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Masayuki Miyazaki

Bio: Masayuki Miyazaki is an academic researcher from Japan Agency for Marine-Earth Science and Technology. The author has contributed to research in topics: Energy source & Microbulbifer. The author has an hindex of 31, co-authored 76 publications receiving 3404 citations.


Papers
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Journal ArticleDOI
TL;DR: Under conventional growth conditions, the isotope fractionation of methanogenesis by M. kandleri strain 116 was similar to values previously reported for other hydrogenotrophic methanogens, but under high hydrostatic pressures, the atom fractionation effect became much smaller, and the kinetic isotope effect was one of the smallest effects ever reported.
Abstract: We have developed a technique for cultivation of chemolithoautotrophs under high hydrostatic pressures that is successfully applicable to various types of deep-sea chemolithoautotrophs, including methanogens. It is based on a glass-syringe-sealing liquid medium and gas mixture used in conjunction with a butyl rubber piston and a metallic needle stuck into butyl rubber. By using this technique, growth, survival, and methane production of a newly isolated, hyperthermophilic methanogen Methanopyrus kandleri strain 116 are characterized under high temperatures and hydrostatic pressures. Elevated hydrostatic pressures extend the temperature maximum for possible cell proliferation from 116°C at 0.4 MPa to 122°C at 20 MPa, providing the potential for growth even at 122°C under an in situ high pressure. In addition, piezophilic growth significantly affected stable carbon isotope fractionation of methanogenesis from CO2. Under conventional growth conditions, the isotope fractionation of methanogenesis by M. kandleri strain 116 was similar to values (−34‰ to−27‰) previously reported for other hydrogenotrophic methanogens. However, under high hydrostatic pressures, the isotope fractionation effect became much smaller (<−12‰), and the kinetic isotope effect at 122°C and 40 MPa was −9.4‰, which is one of the smallest effects ever reported. This observation will shed light on the sources and production mechanisms of deep-sea methane.

684 citations

Journal ArticleDOI
15 Jan 2020-Nature
TL;DR: A hypothetical model for eukaryogenesis is proposed, termed the entangle–engulf–endogenize (also known as E 3 ) model, and isolation and characterization of an Asgard archaeon related to Lokiarchaeota reveals insights into how eukARYotes may have evolved from prokaryotes.
Abstract: The origin of eukaryotes remains unclear1–4. Current data suggest that eukaryotes may have emerged from an archaeal lineage known as ‘Asgard’ archaea5,6. Despite the eukaryote-like genomic features that are found in these archaea, the evolutionary transition from archaea to eukaryotes remains unclear, owing to the lack of cultured representatives and corresponding physiological insights. Here we report the decade-long isolation of an Asgard archaeon related to Lokiarchaeota from deep marine sediment. The archaeon—‘Candidatus Prometheoarchaeum syntrophicum’ strain MK-D1—is an anaerobic, extremely slow-growing, small coccus (around 550 nm in diameter) that degrades amino acids through syntrophy. Although eukaryote-like intracellular complexes have been proposed for Asgard archaea6, the isolate has no visible organelle-like structure. Instead, Ca. P. syntrophicum is morphologically complex and has unique protrusions that are long and often branching. On the basis of the available data obtained from cultivation and genomics, and reasoned interpretations of the existing literature, we propose a hypothetical model for eukaryogenesis, termed the entangle–engulf–endogenize (also known as E3) model. Isolation and characterization of an archaeon that is most closely related to eukaryotes reveals insights into how eukaryotes may have evolved from prokaryotes.

