title: High-voltage electron microscopy tomography and structome analysis of unique spiral bacteria from the deep sea.
abstract: Structome analysis is a useful tool for identification of unknown microorganisms that cannot be cultured. In 2012, we discovered a unique deep-sea microorganism with a cell structure intermediate between those of prokaryotes and eukaryotes and described its features using freeze-substitution electron microscopy and structome analysis (quantitative and three-dimensional structural analysis of a whole cell at the electron microscopic level). We named it Myojin parakaryote Here we describe, using serial ultrathin sectioning and high-voltage electron microscopy tomography of freeze-substituted specimens, the structome analysis and 3D reconstruction of another unique spiral bacteria, found in the deep sea off the coast of Japan. The bacteria, which is named as 'Myojin spiral bacteria' after the discovery location and their morphology, had a total length of 1.768 ± 0.478 µm and a total diameter of 0.445 ± 0.050 µm, and showed either clockwise or counter-clockwise spiral. The cells had a cell surface membrane, thick fibrous layer, ribosomes and inner fibrous structures (most likely DNA). They had no flagella. The bacteria had 322 ± 119 ribosomes per cell. This ribosome number is only 1.2% of that of Escherichia coli and 19.3% of Mycobacterium tuberculosis and may reflect a very slow growth rate of this organism in the deep sea.
authors.affiliation: Medical Mycology Research Center, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8673, Japan yama@faculty.chiba-u.jp.
authors.forename: Masashi
authors.initials: M
authors.lastname: Yamaguchi
authors.affiliation: Department of Mycobacterium Reference and Research, The Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Kiyose, Tokyo 204-8533, Japan.
authors.forename: Hiroyuki
authors.initials: H
authors.lastname: Yamada
authors.affiliation: High Voltage Electron Microscopy Laboratory, Ecotopia Institute, Nagoya University, Nagoya 464-8603, Japan.
authors.forename: Kimitaka
authors.initials: K
authors.lastname: Higuchi
authors.affiliation: High Voltage Electron Microscopy Laboratory, Ecotopia Institute, Nagoya University, Nagoya 464-8603, Japan.
authors.forename: Yuta
authors.initials: Y
authors.lastname: Yamamoto
authors.affiliation: High Voltage Electron Microscopy Laboratory, Ecotopia Institute, Nagoya University, Nagoya 464-8603, Japan.
authors.forename: Shigeo
authors.initials: S
authors.lastname: Arai
authors.affiliation: Section of Electron Microscopy, National Institute for Physiological Sciences, Okazaki, Aichi 444-8585, Japan.
authors.forename: Kazuyoshi
authors.initials: K
authors.lastname: Murata
authors.affiliation: System in Frontier Inc., 2-8-3 Shinsuzuharu Bldg. 4F, Akebono-cho, Tachikawa-shi, Tokyo 190-0012, Japan.
authors.forename: Yuko
authors.initials: Y
authors.lastname: Mori
authors.affiliation: System in Frontier Inc., 2-8-3 Shinsuzuharu Bldg. 4F, Akebono-cho, Tachikawa-shi, Tokyo 190-0012, Japan.
authors.forename: Hiromitsu
authors.initials: H
authors.lastname: Furukawa
authors.affiliation: Medical Mycology Research Center, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8673, Japan Department of Computer Science and Engineering, Jahangirnagar University, Savar, Dhaka 1342, Bangladesh.
authors.forename: Mohammad Shorif
authors.initials: MS
authors.lastname: Uddin
authors.affiliation: Medical Mycology Research Center, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8673, Japan.
authors.forename: Hiroji
authors.initials: H
authors.lastname: Chibana
mesh_terms: D001419:Bacteria / Q000145:classification / Q000302:isolation & purification / Q000648:ultrastructure; D060086:Hydrothermal Vents / Q000382:microbiology*; D046529:Microscopy, Electron, Transmission; D009792:Oceans and Seas; D014057:Tomography, X-Ray Computed
keywords: deep-sea; freeze-substitution fixation; high-voltage electron microscopy; spiral bacteria; structome; tomography