Biomedical subjects

Urumu Tsunogai

Publications and source records attributed to Urumu Tsunogai.

10 recordsLinked to original sources

PubMed2006

Microbial community in a sediment-hosted CO2 lake of the southern Okinawa Trough hydrothermal system.

Increasing levels of CO2 in the atmosphere are expected to cause climatic change with negative effects on the earth's ecosystems and human society. Consequently, a variety of CO2 disposal options are discussed, including injection into the deep ocean. Because the dissolution of CO2 in seawater will decrease ambient pH considerably, negative consequences for deep-water ecosystems have been predicted. Hence, ecosystems associated with natural CO2 reservoirs in the deep sea, and the dynamics of gaseous, liquid, and solid CO2 in such environments, are of great interest to science and society. We report here a biogeochemical and microbiological characterization of a microbial community inhabiting deep-sea sediments overlying a natural CO2 lake at the Yonaguni Knoll IV hydrothermal field, southern Okinawa Trough. We found high abundances (>10(9) cm(-3)) of microbial cells in sediment pavements above the CO2 lake, decreasing to strikingly low cell numbers (10(7) cm(-3)) at the liquid CO2/CO2-hydrate interface. The key groups in these sediments were as follows: (i) the anaerobic methanotrophic archaea ANME-2c and the Eel-2 group of Deltaproteobacteria and (ii) sulfur-metabolizing chemolithotrophs within the Gamma- and Epsilonproteobacteria. The detection of functional genes related to one-carbon assimilation and the presence of highly 13C-depleted archaeal and bacterial lipid biomarkers suggest that microorganisms assimilating CO2 and/or CH4 dominate the liquid CO2 and CO2-hydrate-bearing sediments. Clearly, the Yonaguni Knoll is an exceptional natural laboratory for the study of consequences of CO2 disposal as well as of natural CO2 reservoirs as potential microbial habitats on early Earth and other celestial bodies.

Archaea↗

PubMed2006

Molecular phylogenetic and chemical analyses of the microbial mats in deep-sea cold seep sediments at the northeastern Japan Sea.

Microbial communities inhabiting deep-sea cold seep sediments at the northeastern Japan Sea were characterized by molecular phylogenetic and chemical analyses. White patchy microbial mats were observed along the fault offshore the Hokkaido Island and sediment samples were collected from two stations at the southern foot of the Shiribeshi seamount (M1 site at a depth of 2,961 m on the active fault) and off the Motta Cape site (M2 site at a depth of 3,064 m off the active fault). The phylogenetic and terminal-restriction fragment polymorphism analyses of PCR-amplified 16S rRNA genes revealed that microbial community structures were different between two sampling stations. The members of ANME-2 archaea and diverse bacterial components including sulfate reducers within Deltaproteobacteria were detected from M1 site, indicating the occurrence of biologically mediated anaerobic oxidation of methane, while microbial community at M2 site was predominantly composed of members of Marine Crenarchaeota group I, sulfate reducers of Deltaproteobacteria, and sulfur oxidizers of Epsilonproteobacteria. Chemical analyses of seawater above microbial mats suggested that concentrations of sulfate and methane at M1 site were largely decreased relative to those at M2 site and carbon isotopic composition of methane at M1 site shifted heavier ((13)C-enriched), the results of which are consistent with molecular analyses. These results suggest that the mat microbial communities in deep-sea cold seep sediments at the northeastern Japan Sea are significantly responsible for sulfur and carbon circulations and the geological activity associated with plate movements serves unique microbial habitats in deep-sea environments.

Bacteria↗

PubMed2006

Geomicrobiological exploration and characterization of a novel deep-sea hydrothermal system at the TOTO caldera in the Mariana Volcanic Arc.

Novel hydrothermal activities accompanying effluent white smokers and elemental sulfur chimney structures at the north-east lava dome of the TOTO caldera depression in the Mariana Volcanic Arc have been explored and characterized by geochemical and microbiological surveys. White smoker hydrothermal fluids were observed in the potential hydrothermal activity centre of the field and represented the maximal temperature of 170 degrees C and the lowest pH of 1.6. The chimney structures, all consisting of elemental sulfur (sulfur chimney), were also unique to the TOTO caldera hydrothermal field. Microbial community structures in a sulfur chimney and its formation hydrothermal fluid with a high concentration of hydrogen sulfide (15 mM) have been investigated by culture-dependent and -independent analyses. 16S rRNA gene clone analysis and fluorescence in situ hybridization (FISH) analysis revealed that epsilon-Proteobacteria dominated the microbial communities in the sulfur chimney structure and formed a dense microbial mat covering the sulfur chimney surface. Archaeal phylotypes were consistently minor components in the communities and related to the genera Thermococcus, Pyrodictium, Aeropyrum, and the uncultivated archaeal group of 'deep-sea hydrothermal vent euryarchaeotal group'. Cultivation analysis suggested that the chemolithoautotrophs might play a significant ecological role as primary producers utilizing gas and sulfur compounds provided from hydrothermal fluids.

Archaea↗

PubMed2005

An analytical system for determining delta17O in CO2 using continuous flow-isotope ratio MS.

