Institute of Biogeosciences

Yokosuka, Japan

Institute of Biogeosciences

Yokosuka, Japan
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Nunoura T.,Institute of Biogeosciences | Takaki Y.,Institute of Biogeosciences | Kakuta J.,Institute of Biogeosciences | Nishi S.,Institute of Biogeosciences | And 9 more authors.
Nucleic Acids Research | Year: 2011

The domain Archaea has historically been divided into two phyla, the Crenarchaeota and Euryarchaeota. Although regarded as members of the Crenarchaeota based on small subunit rRNA phylogeny, environmental genomics and efforts for cultivation have recently revealed two novel phyla/divisions in the Archaea; the 'Thaumarchaeota' and 'Korarchaeota'. Here, we show the genome sequence of Candidatus 'Caldiarchaeum subterraneum' that represents an uncultivated crenarchaeotic group. A composite genome was reconstructed from a metagenomic library previously prepared from a microbial mat at a geothermal water stream of a sub-surface gold mine. The genome was found to be clearly distinct from those of the known phyla/divisions, Crenarchaeota (hyperthermophiles), Euryarchaeota, Thaumarchaeota and Korarchaeota. The unique traits suggest that this crenarchaeotic group can be considered as a novel archaeal phylum/division. Moreover, C. subterraneum harbors an ubiquitin-like protein modifier system consisting of Ub, E1, E2 and small Zn RING finger family protein with structural motifs specific to eukaryotic system proteins, a system clearly distinct from the prokaryote-type system recently identified in Haloferax and Mycobacterium. The presence of such a eukaryote-type system is unprecedented in prokaryotes, and indicates that a prototype of the eukaryotic protein modifier system is present in the Archaea. © 2010 The Author(s).

Makita H.,Institute of Biogeosciences | Nakagawa S.,Institute of Biogeosciences | Nakagawa S.,Hokkaido University | Miyazaki M.,Institute of Biogeosciences | And 3 more authors.
Archives of Microbiology | Year: 2012

A novel chemolithoautotrophic hydrogen-oxidizing and sulfur-reducing bacterium, strain 496ChimT, was isolated from a deep-sea hydrothermal vent chimney collected from the hydrothermal Weld at the summit of Nikko Seamount Weld, in the Mariana Arc. Cells were rods or curved rods, motile by means of a single polar Xagellum. Growth was observed between 15 and 45 °C (optimum 37 °C; doubling time, 2.1 h) and between pH 5.3 and 8.0 (optimum pH 6.0). The isolate was a strictly anaerobic, obligate chemolithoautotroph capable of growth using molecular hydrogen as the sole energy source, carbon dioxide as the sole carbon source, ammonium or nitrate as the sole nitrogen source, and elemental sulfur as the electron acceptor. The G+C content of genomic DNA was 35 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the new isolate belonged to the class Epsilonproteobacteria, but the isolate was distantly related to the previously described Epsilonproteobacteria species potentially at the genus level (<90 %). On the basis of its physiological and molecular characteristics, strain 496Chim T (=DSM 22050T = JCM 15747T = NBRC 105224 T) represents the sole species of a new genus, Thiofractor, for which the name Thiofractor thiocaminus is proposed. © Springer-Verlag 2012.

Takai K.,Institute of Biogeosciences | Takai K.,Japan Agency for Marine - Earth Science and Technology | Abe M.,Institute of Biogeosciences | Abe M.,Japan Agency for Marine - Earth Science and Technology | And 9 more authors.
International Journal of Systematic and Evolutionary Microbiology | Year: 2013

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). © 2013 IUMS.

Takaki Y.,Japan Agency for Marine - Earth Science and Technology | Shimamura S.,Institute of Biogeosciences | Nakagawa S.,Institute of Biogeosciences | Nakagawa S.,Hokkaido University | And 10 more authors.
DNA Research | Year: 2010

The complete genome sequence of the thermophilic sulphur-reducing bacterium, Deferribacter desulfuricans SMM1, isolated from a hydrothermal vent chimney has been determined. The genome comprises a single circular chromosome of 2 234 389 bp and a megaplasmid of 308 544 bp. Many genes encoded in the genome are most similar to the genes of sulphur-or sulphate-reducing bacterial species within Deltaproteobacteria. The reconstructed central metabolisms showed a heterotrophic lifestyle primarily driven by C1 to C3 organics, e.g. formate, acetate, and pyruvate, and also suggested that the inability of autotrophy via a reductive tricarboxylic acid cycle may be due to the lack of ATP-dependent citrate lyase. In addition, the genome encodes numerous genes for chemoreceptors, chemotaxis-like systems, and signal transduction machineries. These signalling networks may be linked to this bacterium's versatile energy metabolisms and may provide ecophysiological advantages for D. desulfuricans SSM1 thriving in the physically and chemically fluctuating environments near hydrothermal vents. This is the first genome sequence from the phylum Deferribacteres. © 2010 The Author.

