Strain identifier

BacDive ID: 12717

Type strain: Yes

Species: Azomonas agilis

Strain history: <- ATCC <- N.R. Smith <- D. Burk <- H.W. Reuszer <- A.J. Kluyver (Azotobacter agilis)

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General

@ref: 163

BacDive-ID: 12717

DSM-Number: 375

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

description: Azomonas agilis DSM 375 is a mesophilic, motile bacterium of the family Pseudomonadaceae.

NCBI tax id

NCBI tax idMatching level
116849species
1121031strain

strain history

  • @ref: 163
  • history: <- ATCC <- N.R. Smith <- D. Burk <- H.W. Reuszer <- A.J. Kluyver (Azotobacter agilis)

doi: 10.13145/bacdive12717.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Pseudomonadales
  • family: Pseudomonadaceae
  • genus: Azomonas
  • species: Azomonas agilis
  • full scientific name: Azomonas agilis (Beijerinck 1901) Winogradsky 1938 (Approved Lists 1980)
  • synonyms

    • @ref: 20215
    • synonym: Azotobacter agilis

@ref: 163

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Pseudomonadales

family: Pseudomonadaceae

genus: Azomonas

species: Azomonas agilis

full scientific name: Azomonas agilis (Beijerinck 1901) Winogradsky 1938

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480yes98.03
6948099.998negative

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
163DIAZOTROPHIC MEDIUM (RBA) (DSMZ Medium 441)yeshttps://mediadive.dsmz.de/medium/441Name: DIAZOTROPHIC MEDIUM (RBA) (DSMZ Medium 441) Composition: Agar 14.881 g/l DL-Malate 1.98413 g/l D-Glucose 1.98413 g/l D-Mannitol 1.98413 g/l Na-pyruvate 0.992063 g/l Disodium succinate 0.992063 g/l K2HPO4 0.892857 g/l KH2PO4 0.0992065 g/l NaCl 0.0992065 g/l CaCl2 x 2 H2O 0.0992065 g/l MgSO4 x 7 H2O 0.0992065 g/l Yeast extract 0.0496032 g/l FeSO4 x 7 H2O 0.00992065 g/l MnSO4 x H2O 0.00496032 g/l NaVO3 x H2O 0.00496032 g/l Nicotinic acid 0.00248016 g/l Pyridoxine hydrochloride 0.00248016 g/l Calcium pantothenate 0.00248016 g/l Thiamine-HCl x 2 H2O 0.00248016 g/l H3BO3 0.000892857 g/l CoCl2 x 6 H2O 0.000595238 g/l Riboflavin 0.000496032 g/l ZnSO4 x 7 H2O 0.000297619 g/l MnCl2 x 4 H2O 8.92857e-05 g/l Na2MoO4 x 2 H2O 8.92857e-05 g/l NiCl2 x 6 H2O 5.95238e-05 g/l Vitamin B12 4.96032e-05 g/l CuCl2 x 2 H2O 2.97619e-05 g/l Folic acid 9.92063e-06 g/l Biotin 4.96032e-06 g/l Distilled water
163AZOTOBACTER MEDIUM (DSMZ Medium 3)yeshttps://mediadive.dsmz.de/medium/3Name: AZOTOBACTER MEDIUM (DSMZ Medium 3) Composition: Agar 15.0 g/l CaCO3 5.0 g/l Glucose 5.0 g/l Mannitol 5.0 g/l K2HPO4 0.9 g/l KH2PO4 0.1 g/l MgSO4 x 7 H2O 0.1 g/l CaCl2 x 2 H2O 0.1 g/l FeSO4 x 7 H2O 0.01 g/l Na2MoO4 x 2 H2O 0.005 g/l Distilled water

culture temp

  • @ref: 163
  • growth: positive
  • type: growth
  • temperature: 26
  • range: mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.983

compound production

@refcompound
163fluorescent pigment
163polyhydroxyalkanoic acids

Isolation, sampling and environmental information

taxonmaps

  • @ref: 69479
  • File name: preview.99_115427.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_23;96_18646;97_58772;98_78038;99_115427&stattab=map
  • Last taxonomy: Azomonas agilis subclade
  • 16S sequence: AB681882
  • Sequence Identity:
  • Total samples: 32
  • soil counts: 6
  • aquatic counts: 13
  • animal counts: 9
  • plant counts: 4

Safety information

risk assessment

  • @ref: 163
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Azomonas agilis gene for 16S rRNA, partial sequence, strain: NBRC 102607AB6818821462ena116849
20218Azomonas agilis gene for 16S rRNA, partial sequenceAB1756521451ena116849

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Azomonas agilis DSM 375GCA_007830255scaffoldncbi116849
66792Azomonas agilis strain DSM 375116849.3wgspatric116849
66792Azomonas agilis DSM 3752596583523draftimg116849

GC content

  • @ref: 163
  • GC-content: 51.9

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes86.383no
flagellatedyes67.803no
gram-positiveno98.958no
anaerobicno91.102no
aerobicyes64.746no
halophileno93.649no
spore-formingno94.595no
thermophileno97.778no
glucose-utilno56.033no
glucose-fermentno90.774no

External links

@ref: 163

culture collection no.: DSM 375, ATCC 7494, CCUG 53669, LMG 3842, IAM 15039, LMG 14901, LMG 8754, NCIMB 12097

straininfo link

  • @ref: 81926
  • straininfo: 1012

literature

  • topic: Enzymology
  • Pubmed-ID: 1987127
  • title: Detection of alternative nitrogenases in aerobic gram-negative nitrogen-fixing bacteria.
  • authors: Fallik E, Chan YK, Robson RL
  • journal: J Bacteriol
  • DOI: 10.1128/jb.173.1.365-371.1991
  • year: 1991
  • mesh: Azotobacter/enzymology/genetics, DNA Probes, DNA, Bacterial/genetics/isolation & purification, Escherichia coli/genetics, *Genes, Bacterial, Gram-Negative Aerobic Bacteria/enzymology/*genetics, *Nitrogen Fixation, Nitrogenase/*genetics, Nucleic Acid Hybridization, Pseudomonas/enzymology/genetics, Rhizobium/enzymology/genetics, Species Specificity
  • topic2: Phylogeny

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
163Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 375)https://www.dsmz.de/collection/catalogue/details/culture/DSM-375
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
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
81926Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID1012.1StrainInfo: A central database for resolving microbial strain identifiers