Strain identifier

BacDive ID: 133265

Type strain: Yes

Species: Paenibacillus oryzae

Strain Designation: 1DrF-4

Strain history: X. Zhang; ACCC, China; 1DrF-4.

NCBI tax ID(s): 1844972 (species)

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General

@ref: 25128

BacDive-ID: 133265

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, spore-forming, Gram-positive, motile, rod-shaped, colony-forming

description: Paenibacillus oryzae 1DrF-4 is a facultative anaerobe, spore-forming, Gram-positive bacterium that forms circular colonies and was isolated from rice roots.

NCBI tax id

  • NCBI tax id: 1844972
  • Matching level: species

strain history

  • @ref: 67770
  • history: X. Zhang; ACCC, China; 1DrF-4.

doi: 10.13145/bacdive133265.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Paenibacillaceae
  • genus: Paenibacillus
  • species: Paenibacillus oryzae
  • full scientific name: Paenibacillus oryzae Zhang et al. 2016

@ref: 25128

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Caryophanales

family: Paenibacillaceae

genus: Paenibacillus

species: Paenibacillus oryzae

strain designation: 1DrF-4

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
25128positive1.0-2.5 µm0.5-0.75 µmrod-shapedyes
69480yes97.849
69480positive100

colony morphology

  • @ref: 25128
  • colony color: greyish
  • colony shape: circular
  • medium used: TSA

Culture and growth conditions

culture medium

  • @ref: 25128
  • name: Trypticase Soy Agar (TSA)
  • growth: yes

culture temp

@refgrowthtypetemperaturerange
25128positivegrowth15-40
67770positivegrowth28mesophilic

culture pH

  • @ref: 25128
  • ability: positive
  • type: growth
  • pH: 6.0-11.0
  • PH range: alkaliphile

Physiology and metabolism

oxygen tolerance

  • @ref: 25128
  • oxygen tolerance: facultative anaerobe

spore formation

@reftype of sporespore formationconfidence
25128endosporeyes
69481yes100
69480yes100

halophily

  • @ref: 25128
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-3.0 %

observation

  • @ref: 67770
  • observation: quinones: MK-7

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2512817128adipate-carbon source
251282509agar-hydrolysis
25128casein-hydrolysis
2512817634D-glucose-carbon source
2512817634D-glucose-builds acid from
2512817634D-glucose-assimilation
2512816899D-mannitol-carbon source
2512816899D-mannitol-builds acid from
2512816899D-mannitol-assimilation
2512817924D-sorbitol-carbon source
2512827689decanoate-carbon source
251285291gelatin-hydrolysis
2512830849L-arabinose-builds acid from
2512862345L-rhamnose-carbon source
2512825115malate-carbon source
25128506227N-acetylglucosamine-carbon source
25128506227N-acetylglucosamine-assimilation
2512818401phenylacetate-carbon source
2512832032potassium gluconate-carbon source
2512832032potassium gluconate-assimilation
2512853258sodium citrate-carbon source
2512827897tryptophan-energy source
2512828938ammonium+nitrogen source
2512827613amygdalin+carbon source
2512827613amygdalin+builds acid from
2512816947citrate+carbon source
2512816024D-mannose+carbon source
2512816024D-mannose+assimilation
251284853esculin+hydrolysis
2512830849L-arabinose+carbon source
2512830849L-arabinose+assimilation
2512817306maltose+carbon source
2512828053melibiose+carbon source
2512828053melibiose+builds acid from
2512817632nitrate+reduction
2512828017starch+hydrolysis
2512817992sucrose+carbon source
2512817992sucrose+builds acid from
2512853426tween 80+hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
2512835581indoleno
2512815688acetoinyes

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole testcitrate test
2512815688acetoin+
2512835581indole-
2512816947citrate+

enzymes

@refvalueactivityec
25128arginine dihydrolase-3.5.3.6
25128beta-galactosidase+3.2.1.23
25128catalase-1.11.1.6
25128cytochrome oxidase+1.9.3.1
25128lysine decarboxylase-4.1.1.18
25128ornithine decarboxylase-4.1.1.17
25128tryptophan deaminase-4.1.99.1
25128urease-3.5.1.5

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
25128rice rootsQiyang County of Hunan ProvinceChinaCHNAsia
67770Rice roots from Qiyang County of Hunan ProvinceChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Root (Rhizome)

taxonmaps

  • @ref: 69479
  • File name: preview.99_34286.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15358;96_16515;97_20265;98_25335;99_34286&stattab=map
  • Last taxonomy: Paenibacillus oryzae subclade
  • 16S sequence: KX196453
  • Sequence Identity:
  • Total samples: 160
  • soil counts: 76
  • aquatic counts: 11
  • animal counts: 10
  • plant counts: 63

Sequence information

16S sequences

  • @ref: 25128
  • description: Paenibacillus oryzae strain 1DrF-4 16S ribosomal RNA gene, partial sequence
  • accession: KX196453
  • length: 1423
  • database: nuccore
  • NCBI tax ID: 1844972

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Paenibacillus oryzae strain 1DrF-41844972.5wgspatric1844972
66792Paenibacillus oryzae 1DrF-42791355222draftimg1844972
67770Paenibacillus oryzae 1DrF-4GCA_001675045scaffoldncbi1844972

GC content

@refGC-contentmethod
2512850.16Thermal denaturation, fluorometry
6777050.16thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileyes87.08yes
gram-positiveyes88.636yes
anaerobicno98.09yes
aerobicyes75.504yes
halophileno88.81no
spore-formingyes94.757yes
glucose-utilyes89.171no
flagellatedyes84.379no
glucose-fermentno85.766no
thermophileno99.741yes

External links

@ref: 25128

culture collection no.: ACCC 19927, JCM 30486

Reference

@idauthorstitledoi/urljournalpubmed
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
25128J. M. Zhang, X. T.,Gao, J. S.,Zhao, J. J.,Yin, H. Q.,Zhang, C. W.,Zhang, R. J.,Zhang, X. X.Paenibacillus oryzae sp. nov., isolated from rice roots10.1099/ijsem.0.001459IJSEM 66: 5000-5004 201627565704
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
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa1025Nucleic Acids Res. 49: D498-D508 202033211880
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