Strain identifier

BacDive ID: 13891

Type strain: No

Species: Azospira oryzae

Strain Designation: PS

Strain history: <- J. D. Coates; PS

NCBI tax ID(s): 146939 (species)

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General

@ref: 5030

BacDive-ID: 13891

DSM-Number: 13638

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic

description: Azospira oryzae PS is an aerobe, mesophilic bacterium that was isolated from swine waste primary lagoons.

NCBI tax id

  • NCBI tax id: 146939
  • Matching level: species

strain history

  • @ref: 5030
  • history: <- J. D. Coates; PS

doi: 10.13145/bacdive13891.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Rhodocyclales
  • family: Rhodocyclaceae
  • genus: Azospira
  • species: Azospira oryzae
  • full scientific name: Azospira oryzae Reinhold-Hurek and Hurek 2000

  • synonyms

    @refsynonym
    20215Dechlorisoma suillus
    20215Dechlorosoma suillum
    20215Dechloromonas suillum

@ref: 5030

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Rhizobiales

family: Rhodocyclaceae

genus: Azospira

species: Azospira oryzae

full scientific name: Azospira oryzae Reinhold-Hurek and Hurek 2000 emend. Tan and Reinhold-Hurek 2003

strain designation: PS

type strain: no

Morphology

multimedia

  • @ref: 5030
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_13638.jpg
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5030R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 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
5030MEDIUM FOR CHLORATE RESPIRERS (DSMZ Medium 908)yeshttps://mediadive.dsmz.de/medium/908Name: MEDIUM FOR CHLORATE RESPIRERS (DSMZ Medium 908) Composition: NaHCO3 2.43665 g/l Na-acetate 1.32554 g/l NaClO3 0.974659 g/l NaH2PO4 0.584795 g/l NH4Cl 0.243665 g/l KCl 0.0974659 g/l MgSO4 0.0292398 g/l CaCl2 x 2 H2O 0.00974659 g/l HCl 0.00243665 g/l FeCl2 x 4 H2O 0.00146199 g/l alpha-lipoic acid 0.000243665 g/l p-Aminobenzoic acid 0.000243665 g/l Na2MoO4 0.000243665 g/l Thiamine-HCl x 2 H2O 0.000243665 g/l Na2WO4 x 2 H2O 0.000243665 g/l Vitamin B12 0.000243665 g/l Riboflavin 0.000243665 g/l Pantothenic acid 0.000243665 g/l CoCl2 x 6 H2O 0.000185185 g/l Nicotine amide 0.000121832 g/l Nicotinic acid 0.000121832 g/l Folic acid 9.74659e-05 g/l Biotin 9.74659e-05 g/l MnCl2 x 4 H2O 9.74659e-05 g/l ZnCl2 6.82261e-05 g/l Pyridoxamine hydrochloride 4.87329e-05 g/l Na2MoO4 x 2 H2O 3.50877e-05 g/l NiCl2 x 6 H2O 2.33918e-05 g/l H3BO3 5.84795e-06 g/l CuCl2 x 2 H2O 1.94932e-06 g/l Distilled water

culture temp

  • @ref: 5030
  • growth: positive
  • type: growth
  • temperature: 30
  • range: mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
5030aerobe
5030anaerobe

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
5030---------------+-+--+

Isolation, sampling and environmental information

isolation

  • @ref: 5030
  • sample type: swine waste primary lagoons
  • geographic location: Illinois
  • country: USA
  • origin.country: USA
  • continent: North America

isolation source categories

Cat1Cat2Cat3
#Engineered#Waste
#Host#Mammals#Suidae (Pig,Swine)

taxonmaps

  • @ref: 69479
  • File name: preview.99_4972.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_129;96_2435;97_2968;98_3718;99_4972&stattab=map
  • Last taxonomy: Azospira oryzae subclade
  • 16S sequence: AF170348
  • Sequence Identity:
  • Total samples: 32001
  • soil counts: 5057
  • aquatic counts: 15144
  • animal counts: 9661
  • plant counts: 2139

Safety information

risk assessment

  • @ref: 5030
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 5030
  • description: Dechlorosoma suillum 16S ribosomal RNA gene, complete sequence
  • accession: AF170348
  • length: 1532
  • database: ena
  • NCBI tax ID: 640081

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Azospira oryzae PSGCA_000236665completencbi640081
66792Azospira oryzae PS2508501046completeimg640081

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes93.932no
flagellatedyes84.352no
gram-positiveno99.386no
anaerobicno76.203no
aerobicno80.622no
halophileno97.431no
spore-formingno94.751no
thermophileno94.211no
glucose-utilno80.562no
glucose-fermentno91.445no

External links

@ref: 5030

culture collection no.: DSM 13638, ATCC BAA 33

straininfo link

  • @ref: 83066
  • straininfo: 49498

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny12892141Dechlorosoma suillum Achenbach et al. 2001 is a later subjective synonym of Azospira oryzae Reinhold-Hurek and Hurek 2000.Tan Z, Reinhold-Hurek BInt J Syst Evol Microbiol10.1099/ijs.0.02606-02003Bacterial Proteins/isolation & purification, Betaproteobacteria/*classification/genetics/metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Species Specificity, Terminology as TopicPhenotype
Phylogeny16166710Dechloromonas hortensis sp. nov. and strain ASK-1, two novel (per)chlorate-reducing bacteria, and taxonomic description of strain GR-1.Wolterink A, Kim S, Muusse M, Kim IS, Roholl PJM, van Ginkel CG, Stams AJM, Kengen SWMInt J Syst Evol Microbiol10.1099/ijs.0.63404-02005Chlorates/*metabolism, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Molecular Sequence Data, Nucleic Acid Hybridization, Oxidation-Reduction, Perchlorates/*metabolism, RNA, Ribosomal, 16S/genetics, Rhodocyclaceae/*classification/genetics/isolation & purification/metabolism, Sequence Analysis, DNA, Sewage/*microbiology, *Soil Microbiology, Species Specificity, Waste Disposal, Fluid/methods, Water Pollution, ChemicalMetabolism

Reference

@idauthorscataloguedoi/urltitle
5030Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 13638)https://www.dsmz.de/collection/catalogue/details/culture/DSM-13638
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
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)
68369Automatically annotated from API 20NE
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
83066Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID49498.1StrainInfo: A central database for resolving microbial strain identifiers