We developed a simple measurement system for delta17O in nanomole quantities of CO2 using continuous flow isotope ratio mass spectrometry (CF-IRMS). The analytical system consisted of a sample injection system, a helium-purged CO2 purification line, a capillary GC, a combustion unit, and CF-IRMS. A unique feature of the system is that we use molecular CO2 to determine the isotopic compositions including delta17O. The delta17O of CO2 in a sample is calculated from the mass ratios of both 45/44 and 46/44 of two different kinds of CO2, which have been purified quantitatively from different aliquots of a sample. While one aliquot (rCO2) flows into IRMS directly, the other (eCO2) flows through a CuO unit (900 degrees C) prior to injection into IRMS, to exchange oxygen atoms in the sample CO2 molecules with those in CuO for which we can assume Delta17O = 0. In our system, we introduce both rCO2 and eCO2 alternately to IRMS repeatedly by using an automatic multianalytical system to improve analytical precision statistically. The standard deviation of 0.35 per thousand for Delta17O can be realized using as little as 8.7 nmol CO2 in a approximately 3-h analysis. Based on this system, we have quantified delta17O in the stratospheric CO2 over Japan.

Journal Article↗

PubMed2005

A selective unsaturated hydrocarbon subtraction technique for stable carbon isotopic analysis of atmospheric methyl chloride, methyl bromide, and C2-C5 saturated hydrocarbons using continuous-flow isotope ratio mass spectrometry.

Using continuous-flow isotope ratio mass spectrometry, we have developed a new analytical system which enables us to determine the stable carbon isotopic composition of CH3Cl, CH3Br, and C2-C5 saturated hydrocarbons in gas samples even if they contain substantial amounts of unsaturated hydrocarbons, using an I2O5 reagent for their selective subtraction. The analytical precision of the delta13C determinations is better than 0.5 per thousand for >300 pmolC injections and better than 5 per thousand for 20 pmolC injections. Using the system, delta13C values for CH3Cl and CH3Br were found in burning exhaust that contain a substantial quantity of unsaturated hydrocarbons. CH3Cl and CH3Br measured in exhaust from burning rice plants exhibit highly 13C-depleted values of -56.6 +/- 1.3 per thousand and -48.6 +/- 3.9 per thousand, respectively, while saturated hydrocarbons exhibit delta13C values (-26.4 to -28.9 per thousand) that are comparable with the total delta13C value of the parent material (rice plant; -28.0 per thousand). Using the system, we can determine the delta13C values of methyl halides and hydrocarbons in many kinds of gas samples.

Air Pollutants↗

PubMed2004

Geochemical and microbiological evidence for a hydrogen-based, hyperthermophilic subsurface lithoautotrophic microbial ecosystem (HyperSLiME) beneath an active deep-sea hydrothermal field.

Subsurface microbial communities supported by geologically and abiologically derived hydrogen and carbon dioxide from the Earth's interior are of great interest, not only with regard to the nature of primitive life on Earth, but as potential analogs for extraterrestrial life. Here, for the first time, we present geochemical and microbiological evidence pointing to the existence of hyperthermophilic subsurface lithoautotrophic microbial ecosystem (HyperSLiME) dominated by hyperthermophilic methanogens beneath an active deep-sea hydrothermal field in the Central Indian Ridge. Geochemical and isotopic analyses of gaseous components in the hydrothermal fluids revealed heterogeneity of both concentration and carbon isotopic compositions of methane between the main hydrothermal vent (0.08 mM and -13.8 per thousand PDB, respectively) and the adjacent divergent vent site (0.2 mM and -18.5 per thousand PDB, respectively), representing potential subsurface microbial methanogenesis, at least in the divergent vent emitting more 13C-depleted methane. Extremely high abundance of magmatic energy sources such as hydrogen (2.5 mM) in the fluids also encourages a hydrogen-based, lithoautotrophic microbial activity. Both cultivation and cultivation-independent molecular analyses suggested the predominance of Methanococcales members in the superheated hydrothermal emissions and chimney interiors along with the other major microbial components of Thermococcales members. These results imply that a HyperSLiME, consisting of methanogens and fermenters, occurs in this tectonically active subsurface zone, strongly supporting the existence of hydrogen-driven subsurface microbial communities.

Archaea↗

PubMed2004

Stable carbon and oxygen isotopic determination of sub-microgram quantities of CaCO3 to analyze individual foraminiferal shells.

We have developed an analytical system to determine stable isotopic compositions (delta13C and delta18O) of sub-microgram quantities of CaCO3 for the purpose of analyzing individual foraminiferal shells, using continuous-flow isotope ratio mass spectrometry (CF-IRMS). The system consists of a micro-volume CaCO3 decomposition tube, stainless steel CO2 purification vacuum line with a quantity-regulating unit, helium-purged CO2 purification line, gas chromatograph, and a CF-IRMS system. By using this system, we can determine stable carbon and oxygen isotopic compositions as low as 0.2 microg of CaCO3, with standard deviations of +/-0.10 per thousand for delta13C and +/-0.18 per thousand for delta18O within a 4-h reaction time and 30-min analysis period.

