Strain identifier

BacDive ID: 131421

Type strain: Yes

Species: Oryzobacter terrae

Strain Designation: PSGM2-16

Strain history: <- S.-W. Kwon, KACC; PSGM2-16

NCBI tax ID(s): 1620385 (species)

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General

@ref: 22648

BacDive-ID: 131421

DSM-Number: 27137

keywords: 16S sequence, Bacteria, mesophilic

description: Oryzobacter terrae PSGM2-16 is a mesophilic bacterium that was isolated from pot of paddy soil planted with rice.

NCBI tax id

  • NCBI tax id: 1620385
  • Matching level: species

strain history

  • @ref: 22648
  • history: <- S.-W. Kwon, KACC; PSGM2-16

doi: 10.13145/bacdive131421.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Intrasporangiaceae
  • genus: Oryzobacter
  • species: Oryzobacter terrae
  • full scientific name: Oryzobacter terrae Kim et al. 2015

@ref: 22648

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Intrasporangiaceae

genus: Oryzobacter

species: Oryzobacter terrae

full scientific name: Oryzobacter terrae Kim et al. 2015

strain designation: PSGM2-16

type strain: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
22648R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
22648RICH MEDIUM (DSMZ Medium 736)yeshttps://mediadive.dsmz.de/medium/736Name: RICH MEDIUM (DSMZ Medium 736) Composition: Agar 20.0 g/l Bacto peptone 10.0 g/l Yeast extract 5.0 g/l Malt extract 5.0 g/l Casamino acids 5.0 g/l Glycerol 2.0 g/l Meat extract 2.0 g/l MgSO4 x 7 H2O 1.0 g/l Tween 80 0.05 g/l Distilled water

culture temp

  • @ref: 22648
  • growth: positive
  • type: growth
  • temperature: 28
  • range: mesophilic

Isolation, sampling and environmental information

isolation

  • @ref: 22648
  • sample type: pot of paddy soil planted with rice
  • geographic location: Suwon region
  • country: Republic of Korea
  • origin.country: KOR
  • continent: Asia

isolation source categories

Cat1Cat2Cat3
#Engineered#Agriculture#Field
#Environmental#Terrestrial#Soil
#Host#Plants#Herbaceous plants (Grass,Crops)

taxonmaps

  • @ref: 69479
  • File name: preview.99_16269.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_8267;97_9950;98_12233;99_16269&stattab=map
  • Last taxonomy: uncultured bacterium subclade
  • 16S sequence: KP100643
  • Sequence Identity:
  • Total samples: 282
  • soil counts: 91
  • aquatic counts: 38
  • animal counts: 149
  • plant counts: 4

Safety information

risk assessment

  • @ref: 22648
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 22648
  • description: Oryzobacter terrae strain PSGM2-16 16S ribosomal RNA gene, partial sequence
  • accession: KP100643
  • length: 1467
  • database: ena
  • NCBI tax ID: 1620385

GC content

  • @ref: 22648
  • GC-content: 70.0
  • method: fluorimetric

External links

@ref: 22648

culture collection no.: DSM 27137, KACC 17299, NBRC 109598

straininfo link

  • @ref: 89849
  • straininfo: 401381

literature

  • topic: Phylogeny
  • Pubmed-ID: 26297674
  • title: Oryzobacter terrae gen. nov., sp. nov., isolated from paddy soil.
  • authors: Kim SJ, Lim JM, Hamada M, Ahn JH, Weon HY, Suzuki KI, Ahn TY, Kwon SW
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.000398
  • year: 2015
  • mesh: *Actinomycetales/classification, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Soil, Soil Microbiology
  • topic2: Genetics

Reference

@idauthorstitledoi/urlcatalogue
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
22648Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-27137Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 27137)
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
89849Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID401381.1