Strain identifier
BacDive ID: 1796
Type strain: 
Species: Nitrobacter winogradskyi
Strain Designation: 255
Strain history: <- E. Spiek <- E. Bock
NCBI tax ID(s): 913 (species)
version 8.1 (current version)
General
@ref: 3860
BacDive-ID: 1796
DSM-Number: 10237
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative
description: Nitrobacter winogradskyi 255 is a mesophilic, Gram-negative bacterium of the family Nitrobacteraceae.
NCBI tax id
- NCBI tax id: 913
- Matching level: species
strain history
- @ref: 3860
- history: <- E. Spiek <- E. Bock
doi: 10.13145/bacdive1796.20230509.8.1
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 winogradskyi
- full scientific name: Nitrobacter winogradskyi Winslow et al. 1917 (Approved Lists 1980)
@ref: 3860
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhizobiales
family: Nitrobacteraceae
genus: Nitrobacter
species: Nitrobacter winogradskyi
full scientific name: Nitrobacter winogradskyi Winslow et al. 1917
strain designation: 255
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 100
Culture and growth conditions
culture medium
- @ref: 3860
- name: MIXOTROPHIC NITROBACTER MEDIUM (DSMZ Medium 756a)
- growth: yes
- link: https://mediadive.dsmz.de/medium/756a
- composition: Name: 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
culture temp
- @ref: 3860
- growth: positive
- type: growth
- temperature: 28
- range: mesophilic
Physiology and metabolism
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 99.998 |
Isolation, sampling and environmental information
taxonmaps
- @ref: 69479
- File name: preview.99_2433.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_86;96_297;97_329;98_1900;99_2433&stattab=map
- Last taxonomy: Nitrobacter
- 16S sequence: NR_074324
- Sequence Identity:
- Total samples: 8985
- soil counts: 5887
- aquatic counts: 1315
- animal counts: 625
- plant counts: 1158
Safety information
risk assessment
- @ref: 3860
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 3860
- description: Nitrobacter winogradskyi strain Nb-255 16S ribosomal RNA, partial sequence
- accession: NR_074324
- length: 1490
- database: nuccore
- NCBI tax ID: 913
Genome sequences
- @ref: 66792
- description: Nitrobacter winogradskyi Nb-255
- accession: 323098.6
- assembly level: complete
- database: patric
- NCBI tax ID: 323098
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| gram-positive | no | 98.71 | no |
| anaerobic | no | 96.317 | no |
| halophile | no | 93.445 | no |
| spore-forming | no | 94.814 | no |
| glucose-util | yes | 59.627 | no |
| motile | yes | 71.135 | no |
| flagellated | no | 84.677 | no |
| thermophile | no | 91.082 | yes |
| aerobic | yes | 67.261 | no |
| glucose-ferment | no | 93.118 | no |
External links
@ref: 3860
culture collection no.: DSM 10237, ATCC 25391
straininfo link
- @ref: 71443
- straininfo: 38533
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Genetics | 16517654 | Genome sequence of the chemolithoautotrophic nitrite-oxidizing bacterium Nitrobacter winogradskyi Nb-255. | Starkenburg SR, Chain PS, Sayavedra-Soto LA, Hauser L, Land ML, Larimer FW, Malfatti SA, Klotz MG, Bottomley PJ, Arp DJ, Hickey WJ | Appl Environ Microbiol | 10.1128/AEM.72.3.2050-2063.2006 | 2006 | Bacterial Proteins/genetics/metabolism, Carbon Dioxide/metabolism, *Genome, Bacterial, Molecular Sequence Data, Nitrites/*metabolism, *Nitrobacter/classification/genetics/metabolism/physiology, Oxidation-Reduction, Phylogeny, *Sequence Analysis, DNA | Metabolism |
| Phylogeny | 18023467 | Distribution of Nitrosomonas europaea and Nitrobacter winogradskyi in an autotrophic nitrifying biofilm reactor as depicted by molecular analyses and mathematical modelling. | Montras A, Pycke B, Boon N, Godia F, Mergeay M, Hendrickx L, Perez J | Water Res | 10.1016/j.watres.2007.10.025 | 2007 | Base Sequence, *Biofilms, *Bioreactors, DNA Primers, In Situ Hybridization, Fluorescence, *Models, Theoretical, Nitrobacter/genetics/*isolation & purification, Nitrosomonas/genetics/*isolation & purification, Polymerase Chain Reaction, RNA, Ribosomal, 16S/genetics | Enzymology |
Reference
| @id | authors | catalogue | doi/url | title |
|---|---|---|---|---|
| 3860 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 10237) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-10237 | |
| 20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |
| 69479 | João 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 | |
| 69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |
| 69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |
| 71443 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID38533.1 | StrainInfo: A central database for resolving microbial strain identifiers |