Strain identifier
BacDive ID: 131945
Type strain: 
Species: Sphingomonas sp.
Strain Designation: Leaf21
Strain history: <- J. A. Vorholt, Institute of Microbiology, ETH Zurich, Switzerland; Leaf21 <- D. B. Müller, E. Potthoff and M. Remus-Emsermann
NCBI tax ID(s): 28214 (species)
version 8.1 (current version)
General
@ref: 23737
BacDive-ID: 131945
DSM-Number: 102728
keywords: genome sequence, Bacteria, mesophilic
description: Sphingomonas sp. Leaf21 is a mesophilic bacterium that was isolated from leaf of wild-type Arabidopsis thaliana.
NCBI tax id
- NCBI tax id: 28214
- Matching level: species
strain history
- @ref: 23737
- history: <- J. A. Vorholt, Institute of Microbiology, ETH Zurich, Switzerland; Leaf21 <- D. B. Müller, E. Potthoff and M. Remus-Emsermann
doi: 10.13145/bacdive131945.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Sphingomonadales
- family: Sphingomonadaceae
- genus: Sphingomonas
- species: Sphingomonas sp.
- full scientific name: Sphingomonas Yabuuchi et al. 1990
@ref: 23737
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Pseudomonadales
family: Sphingomonadaceae
genus: Sphingomonas
species: Sphingomonas sp.
full scientific name: Sphingomonas sp.
strain designation: Leaf21
type strain: no
Culture and growth conditions
culture medium
- @ref: 23737
- 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: 23737
- 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 |
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 |
|---|---|---|---|
| 68369 | cytochrome oxidase | - | 1.9.3.1 |
| 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 | OX |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 23737 | - | - | - | - | - | + | - | + | + | + | + | - | + | + | + | - | - | + | - | - | - |
Isolation, sampling and environmental information
isolation
- @ref: 23737
- sample type: leaf of wild-type Arabidopsis thaliana
- host species: Arabidopsis thaliana
- geographic location: Brugg (47.4816806N 8.217547222E)
- country: Switzerland
- origin.country: CHE
- continent: Europe
- latitude: 47.4817
- longitude: 8.2176
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Host | #Plants | #Herbaceous plants (Grass,Crops) |
| #Host Body-Site | #Plant | #Leaf (Phyllosphere) |
Sequence information
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Sphingomonas sp. Leaf21 Leaf21 | GCA_916858675 | scaffold | ncbi | 2876550 |
| 66792 | Sphingomonas sp. Leaf21 | 2876550.4 | wgs | patric | 2876550 |
| 66792 | Sphingomonas sp. Leaf21 | 2876550.3 | wgs | patric | 2876550 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| aerobic | yes | 91.35 | no |
| flagellated | no | 89.343 | no |
| gram-positive | no | 97.098 | no |
| anaerobic | no | 99.176 | no |
| halophile | no | 95.69 | no |
| spore-forming | no | 94.405 | no |
| thermophile | no | 98.72 | yes |
| glucose-util | yes | 92.127 | yes |
| motile | yes | 73.51 | no |
| glucose-ferment | no | 90.92 | yes |
External links
@ref: 23737
culture collection no.: DSM 102728
straininfo link
- @ref: 90332
- straininfo: 399653
Reference
| @id | authors | title | doi/url | catalogue |
|---|---|---|---|---|
| 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 | |
| 23737 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-102728 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 102728) | |
| 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 | |
| 68369 | Automatically annotated from API 20NE | |||
| 90332 | 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-ID399653.1 |