Strain identifier
BacDive ID: 1783
Type strain: 
Species: Afipia sp.
Strain Designation: 1NLS2
Strain history: <- S. Green, Oceanography Dept., Florida State Univ., Tallahassee, USA; 1NLS2 <- O. Prakash
NCBI tax ID(s): 1871052 (species)
version 8.1 (current version)
General
@ref: 17295
BacDive-ID: 1783
DSM-Number: 23597
keywords: genome sequence, 16S sequence, Bacteria, mesophilic
description: Afipia sp. 1NLS2 is a mesophilic bacterium that was isolated from contaminated surface sediment.
NCBI tax id
- NCBI tax id: 1871052
- Matching level: species
strain history
- @ref: 17295
- history: <- S. Green, Oceanography Dept., Florida State Univ., Tallahassee, USA; 1NLS2 <- O. Prakash
doi: 10.13145/bacdive1783.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Hyphomicrobiales
- family: Nitrobacteraceae
- genus: Afipia
- species: Afipia sp.
- full scientific name: Afipia Brenner et al. 1992
synonyms
- @ref: 20215
- synonym: Oligotropha
@ref: 17295
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhizobiales
family: Nitrobacteraceae
genus: Afipia
species: Afipia sp.
full scientific name: Afipia sp.
strain designation: 1NLS2
type strain: no
Culture and growth conditions
culture medium
- @ref: 17295
- name: R2A MEDIUM (DSMZ Medium 830)
- growth: yes
- link: https://mediadive.dsmz.de/medium/830
- composition: Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
culture temp
- @ref: 17295
- growth: positive
- type: growth
- temperature: 28
- range: mesophilic
Physiology and metabolism
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 68369 | 25115 | malate | + | assimilation |
| 68369 | 17128 | adipate | - | assimilation |
| 68369 | 27689 | decanoate | - | assimilation |
| 68369 | 24265 | gluconate | - | assimilation |
| 68369 | 17306 | maltose | - | assimilation |
| 68369 | 59640 | N-acetylglucosamine | - | assimilation |
| 68369 | 16899 | D-mannitol | - | assimilation |
| 68369 | 16024 | D-mannose | - | assimilation |
| 68369 | 30849 | L-arabinose | - | assimilation |
| 68369 | 17634 | D-glucose | - | assimilation |
| 68369 | 5291 | gelatin | - | hydrolysis |
| 68369 | 4853 | esculin | - | hydrolysis |
| 68369 | 16199 | urea | - | hydrolysis |
| 68369 | 29016 | arginine | - | hydrolysis |
| 68369 | 17634 | D-glucose | - | fermentation |
| 68369 | 27897 | tryptophan | - | energy source |
| 68369 | 17632 | nitrate | + | reduction |
| 68377 | 17634 | D-glucose | - | builds acid from |
| 68377 | 15824 | D-fructose | - | builds acid from |
| 68377 | 17306 | maltose | - | builds acid from |
metabolite production
- @ref: 68369
- Chebi-ID: 35581
- metabolite: indole
- production: no
metabolite tests
- @ref: 68369
- Chebi-ID: 35581
- metabolite: indole
- indole test: -
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 68377 | gamma-glutamyltransferase | - | 2.3.2.2 |
| 68377 | proline-arylamidase | - | 3.4.11.5 |
| 68377 | beta-galactosidase | - | 3.2.1.23 |
| 68377 | alkaline phosphatase | - | 3.1.3.1 |
| 68369 | gelatinase | - | |
| 68369 | beta-glucosidase | - | 3.2.1.21 |
| 68369 | urease | - | 3.5.1.5 |
| 68369 | arginine dihydrolase | - | 3.5.3.6 |
API 20NE
| @ref | NO3 | TRP | GLU_ Ferm | ADH Arg | URE | ESC | GEL | PNPG | GLU_ Assim | ARA | MNE | MAN | NAG | MAL | GNT | CAP | ADI | MLT | CIT | PAC |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 17295 | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | - | - |
API NH
| @ref | PEN | GLU | FRU | MAL | SAC | ODC | URE | LIP | PAL | beta GAL | ProA | GGT | IND |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 17295 | - | - | - | - | + | - | + | - | - | - | - | - | + |
| 17295 | + | - | - | - | - | + | - | + | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
- @ref: 17295
- sample type: contaminated surface sediment
- geographic location: Oak Ridge, TN
- country: USA
- origin.country: USA
- continent: North America
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Engineered | #Contamination | |
| #Environmental | #Terrestrial | #Sediment |
taxonmaps
- @ref: 69479
- File name: preview.99_1530.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_86;96_297;97_329;98_1207;99_1530&stattab=map
- Last taxonomy: Afipia
- 16S sequence: FJ851425
- Sequence Identity:
- Total samples: 807
- soil counts: 269
- aquatic counts: 275
- animal counts: 203
- plant counts: 60
Sequence information
16S sequences
- @ref: 17295
- description: Afipia sp. 1NLS2 16S ribosomal RNA gene, partial sequence
- accession: FJ851425
- length: 1217
- database: ena
- NCBI tax ID: 666684
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Afipia sp. 1NLS2 | GCA_000178995 | contig | ncbi | 666684 |
| 66792 | Afipia sp. 1NLS2 | 666684.3 | wgs | patric | 666684 |
| 66792 | Afipia sp. 1NLS2 | 648276616 | draft | img | 666684 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| gram-positive | no | 97.951 | no |
| anaerobic | no | 95.37 | no |
| halophile | no | 96.232 | no |
| spore-forming | no | 96.142 | no |
| glucose-util | no | 57.819 | yes |
| thermophile | no | 97.501 | yes |
| flagellated | no | 85.819 | no |
| aerobic | yes | 80.014 | no |
| glucose-ferment | no | 93.294 | yes |
| motile | yes | 72.631 | no |
External links
@ref: 17295
culture collection no.: DSM 23597
straininfo link
- @ref: 71430
- straininfo: 397021
literature
- topic: Genetics
- Pubmed-ID: 23833140
- title: Genome sequences for three denitrifying bacterial strains isolated from a uranium- and nitrate-contaminated subsurface environment.
- authors: Venkatramanan R, Prakash O, Woyke T, Chain P, Goodwin LA, Watson D, Brooks S, Kostka JE, Green SJ
- journal: Genome Announc
- DOI: 10.1128/genomeA.00449-13
- year: 2013
- topic2: Phylogeny
Reference
| @id | authors | catalogue | doi/url | title |
|---|---|---|---|---|
| 17295 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23597) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-23597 | |
| 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) | |
| 68369 | Automatically annotated from API 20NE | |||
| 68377 | Automatically annotated from API NH | |||
| 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 | |
| 71430 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID397021.1 | StrainInfo: A central database for resolving microbial strain identifiers |