Strain identifier

BacDive ID: 17955

Type strain: Yes

Species: Ideonella azotifigens

Strain Designation: 1a22

Strain history: D. H. Buckley 1a22.

NCBI tax ID(s): 513160 (species)

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General

@ref: 15705

BacDive-ID: 17955

DSM-Number: 21438

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

description: Ideonella azotifigens 1a22 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from grass rhizosphere soil.

NCBI tax id

  • NCBI tax id: 513160
  • Matching level: species

strain history

@refhistory
15705<- D.H. Buckley, Cornell University <- J. D. Noar, Cornell University; 1a22
67770D. H. Buckley 1a22.

doi: 10.13145/bacdive17955.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Burkholderiales
  • family: Comamonadaceae
  • genus: Ideonella
  • species: Ideonella azotifigens
  • full scientific name: Ideonella azotifigens Noar and Buckley 2009

@ref: 15705

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Comamonadaceae

genus: Ideonella

species: Ideonella azotifigens

full scientific name: Ideonella azotifigens Noar and Buckley 2009

strain designation: 1a22

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
28994negative4 µm0.75 µmrod-shapedyes
69480yes93.672
69480negative99.998

Culture and growth conditions

culture medium

  • @ref: 15705
  • 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
15705positivegrowth28mesophilic
28994positivegrowth04-35
28994positiveoptimum06-08psychrophilic
67770positivegrowth30mesophilic

culture pH

  • @ref: 28994
  • ability: positive
  • type: optimum
  • pH: 6.5

Physiology and metabolism

oxygen tolerance

  • @ref: 28994
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no99
69480no99.992

halophily

  • @ref: 28994
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-0.5 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2899430089acetate+carbon source
2899417057cellobiose+carbon source
2899417234glucose+carbon source
2899429987glutamate+carbon source
2899425115malate+carbon source
2899429864mannitol+carbon source
2899437684mannose+carbon source
28994506227N-acetylglucosamine+carbon source
2899453424tween 20+carbon source
2899453423tween 40+carbon source
2899453425tween 60+carbon source
2899453426tween 80+carbon source

enzymes

@refvalueactivityec
28994catalase+1.11.1.6
28994gelatinase+
28994cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
15705grass rhizosphere soilIthaca, NYUSAUSANorth America
67770Soil in association with the rhizosphere of a perennial grass

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Rhizosphere

Safety information

risk assessment

  • @ref: 15705
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
15705Ideonella sp. 1a22 16S ribosomal RNA gene, partial sequenceEU5425761396ena513160
67770Ideonella azotifigens JCM 15503 gene for 16S ribosomal RNA, partial sequenceLC5087971451ena513160

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Ideonella azotifigens DSM 21438GCA_006519715contigncbi513160
66792Ideonella azotifigens strain DSM 21438513160.3wgspatric513160

GC content

@refGC-contentmethod
1570567.4
6777067.4high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno99no
gram-positiveno98.052yes
anaerobicno98.767yes
halophileno96.345yes
spore-formingno91.45no
glucose-utilyes89yes
aerobicyes93.565yes
thermophileno99.417yes
motileyes88.595yes
flagellatedyes50.916no
glucose-fermentno91.467no

External links

@ref: 15705

culture collection no.: DSM 21438, JCM 15503

straininfo link

  • @ref: 86942
  • straininfo: 401901

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19567574Ideonella azotifigens sp. nov., an aerobic diazotroph of the Betaproteobacteria isolated from grass rhizosphere soil, and emended description of the genus Ideonella.Noar JD, Buckley DHInt J Syst Evol Microbiol10.1099/ijs.0.003368-02009Bacterial Typing Techniques, Base Composition, Betaproteobacteria/*classification/genetics/*isolation & purification/physiology, Catalase/metabolism, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Hydroxybutyrates/metabolism, Locomotion, Molecular Sequence Data, New York, Nitrogen Fixation, Nucleic Acid Hybridization, Oxidoreductases/metabolism, Phylogeny, Plant Roots/*microbiology, Poaceae/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil MicrobiologyMetabolism
Phylogeny27045688Ideonella sakaiensis sp. nov., isolated from a microbial consortium that degrades poly(ethylene terephthalate).Tanasupawat S, Takehana T, Yoshida S, Hiraga K, Oda KInt J Syst Evol Microbiol10.1099/ijsem.0.0010582016Bacterial Typing Techniques, Base Composition, Betaproteobacteria/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Japan, *Microbial Consortia, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Polyethylene Terephthalates/*chemistry, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Ubiquinone/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
15705Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21438)https://www.dsmz.de/collection/catalogue/details/culture/DSM-21438
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
28994Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2542728776041
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
86942Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID401901.1StrainInfo: A central database for resolving microbial strain identifiers