A5101576861- Methane Hydrates and Related Phenomena
- Microbial Community Ecology and Physiology
- Wastewater Treatment and Nitrogen Removal
- Geology and Paleoclimatology Research
- Hydrocarbon exploration and reservoir analysis
- Offshore Engineering and Technologies
- Anaerobic Digestion and Biogas Production
- Protist diversity and phylogeny
- Atmospheric and Environmental Gas Dynamics
- Marine and coastal ecosystems
- Genomics and Phylogenetic Studies
- Electron and X-Ray Spectroscopy Techniques
- Calcium Carbonate Crystallization and Inhibition
- Geotechnical and Geomechanical Engineering
- Environmental DNA in Biodiversity Studies
- Diatoms and Algae Research
- Microbial Fuel Cells and Bioremediation
- Spectroscopy Techniques in Biomedical and Chemical Research
- Bee Products Chemical Analysis
- Spectroscopy and Chemometric Analyses
- Advanced Electron Microscopy Techniques and Applications
- Single-cell and spatial transcriptomics
- Nuclear and radioactivity studies
- Microbial bioremediation and biosurfactants
- Mechanical and Thermal Properties Analysis
Japan Steel Works (Japan)
2012-2023
Japan Agency for Marine-Earth Science and Technology
2014
National Institute of Advanced Industrial Science and Technology
2006-2012
Microbial life inhabits deeply buried marine sediments, but the extent of this vast ecosystem remains poorly constrained. Here we provide evidence for existence microbial communities in ~40° to 60°C sediment associated with lignite coal beds at ~1.5 2.5 km below seafloor Pacific Ocean off Japan. methanogenesis was indicated by isotopic compositions methane and carbon dioxide, biomarkers, cultivation data, gas compositions. Concentrations indigenous cells 1.5 ranged from <10 ~10(4) cm(-3)....
Remarkable numbers of microbial cells have been observed in global shallow to deep subseafloor sediments. Accumulating evidence indicates that and ancient sediments harbor living life, where the flux nutrients energy are extremely low. However, their physiology requirements remain largely unknown. We used stable isotope tracer incubation nanometer-scale secondary ion MS investigate dynamics carbon nitrogen assimilation activities individual from 219-m-deep lower Pleistocene (460,000 y old)...
Development of an improved technique for separating microbial cells from marine sediments and standardization a high-throughput discriminative cell enumeration method were conducted. We separated various types sediment then recovered the using multilayer density gradients sodium polytungstate and/or Nycodenz, resulting in notably higher percent recovery than previous methods. The efficiency extraction generally depends on depth; new we developed, more 80% total shallow samples (down to 100...
Abstract Sparse microbial populations persist from seafloor to basement in the slowly accumulating oxic sediment of oligotrophic South Pacific Gyre (SPG). The physiological status these communities, including their substrate metabolism, is previously unconstrained. Here we show that diverse aerobic members communities SPG sediments (4.3‒101.5 Ma) are capable readily incorporating carbon and nitrogen substrates dividing. Most 6986 individual cells analyzed with nanometer-scale secondary ion...
Scientific drilling at a submarine mud volcano shows that geofluid migration stimulates methanogenesis in the deep biosphere.
A comprehensive survey of bacterial and archaeal community structures within granular sludges taken from twelve different types full-scale, food-processing wastewater-treating, upflow anaerobic sludge blanket (UASB) reactors was performed with a 16S rRNA gene-based clone library method. In total, 1,282 gene clones 722 were analyzed, their identities determined by phylogenetic analyses. Overall, belonging to the phyla Proteobacteria (the class Deltaproteobacteria in particular), Firmicutes,...
Halogenated organic compounds serve as terminal electron acceptors for anaerobic respiration in a diverse range of microorganisms. Here, we report on the widespread distribution and diversity reductive dehalogenase homologous (rdhA) genes marine subsurface sediments. A total 32 putative rdhA phylotypes were detected sediments from southeast Pacific off Peru, eastern equatorial Pacific, Juan de Fuca Ridge flank Oregon, northwest Japan, collected at maximum depth 358 m below seafloor. In...
Spore-forming bacteria accumulate dipicolinic acid (DPA) to form spores survive in extreme environments. Vibrational spectroscopy is widely used detect DPA and elucidate the existence of bacteria, while vegetative cells, another spore-forming have not been studied extensively. Herein, we applied coherent anti-Stokes Raman scattering (CARS) microscopy spectroscopically identify both cells without staining or molecular tagging. The were identified by strong CARS signals due DPA. Furthermore,...
A prerequisite for DNA-based microbial community analysis is even and effective cell disruption DNA extraction. With a commonly used extraction kit, roughly two-thirds of subseafloor sediment cells remain intact on average (i.e., the are not disrupted), indicating that analyses may be biased at step, prior to subsequent molecular analyses. To address this issue, we standardized new method using alkaline treatment heating. Upon with 1 M NaOH 98°C 20 min, over 98% in samples collected...
