A5020252414- Microbial Community Ecology and Physiology
- Genomics and Phylogenetic Studies
- Methane Hydrates and Related Phenomena
- Wastewater Treatment and Nitrogen Removal
- Anaerobic Digestion and Biogas Production
- Gut microbiota and health
- Probiotics and Fermented Foods
- Protist diversity and phylogeny
- Atmospheric and Environmental Gas Dynamics
- Constructed Wetlands for Wastewater Treatment
- Microbial metabolism and enzyme function
- Hydrocarbon exploration and reservoir analysis
- Bacteriophages and microbial interactions
- Plant-Microbe Interactions and Immunity
- Biofuel production and bioconversion
- Environmental DNA in Biodiversity Studies
- Enzyme Production and Characterization
- Microbial Fuel Cells and Bioremediation
- Legume Nitrogen Fixing Symbiosis
- Plant Pathogens and Fungal Diseases
- Coastal wetland ecosystem dynamics
- Chromium effects and bioremediation
- Mine drainage and remediation techniques
- Fungal Biology and Applications
- Microbial Metabolic Engineering and Bioproduction
National Institute of Advanced Industrial Science and Technology
2016-2025
University of Tsukuba
2003-2024
The University of Tokyo
2016-2023
National Bioproducts Institute (South Africa)
2020
Urbana University
2019
University of Illinois Urbana-Champaign
2011-2014
Gifu University
2012
Asahi Kasei (Japan)
2010
Institute of Applied Biochemistry
2003-2004
The origin of eukaryotes remains unclear1–4. Current data suggest that may have emerged from an archaeal lineage known as 'Asgard' archaea5,6. Despite the eukaryote-like genomic features are found in these archaea, evolutionary transition archaea to unclear, owing lack cultured representatives and corresponding physiological insights. Here we report decade-long isolation Asgard archaeon related Lokiarchaeota deep marine sediment. archaeon—'Candidatus Prometheoarchaeum syntrophicum' strain...
Coal-bed methane is one of the largest unconventional natural gas resources. Although microbial activity may greatly contribute to coal-bed formation, it unclear whether complex aromatic organic compounds present in coal can be used for methanogenesis. We show that deep subsurface-derived Methermicoccus methanogens produce from more than 30 types methoxylated (MACs) as well coals containing MACs. In contrast known methanogenesis pathways involving one- and two-carbon compounds, this...
16S rRNA gene pyrosequencing approach has revolutionized studies in microbial ecology. While primer selection and short read length can affect the resulting community profile, little is known about influence of methods on sequencing throughput outcome analyses. The aim this study to compare differences output, ease, cost among three different amplicon for Roche/454 Titanium platformThe following genes were selected study: Method-1 (standard method) recommended method bi-directional using...
ABSTRACT Microbiologists have been using agar growth medium for over 120 years. It revolutionized microbiology in the 1890s when microbiologists were seeking effective methods to isolate microorganisms, which led successful cultivation of microorganisms as single clones. But there has a disparity between total cell counts and cultivable on plates, often referred “great plate count anomaly,” that long phenomenon still remains unsolved. Here, we report common practice employed prepare hidden...
The class Thermoplasmata harbors huge uncultured archaeal lineages at the order level, so-called Groups E2 and E3. A novel archaeon Kjm51a affiliated with Group was enriched from anaerobic sludge in present study. Clone library analysis of 16S rRNA mcrA genes confirmed a unique population enrichment culture. gene-based phylogeny revealed that formed distinct cluster within together Methanomassiliicoccus luminyensis B10(T) environmental clone sequences derived digesters, bovine rumen,...
A novel, strictly anaerobic, short rod-shaped bacterium, designated strain TBC1T, was isolated from methanogenic granular sludge in a full-scale mesophilic upflow anaerobic blanket reactor treating high-strength starch-based organic wastewater. Cells of this were 2-4 µm long and 0.4-0.6 wide. They non-motile Gram-stain-negative. The optimum growth temperature 30-37 °C, with range 20-40 °C. pH for around 7.0, while occurred 6.5-9.0. Strain TBC1T grew chemo-organotrophically on narrow...
Comparative analysis of bacterial diversity in freshwater sediment collected from a shallow eutrophic lake was performed by using 16S rRNA gene clone library and improved cultivation-based techniques. Our study demonstrated that the use gellan gum as gelling reagent instead agar more effective at increasing culturability, cultivating diverse array novel microbes, reducing gaps results between molecular analyses.
A novel aerobic, chemoheterotrophic bacterium, strain YO-36(T), isolated from the rhizoplane of an aquatic plant (a reed, Phragmites australis) inhabiting a freshwater lake in Japan, was morphologically, physiologically and phylogenetically characterized. Strain YO-36(T) Gram-negative ovoid to rod-shaped, formed pinkish hard colonies on agar plates. grew at 20-40 °C with optimum growth 30-35 °C, whilst no observed 15 or 45 °C. The pH range for 5.5-8.5 6.5. utilized limited substrates, such...
Summary Viruses have been detected in the different stages of wastewater treatment plants (WWTPs) at concentrations 10 8 –10 ml −1 virus‐like particles (VLPs), 10–1000 times higher than natural aquatic environments, suggesting that WWTPs can be considered as an important reservoir and source viruses. This study revealed novel diversity function with DNA viral communities influent, activated sludge, anaerobic digester, effluent a domestic WWTP using metagenomics. was very specific...
Deep subsurface formations (for example, high-temperature oil reservoirs) are candidate sites for carbon capture and storage technology. However, very little is known about how the microbial community would respond to an increase in CO2 pressure resulting from storage. Here we construct microcosms mimicking reservoir conditions (55 °C, 5 MPa) using samples. Methanogenesis occurs under both high low microcosms. accelerates rate of methanogenesis more than twice that conditions. Isotope tracer...
