Strain identifier

BacDive ID: 10421

Type strain: No

Species: Plesiocystis pacifica

Strain Designation: SHI-1

Strain history: T. Iizuka SHI-1.

NCBI tax ID(s): 191768 (species)

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General

@ref: 5592

BacDive-ID: 10421

DSM-Number: 14876

keywords: 16S sequence, Bacteria, mesophilic

description: Plesiocystis pacifica SHI-1 is a mesophilic bacterium that was isolated from coastal sands.

NCBI tax id

  • NCBI tax id: 191768
  • Matching level: species

strain history

@refhistory
5592<- T. Iizuka; SHI-1
67770T. Iizuka SHI-1.

doi: 10.13145/bacdive10421.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Deltaproteobacteria
  • order: Myxococcales
  • family: Nannocystaceae
  • genus: Plesiocystis
  • species: Plesiocystis pacifica
  • full scientific name: Plesiocystis pacifica Iizuka et al. 2003

@ref: 5592

domain: Bacteria

phylum: Proteobacteria

class: Deltaproteobacteria

order: Myxococcales

family: Nannocystaceae

genus: Plesiocystis

species: Plesiocystis pacifica

full scientific name: Plesiocystis pacifica Iizuka et al. 2003

strain designation: SHI-1

type strain: no

Culture and growth conditions

culture medium

  • @ref: 5592
  • name: VY/4-SWS AGAR (DSMZ Medium 958)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/958
  • composition: Name: VY/4-SWS AGAR (DSMZ Medium 958) Composition: NaCl 20.0 g/l Agar 15.0 g/l MgSO4 x 7 H2O 8.0 g/l Yeast cell paste 2.5 g/l CaCl2 x 2 H2O 1.0 g/l KCl 0.5 g/l NaHCO3 0.16 g/l KBr 0.08 g/l SrCl2 x 6 H2O 0.03 g/l Sodium beta-glycerophosphate 0.01 g/l Ferric citrate 0.01 g/l Cyanocobalamine 0.0005 g/l EDTA 0.0005 g/l FeSO4 x 7 H2O 0.0002 g/l H3BO3 3e-05 g/l CoCl2 x 6 H2O 2e-05 g/l ZnSO4 x 7 H2O 1e-05 g/l Na2MoO4 x 2 H2O 3e-06 g/l MnCl2 x 4 H2O 3e-06 g/l NiCl2 x 6 H2O 2e-06 g/l CuCl2 x 2 H2O 1e-06 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
5592positivegrowth30mesophilic
67770positivegrowth30mesophilic

Physiology and metabolism

observation

  • @ref: 67770
  • observation: quinones: MK-8(H2)

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
5592coastal sandsHachijyo Island, TokyoJapanJPNAsia
67770SandHachijo-jima IslandJapanJPNAsia

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Sandy

taxonmaps

  • @ref: 69479
  • File name: preview.99_3266.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_385;96_1701;97_2036;98_2502;99_3266&stattab=map
  • Last taxonomy: Plesiocystis pacifica subclade
  • 16S sequence: AB016469
  • Sequence Identity:
  • Total samples: 3138
  • soil counts: 471
  • aquatic counts: 1671
  • animal counts: 937
  • plant counts: 59

Safety information

risk assessment

  • @ref: 5592
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 5592
  • description: Myxobacterium SHI-1 16S rRNA gene, partial sequence
  • accession: AB016469
  • length: 1483
  • database: ena
  • NCBI tax ID: 80815

GC content

@refGC-contentmethod
559269.3-70.0high performance liquid chromatography (HPLC)
6777070high performance liquid chromatography (HPLC)

External links

@ref: 5592

culture collection no.: DSM 14876, AJ 13393, JCM 11592

straininfo link

  • @ref: 79703
  • straininfo: 111749

literature

  • topic: Phylogeny
  • Pubmed-ID: 12656172
  • title: Plesiocystis pacifica gen. nov., sp. nov., a marine myxobacterium that contains dihydrogenated menaquinone, isolated from the Pacific coasts of Japan.
  • authors: Iizuka T, Jojima Y, Fudou R, Hiraishi A, Ahn JW, Yamanaka S
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.02418-0
  • year: 2003
  • mesh: Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/genetics, Japan, Microscopy, Electron, Scanning, Molecular Sequence Data, Myxococcales/*classification/genetics/isolation & purification/*metabolism, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Vitamin K 2/*analogs & derivatives/*metabolism
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitle
5592Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 14876)https://www.dsmz.de/collection/catalogue/details/culture/DSM-14876
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
69479João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.https://microbeatlas.org/MicrobeAtlas 1.0 beta
79703Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID111749.1StrainInfo: A central database for resolving microbial strain identifiers