370 citations

Journal ArticleDOI
TL;DR: Strain GO25(T) represents the first deep-sea epsilonproteobacterium capable of growth by both hydrogen and sulfur oxidation and is proposed as the reclassification of Thiomicrospira denitrificans as Sulfurimonas denitRificans comb.
Abstract: A novel mesophilic bacterium, strain GO25T, was isolated from a nest of hydrothermal vent polychaetes, Paralvinella sp., at the Iheya North field in the Mid-Okinawa Trough. Cells were motile short rods with a single polar flagellum. Growth was observed between 4 and 35 °C (optimum 30 °C; 13–16 h doubling time) and between pH 5.4 and 8.6 (optimum pH 6.1). The isolate was a facultatively anaerobic chemolithoautotroph capable of growth using molecular hydrogen, elemental sulfur or thiosulfate as the sole energy source, carbon dioxide as the sole carbon source, ammonium or nitrate as the sole nitrogen source and elemental sulfur, thiosulfate or yeast extract as the sole sulfur source. Strain GO25T represents the first deep-sea epsilonproteobacterium capable of growth by both hydrogen and sulfur oxidation. Nitrate or molecular oxygen (up to 10 % partial pressure) could serve as the sole electron acceptor to support growth. Metabolic products of nitrate reduction shifted in response to the electron donor provided. The G+C content of genomic DNA was 37.6 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the novel isolate belonged to the genus Sulfurimonas and was most closely related to Sulfurimonas autotrophica OK10T (96.3 % sequence similarity). DNA–DNA hybridization demonstrated that the novel isolate could be differentiated genotypically from Sulfurimonas autotrophica OK10T. On the basis of the physiological and molecular properties of the novel isolate, the name Sulfurimonas paralvinellae sp. nov. is proposed, with strain GO25T (=JCM 13212T=DSM 17229T) as the type strain. Thiomicrospira denitrificans DSM 1251T (=ATCC 33889T) is phylogenetically associated with Sulfurimonas autotrophica OK10T and Sulfurimonas paralvinellae GO25T. Based on the phylogenetic relationship between Thiomicrospira denitrificans DSM 1251T, Sulfurimonas autotrophica OK10T and Sulfurimonas paralvinellae GO25T, we propose the reclassification of Thiomicrospira denitrificans as Sulfurimonas denitrificans comb. nov. (type strain DSM 1251T=ATCC 33889T). In addition, an emended description of the genus Sulfurimonas is proposed.

229 citations

Journal ArticleDOI
02 Feb 2018-Science
TL;DR: Phylometabolic evaluation suggests that the TCA cycle with reversible CS may represent an ancestral mode of the rTCA cycle and raises the possibility of a facultatively chemolithomixotrophic origin of life.
Abstract: Inorganic carbon fixation is essential to sustain life on Earth, and the reductive tricarboxylic acid (rTCA) cycle is one of the most ancient carbon fixation metabolisms A combination of genomic, enzymatic, and metabolomic analyses of a deeply branching chemolithotrophic Thermosulfidibacter takaii ABI70S6 T revealed a previously unknown reversible TCA cycle whose direction was controlled by the available carbon source(s) Under a chemolithoautotrophic condition, a rTCA cycle occurred with the reverse reaction of citrate synthase (CS) and not with the adenosine 5′-triphosphate–dependent citrate cleavage reactions that had been regarded as essential for the conventional rTCA cycle Phylometabolic evaluation suggests that the TCA cycle with reversible CS may represent an ancestral mode of the rTCA cycle and raises the possibility of a facultatively chemolithomixotrophic origin of life

134 citations

Journal ArticleDOI
TL;DR: Benthic communities were similar across all the carcasses studied, although the body sizes of the whales were very different, and the succession of epifaunal communities was relatively rapid and the sulphophilic stage was considerably shorter than that of other known whale falls.
Abstract: We report the first study of sperm whale-fall ecosystems, based on mass sinking of whale carcasses at shelf depths in the northwest Pacific. We conducted three observations over a 2-year period on replicate sperm-whale carcasses implanted at depths of 219‐254 m off the southern part of Japan from July 2003 to August 2005. The study was made possible by a mass stranding of sperm whales in January 2002, and the subsequent sinking of 12 carcasses in the waters off Cape Nomamisaki. Dense aggregations of unique chemosynthesis-based fauna had formed around the whale carcasses after 18 months (July 2003). The mytilid mussel Adipicola pacifica was the most abundant macrofaunal species and covered most of the exposed bone surfaces. The general composition of the fauna was similar to that of deep-water reducing habitats, but none of the species appearing in this study has been found at hydrothermal vents, cold seeps or deep-water whale falls. A new species of lancelet, which was the first record of the subphylum Cephalochordata from reducing environments, a new species of Osedax; a rarely encountered benthic ctenophore, and a rare gastropod species were discovered at this sperm whale-fall site. Benthic communities were similar across all the carcasses studied, although the body sizes of the whales were very different. The succession of epifaunal communities was relatively rapid and the sulphophilic stage was considerably shorter than that of other known whale falls.