Watsuji T.-O.,Japan Agency for Marine - Earth Science and Technology | Yamamoto A.,Japan Agency for Marine - Earth Science and Technology | Yamamoto A.,Nihon University | Takaki Y.,Institute of Biogeosciences | And 3 more authors.
ISME Journal | Year: 2014

Shinkaia crosnieri is a galatheid crab that predominantly dwells in deep-sea hydrothermal systems in the Okinawa Trough, Japan. In this study, the phylogenetic diversity of active methanotrophs in the epibiotic microbial community on the setae of S. Crosnieri was characterized by reverse transcription-polymerase chain reaction (RT-PCR) of a functional gene (pmoA) encoding a subunit of particulate methane monooxygenase. Phylogenetic analysis of pmoA transcript sequences revealed that the active epibiotic methanotrophs on S. Crosnieri setae consisted of gammaproteobacterial type Ia and Ib methanotrophs. The effect of different RNA stabilization procedures on the abundance of pmoA and 16S rRNA transcripts in the epibiotic community was estimated by quantitative RT-PCR. Our novel RNA fixation method performed immediately after sampling effectively preserved cellular RNA assemblages, particularly labile mRNA populations, including pmoA mRNA. Methane consumption in live S. Crosnieri was also estimated by continuous-flow incubation under atmospheric and in situ hydrostatic pressures, and provided a clear evidence of methane oxidation activity of the epibiotic microbial community, which was not significantly affected by hydrostatic pressure. Our study revealed the significant ecological function and nutritional contribution of epibiotic methanotrophs to the predominant S. Crosnieri populations in the Okinawa Trough deep-sea hydrothermal systems. In conclusion, our study gave clear facts about diversity and methane oxidation of active methanotrophs in the epibiotic community associated with invertebrates. © 2014 International Society for Microbial Ecology All rights reserved.

Zhou Y.,Curtin University Australia | Zhou Y.,Australian National University | Zhou Y.,CAS Institute of Earth Environment | Grice K.,Curtin University Australia | And 4 more authors.
Phytochemistry | Year: 2011

The hydrogen isotopic ratios (2H/1H) of land plant leaf water and the carbon-bound hydrogen of leaf wax lipids are valuable indicators for climatic, physiological, metabolic and geochemical studies. Temperature will exert a profound effect on the stable isotopic composition of leaf water and leaf lipids as it directly influences the isotopic equilibrium (IE) during leaf water evaporation and cellular water dissociation. It is also expected to affect the kinetics of enzymes involved in lipid biosynthesis, and therefore the balance of hydrogen inputs along different biochemical routes. We conducted a controlled growth experiment to examine the effect of temperature on the stable hydrogen isotopic composition of leaf water and the biological and biochemical isotopic fractionations during lipid biosynthesis. We find that leaf water 2H enrichment at 20 °C is lower than that at 30 °C. This is contrary to the expectation that at lower temperatures leaf water should be more enriched in 2H due to a larger equilibrium isotope effect associated with evapotranspiration from the leaf if all other variables are held constant. A hypothesis is presented to explain the apparent discrepancy whereby lower temperature-induced down-regulation of available aquaporin water channels and/or partial closure of transmembrane water channel forces water flow to "detour" to a more convoluted apoplastic pathway, effectively increasing the length over which diffusion acts against advection as described by the Péclet effect (Farquhar and Lloyd, 1993) and decreasing the average leaf water enrichment. The impact of temperature on leaf water enrichment is not reflected in the biological isotopic fractionation or the biochemical isotopic fractionation during lipid biosynthesis. Neither the biological nor biochemical fractionations at 20 °C are significantly different from that at 30 °C, implying that temperature has a negligible effect on the isotopic fractionation during lipid biosynthesis. © 2010 Elsevier Ltd. All rights reserved.

PubMed | Institute of Biogeosciences
Type: Journal Article | Journal: Applied and environmental microbiology | Year: 2010

A variety of archaeal lineages have been identified using culture-independent molecular phylogenetic surveys of microbial habitats occurring in deep-sea hydrothermal environments such as chimney structures, sediments, vent emissions, and chemosynthetic macrofauna. With the exception of a few taxa, most of these archaea have not yet been cultivated, and their physiological and metabolic traits remain unclear. In this study, phylogenetic diversity and distribution profiles of the archaeal genes encoding small subunit (SSU) rRNA, methyl coenzyme A (CoA) reductase subunit A, and the ammonia monooxygenase large subunit were characterized in hydrothermally influenced sediments at the Yonaguni Knoll IV hydrothermal field in the Southern Okinawa Trough. Sediment cores were collected at distances of 0.5, 2, or 5 m from a vent emission (90 degrees C). A moderate temperature gradient extends both horizontally and vertically (5 to 69 degrees C), indicating the existence of moderate mixing between the hydrothermal fluid and the ambient sediment pore water. The mixing of reductive hot hydrothermal fluid and cold ambient sediment pore water establishes a wide spectrum of physical and chemical conditions in the microbial habitats that were investigated. Under these different physico-chemical conditions, variability in archaeal phylotype composition was observed. The relationship between the physical and chemical parameters and the archaeal phylotype composition provides important insight into the ecophysiological requirements of uncultivated archaeal lineages in deep-sea hydrothermal vent environments, giving clues for approximating culture conditions to be used in future culturing efforts.

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