Strain identifier

BacDive ID: 1794

Type strain: Yes

Species: Nitrobacter hamburgensis

Strain Designation: X14

Strain history: <- E. Spieck <- E. Bock; X14

NCBI tax ID(s): 912 (species)

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General

@ref: 3854

BacDive-ID: 1794

DSM-Number: 10229

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

description: Nitrobacter hamburgensis X14 is a mesophilic bacterium of the family Nitrobacteraceae.

NCBI tax id

  • NCBI tax id: 912
  • Matching level: species

strain history

  • @ref: 3854
  • history: <- E. Spieck <- E. Bock; X14

doi: 10.13145/bacdive1794.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Hyphomicrobiales
  • family: Nitrobacteraceae
  • genus: Nitrobacter
  • species: Nitrobacter hamburgensis
  • full scientific name: Nitrobacter hamburgensis Bock et al. 2001

@ref: 3854

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Nitrobacteraceae

genus: Nitrobacter

species: Nitrobacter hamburgensis

full scientific name: Nitrobacter hamburgensis Bock et al. 2001

strain designation: X14

type strain: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
3854AUTOTROPHIC NITROBACTER MEDIUM (DSMZ Medium 756c)yeshttps://mediadive.dsmz.de/medium/756cName: AUTOTROPHIC NITROBACTER MEDIUM (DSMZ Medium 756c) Composition: NaNO2 2.0 g/l NaCl 0.5 g/l KH2PO4 0.15 g/l MgSO4 x 7 H2O 0.05 g/l CaCO3 0.007 g/l FeSO4 x 7 H2O 9.73e-05 g/l H3BO3 4.94e-05 g/l ZnSO4 x 7 H2O 4.31e-05 g/l (NH4)6Mo7O24 3.71e-05 g/l MnSO4 x H2O 3.38e-05 g/l CuSO4 x 5 H2O 2.5e-05 g/l Distilled water
385410% MIXOTROPHIC NITROBACTER MEDIUM (DSMZ Medium 756b)yeshttps://mediadive.dsmz.de/medium/756bName: 10% MIXOTROPHIC NITROBACTER MEDIUM (DSMZ Medium 756b) Composition: NaNO2 2.0 g/l NaCl 0.5 g/l KH2PO4 0.15 g/l Peptone 0.15 g/l Yeast extract 0.15 g/l Na-pyruvate 0.055 g/l MgSO4 x 7 H2O 0.05 g/l CaCO3 0.007 g/l FeSO4 x 7 H2O 9.73e-05 g/l H3BO3 4.94e-05 g/l ZnSO4 x 7 H2O 4.31e-05 g/l (NH4)6Mo7O24 3.71e-05 g/l MnSO4 x H2O 3.38e-05 g/l CuSO4 x 5 H2O 2.5e-05 g/l Distilled water
3854MIXOTROPHIC NITROBACTER MEDIUM (DSMZ Medium 756a)yeshttps://mediadive.dsmz.de/medium/756aName: MIXOTROPHIC NITROBACTER MEDIUM (DSMZ Medium 756a) Composition: NaNO2 2.0 g/l Yeast extract 1.5 g/l Peptone 1.5 g/l Na-pyruvate 0.55 g/l NaCl 0.5 g/l KH2PO4 0.15 g/l MgSO4 x 7 H2O 0.05 g/l CaCO3 0.007 g/l FeSO4 x 7 H2O 9.73e-05 g/l H3BO3 4.94e-05 g/l ZnSO4 x 7 H2O 4.31e-05 g/l (NH4)6Mo7O24 3.71e-05 g/l MnSO4 x H2O 3.38e-05 g/l CuSO4 x 5 H2O 2.5e-05 g/l Distilled water
3854HETEROTROPHIC NITROBACTER MEDIUM (DSMZ Medium 756)yeshttps://mediadive.dsmz.de/medium/756Name: HETEROTROPHIC NITROBACTER MEDIUM (DSMZ Medium 756) Composition: Yeast extract 1.5 g/l Peptone 1.5 g/l Na-pyruvate 0.55 g/l NaCl 0.5 g/l KH2PO4 0.15 g/l MgSO4 x 7 H2O 0.05 g/l CaCO3 0.007 g/l FeSO4 x 7 H2O 9.73e-05 g/l H3BO3 4.94e-05 g/l ZnSO4 x 7 H2O 4.31e-05 g/l (NH4)6Mo7O24 3.71e-05 g/l MnSO4 x H2O 3.38e-05 g/l CuSO4 x 5 H2O 2.5e-05 g/l Distilled water

culture temp

  • @ref: 3854
  • growth: positive
  • type: growth
  • temperature: 28
  • range: mesophilic

Isolation, sampling and environmental information

taxonmaps

  • @ref: 69479
  • File name: preview.99_7140.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_86;96_297;97_329;98_1900;99_7140&stattab=map
  • Last taxonomy: Nitrobacter
  • 16S sequence: L11663
  • Sequence Identity:
  • Total samples: 920
  • soil counts: 652
  • aquatic counts: 159
  • animal counts: 42
  • plant counts: 67

Safety information

risk assessment

  • @ref: 3854
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 3854
  • description: Nitrobacter hamburgensis 16S ribosomal RNA (16S rRNA) gene
  • accession: L11663
  • length: 1462
  • database: ena
  • NCBI tax ID: 323097

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nitrobacter hamburgensis X14GCA_000013885completencbi323097
66792Nitrobacter hamburgensis X14323097.20plasmidpatric323097
66792Nitrobacter hamburgensis X14323097.21plasmidpatric323097
66792Nitrobacter hamburgensis X14323097.22plasmidpatric323097
66792Nitrobacter hamburgensis X14323097.6completepatric323097
66792Nitrobacter hamburgensis X14637000192completeimg323097

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes70.394no
flagellatedno85.051no
gram-positiveno98.259no
anaerobicno94.576no
halophileno95.444no
spore-formingno92.38no
thermophileno98.411yes
glucose-utilyes62.116no
aerobicyes76.434no
glucose-fermentno92.634no

External links

@ref: 3854

culture collection no.: DSM 10229

straininfo link

  • @ref: 71441
  • straininfo: 48782

Reference

@idauthorscataloguedoi/urltitle
3854Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 10229)https://www.dsmz.de/collection/catalogue/details/culture/DSM-10229
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)
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
71441Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID48782.1StrainInfo: A central database for resolving microbial strain identifiers