130 citations


Cited by
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01 Jun 2012
TL;DR: SPAdes as mentioned in this paper is a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler and on popular assemblers Velvet and SoapDeNovo (for multicell data).
Abstract: The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

10,124 citations

Journal ArticleDOI

3,734 citations

Journal ArticleDOI
TL;DR: There are two kinds of tutorial articles: those that provide a primer on an established topic and those that let us in on the ground floor of something of emerging importance.
Abstract: There are two kinds of tutorial articles: those that provide a primer on an established topic and those that let us in on the ground floor of something of emerging importance. The first type of tutorial can have a noted expert who has been gracious (and brave) enough to write a field guide about a particular topic. The other sort of tutorial typically involves researchers who have each been laboring on a topic for some years. Both sorts of tutorial articles are very much desired. But we, as an editorial board for both Systems and Transactions, know that there has been no logical place for them in the AESS until this series was started several years ago. With these tutorials, we hope to continue to give them a home, a welcome, and provide a service to our membership. We do not intend to publish tutorials on a regular basis, but we hope to deliver them once or twice per year. We need and welcome good, useful tutorial articles (both kinds) in relevant AESS areas. If you, the reader, can offer a topic of interest and an author to write about it, please contact us. Self-nominations are welcome, and even more ideal is a suggestion of an article that the editor(s) can solicit. All articles will be reviewed in detail. Criteria on which they will be judged include their clarity of presentation, relevance, and likely audience, and, of course, their correctness and scientific merit. As to the mathematical level, the articles in this issue are a good guide: in each case the author has striven to explain complicated topics in simple-well, tutorial-terms. There should be no (or very little) novel material: the home for archival science is the Transactions Magazine, and submissions that need to be properly peer reviewed would be rerouted there. Likewise, articles that are interesting and descriptive, but lack significant tutorial content, ought more properly be submitted to the Systems Magazine.

955 citations

Journal ArticleDOI
TL;DR: The diversity of chemosynthetic symbionts and their hosts is focused on, and phylogenetic analyses have shown that these associations have evolved on multiple occasions by convergent evolution.
Abstract: Chemosynthetic symbioses occur in a wide range of ocean habitats, from deep-sea vents and cold seeps to whale falls and shallow-water sediments. This Review reveals the diversity and complexity of these symbioses, some of which include multiple symbiotic partners. Chemosynthetic symbioses between bacteria and marine invertebrates were discovered 30 years ago at hydrothermal vents on the Galapagos Rift. Remarkably, it took the discovery of these symbioses in the deep sea for scientists to realize that chemosynthetic symbioses occur worldwide in a wide range of habitats, including cold seeps, whale and wood falls, shallow-water coastal sediments and continental margins. The evolutionary success of these symbioses is evident from the wide range of animal groups that have established associations with chemosynthetic bacteria; at least seven animal phyla are known to host these symbionts. The diversity of the bacterial symbionts is equally high, and phylogenetic analyses have shown that these associations have evolved on multiple occasions by convergent evolution. This Review focuses on the diversity of chemosynthetic symbionts and their hosts, and examines the traits that have resulted in their evolutionary success.

852 citations

Journal ArticleDOI
TL;DR: This work shows that total microbial cell abundance in subseafloor sediment varies between sites by ca.
Abstract: The global geographic distribution of subseafloor sedimentary microbes and the cause(s) of that distribution are largely unexplored. Here, we show that total microbial cell abundance in subseafloor sediment varies between sites by ca. five orders of magnitude. This variation is strongly correlated with mean sedimentation rate and distance from land. Based on these correlations, we estimate global subseafloor sedimentary microbial abundance to be 2.9⋅1029 cells [corresponding to 4.1 petagram (Pg) C and ∼0.6% of Earth’s total living biomass]. This estimate of subseafloor sedimentary microbial abundance is roughly equal to previous estimates of total microbial abundance in seawater and total microbial abundance in soil. It is much lower than previous estimates of subseafloor sedimentary microbial abundance. In consequence, we estimate Earth’s total number of microbes and total living biomass to be, respectively, 50–78% and 10–45% lower than previous estimates.

791 citations