Hiroyuki Ohta

Limnobacter litoralis sp. nov., a thiosulfate-oxidizing, heterotrophic bacterium isolated from a volcanic deposit, and emended description of the genus Limnobacter.

A Gram-negative, aerobic, heterotrophic bacterium, designated KP1-19(T), was isolated from a 22-year-old volcanic deposit at a site lacking vegetation on the island of Miyake, Japan. Strain KP1-19(T) was able to use thiosulfate (optimum concentration 10 mM) as an additional energy source. 16S rRNA gene sequence analysis indicated that strain KP1-19(T) was closely related to Limnobacter thiooxidans CS-K2(T) within the class Betaproteobacteria (97.7u200a% 16S rRNA gene sequence similarity). The cellular fatty acid profile was characteristic of the genus Limnobacter: the major fatty acids (>5u200a%) were C(16u200a:u200a0), C(16u200a:u200a1)ω7c and C(18u200a:u200a1)ω7c and minor amounts of C(10u200a:u200a0) 3-OH were also found. DNA-DNA relatedness between strain KP1-19(T) and L. thiooxidans LMG 19593(T) was 18u200a%. Therefore, strain KP1-19(T) represents a novel species, for which the name Limnobacter litoralis sp. nov. is proposed. The type strain is KP1-19(T) (=LMG 24869(T) =NBRC 105857(T) =CIP 109929(T)).

Analysis of Early Bacterial Communities on Volcanic Deposits on the Island of Miyake (Miyake-jima), Japan : a 6-year Study at a Fixed Site

Microbial colonization on new terrestrial substrates represents the initiation of new soil ecosystem formation. In this study, we analyzed early bacterial communities growing on volcanic ash deposits derived from the 2000 Mount Oyama eruption on the island of Miyake (Miyake-jima), Japan. A site was established in an unvegetated area near the summit and investigated over a 6-year period from 2003 to 2009. Collected samples were acidic (pH 3.0–3.6), did not utilize any organic substrates in ECO microplate assays (Biolog), and harbored around 106 cells (g dry weight)−1 of autotrophic Fe(II) oxidizers by most-probable-number (MPN) counts. Acidithiobacillus ferrooxidans, Acidithiobacillus ferrivorans, and the Leptospirillum groups I, II and III were found to be abundant in the deposits by clone library analysis of bacterial 16S rRNA genes. The numerical dominance of Acidithiobacillus ferrooxidans was also supported by analysis of the gene coding for the large subunit of the form I ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO). Comparing the 16S rRNA gene clone libraries from samples differing in age, shifts in Fe(II)-oxidizing populations seemed to occur with deposit aging. The detection of known 16S rRNA gene sequences from Fe(III)-reducing acidophiles promoted us to propose the acidity-driven iron cycle for the early microbial ecosystem on the deposit.

Mycoavidus cysteinexigens gen. nov., sp. nov., an endohyphal bacterium isolated from a soil isolate of the fungus Mortierella elongata.

An endohyphal bacterium (strain B1-EBT) living in association with the fungus Mortierella elongata FMR23-6 I-B1 was isolated from a fungal cell homogenate and studied for its taxonomic allocation. Cells were Gram-stain-negative, rod-shaped, non-spore-forming, non-motile, and negative for oxidase and catalase. Strain B1-EBT required cysteine for growth and grew at temperatures between 4 and 35u2009°C. A comparative analysis of 16S rRNA gene sequences revealed that strain B1-EBT forms a distinct clade in the family Burkholderiaceae, encompassing a group of endosymbionts associated with several soil isolates of M. elongata. The most closely related genus is Candidatus Glomeribacter gigasporarum, an endosymbiont of the arbuscular mycorrhizal fungus Gigaspora margarita. The major cellular fatty acids of strain B1-EBT were C16u2009:u20090, summed feature 3 (C16u2009:u20091ω7c and C16u2009:u20091ω6c) and summed feature 8 (C18u2009:u20091ω7c or C18u2009:u20091ω6c). Ubiquinone Q-8 was the only quinone detected. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, an unknown aminophospholipid and two unknown aminolipids. The DNA G+C content was 49.8u200amol%. On the basis of phenotypic, chemotaxonomic, and phylogenetic characteristics, strain B1-EBT represents a novel genus and novel species in the family Burkholderiaceae, for which the name Mycoavidus cysteinexigens gen. nov., sp. nov. is proposed. The type strain is B1-EBT (u2009=u2009JCM 30646Tu2009=u2009LMG 28693Tu2009=u2009NBRC 110909T).

