Strain identifier

BacDive ID: 134147

Type strain: Yes

Species: Zoogloea oryzae

Strain Designation: A-7

Strain history: IAM 15218 <-- C.-H. Xie and A. Yokota A-7.

NCBI tax ID(s): 310767 (species)

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General

@ref: 31534

BacDive-ID: 134147

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

description: Zoogloea oryzae A-7 is an aerobe, Gram-negative, motile bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 310767
  • Matching level: species

strain history

  • @ref: 67770
  • history: IAM 15218 <-- C.-H. Xie and A. Yokota A-7.

doi: 10.13145/bacdive134147.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Rhodocyclales
  • family: Zoogloeaceae
  • genus: Zoogloea
  • species: Zoogloea oryzae
  • full scientific name: Zoogloea oryzae Xie and Yokota 2006

@ref: 31534

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Rhodocyclales

family: Zoogloeaceae

genus: Zoogloea

species: Zoogloea oryzae

strain designation: A-7

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31534negative1.5-2 µm0.5-0.7 µmrod-shapedyes
69480negative99.955

pigmentation

  • @ref: 31534
  • production: yes

Culture and growth conditions

culture temp

@refgrowthtypetemperaturerange
31534positivegrowth10-37
31534positiveoptimum30-37mesophilic
67770positivegrowth30mesophilic

culture pH

@refabilitytypepH
31534positivegrowth7
31534positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 31534
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
31534no
69481no100
69480no99.996

observation

@refobservation
31534aggregates in chains
67770quinones: Q-8

enzymes

@refvalueactivityec
31534catalase+1.11.1.6
31534cytochrome oxidase+1.9.3.1
31534urease+3.5.1.5

Isolation, sampling and environmental information

isolation

@refsample type
31534soil
67770Soil from a rice paddy field

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_12668.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_129;96_3402;97_7763;98_9548;99_12668&stattab=map
  • Last taxonomy: Zoogloea oryzae
  • 16S sequence: AB201043
  • Sequence Identity:
  • Total samples: 395
  • soil counts: 6
  • aquatic counts: 371
  • animal counts: 14
  • plant counts: 4

Sequence information

16S sequences

  • @ref: 31534
  • description: Zoogloea oryzae gene for 16S rRNA, partial sequence, strain: A-7
  • accession: AB201043
  • length: 1487
  • database: nuccore
  • NCBI tax ID: 310767

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Zoogloea oryzae NBRC 102407GCA_003290265completencbi310767
66792Zoogloea oryzae strain NBRC 102407310767.3completepatric310767
66792Zoogloea oryzae NBRC 1024072832915741completeimg310767

GC content

@refGC-contentmethod
3153465.1
6777065.1high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno80.899no
flagellatedno95.3no
gram-positiveno96.277no
anaerobicno91.076no
aerobicyes81.429yes
halophileno76.62no
spore-formingno98.514yes
glucose-utilyes74.968no
thermophileno83.171no
glucose-fermentno60.278no

External links

@ref: 31534

culture collection no.: IAM 15218, CCTCC AB 2052005, JCM 21672, NBRC 102407

straininfo link

  • @ref: 91745
  • straininfo: 291019

literature

  • topic: Phylogeny
  • Pubmed-ID: 16514038
  • title: Zoogloea oryzae sp. nov., a nitrogen-fixing bacterium isolated from rice paddy soil, and reclassification of the strain ATCC 19623 as Crabtreella saccharophila gen. nov., sp. nov.
  • authors: Xie CH, Yokota A
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.63755-0
  • year: 2006
  • mesh: Alphaproteobacteria/chemistry/*classification/genetics/isolation & purification, DNA, Ribosomal/chemistry, Fatty Acids/analysis, *Nitrogen Fixation, Oryza/*microbiology, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Zoogloea/chemistry/*classification/genetics/isolation & purification
  • topic2: Enzymology

Reference

@idauthorstitledoi/urlID_cross_referencepubmed
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
31534Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172782728776041
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
91745Reimer, 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-ID291019.1