Halogenated organic matter buried in marine subsurface sediment may serve as a source of electron acceptors for anaerobic respiration subseafloor microbes. Detection diverse array reductive dehalogenase-homologous (rdhA) genes suggests that organohalide-respiring microbial communities play significant ecological roles the biogeochemical carbon and halogen cycle biosphere. We report here spatial distribution dehalogenation activity Nankai Trough plate-subduction zone northwest Pacific off Kii...
ABSTRACT In situ detection of methanogens within the family Methanobacteriaceae is sometimes known to be unsuccessful due difficulty in permeability oligonucleotide probes. Pseudomurein endoisopeptidase (Pei), a lytic enzyme that specifically acts on their cell walls, was applied prior 16S rRNA-targeting fluorescence hybridization (FISH). For this purpose, pure cultured family, Methanobacterium bryantii , Methanobrevibacter ruminantium Methanosphaera stadtmanae and Methanothermobacter...
The study of environmental samples requires a preservation system that stabilizes the sample structure, including cells and biomolecules. To address this fundamental issue, we tested cell alive (CAS)-freezing technique for subseafloor sediment core samples. In CAS-freezing technique, an alternating magnetic field is applied during freezing process to produce vibration water molecules achieve stable, super-cooled liquid phase. Upon further cooling, temperature decreases further, achieving...
Subseafloor sedimentary environments harbor remarkably diverse microbial communities. However, it remains unknown if the deeply buried fossils in these sediments play ecological roles deep habitats, or whether communities inhabiting such differ from those surrounding sediment matrix. Here we compare community structures of subseafloor microbes coldwater coral carbonates (Madrepora oculata and Lophelia pertusa) clay Samples were obtained Challenger Mound Porcupine Seabight at Site U1317 Hole...
Hydraulic fracturing is a prominent method of natural gas production that uses injected, high-pressure fluids to fracture low permeability, hydrocarbon rich strata such as shale. Upon completion well, the fluid returns surface (produced water) and contains gas, subsurface constituents, microorganisms (Barbot et al., 2013, Daley 2016). While microbial community produced has been studied in multiple wells, activity these their relation biogeochemical not well understood. In this experiment, we...
In upflow anaerobic sludge blanket (UASB) reactors treating high-strength organic wastewaters, uncultured phylotypes belonging to the phylum Nitrospirae were assumed play a key role in treatment processes because of their high abundance as determined by 16S rRNA gene-based clone library analyses (Narihiro et al. (27)). A comparative nucleotide sequence analysis phylotypes, commonly found mesophilic sludges, revealed that these formed coherent clade at family genus levels with no cultured...
Experimental contamination by exogenous DNA is a major issue in molecular biological studies for data quality and its management. We herein assessed aerosols the risk of tested capacity clean air filters to trap remove aerosols. were generated atomizing solution introduced into laminar flow unit. Capture detection performed upstream downstream unit showed that significant fraction (>99.96%) molecules was trapped removed filter. Although appear be an avoidable source contamination, clearer...
Fluorescence in situ hybridization (FISH) is a widely used molecular technique microbial ecology. However, the non-specific adsorption of fluorescent probes and resulting high intensity background signals from mineral particles hampers specific detection cells grain-rich environmental samples, such as subseafloor sediments. We herein demonstrated that new buffer composition containing EDTA efficiently reduced without compromising properties FISH-based probing microbes. The inclusion...
Abstract It is necessary to purify diatom frustules by taxon perform accurate geochemical analyses of fossils preserved in sediments. However, the small size diatoms has hitherto prevented taxon-specific purification; therefore, previous have been performed with mixtures various taxa. In this study, we developed a taxon-selective collection method that uses cell sorter. The experimental material comprised six samples from sediment core Hole U1538A Scotia Sea, Atlantic sector Southern Ocean...
Continuous denitrification experiments were carried out in an aerobic canal using water-insoluble fatty acid compounds as hydrogen doors. After about one year, the results showed that total nitrogen (T-N) removal efficiencies 10 to 40% and maximum rates 1920 5760mg-N·m-2·d-1 per unit area from April Jun. Statistical analysis revealed sufficient nitrification treatment was most important factor for maintaining a high rate. Denitrification medias, which gathered bacteria with precedence,...
Microbial cell counting provides essential information for the study of abundance profiles and biogeochemical interactions with surrounding environments. However, it often requires labor-intensive time-consuming processes, particularly subseafloor sediment samples, in which non-cell particles are abundant. We developed a rapid straightforward method staining microbial intracellular DNA by SYBR Green I (SYBR-I) to enumerate cells flow cytometry (FCM). initially examined efficiency at various...