Publications (129) View all
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Article: 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.
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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)).Microbes and Environments 05/2013; · 1.91 Impact Factor -
Article: Genome sequence of a novel deep-sea vent epsilonproteobacterial phage provides new insight into the co-evolution of Epsilonproteobacteria and their phages.
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ABSTRACT: Epsilonproteobacteria are among the predominant primary producers in deep-sea hydrothermal vent ecosystems. However, phages infecting deep-sea vent Epsilonproteobacteria have never been isolated and characterized. Here, we successfully isolated a novel temperate phage, NrS-1, that infected a deep-sea vent chemolithoautotrophic isolate of Epsilonproteobacteria, Nitratiruptor sp. SB155-2, and its entire genome sequence was obtained and analyzed. The NrS-1 genome is linear, circularly permuted, and terminally redundant. The NrS-1 genome is 37,159 bp in length and contains 51 coding sequences. Five major structural proteins including major capsid protein and tape measure protein were identified by SDS-PAGE and mass spectrometry analysis. NrS-1 belongs to the family Siphoviridae, but its sequence and genomic organization are distinct from those of any other previously known Siphoviridae phages. Homologues of genes encoded in the NrS-1 genome were widely distributed among the genomes of diverse Epsilonproteobacteria. The distribution patterns had little relation to the evolutionary traits and ecological and physiological differentiation of the host epsilonproteobacterial species. The widespread occurrence of phage genes in diverse Epsilonproteobacteria supports early co-evolution between temperate phages and Epsilonproteobacteria prior to the divergence of their habitats and physiological adaptation.Extremophiles 03/2013; · 2.94 Impact Factor -
Article: Metagenomic analysis of viral communities in (hado)pelagic sediments.
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ABSTRACT: In this study, we analyzed viral metagenomes (viromes) in the sedimentary habitats of three geographically and geologically distinct (hado)pelagic environments in the northwest Pacific; the Izu-Ogasawara Trench (water depth = 9,760 m) (OG), the Challenger Deep in the Mariana Trench (10,325 m) (MA), and the forearc basin off the Shimokita Peninsula (1,181 m) (SH). Virus abundance ranged from 10 to 10 viruses/cm of sediments (down to 30 cm below the seafloor [cmbsf]). We recovered viral DNA assemblages (viromes) from the (hado)pelagic sediment samples and obtained a total of 37,458, 39,882, and 70,882 sequence reads by 454 GS FLX Titanium pyrosequencing from the virome libraries of the OG, MA, and SH (hado)pelagic sediments, respectively. Only 24-30% of the sequence reads from each virome library exhibited significant similarities to the sequences deposited in the public nr protein database (E-value <10 in BLAST). Among the sequences identified as potential viral genes based on the BLAST search, 95-99% of the sequence reads in each library were related to genes from single-stranded DNA (ssDNA) viral families, including , , and . A relatively high abundance of sequences related to the genetic markers (major capsid protein [VP1] and replication protein [Rep]) of two ssDNA viral groups were also detected in these libraries, thereby revealing a high genotypic diversity of their viruses (833 genotypes for VP1 and 2,551 genotypes for Rep). A majority of the viral genes predicted from each library were classified into three ssDNA viral protein categories: Rep, VP1, and minor capsid protein. The deep-sea sedimentary viromes were distinct from the viromes obtained from the oceanic and fresh waters and marine eukaryotes, and thus, deep-sea sediments harbor novel viromes, including previously unidentified ssDNA viruses.PLoS ONE 01/2013; 8(2):e57271. · 4.09 Impact Factor -
Article: Biogeography of Persephonella in deep-sea hydrothermal vents of the Western Pacific.
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ABSTRACT: Deep-sea hydrothermal vent fields are areas on the seafloor with high biological productivity fueled by microbial chemosynthesis. Members of the Aquificales genus Persephonella are obligately chemosynthetic bacteria, and appear to be key players in carbon, sulfur, and nitrogen cycles in high temperature habitats at deep-sea vents. Although this group of bacteria has cosmopolitan distribution in deep-sea hydrothermal ecosystem around the world, little is known about their population structure such as intraspecific genomic diversity, distribution pattern, and phenotypic diversity. We developed the multi-locus sequence analysis (MLSA) scheme for their genomic characterization. Sequence variation was determined in five housekeeping genes and one functional gene of 36 Persephonella hydrogeniphila strains originated from the Okinawa Trough and the South Mariana Trough (SNT). Although the strains share >98.7% similarities in 16S rRNA gene sequences, MLSA revealed 35 different sequence types (ST), indicating their extensive genomic diversity. A phylogenetic tree inferred from all concatenated gene sequences revealed the clustering of isolates according to the geographic origin. In addition, the phenotypic clustering pattern inferred from whole-cell matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF/MS) analysis can be correlated to their MLSA clustering pattern. This study represents the first MLSA combined with phenotypic analysis indicative of allopatric speciation of deep-sea hydrothermal vent bacteria.Frontiers in microbiology. 01/2013; 4:107. -
Article: Effects of Hydrogen Sulfide on Bacterial Communities on the Surface of Galatheid Crab, Shinkaia crosnieri, and in a Bacterial Mat Cultured in Rearing Tanks.
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ABSTRACT: To investigate the effects of H(2)S on the bacterial consortia on the galatheid crab, Shinkaia crosnieri, crabs of this species were cultivated in the laboratory under two different conditions, with and without hydrogen sulfide feeding. We developed a novel rearing tank system equipped with a feedback controller using a semiconductor sensor for hydrogen sulfide feeding. H(2)S aqueous concentration was successfully maintained between 5 to 40 μM for 80 d with the exception of brief periods of mechanical issues. According to real-time PCR analysis, the numbers of copies of partial 16S rRNA gene of an episymbiont of the crabs with H(2)S feeding was three orders of magnitude larger than that without feeding. By phylogenetic analysis of partial 16S rRNA gene, we detected several clones related to symbionts of deep sea organisms in Alphaproteobacteria, Gammaproteobacteria, Epsilonproteobacteria, and Flavobacteria, from a crab with H(2)S feeding. The symbiont-related clones were grouped into four different groups: Gammaproteobacteria in marine epibiont group I, Sulfurovum-affiliated Epsilonproteobacteria, Osedax mucofloris endosymbiont-affiliated Epsilonproteobacteria, and Flavobacteria closely related to CFB group bacterial epibiont of Rimicaris exoculata. The other phylotypes were related to Roseobacter, and some Flavobacteria, seemed to be free-living psychrophiles. Furthermore, white biofilm occurred on the surface of the rearing tank with H(2)S feeding. The biofilms contained various phylotypes of Gammaproteobacteria, Epsilonproteobacteria, and Flavobacteria, as determined by phylogenetic analysis. Interestingly, major clones were related to symbionts of Alviniconcha sp. type 2 and to endosymbionts of Osedax mucofloris, in Epsilonproteobacteria.Microbes and Environments 10/2012; · 1.91 Impact Factor