Animals↗

PubMed2004

Characterization of C1-metabolizing prokaryotic communities in methane seep habitats at the Kuroshima Knoll, southern Ryukyu Arc, by analyzing pmoA, mmoX, mxaF, mcrA, and 16S rRNA genes.

Samples from three submerged sites (MC, a core obtained in the methane seep area; MR, a reference core obtained at a distance from the methane seep; and HC, a gas-bubbling carbonate sample) at the Kuroshima Knoll in the southern Ryuku arc were analyzed to gain insight into the organisms present and the processes involved in this oxic-anoxic methane seep environment. 16S rRNA gene analyses by quantitative real-time PCR and clone library sequencing revealed that the MC core sediments contained abundant archaea (approximately 34% of the total prokaryotes), including both mesophilic methanogens related to the genus Methanolobus and ANME-2 members of the Methanosarcinales, as well as members of the delta-Proteobacteria, suggesting that both anaerobic methane oxidation and methanogenesis occurred at this site. In addition, several functional genes connected with methane metabolism were analyzed by quantitative competitive-PCR, including the genes encoding particulate methane monooxygenase (pmoA), soluble methane monooxygenase (mmoX), methanol dehydrogenese (mxaF), and methyl coenzyme M reductase (mcrA). In the MC core sediments, the most abundant gene was mcrA (2.5 x 10(6) copies/g [wet weight]), while the pmoA gene of the type I methanotrophs (5.9 x 10(6) copies/g [wet weight]) was most abundant at the surface of the MC core. These results indicate that there is a very complex environment in which methane production, anaerobic methane oxidation, and aerobic methane oxidation all occur in close proximity. The HC carbonate site was rich in gamma-Proteobacteria and had a high copy number of mxaF (7.1 x 10(6) copies/g [wet weight]) and a much lower copy number of the pmoA gene (3.2 x 10(2) copies/g [wet weight]). The mmoX gene was never detected. In contrast, the reference core contained familiar sequences of marine sedimentary archaeal and bacterial groups but not groups specific to C1 metabolism. Geochemical characterization of the amounts and isotopic composition of pore water methane and sulfate strongly supported the notion that in this zone both aerobic methane oxidation and anaerobic methane oxidation, as well as methanogenesis, occur.

Alcohol Oxidoreductases↗

PubMed2003

A simple method for oxygen-18 determination of milligram quantities of water using NaHCO3 reagent.

This paper presents a modified H(2)O-CO(2) equilibration method for stable oxygen isotopic composition (delta(18)O) analysis of water. This method enables rapid and simple delta(18)O analysis of milligram quantities of water, by employing solid reagent NaHCO(3) as the CO(2) source, a small (0.6 mL) glass vial for the equilibration chamber, and an isotope-monitoring gas chromatography/mass spectrometry (irm-GC/MS) system for delta 18O(CO2) analysis. This method has several advantages, including simple handling for the H(2)O-CO(2) equilibration (without purging and/or evacuation treatments), rapid and easy delta(18)O analysis of equilibrated CO(2), and highly sensitive and highly precise delta(18)O analysis of H(2)O, using samples as small as 10 mg and with a precision of less than +/-0.12 per thousand. The time needed to attain oxygen isotopic equilibration between CO(2) and water is also comparable (17 h for 10 mg H(2)O and 10 h for 100 mg H(2)O) to other previous methods using CO(2) gas for the CO(2) source. The extent of delta(18)O variation of sample water from its initial delta(18)O value due to isotope exchange with added NaHCO(3) is also discussed. It is concluded that the correction needed is negligible (less than 0.1 per thousand ) as long as the oxygen atom ratio (O(NaHCO3)/O(H2O)) is less than 3.3 +/- 10(-3) and provided the delta18O(H2O) determination is made by comparing delta(18)O of CO(2) equilibrated with sample water and that equilibrated with standard water of a moderately close delta(18)O value, less than 30 per thousand difference.

Journal Article↗

PubMed2002

Stable carbon and oxygen isotopic analysis of atmospheric carbon monoxide using continuous-flow isotope ratio MS by isotope ratio monitoring of CO.

We have developed a rapid and simple measurement system for both content and stable isotopic compositions (13C and 18O) of atmospheric CO, using continuous-flow isotope ratio mass spectrometry by simultaneously monitoring the CO+ ion currents at masses 28, 29, and 30. The analytical system consisted sequentially of a sample trapping port (liquid nitrogen temperature silica gel and molecular sieve 5A), a gas dryer, a CO purification column (molecular sieve 5A), a cryofocusing unit, and a final purification column using a GC capillary. Analytical precision of 0.2 per thousand for 13C and 0.4 per thousand for 18O can be realized for samples that contain as little as 300 pmol of CO within 40 min for one sample analysis. Analytical blanks associated with the method are less than 1 pmol. The extent of analytical error in delta13C due to mass-independent fractionation of oxygen in natural CO is estimated to be less than 0.3 per thousand. Based on this system, we report herein a kinetic isotopic effect during CO consumption in soil.

Air Pollutants, Occupational↗