Abstract A key feature that differentiates prokaryotic cells from eukaryotes is the absence of an intracellular membrane surrounding chromosomal DNA. Here, we isolate a member ubiquitous, yet-to-be-cultivated phylum ‘ Candidatus Atribacteria’ (also known as OP9) has intracytoplasmic apparently nucleoid. The isolate, RT761, subsurface-derived anaerobic bacterium appears to have three lipid membrane-like layers, shown by cryo-electron tomography. Our observations are consistent with classical...
Abstract The origin of eukaryotes remains enigmatic. Current data suggests that may have risen from an archaeal lineage known as “Asgard archaea”. Despite the eukaryote-like genomic features found in these archaea, evolutionary transition archaea to unclear due lack cultured representatives and corresponding physiological insight. Here we report decade-long isolation a Lokiarchaeota-related Asgard archaeon deep marine sediment. archaeon, “ Candidatus Prometheoarchaeum syntrophicum strain...
Methane-generating archaea drive the final step in anaerobic organic compound mineralization and dictate carbon flow of Earth's diverse anoxic ecosystems absence inorganic electron acceptors. Although such Archaea were presumed to be restricted life on simple compounds like hydrogen (H
Summary Since Robert Koch and colleagues found agar to be an effective gelling agent over a century ago, the pure culture method using plates has long been standard of microbiology. Agar is undoubtedly easy handle useful for microorganisms, but recent discovery ubiquity microorganisms that cannot cultured on raises question: really best agent? In this study, we investigated effect two agents, gellan gum, colony formation diverse array (total 108 strains) newly isolated from freshwater...
A novel obligately anaerobic bacterium, designated strain TC1T, was isolated from methanogenic granular sludge in a full-scale mesophilic upflow blanket reactor treating high-strength starch-based wastewater. Cells had multicellular filamentous morphology, stained Gram-negative and were non-motile. The filaments flexible, generally >100 μm long 0.3-0.4 wide. Growth of the isolate observed at 25-43 °C (optimum 37 °C) pH 6.0-8.5 7.0). Strain TC1T grew chemo-organotrophically on range...
Most microorganisms living in the environment have yet to be cultured, owing at least part their slow and poor propagation properties susceptibility oxidative stress. Our previous studies demonstrated that a simple modification preparation of agar media, i.e., autoclaving phosphate separately (termed "PS" medium), can greatly improve culturability by mitigating stress compared with use "PT" medium (autoclaving together). Here, we attempted isolate phylogenetically novel bacteria combining PS...
How aromatic compounds are degraded in various anaerobic ecosystems (e.g. groundwater, sediments, soils and wastewater) is currently poorly understood. Under methanogenic conditions (i.e. groundwater wastewater treatment), syntrophic metabolizers known to play an important role. This study explored the draft genome of Syntrophorhabdus aromaticivorans strain UI identified first phenol-degrading phenylphosphate synthase (PpsAB) carboxylase (PpcABCD) terephthalate-degrading decarboxylase...
Here we employed quantitative real-time PCR (qPCR) assays for polyphosphate kinase 1 (ppk1) and 16S rRNA genes to assess relative abundances of dominant clades Candidatus Accumulibacter phosphatis (referred Accumulibacter) in 18 globally distributed full-scale wastewater treatment plants (WWTPs) from six countries. were not only detected the 6 WWTPs performing biological phosphorus removal, but also inhabited other 11 employing conventional activated sludge (AS) with ranging 0.02% 7.0%....
ABSTRACT Despite their importance as a biofuel production platform, only very limited number of butanol-tolerant bacteria have been identified thus far. Here, we extensively explored butanol- and isobutanol-tolerant from various environmental samples. A total 16 aerobic anaerobic that could tolerate greater than 2.0% (vol/vol) butanol isobutanol were isolated. 16S rRNA gene sequencing analysis revealed the isolates phylogenetically distributed over at least nine genera: Bacillus ,...
An aerobic, methane-oxidizing bacterium (strain S8 T ) was isolated from marine sediments in Kagoshima Bay, Japan. Phylogenetic analysis based on 16S rRNA gene sequences indicated that this strain is closely related to members of the genus Methylocaldum (97.6–97.9 % similarity) within class Gammaproteobacteria . Strain a Gram-staining-negative, non-motile, coccoid or short rod-shaped organism. The temperature range for growth 20–47 °C (optimum at 36 °C). It required NaCl (>0.5 %),...
Deciphering unclear microbial interactions is key to improving biological wastewater treatment processes. Microbial predation and parasitism in ecosystems are unexplored survival strategies that have long been known recently attracted attention because these interspecies may contribute the reduction of excess sludge. Here, community profiling 600 activated sludge samples taken from six industrial one municipal processes (WWTPs) was conducted. To identify shared lineages WWTPs, constituents...
Three novel strains of cold-adapted bacteria, ST-82T, ST-10 and ST-92, were isolated from freshwater sediments. These three isolates very similar to each other in phenotypic chemotaxonomic traits, as well 16S rDNA sequence. The Gram-negative, elongated filament-like rods that formed bright yellow colonies. They showed neither flexirubin pigments nor gliding motility. able hydrolyse casein, gelatin, starch, agar, aesculin, urea, uric acid tyrosine. also lysed cells Escherichia coil...
Potato scab is a serious plant disease caused by several Streptomyces sp., and effective control methods remain unavailable. Although antagonistic bacteria phages against potato pathogens have been reported, to the best of our knowledge, there no information about fungi that are pathogens. The aim this study was isolate fungal antagonists, characterize their phylogenetic positions, determine activities pathogens, highlight potential use as agents under lower pH conditions. Fifteen stains...