Strain identifier

BacDive ID: 7226

Type strain: Yes

Species: Pleomorphomonas oryzae

Strain Designation: F-7

Strain history: IAM 15079 <-- Y. Masuchi F-7.

NCBI tax ID(s): 1122963 (strain), 261934 (species)

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General

@ref: 6350

BacDive-ID: 7226

DSM-Number: 16300

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

description: Pleomorphomonas oryzae F-7 is a mesophilic, Gram-negative, rod-shaped bacterium that was isolated from Oryza sativa.

NCBI tax id

NCBI tax idMatching level
261934species
1122963strain

strain history

@refhistory
6350<- CH.-H. Xie; F-7 <- 1982
67770IAM 15079 <-- Y. Masuchi F-7.

doi: 10.13145/bacdive7226.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Hyphomicrobiales
  • family: Pleomorphomonadaceae
  • genus: Pleomorphomonas
  • species: Pleomorphomonas oryzae
  • full scientific name: Pleomorphomonas oryzae Xie and Yokota 2005

@ref: 6350

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Pleomorphomonadaceae

genus: Pleomorphomonas

species: Pleomorphomonas oryzae

full scientific name: Pleomorphomonas oryzae Xie and Yokota 2005

strain designation: F-7

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31363negative3 µm0.75 µmrod-shapedno
69480yes96.908
69480negative99.978

pigmentation

  • @ref: 31363
  • production: no

multimedia

@refmultimedia contentcaptionintellectual property rights
66793EM_DSM_16300_1.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_16300_2.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_16300_3.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_16300_4.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_16300_5.jpgelectron microscopic image© HZI/Manfred Rohde

Culture and growth conditions

culture medium

  • @ref: 6350
  • name: NUTRIENT AGAR (DSMZ Medium 1)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/1
  • composition: Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
6350positivegrowth27mesophilic
67770positivegrowth25mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
31363no
69481no100
69480no99.942

observation

  • @ref: 67770
  • observation: quinones: Q-10

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3136330089acetate+carbon source
3136322599arabinose+carbon source
3136335391aspartate+carbon source
3136317057cellobiose+carbon source
3136328757fructose+carbon source
3136328260galactose+carbon source
3136324265gluconate+carbon source
3136317234glucose+carbon source
3136317754glycerol+carbon source
3136317716lactose+carbon source
3136325115malate+carbon source
3136329864mannitol+carbon source
3136337684mannose+carbon source
3136326271proline+carbon source
3136315361pyruvate+carbon source
3136316634raffinose+carbon source
3136326546rhamnose+carbon source
3136333942ribose+carbon source
3136317814salicin+carbon source
3136317822serine+carbon source
3136330911sorbitol+carbon source
3136317992sucrose+carbon source
3136327082trehalose+carbon source
3136318222xylose+carbon source
3136317632nitrate+reduction

metabolite production

  • @ref: 31363
  • Chebi-ID: 35581
  • metabolite: indole
  • production: yes

metabolite tests

  • @ref: 31363
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: +

enzymes

@refvalueactivityec
31363catalase+1.11.1.6
31363cytochrome oxidase+1.9.3.1
31363urease+3.5.1.5

Isolation, sampling and environmental information

isolation

@refsample typehost speciescountryorigin.countrycontinent
6350Oryza sativaOryza sativaJapanJPNAsia
67770Rice, Oryza sativa C5444Oryza sativa

isolation source categories

  • Cat1: #Host
  • Cat2: #Plants
  • Cat3: #Herbaceous plants (Grass,Crops)

taxonmaps

  • @ref: 69479
  • File name: preview.99_3720.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_5;96_1902;97_2285;98_2811;99_3720&stattab=map
  • Last taxonomy: Pleomorphomonas
  • 16S sequence: AB159680
  • Sequence Identity:
  • Total samples: 2970
  • soil counts: 978
  • aquatic counts: 901
  • animal counts: 721
  • plant counts: 370

Safety information

risk assessment

  • @ref: 6350
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 6350
  • description: Pleomorphomonas oryzae gene for 16S rRNA, partial sequence, strain:F-7
  • accession: AB159680
  • length: 1435
  • database: ena
  • NCBI tax ID: 261934

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pleomorphomonas oryzae DSM 163001122963.3wgspatric1122963
66792Pleomorphomonas oryzae DSM 163002523231067draftimg1122963
67770Pleomorphomonas oryzae DSM 16300GCA_000422965scaffoldncbi1122963

GC content

@refGC-contentmethod
3136362.6
6777063.1high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes84.666yes
flagellatedno84.549yes
gram-positiveno98.08yes
anaerobicno92.547no
aerobicno75.438no
halophileno96.221no
spore-formingno90.837no
glucose-utilyes93.602no
thermophileno98.465no
glucose-fermentno78.486no

External links

@ref: 6350

culture collection no.: DSM 16300, IAM 15079, JCM 21540, ATCC BAA 940, NBRC 102288

straininfo link

  • @ref: 76678
  • straininfo: 139008

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15879261Pleomorphomonas oryzae gen. nov., sp. nov., a nitrogen-fixing bacterium isolated from paddy soil of Oryza sativa.Xie CH, Yokota AInt J Syst Evol Microbiol10.1099/ijs.0.63406-02005Alphaproteobacteria/*classification/cytology/*isolation & purification/physiology, Bacterial Proteins/genetics, Base Composition, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Fatty Acids/analysis/isolation & purification, Genes, Bacterial, Genes, rRNA, Japan, Molecular Sequence Data, *Nitrogen Fixation, Nucleic Acid Hybridization, Oryza/*microbiology, Oxidoreductases/genetics, Phylogeny, Quinones/analysis/isolation & purification, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil MicrobiologyEnzymology
Phylogeny27902265Oharaeibacter diazotrophicus gen. nov., sp. nov., a diazotrophic and facultatively methylotrophic bacterium, isolated from rice rhizosphere.Lv H, Masuda S, Fujitani Y, Sahin N, Tani AInt J Syst Evol Microbiol10.1099/ijsem.0.0016602017Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Japan, Methylocystaceae/*classification/genetics/isolation & purification, Oryza/*microbiology, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
6350Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16300)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16300
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
31363Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2767628776041
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)
66793Mukherjee et al.10.1038/nbt.3886GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life28604660 35: 676-683 2017
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
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
76678Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID139008.1StrainInfo: A central database for resolving microbial strain identifiers