Strain identifier

BacDive ID: 14268

Type strain: Yes

Species: Sphingomonas oryziterrae

Strain Designation: YC6722

Strain history: CIP <- 2012, DSMZ <- Y.R. Chung, GSNU Gyeongsang Nat. Univ., Jinju, Korea: strain YC6722 <- Z. Aslam

NCBI tax ID(s): 535906 (species)

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General

@ref: 15716

BacDive-ID: 14268

DSM-Number: 21455

keywords: 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative

description: Sphingomonas oryziterrae YC6722 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from rhizosphere soil from no-tillage rice field.

NCBI tax id

  • NCBI tax id: 535906
  • Matching level: species

strain history

@refhistory
15716<- Y. R. Chung, Gyeongsang Nat. Univ. (GSNU), Jinju, Korea; YC6722 <- Z. Aslam
67771<- YR Chung, Kyeongsang Univ.
121456CIP <- 2012, DSMZ <- Y.R. Chung, GSNU Gyeongsang Nat. Univ., Jinju, Korea: strain YC6722 <- Z. Aslam

doi: 10.13145/bacdive14268.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Sphingomonadales
  • family: Sphingomonadaceae
  • genus: Sphingomonas
  • species: Sphingomonas oryziterrae
  • full scientific name: Sphingomonas oryziterrae Chung et al. 2011

@ref: 15716

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Sphingomonadales

family: Sphingomonadaceae

genus: Sphingomonas

species: Sphingomonas oryziterrae

full scientific name: Sphingomonas oryziterrae Chung et al. 2011

strain designation: YC6722

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotility
67771negative
121456negativerod-shapedno

colony morphology

  • @ref: 15716
  • incubation period: 3-7 days

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
15716NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
40623MEDIUM 566- Reasoner's 2A agar for Flavobacterium micromatiyesDistilled water make up to (1000.000 ml);R2A agar (18.200 g)
121456CIP Medium 566yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=566

culture temp

@refgrowthtypetemperaturerange
15716positivegrowth28mesophilic
40623positivegrowth30mesophilic
67771positivegrowth28mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 67771
  • oxygen tolerance: aerobe

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836925115malate+assimilation
6836917128adipate+assimilation
6836927689decanoate-assimilation
6836924265gluconate-assimilation
6836917306maltose+assimilation
6836959640N-acetylglucosamine+assimilation
6836916899D-mannitol-assimilation
6836916024D-mannose+assimilation
6836930849L-arabinose+assimilation
6836917634D-glucose+assimilation
683695291gelatin-hydrolysis
683694853esculin+hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction

metabolite production

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase+3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
15716-----+-++++-++--++--+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
15716rhizosphere soil from no-tillage rice fieldJinjuRepublic of KoreaKORAsia
67771From rice fieldJinjuRepublic of KoreaKORAsia
121456Environment, Rhizosphere soil from no-tillage rice fieldJinjuRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Agriculture#Field
#Environmental#Terrestrial#Soil
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Rhizosphere

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
157161Risk group (German classification)
1214561Risk group (French classification)

Sequence information

16S sequences

  • @ref: 15716
  • description: Sphingomonas oryziterrae strain YC6722 16S ribosomal RNA gene, partial sequence
  • accession: EU707560
  • length: 1365
  • database: ena
  • NCBI tax ID: 535906

GC content

  • @ref: 67771
  • GC-content: 66.17

External links

@ref: 15716

culture collection no.: DSM 21455, CIP 110408, KCTC 22476

straininfo link

  • @ref: 83425
  • straininfo: 378359

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny21057052Sphingomonas oryziterrae sp. nov. and Sphingomonas jinjuensis sp. nov. isolated from rhizosphere soil of rice (Oryza sativa L.).Chung EJ, Jo EJ, Yoon HS, Song GC, Jeon CO, Chung YRInt J Syst Evol Microbiol10.1099/ijs.0.023846-02010Bacterial Typing Techniques, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Hydrogen-Ion Concentration, Korea, Molecular Sequence Data, Oryza/growth & development, Phospholipids/analysis, Phylogeny, Pigments, Biological/metabolism, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Sphingomonas/*classification/genetics/*isolation & purification/physiology, TemperatureGenetics
Phylogeny31596192Sphingomonas edaphi sp. nov., a novel species isolated from beach soil in the Republic of Korea.Kim H, Chhetri G, Seo TInt J Syst Evol Microbiol10.1099/ijsem.0.0037802020Bacterial Typing Techniques, Base Composition, *Bathing Beaches, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Spermidine/analogs & derivatives/chemistry, Sphingomonas/*classification/isolation & purification, Ubiquinone/analogs & derivatives/chemistryTranscriptome
Phylogeny33146742Sphingomonas xanthus sp. nov., Isolated from Beach Soil.Kim H, Chhetri G, Seo TCurr Microbiol10.1007/s00284-020-02273-z2020Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/analysis, Phospholipids, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil, Soil Microbiology, *Sphingomonas/geneticsTranscriptome
Phylogeny34323678Sphingomonas sabuli sp. nov., a carotenoid-producing bacterium isolated from beach sand.Kang M, Chhetri G, Kim J, Kim I, Seo TInt J Syst Evol Microbiol10.1099/ijsem.0.0048962021Bacterial Typing Techniques, Base Composition, Carotenoids, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phospholipids, Phylogeny, RNA, Ribosomal, 16S/genetics, Sand, Sequence Analysis, DNA, Soil Microbiology, Spermidine, *Sphingomonas/geneticsTranscriptome

Reference

@idauthorscataloguedoi/urltitle
15716Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21455)https://www.dsmz.de/collection/catalogue/details/culture/DSM-21455
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
40623Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/8264
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68369Automatically annotated from API 20NE
83425Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID378359.1StrainInfo: A central database for resolving microbial strain identifiers
121456Curators of the CIPCollection of Institut Pasteur (CIP 110408)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110408