Alsobacter metallidurans gen. nov., sp. nov., a thallium-tolerant soil bacterium in the order Rhizobiales.

A thallium-tolerant, aerobic bacterium, designated strain SK200a-9(T), isolated from a garden soil sample was characterized using a polyphasic approach. Comparative analysis of 16S rRNA gene sequences revealed that strain SK200a-9(T) was affiliated with an uncultivated lineage within the Alphaproteobacteria and the nearest cultivated neighbours were bacteria in genera in the family Methylocystaceae (93.3-94.4% 16S rRNA gene sequence similarity) and the family Beijerinckiaceae (92.3-93.1%) in the order Rhizobiales. Cells of strain SK200a-9(T) were Gram-stain-negative, non-motile, non-spore-forming, poly-β-hydroxybutyrate-accumulating rods. The strain was a chemo-organotrophic bacterium, which was incapable of growth on C1 substrates. Catalase and oxidase were positive. Atmospheric nitrogen fixation and nitrate reduction were negative. The strain contained ubiquinone Q-10 and cellular fatty acids C18u200a:u200a1ω7c, C18u200a:u200a0, C16u200a:u200a1ω7c and C16u200a:u200a0 as predominant components. The major polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine and phosphatidylglycerol. The DNA G+C content was 64.8 mol%. On the basis of the information described above, strain SK200a-9(T) is considered to represent a novel species of a new genus in the order Rhizobiales, for which the name Alsobacter metallidurans gen. nov., sp. nov. is proposed. The type strain of Alsobacter metallidurans is SK200a-9(T) (u200a=u200aNBRC 107718(T)u200a=u200aCGMCC 1.12214(T)).

Efficient butanol recovery from acetone-butanol-ethanol fermentation cultures grown on sweet sorghum juice by pervaporation using silicalite-1 membrane.

We investigated butanol recovery by pervaporation separation, using a silicalite-1 membrane, from batch cultures of butanol-producing Clostridium beijerinckii SBP2 grown on sweet sorghum juice as a fermentation medium. The pervaporation system yielded 73% (w/v) butanol from intact feed cultures containing 1% (w/v) butanol, and had a butanol permeation flux of 11xa0gxa0m(-2)xa0h(-1). Upon neutralization and activated charcoal treatment of the feed cultures, butanol yield and total flux increased to 82% (w/v) and 40xa0gxa0m(-2)xa0h(-1), respectively. This system is applicable to refining processes for practical biobutanol production from a promising energy crop, sweet sorghum.

Characterization of Early Microbial Communities on Volcanic Deposits along a Vegetation Gradient on the Island of Miyake, Japan

The 2000 eruption of Mount Oyama on the island of Miyake (Miyake-jima) created a unique opportunity to study the early ecosystem development on newly exposed terrestrial substrates. In this study, bacterial and fungal communities on 9- and 11-year-old volcanic deposits at poorly to fully vegetation-recovered sites in Miyake-jima, Japan, were characterized by conventional culture-based methods and pyrosequencing of 16S rRNA and 18S rRNA genes. Despite the differences in the vegetation cover, the upper volcanic deposit layer samples displayed low among-site variation for chemical properties (pH, total organic carbon, and total nitrogen) and microbial population densities (total direct count and culturable count). Statistical analyses of pyrosequencing data revealed that the microbial communities of volcanic deposit samples were phylogenetically diverse, in spite of very low-carbon environmental conditions, and their diversity was comparable to that in the lower soil layer (buried soil) samples. Comparing with the microbial communities in buried soil, the volcanic deposit communities were characterized by the presence of Betaproteobacteria and Gammaproteobacteria as the main bacterial class, Deinococcus- Thermus as the minor bacterial phyla, and Ascomycota as the major fungal phyla. Multivariate analysis revealed that several bacterial families and fungal classes correlated positively or negatively with plant species.

Draft genome sequences of Aggregatibacter actinomycetemcomitans strains 310a and 310b

ABSTRACT We report the draft genome sequences of Aggregatibacter actinomycetemcomitans strains 310a (310-TR) and 310b (310-OS). Strain 310a is a clinical isolate with a rough phenotype. Strain 310b is a laboratory-adapted isolate derived from the passage of 310a and displays a smooth phenotype.

Complete Genome Sequence of the Nonylphenol-Degrading Bacterium Sphingobium cloacae JCM 10874 T

ABSTRACT Sphingobium cloacae JCM 10874T can degrade phenolic endocrine-disrupting chemicals, nonylphenol, and octylphenol. Here, we report the complete genome sequence of the JCM 10874T strain.