Strain identifier

BacDive ID: 12725

Type strain: Yes

Species: Azotobacter beijerinckii

Strain Designation: 3, M.B. 2.3.

Strain history: CIP <- 1999, NCAIM <- DSMZ <- ATCC <- NCIB <- C.B. van Niel: strain M.B. 2.3. <- S. Soriano: strain 3

NCBI tax ID(s): 170623 (species)

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General

@ref: 165

BacDive-ID: 12725

DSM-Number: 378

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, mesophilic, Gram-negative

description: Azotobacter beijerinckii 3 is an obligate aerobe, mesophilic, Gram-negative bacterium that was isolated from activated sludge.

NCBI tax id

  • NCBI tax id: 170623
  • Matching level: species

strain history

@refhistory
165<- ATCC <- NCIB <- C.B. van Niel, M.B. 2.3. <- S. Soriano, 3
67770IAM 12683 <-- I. Niou <-- DSM 378 <-- ATCC 19360 <-- NCIB 8948 <-- C. B. van Niel M.B.2.3 <-- S. Soriano.
116773CIP <- 1999, NCAIM <- DSMZ <- ATCC <- NCIB <- C.B. van Niel: strain M.B. 2.3. <- S. Soriano: strain 3

doi: 10.13145/bacdive12725.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Pseudomonadales
  • family: Pseudomonadaceae
  • genus: Azotobacter
  • species: Azotobacter beijerinckii
  • full scientific name: Azotobacter beijerinckii Lipman 1904 (Approved Lists 1980)

@ref: 165

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Pseudomonadales

family: Pseudomonadaceae

genus: Azotobacter

species: Azotobacter beijerinckii

full scientific name: Azotobacter beijerinckii Lipman 1904

strain designation: 3, M.B. 2.3.

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480negative99.989
116773negativerod-shapedno

colony morphology

  • @ref: 116773

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
32950MEDIUM 1 - for Acetobacter, Azotobacter, Gluconobacter, Gluconacetobacter, Mesorhizodium ciceri and Pseudomonas doudoroffiiyesDistilled water make up to (1000.000 ml);Agar (15.000 g);Yeast extract (5.000 g);Peptone (3.000 g);Mannitol (25.000 g)
165DIAZOTROPHIC MEDIUM (RBA) (DSMZ Medium 441)yesName: 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 waterhttps://mediadive.dsmz.de/medium/441
116773CIP Medium 314yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=314
116773CIP Medium 1yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=1

culture temp

@refgrowthtypetemperaturerange
165positivegrowth30mesophilic
32950positivegrowth30mesophilic
67770positivegrowth30mesophilic
116773positivegrowth25-37mesophilic
116773nogrowth5psychrophilic
116773nogrowth15psychrophilic
116773nogrowth41thermophilic
116773nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 116773
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.879

halophily

@refsaltgrowthtested relationconcentration
116773NaClpositivegrowth0 %
116773NaClnogrowth2 %
116773NaClnogrowth4 %
116773NaClnogrowth6 %
116773NaClnogrowth8 %
116773NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1167734853esculin+hydrolysis
116773606565hippurate-hydrolysis
11677317632nitrate-builds gas from
11677317632nitrate-reduction
11677316301nitrite-builds gas from
11677316301nitrite-reduction
11677317632nitrate-respiration

metabolite production

  • @ref: 116773
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11677315688acetoin-
11677317234glucose+

enzymes

@refvalueactivityec
116773oxidase+
116773beta-galactosidase-3.2.1.23
116773alcohol dehydrogenase-1.1.1.1
116773gelatinase-
116773DNase-
116773caseinase-3.4.21.50
116773catalase+1.11.1.6
116773gamma-glutamyltransferase-2.3.2.2
116773lecithinase-
116773lipase-
116773lysine decarboxylase-4.1.1.18
116773ornithine decarboxylase-4.1.1.17
116773phenylalanine ammonia-lyase-4.3.1.24
116773tryptophan deaminase-
116773urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase-3.1.3.2
68382naphthol-AS-BI-phosphohydrolase-
68382alpha-galactosidase+3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
116773-+++-++-----+--+----

Isolation, sampling and environmental information

isolation

@refsample type
165activated sludge
59970Sludge,activated
67770Activated sludge
116773Environment, Activated sludge

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Waste
  • Cat3: #Activated sludge

taxonmaps

  • @ref: 69479
  • File name: preview.99_61430.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_23;96_646;97_749;98_43592;99_61430&stattab=map
  • Last taxonomy: Azotobacter
  • 16S sequence: AJ308319
  • Sequence Identity:
  • Total samples: 186
  • soil counts: 93
  • aquatic counts: 56
  • animal counts: 28
  • plant counts: 9

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
1651Risk group (German classification)
1167731Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Azotobacter beijerinckii partial 16S rRNA gene, isolate ICMP 8673; ATCC 19360AJ3083191384ena170623
20218Azotobacter beijerinckii strain ICMP 8673 16S ribosomal RNA gene, partial sequenceEF1001521372ena170623
20218Azotobacter beijerinckii DSM378 16S ribosomal RNA gene, partial sequenceAY336566863ena170623
20218Azotobacter beijerinckii strain ICMP 8673 16S ribosomal RNA gene, partial sequenceKC1728551248ena170623

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Azotobacter beijerinckii strain DSM 378170623.6wgspatric170623
66792Azotobacter beijerinckii DSM 3782597490340draftimg170623
67770Azotobacter beijerinckii DSM 378GCA_900110885scaffoldncbi170623

GC content

  • @ref: 165
  • GC-content: 66.2

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno66.263no
gram-positiveno98.752no
anaerobicno97.979no
aerobicyes80.719no
halophileno89.41no
spore-formingno93.9no
thermophileno99.013no
glucose-utilyes86.788no
flagellatedno80.859no
glucose-fermentno89.644no

External links

@ref: 165

culture collection no.: DSM 378, ATCC 19360, NCIB 8948, VKM B-1615, CCUG 53670, LMG 1265, BCRC 14360, CIP 106282, IAM 12683, JCM 20742, CECT 9204, ICMP 8673, NCAIM B.01800, NCIMB 8948, NRRL B-14367, NRRL B-14640

straininfo link

  • @ref: 81934
  • straininfo: 1067

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
165Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 378)https://www.dsmz.de/collection/catalogue/details/culture/DSM-378
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
32950Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18395
59970Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 53670)https://www.ccug.se/strain?id=53670
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/
68382Automatically annotated from API zym
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
81934Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID1067.1StrainInfo: A central database for resolving microbial strain identifiers
116773Curators of the CIPCollection of Institut Pasteur (CIP 106282)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106282