Geo-Biological Coupling of Authigenic Carbonate Formation and Autotrophic Faunal Colonization at Deep-Sea Methane Seeps I: Geo-Biological Settings

Methane (CH4) in sub-seafloor sediment is generated both biologically and non-biologically from organic and inorganic sources. A major part of the sub-seafloor methane is oxidized before leakage via “anaerobic oxidation of methane” (AOM) in the subsurface. The AOM-survivor methane, which is relatively minor part of the subsurface methane, leaches to the overlying water column and is eventually subject to thorough anaerobic and aerobic oxidation in the water column. The AOM with sulfate results in the generation of carbon dioxide and sulfide; the former (CO2) is incorporated into authigenic carbonate and autotrophic biomass, and the autotrophy is energetically driven by oxidation of the latter (H2S). These processes are typically observed at focused sites that are generally known as “methane seeps” or hydrocarbon seeps, or occasionally called as cold seeps in comparison with hydrothermal vents. Methane seeps are typically formed in passive and active continental margins, occasionally with unique features such as exposed methane hydrates, mud volcanoes, asphalt volcanoes, salt diapirs, and brine pools. Accordingly, authigenic carbonates and unique biological communities are shaped at respective methane seeps. This chapter overviews geological and biological setting for the formation of methane seeps associated with unique landscapes of carbonates and biomes

Geo-Biological Coupling of Authigenic Carbonate Formation and Autotrophic Faunal Colonization at Deep-Sea Methane Seeps II. Geo-Biological Landscapes

Deep-sea methane seeps are typically shaped with authigenic carbonates and unique biomes depending on methane-driven and methane-derived metabolisms. Authigenic carbonates vary in δ13C values due probably to δ13C variation in the carbon sources (directly carbon dioxide and bicarbonate, and ultimately methane) which is affected by the generation and degradation (oxidation) of methane at respective methane seeps. Anaerobic oxidation of methane (AOM) by specially developed microbial consortia has significant influences on the carbonate δ13C variation as well as the production of carbon dioxide and hydrogen sulfide for chemoautotrophic biomass production. Authigenesis of carbonates and faunal colonization are thus connected. Authigenic carbonates also vary in Mg contents that seem correlated again to faunal colonization. Among the colonizers, mussels tend to colonize low δ13C carbonates, while gutless tubeworms colonize high-Mg carbonates. The types and varieties of such geo-biological landscapes of methane seeps are overviewed in this chapter. A unique feature of a high-Mg content of the rock-tubeworm conglomerates is also discussed

The population dynamics of the bacterioplankton communities in the mesotrophic bog environments

Thesis--University of Tsukuba, D.Sc.(A), no. 619, 1989. 3. 2

Phylogenetic similarity of aerobic gram-negative halophilic bacteria from a deep-sea hydrothermal mound and Antarctic habitats

Deep-sea halophilic strains, 4 halomonads and 1 pseudoalteromonad, were isolated from high-temperature hydrothermal fluids of the TAG hydrothermal mound in the Mid-Atlantic Ridge. Two of the TAG halomonads were closely related to Antarctic halomonads based on 16S rDNA sequences (1350bp). Subhydrothermal vents and Antarctic terrains are known to provide high-salinity habitats for halophilic life. The TAG-Antarctic halomonad kinship indicates the wide distribution of halophiles over globally distant habitats, regardless of large differences in temperatures of the habitats. This suggests that microbial eco-physiology in Antarctica (and sub-hydrothermal vent), which has been studied in terms of temperature adapation, may be complemented by halotolerance and halophilism studies

Enhanced Bacterial Growth and Gene Expression of D-Amino Acid Dehydrogenase With D-Glutamate as the Sole Carbon Source

In a search for life-supporting, not life-assisting, D-amino acid metabolism, an environmental strain that grows better with D-glutamate as the sole carbon source was isolated from an ordinary river. The strain, designated as A25, exhibited a faster growth rate and greater cell yield with D-glutamate than with L-glutamate. Conversely, the D/L ratio of total cellular glutamate was as low as 4/96, which suggests that D-glutamate is more likely catabolized than anabolized. Strain A25 was phylogenetically most closely related to the gamma-proteobacterial species Raoultella ornithinolytica, with a 16S rRNA gene sequence similarity of 100%. A standard strain, R. ornithinolytica JCM 6096T, also showed similarly enhanced growth with D-glutamate, which was proven for the first time. Gene expression of the enzymes involved in D-amino acid metabolism was assayed by reverse-transcription quantitative PCR (RT-qPCR) using specifically designed primers. The targets were the genes encoding D-amino acid dehydrogenase (DAD; EC 1.4.99.1), glutamate racemase (EC 5.1.1.3), D-glutamate oxidase (EC 1.4.3.7 or EC 1.4.3.15), and UDP-N-acetyl-α-D-muramoyl-L-alanyl-D-glutamate ligase (EC 6.3.2.9). As a result, the growth of strains A25 and R. ornithinolytica JCM 6096T on D-glutamate was conspicuously associated with the enhanced expression of the DAD gene (dadA) in the exponential phase compared with the other enzyme genes. Pseudomonas aeruginosa is also known to grow on D-glutamate as the sole carbon source but to a lesser degree than with L-glutamate. A standard strain of P. aeruginosa, JCM 5962T, was tested for gene expression of the relevant enzymes by RT-qPCR and also showed enhanced dadA expression, but in the stationary phase. Reduction of ferricyanide with D-glutamate was detected in cell extracts of the tested strains, implying probable involvement of DAD in the D-glutamate catabolizing activity. DAD-mediated catalysis may have advantages in the one-step production of α-keto acids and non-production of H2O2 over other enzymes such as racemase and D-amino acid oxidase. The physiological and biochemical importance of DAD in D-amino acid metabolism is discussed

