Strain identifier

BacDive ID: 17448

Type strain: Yes

Species: Arenimonas oryziterrae

Strain Designation: YC6267, Z0-2

Strain history: <- Y. R. Chung, Gyeongsang Natl. Univ., Jinju, Korea <- Z. Aslam

NCBI tax ID(s): 1121015 (strain), 498055 (species)

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General

@ref: 15536

BacDive-ID: 17448

DSM-Number: 21050

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

description: Arenimonas oryziterrae YC6267 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from rice rhizosphere soil from a no-tillage field.

NCBI tax id

NCBI tax idMatching level
1121015strain
498055species

strain history

  • @ref: 15536
  • history: <- Y. R. Chung, Gyeongsang Natl. Univ., Jinju, Korea <- Z. Aslam

doi: 10.13145/bacdive17448.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Lysobacterales
  • family: Lysobacteraceae
  • genus: Arenimonas
  • species: Arenimonas oryziterrae
  • full scientific name: Arenimonas oryziterrae Aslam et al. 2009

@ref: 15536

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Xanthomonadales

family: Lysobacteraceae

genus: Arenimonas

species: Arenimonas oryziterrae

full scientific name: Arenimonas oryziterrae Aslam et al. 2009

strain designation: YC6267, Z0-2

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
29092negative2.45 µm0.7 µmrod-shapedno
69480negative99.997

pigmentation

  • @ref: 29092
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 15536
  • name: REACTIVATION WITH LIQUID MEDIUM 830 (DSMZ Medium 830c)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/830c
  • composition: Name: REACTIVATION WITH LIQUID MEDIUM 830 (DSMZ Medium 830c) Composition: Agar 15.0 g/l Yeast extract 0.5 g/l Proteose peptone 0.5 g/l Casamino acids 0.5 g/l Glucose 0.5 g/l Starch 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

culture temp

@refgrowthtypetemperaturerange
15536positivegrowth28mesophilic
29092positivegrowth15-37
29092positiveoptimum28mesophilic

culture pH

@refabilitytypepHPH range
29092positivegrowth05-10alkaliphile
29092positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

  • @ref: 29092
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
29092no
69481no100
69480no99.995

observation

  • @ref: 29092
  • observation: aggregates in clumps

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2909235391aspartate+carbon source
2909253423tween 40+carbon source

enzymes

@refvalueactivityec
29092acid phosphatase+3.1.3.2
29092alkaline phosphatase+3.1.3.1
29092catalase+1.11.1.6
29092gelatinase+
29092cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

  • @ref: 15536
  • sample type: rice (Oryza sativa L.) rhizosphere soil from a no-tillage field
  • host species: Oryza sativa
  • geographic location: Jinju
  • 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)
#Host Body-Site#Plant#Rhizosphere

taxonmaps

  • @ref: 69479
  • File name: preview.99_3553.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_17;96_1849;97_2219;98_2724;99_3553&stattab=map
  • Last taxonomy: Arenimonas oryziterrae subclade
  • 16S sequence: EU376961
  • Sequence Identity:
  • Total samples: 2232
  • soil counts: 871
  • aquatic counts: 1120
  • animal counts: 148
  • plant counts: 93

Safety information

risk assessment

  • @ref: 15536
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 15536
  • description: Arenimonas oryziterrae strain YC6267 16S ribosomal RNA gene, partial sequence
  • accession: EU376961
  • length: 1430
  • database: ena
  • NCBI tax ID: 498055

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Arenimonas oryziterrae DSM 21050 = YC6267GCA_000420545contigncbi1121015
66792Arenimonas oryziterrae DSM 21050 = YC6267GCA_000747135contigncbi1121015
66792Arenimonas oryziterrae DSM 210501121015.3wgspatric1121015
66792Arenimonas oryziterrae DSM 21050 = YC62671121015.4wgspatric1121015
66792Arenimonas oryziterrae YC6267, DSM 210502627854209draftimg1121015
66792Arenimonas oryziterrae YC6267, DSM 210502524614729draftimg1121015

GC content

@refGC-contentmethod
1553665.8high performance liquid chromatography (HPLC)
2909265.8

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno89.026yes
flagellatedno96.865no
gram-positiveno98.459yes
anaerobicno98.799yes
aerobicyes88.728yes
halophileno95.545no
spore-formingno97.428no
thermophileno95.344yes
glucose-utilyes79.324no
glucose-fermentno90.028no

External links

@ref: 15536

culture collection no.: DSM 21050, KCTC 22247

straininfo link

  • @ref: 86444
  • straininfo: 397665

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19628604Arenimonas oryziterrae sp. nov., isolated from a field of rice (Oryza sativa L.) managed under a no-tillage regime, and reclassification of Aspromonas composti as Arenimonas composti comb. nov.Aslam Z, Park JH, Kim SW, Jeon CO, Chung YRInt J Syst Evol Microbiol10.1099/ijs.0.006031-02009Agriculture/methods, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Korea, Molecular Sequence Data, *Oryza, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, Xanthomonadaceae/*classification/genetics/*isolation & purification/metabolismGenetics
Phylogeny22493175Arenimonas daechungensis sp. nov., isolated from the sediment of a eutrophic reservoir.Huy H, Jin L, Lee YK, Lee KC, Lee JS, Yoon JH, Ahn CY, Oh HMInt J Syst Evol Microbiol10.1099/ijs.0.035410-02012Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Geologic Sediments/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Xanthomonadaceae/*classification/genetics/isolation & purificationGenetics
Phylogeny25795065Arenimonas subflava sp. nov., isolated from a drinking water network, and emended description of the genus Arenimonas.Makk J, Homonnay ZG, Keki Z, Nemes-Barnas K, Marialigeti K, Schumann P, Toth EMInt J Syst Evol Microbiol10.1099/ijs.0.0002012015Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Drinking Water/*microbiology, Fatty Acids/chemistry, Hungary, Lysobacter/genetics, Molecular Sequence Data, Phosphatidylethanolamines/chemistry, Phosphatidylglycerols/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Ubiquinone/chemistry, Water Supply, Xanthomonadaceae/*classification/genetics/isolation & purificationGenetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
15536Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21050)https://www.dsmz.de/collection/catalogue/details/culture/DSM-21050
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
29092Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2552128776041
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updates33211880Nucleic Acids Res. 49: D498-D508 2020
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
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
86444Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID397665.1StrainInfo: A central database for resolving microbial strain identifiers