Strain identifier
BacDive ID: 24668
Type strain: 
Species: Azorhizobium oxalatiphilum
Strain Designation: NS12
Strain history: <- N. Sahin, Mugla University, Kötekli, Turkey; NS12 <- N. Sahin; NS12
NCBI tax ID(s): 980631 (species)
version 8.1 (current version)
General
@ref: 20925
BacDive-ID: 24668
DSM-Number: 18749
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, motile, rod-shaped
description: Azorhizobium oxalatiphilum NS12 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from macerated Rumex sp. petioles.
NCBI tax id
- NCBI tax id: 980631
- Matching level: species
strain history
- @ref: 20925
- history: <- N. Sahin, Mugla University, Kötekli, Turkey; NS12 <- N. Sahin; NS12
doi: 10.13145/bacdive24668.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Hyphomicrobiales
- family: Xanthobacteraceae
- genus: Azorhizobium
- species: Azorhizobium oxalatiphilum
- full scientific name: Azorhizobium oxalatiphilum Lang et al. 2013
@ref: 20925
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhizobiales
family: Xanthobacteraceae
genus: Azorhizobium
species: Azorhizobium oxalatiphilum
full scientific name: Azorhizobium oxalatiphilum Lang et al. 2013
strain designation: NS12
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell width | cell shape | motility | confidence |
|---|---|---|---|---|---|---|
| 30820 | negative | 2.75 µm | 1 µm | rod-shaped | yes | |
| 69480 | negative | 99.996 |
pigmentation
- @ref: 30820
- production: no
Culture and growth conditions
culture medium
- @ref: 20925
- name: REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a)
- growth: yes
- link: https://mediadive.dsmz.de/medium/1a
- composition: Name: REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 20925 | positive | growth | 30 | mesophilic |
| 30820 | positive | growth | 10-36 |
Physiology and metabolism
oxygen tolerance
- @ref: 30820
- oxygen tolerance: aerobe
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 30820 | no | |
| 69481 | no | 100 |
| 69480 | no | 99.986 |
halophily
- @ref: 30820
- salt: NaCl
- growth: positive
- tested relation: optimum
- concentration: 2 %
observation
- @ref: 30820
- observation: aggregates in chains
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 30820 | 16449 | alanine | + | carbon source |
| 30820 | 16947 | citrate | + | carbon source |
| 30820 | 24175 | galacturonate | + | carbon source |
| 30820 | 24265 | gluconate | + | carbon source |
| 30820 | 29987 | glutamate | + | carbon source |
| 30820 | 17754 | glycerol | + | carbon source |
| 30820 | 24996 | lactate | + | carbon source |
| 30820 | 25115 | malate | + | carbon source |
| 30820 | 17272 | propionate | + | carbon source |
| 30820 | 15361 | pyruvate | + | carbon source |
| 30820 | 30031 | succinate | + | carbon source |
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 30820 | catalase | + | 1.11.1.6 |
| 30820 | cytochrome oxidase | + | 1.9.3.1 |
| 30820 | urease | + | 3.5.1.5 |
Isolation, sampling and environmental information
isolation
- @ref: 20925
- sample type: macerated Rumex sp. petioles
- host species: Rumex
- geographic location: Mugla
- country: Turkey
- origin.country: TUR
- continent: Asia
isolation source categories
- Cat1: #Host
- Cat2: #Plants
- Cat3: #Herbaceous plants (Grass,Crops)
Safety information
risk assessment
- @ref: 20925
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 20925
- description: Azorhizobium oxalatiphilum partial 16S rRNA gene, strain NS12
- accession: FR799325
- length: 1443
- database: ena
- NCBI tax ID: 980631
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Azorhizobium oxalatiphilum CCM 7897 | GCA_014635325 | scaffold | ncbi | 980631 |
| 66792 | Azorhizobium oxalatiphilum strain CCM 7897 | 980631.3 | wgs | patric | 980631 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| flagellated | no | 63.408 | no |
| gram-positive | no | 98.412 | yes |
| anaerobic | no | 97.686 | yes |
| aerobic | yes | 92.678 | yes |
| halophile | no | 91.313 | no |
| spore-forming | no | 93.391 | no |
| thermophile | no | 98.702 | yes |
| glucose-util | yes | 88.002 | no |
| motile | yes | 84.394 | yes |
| glucose-ferment | no | 90.744 | no |
External links
@ref: 20925
culture collection no.: DSM 18749, CCM 7897, NEU 1219
straininfo link
- @ref: 88507
- straininfo: 405515
literature
- topic: Phylogeny
- Pubmed-ID: 22888185
- title: Azorhizobium oxalatiphilum sp. nov., and emended description of the genus Azorhizobium.
- authors: Lang E, Schumann P, Adler S, Sproer C, Sahin N
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.045229-0
- year: 2012
- mesh: Azorhizobium/*classification/genetics/isolation & purification, Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/analysis, Genotype, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, *Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Rumex/*microbiology, Sequence Analysis, DNA
- topic2: Genetics
Reference
| @id | authors | title | doi/url | catalogue | ID_cross_reference | pubmed |
|---|---|---|---|---|---|---|
| 20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | 10.1099/ijsem.0.004332 | |||
| 20925 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-18749 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18749) | |||
| 30820 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 10.1128/mSphere.00237-17 | 27151 | 28776041 | |
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |||
| 69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |||
| 69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | Predictions based on the model GenomeNet Sporulation v. 1 | 10.21203/rs.3.rs-2527258/v1 | |||
| 88507 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | StrainInfo: A central database for resolving microbial strain identifiers | 10.60712/SI-ID405515.1 |