Strain identifier

BacDive ID: 11857

Type strain: Yes

Species: Aminobacter aminovorans

Strain Designation: TK3001, TK 3001

Strain history: CIP <- 2000, JCM <- T. Urakami, strain TK 3001 <- NCIMB <- LMD <- L. E. den Dooren de Jong

NCBI tax ID(s): 83263 (species)

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General

@ref: 2959

BacDive-ID: 11857

DSM-Number: 7048

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

description: Aminobacter aminovorans TK3001 is an obligate aerobe, mesophilic, Gram-negative bacterium that was isolated from garden soil by enrichment with trimethylamine.

NCBI tax id

  • NCBI tax id: 83263
  • Matching level: species

strain history

@refhistory
2959<- JCM <- T. Urakami, TK3001 <- NCIB <- LMD <- L.E. den Dooren de Jong
67770T. Urakami TK3001 <-- NCIB 9039 <-- LMD <-- L. E. den Dooren de Jong.
116335CIP <- 2000, JCM <- T. Urakami, strain TK 3001 <- NCIMB <- LMD <- L. E. den Dooren de Jong

doi: 10.13145/bacdive11857.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Hyphomicrobiales
  • family: Phyllobacteriaceae
  • genus: Aminobacter
  • species: Aminobacter aminovorans
  • full scientific name: Aminobacter aminovorans (den Dooren de Jong 1926) Urakami et al. 1992

  • synonyms

    @refsynonym
    20215Pseudomonas aminovorans
    20215Aminobacter heintzii
    20215Chelatobacter heintzii

@ref: 2959

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Phyllobacteriaceae

genus: Aminobacter

species: Aminobacter aminovorans

full scientific name: Aminobacter aminovorans (den Dooren de Jong 1926) Urakami et al. 1992 emend. Kämpfer et al. 2002

strain designation: TK3001, TK 3001

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480negative99.976
116335negativerod-shapedyes

pigmentation

  • @ref: 116335
  • production: no
  • name: Pyocyanin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
2959NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
39567MEDIUM 328- for nutrient agaryesDistilled water make up to (1000.000 ml);Agar (15.000 g);Peptone (5.000g);Beef extract (3.000 g)
116335CIP Medium 328yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=328

culture temp

@refgrowthtypetemperaturerange
2959positivegrowth30mesophilic
39567positivegrowth30mesophilic
67770positivegrowth30mesophilic
116335positivegrowth25-30mesophilic
116335nogrowth5psychrophilic
116335nogrowth10psychrophilic
116335nogrowth37mesophilic
116335nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 116335
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.999

halophily

@refsaltgrowthtested relationconcentration
116335NaClpositivegrowth0-4 %
116335NaClnogrowth6 %
116335NaClnogrowth8 %
116335NaClnogrowth10 %

observation

  • @ref: 67770
  • observation: quinones: Q-10

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
11633516947citrate-carbon source
1163354853esculin-hydrolysis
11633517632nitrate-reduction
11633516301nitrite-reduction
11633517632nitrate-respiration

antibiotic resistance

  • @ref: 116335
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 116335
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
116335oxidase+
116335beta-galactosidase-3.2.1.23
116335alcohol dehydrogenase-1.1.1.1
116335gelatinase-
116335amylase-
116335DNase-
116335caseinase-3.4.21.50
116335catalase+1.11.1.6
116335tween esterase-
116335lecithinase-
116335lipase-
116335lysine decarboxylase-4.1.1.18
116335ornithine decarboxylase-4.1.1.17
116335protease-
116335tryptophan deaminase-
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
116335-+++-++-+-++---+----

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
116335+++++--+--+----++-++++-++-+----+++-++------------+------+-++-----------+-+-+--+---+---+--+++-++--++

Isolation, sampling and environmental information

isolation

@refsample type
2959garden soil by enrichment with trimethylamine
44478Garden soil by enrichment with trimethylamine 30°C
67770Garden soil by enrichment with trimethylamine
116335Environment, Garden soil, enrichment with trimethylamine

isolation source categories

Cat1Cat2Cat3
#Engineered#Agriculture#Garden
#Environmental#Terrestrial#Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_1038.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_5;96_220;97_697;98_812;99_1038&stattab=map
  • Last taxonomy: Mesorhizobium
  • 16S sequence: AJ011759
  • Sequence Identity:
  • Total samples: 1264
  • soil counts: 780
  • aquatic counts: 308
  • animal counts: 145
  • plant counts: 31

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
29591Risk group (German classification)
1163351Risk group (French classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: Aminobacter aminovorans strain DSM7048T, 16S rRNA gene, partial
  • accession: AJ011759
  • length: 1470
  • database: ena
  • NCBI tax ID: 83263

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Aminobacter aminovorans NCTC10684GCA_900445235contigncbi83263
66792Aminobacter aminovorans strain DSM 704883263.12wgspatric83263
66792Aminobacter aminovorans strain NCTC1068483263.10wgspatric83263
66792Aminobacter aminovorans DSM 70482784746775draftimg83263
66792Aminobacter aminovorans NCTC 106842808606775draftimg83263
67770Aminobacter aminovorans DSM 7048GCA_004341645scaffoldncbi83263

GC content

  • @ref: 67770
  • GC-content: 62.5
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes90.437no
flagellatedno65.476no
gram-positiveno98.105no
anaerobicno99.036no
halophileno89.595no
spore-formingno95.354no
glucose-utilyes93.78no
aerobicyes94.691no
thermophileno97.994yes
glucose-fermentno90.055no

External links

@ref: 2959

culture collection no.: DSM 7048, ATCC 23314, JCM 7852, NCIB 9039, CCUG 2081, NCTC 2871, LMG 2122, CIP 106737, NCTC 10684, BCRC 15819, CCM 4329, CFBP 6720, IAM 15264, NCCB 26039, NCIMB 9039, VKM B-2058

straininfo link

  • @ref: 81075
  • straininfo: 13573

literature

  • topic: Phylogeny
  • Pubmed-ID: 19666787
  • title: Chelativorans multitrophicus gen. nov., sp. nov. and Chelativorans oligotrophicus sp. nov., aerobic EDTA-degrading bacteria.
  • authors: Doronina NV, Kaparullina EN, Trotsenko YA, Nortemann B, Bucheli-Witschel M, Weilenmann HU, Egli T
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.003152-0
  • year: 2009
  • mesh: Aerobiosis, Alphaproteobacteria/*classification/genetics/metabolism/physiology, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Edetic Acid/*metabolism, Fatty Acids/analysis, Genes, rRNA, Genotype, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Russia, Sequence Analysis, DNA, Sewage/*microbiology, Species Specificity, Switzerland
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
2959Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 7048)https://www.dsmz.de/collection/catalogue/details/culture/DSM-7048
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
39567Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18901
44478Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 2081)https://www.ccug.se/strain?id=2081
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
81075Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID13573.1StrainInfo: A central database for resolving microbial strain identifiers
116335Curators of the CIPCollection of Institut Pasteur (CIP 106737)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106737