Characterization of bacteria associated with lichens found in cold environment

第6回極域科学シンポジウム分野横断セッション：[IB2] 地球環境変動の解析と地球生命システム学の構築11月19日（木）　統計数理研究所 セミナー室1（D305

Re-classification of the Apostichopus holothurians from Sagami Bay, central Japan

相模湾より得られたマナマコ属genus Apostichopus（Liao, 1980）を再検討した結果，これまでマナマコApostichopus japonicus（Selenka, 1867）とされていた種類には，真のマナマコApostichopus armata（Selenka, 1867）とアカナマコ Apostichopus japonicus（Selenka, 1867）の2種類が含まれている結果が得られた。この結果は，Kanno et al.（2003）により報告された遺伝的に異なる日本産Apostichopus属の2つの集団（アカとアオ・クロ）と一致する。We reviewed classifications of the sea cucumbers (holothurians) belonging to the genus Apostichopus Liao, 1980, collected from the Sagami Bay, central Japan. Detailed examinations have led to a conclusion that some of the specimens that had once been identified as Apostichopus japonicus (Selenka, 1867) should be re-classified as Apostichopus armata (Selenka, 1867). This conclusion agrees with the report that the Japanese Apostichopus holothurians are divided into two major groups (Kanno et al., 2003)

Abundance of planktonic thraustochytrids and bacteria and the concentration of particulate ATP in the Greenland and Norwegian Seas

Surface water samples were collected at 15 sites in the Greenland and Norwegian Seas, and total planktonic thraustochytrids and bacteria were directly counted by epifluorescence microscopy. Particulate (>0.2 μm) adenosine 5\u27-triphosphate (ATP) was also determined by bioluminescence photometry. Abundance of planktonic thraustochytrids varied from below the detection limit (<8.1×102 l^(-1)) to 2.3×105 l^(-1) with an overall average of 3.1×104 l^(-1). Abundance of bacterioplankton ranged from 2.2×107 l^(-1) at the northernmost site to 6.0×108 l^(-1) at the southernmost site with an overall average of 2.1×108 l^(-1). Particulate ATP concentration ranged from 79 pmol to 676 pmol at the mid-transect (68°N) and southernmost (62°N) sites, respectively, with an overall average of 222 pmol. The measured ATP concentrations were too low to account for the abundance of thraustochytrids and bacteria estimated from total counts and carbon-per-cell factors. However, particulate ATP was correlated with the abundance of bacterioplankton, but not that of planktonic thraustochytrids. These differing relationships suggest different physiological and biochemical strategies of starvation survival and differing substrate availability in the Arctic and sub-Arctic surface waters

Elemental composition of black deposits on the shells of Phenacolepas pulchella (Mollusca: Gastropoda: Neritopsina) collected from the Aso-kai lagoon, Kyoto, Japan

阿蘇海は宮津湾の西部の湾入部が堆砂によって仕切られた海跡湖である。その阿蘇海内に形成されたカキ礁内部に生息するアマオブネガイ目の巻貝ミヤコドリ（Phenacolepas pulchella）を採集した。海跡湖に生息するカキ礁を生息環境とするミヤコドリの報告は初めてである。採集したミヤコドリの殻表面は黒色沈着物で覆われていた。この黒色沈着物について，電子プローブマイクロアナライザー（EPMA）を用いて電子像による形態観察，定性分析および定量分析を行ったところ，顕著なマンガン（Mn）のピークが検出され，沈着物の主成分は酸化マンガン（MnOn）であることが示された。これまでミヤコドリの殻表上の付着物は還元鉄が付着して茶色になる（土屋，2000）とされていたが，分析の結果，阿蘇海で採集されたミヤコドリの殻表面には酸化マンガンが濃集していることがわかった。阿蘇海のミヤコドリ生息域における酸化還元条件が，酸化還元に敏感な元素であるマンガン（Mn）の沈着に深く関与している可能性が考えられる。Aso-kai is a lagoon separated by sand spit from the Miyazu Bay, a marginal water of the Sea of Japan. We collected individuals of Phenacolepas pulchella, belonging to the order Neritimorpha, from inside of oyster reefs, as the first record of such inhabitation. Shell surface of P. pulchella accumulated blackish deposits. Electron probe micro-analysis revealed that the deposits consist mainly of manganese oxides (MnOn). Geochemical setting of the habitat may facilitate accumulation of the redox-sensitive element, Mn