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Strain identifier

BacDive ID: 6945

Type strain: Yes

Species: Methanobacterium oryzae

Strain Designation: FPi

Strain history: <- C. Joulian, Université de Provence, Marseille, France; FPi <- C. Joulian {1995}

NCBI tax ID(s): 69540 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 4204

BacDive-ID: 6945

DSM-Number: 11106

keywords: genome sequence, 16S sequence, Archaea, anaerobe, mesophilic

description: Methanobacterium oryzae FPi is an anaerobe, mesophilic archaeon that was isolated from ricefield soil.

NCBI tax id

  • NCBI tax id: 69540
  • Matching level: species

strain history: <- C. Joulian, Université de Provence, Marseille, France; FPi <- C. Joulian {1995}

doi: 10.13145/bacdive6945.20221219.7.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/archaea
  • keyword: phylum/euryarchaeota
  • domain: Archaea
  • phylum: Euryarchaeota
  • class: Methanobacteria
  • order: Methanobacteriales
  • family: Methanobacteriaceae
  • genus: Methanobacterium
  • species: Methanobacterium oryzae
  • full scientific name: Methanobacterium oryzae Joulian et al. 2000

@ref: 4204

domain: Archaea

phylum: Euryarchaeota

class: Methanobacteria

order: Methanobacteriales

family: Methanobacteriaceae

genus: Methanobacterium

species: Methanobacterium oryzae

full scientific name: Methanobacterium oryzae Joulian et al. 2000

strain designation: FPi

type strain: yes

Morphology

colony morphology

  • @ref: 4204
  • incubation period: 2-3 days

Culture and growth conditions

culture medium

  • @ref: 4204
  • name: METHANOBACTERIUM II MEDIUM (N2/CO2) (DSMZ Medium 825a)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/825a
  • composition: Name: METHANOBACTERIUM II MEDIUM (N2/CO2) (DSMZ Medium 825a; with strain-specific modifications) Composition: Methanol 7.7571 g/l NaHCO3 3.91773 g/l Na-formate 2.9383 g/l Trypticase peptone 0.979432 g/l NH4Cl 0.979432 g/l Yeast extract 0.979432 g/l Na2S x 9 H2O 0.489716 g/l L-Cysteine HCl x H2O 0.489716 g/l Na-acetate 0.489716 g/l K2HPO4 0.29383 g/l KH2PO4 0.29383 g/l MgCl2 x 6 H2O 0.195886 g/l KCl 0.0979432 g/l MgSO4 x 7 H2O 0.029383 g/l Nitrilotriacetic acid 0.0146915 g/l NaCl 0.00979432 g/l MnSO4 x H2O 0.00489716 g/l ZnSO4 x 7 H2O 0.00176298 g/l CoSO4 x 7 H2O 0.00176298 g/l CaCl2 x 2 H2O 0.000979432 g/l FeSO4 x 7 H2O 0.000979432 g/l Sodium resazurin 0.000489716 g/l NiCl2 x 6 H2O 0.00029383 g/l AlK(SO4)2 x 12 H2O 0.000195886 g/l Na2MoO4 x 2 H2O 9.79432e-05 g/l CuSO4 x 5 H2O 9.79432e-05 g/l H3BO3 9.79432e-05 g/l Pyridoxine hydrochloride 9.79432e-05 g/l (DL)-alpha-Lipoic acid 4.89716e-05 g/l p-Aminobenzoic acid 4.89716e-05 g/l Thiamine HCl 4.89716e-05 g/l Riboflavin 4.89716e-05 g/l Nicotinic acid 4.89716e-05 g/l Calcium D-(+)-pantothenate 4.89716e-05 g/l Biotin 1.95886e-05 g/l Folic acid 1.95886e-05 g/l Na2WO4 x 2 H2O 3.91773e-06 g/l Na2SeO3 x 5 H2O 2.9383e-06 g/l Vitamin B12 9.79432e-07 g/l Distilled water

culture temp

  • @ref: 4204
  • growth: positive
  • type: growth
  • temperature: 37
  • range: mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 4204
  • oxygen tolerance: anaerobe

Isolation, sampling and environmental information

isolation

  • @ref: 4204
  • sample type: ricefield soil
  • country: Philippines
  • origin.country: PHL
  • continent: Asia

isolation source categories

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

Safety information

risk assessment

  • @ref: 4204
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 4204
  • description: Methanobacterium oryzae 16S ribosomal RNA, complete sequence
  • accession: AF028690
  • length: 1446
  • database: ena
  • NCBI tax ID: 69540

Genome sequences

  • @ref: 66792
  • description: Methanobacterium oryzae DSM 11106
  • accession: 2913351602
  • assembly level: draft
  • database: img
  • NCBI tax ID: 69540

GC content

  • @ref: 4204
  • GC-content: 31
  • method: high performance liquid chromatography (HPLC)

External links

@ref: 4204

culture collection no.: DSM 11106, NBRC 105229

straininfo link

  • @ref: 20218
  • passport: http://www.straininfo.net/strains/162481

literature

  • topic: Phylogeny
  • Pubmed-ID: 10758856
  • title: Methanobacterium oryzae sp. nov., a novel methanogenic rod isolated from a Philippines ricefield.
  • authors: Joulian C, Patel BK, Ollivier B, Garcia JL, Roger PA
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/00207713-50-2-525
  • year: 2000
  • mesh: Agriculture, Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Genes, rRNA, Methane/metabolism, Methanobacterium/*classification/genetics/isolation & purification/physiology, Molecular Sequence Data, *Oryza, Philippines, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Temperature
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
4204Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 11106)https://www.dsmz.de/collection/catalogue/details/culture/DSM-11106
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)