese waters. Cells were non-motile rods and colonies were smooth, convex, circular and vermilion. The conditions for growth were 15–35 °C, pH 5.5–7.5 and 1–8 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences confirmed that strain LL-001T belonged to the genus Loktanella within the family Rhodobacteraceae of the class Alphaproteobacteria . 16S rRNA gene sequence similarity between strain LL-001T and members of the genus Loktanella was 94.5–98.5 %; the highest sequence similarity was with Loktanella hongkongensis UST950701-009PT. DNA–DNA relatedness between strain LL-001T and L. hongkongensis UST950701-009PT was 41.5–43.6 %. The DNA G+C content of strain LL-001T was 69.3 mol%. On the basis of biochemical features and 16S rRNA gene sequence comparison, strain LL-001T is considered to represent a novel species of the genus Loktanella , for which the name Loktanella cinnabarina sp. nov. is proposed. The type strain is LL-001T ( = JCM 18161T = CECT 8072T). The description of the genus Loktanella is also emended.

Salinisphaera japonica sp. nov., a moderately halophilic bacterium isolated from the surface of a deep-sea fish, Malacocottus gibber, and emended description of the genus Salinisphaera

Abstract: A moderately halophilic, slightly acidophilic, aerobic bacterium, designated strain YTM-1(T), was isolated from the body surface of Malacocottus gibber. Cells were Gram-stain-negative, short rods or cocci, approximately 0.9-1.1 µm long and 1.0-1.8 µm wide. Strain YTM-1(T) was able to grow with 1-30% NaCl (optimum, 7.5-10%, w/v), at 4-30 °C (optimum, 20-25 °C) and at pH 3.8-9.5 (optimum, pH 5.0-5.5). Phylogenetic analysis based on 16S rRNA gene sequence similarities showed that strain YTM-1(T) belonged to the genus Salinisphaera with low similarity values to the type strains of recognized species of this genus (<94.8-94.4%). The polar lipids of strain YTM-1(T) consisted of diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylserine, three unknown phospholipids and one unknown lipid. The predominant isoprenoid quinone was Q-8. The major fatty acids were C19:0ω8c cyclo, C18:1ω7c, C16:1ω5c and C16:0. The DNA G+C content of strain YTM-1(T) was 67.3 mol%. These phylogenetic, physiological and chemotaxonomic data indicated that strain YTM-1(T) represents a novel species of the genus Salinisphaera, for which the name Salinisphaera japonica sp. nov. is proposed. The type strain is YTM-1(T) (=JCM 18087(T)=CECT 8012(T)). An emended description of the genus Salinisphaera is also proposed.