Strain identifier
BacDive ID: 14269
Type strain: 
Species: Sphingomonas alpina
Strain Designation: S8-3
Strain history: <- R. Margesin, Inst. Microbiology, Univ. Innsbruck, Austria; S8-3
NCBI tax ID(s): 653931 (species)
version 8.1 (current version)
General
@ref: 16384
BacDive-ID: 14269
DSM-Number: 22537
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, motile, rod-shaped
description: Sphingomonas alpina S8-3 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from alpine soil.
NCBI tax id
- NCBI tax id: 653931
- Matching level: species
strain history
- @ref: 16384
- history: <- R. Margesin, Inst. Microbiology, Univ. Innsbruck, Austria; S8-3
doi: 10.13145/bacdive14269.20230509.8.1
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 alpina
- full scientific name: Sphingomonas alpina Margesin et al. 2012
@ref: 16384
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Sphingomonadales
family: Sphingomonadaceae
genus: Sphingomonas
species: Sphingomonas alpina
full scientific name: Sphingomonas alpina Margesin et al. 2012
strain designation: S8-3
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell width | cell shape | motility | confidence |
|---|---|---|---|---|---|---|
| 30431 | negative | 1.2 µm | 0.7 µm | rod-shaped | yes | |
| 69480 | negative | 99.892 |
pigmentation
- @ref: 30431
- production: yes
Culture and growth conditions
culture medium
- @ref: 16384
- 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 | growth | type | temperature | range |
|---|---|---|---|---|
| 16384 | positive | growth | 25 | mesophilic |
| 30431 | positive | growth | 1-25 | |
| 16384 | positive | growth | 28 | mesophilic |
culture pH
| @ref | ability | type | pH | PH range |
|---|---|---|---|---|
| 30431 | positive | growth | 06-10 | alkaliphile |
| 30431 | positive | optimum | 7.5 |
Physiology and metabolism
oxygen tolerance
- @ref: 30431
- oxygen tolerance: aerobe
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 99.669 |
halophily
- @ref: 30431
- salt: NaCl
- growth: positive
- tested relation: growth
- concentration: 0-1 %
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 30431 | 22599 | arabinose | + | carbon source |
| 30431 | 17234 | glucose | + | carbon source |
| 30431 | 25115 | malate | + | carbon source |
| 30431 | 17306 | maltose | + | carbon source |
| 30431 | 37684 | mannose | + | carbon source |
| 30431 | 4853 | esculin | + | hydrolysis |
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 30431 | acid phosphatase | + | 3.1.3.2 |
| 30431 | alkaline phosphatase | + | 3.1.3.1 |
| 30431 | catalase | + | 1.11.1.6 |
| 30431 | gelatinase | + | |
| 30431 | cytochrome oxidase | + | 1.9.3.1 |
Isolation, sampling and environmental information
isolation
- @ref: 16384
- sample type: alpine soil
- geographic location: Grossglockner, Hohe Tauern
- country: Austria
- origin.country: AUT
- continent: Europe
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Terrestrial | #Soil |
| #Climate | #Cold | #Alpine |
taxonmaps
- @ref: 69479
- File name: preview.99_5646.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_20;96_2717;97_3339;98_4208;99_5646&stattab=map
- Last taxonomy: Sphingomonas alpina subclade
- 16S sequence: GQ161989
- Sequence Identity:
- Total samples: 630
- soil counts: 156
- aquatic counts: 86
- animal counts: 163
- plant counts: 225
Safety information
risk assessment
- @ref: 16384
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 16384
- description: Sphingomonas alpina strain S8-3 16S ribosomal RNA gene, partial sequence
- accession: GQ161989
- length: 1481
- database: ena
- NCBI tax ID: 653931
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Sphingomonas alpina DSM 22537 | GCA_014490665 | complete | ncbi | 653931 |
| 66792 | Sphingomonas alpina strain S8-3T strain DSM 22537 | 653931.5 | complete | patric | 653931 |
| 66792 | Sphingomonas alpina DSM 22537 | GCA_025370095 | contig | ncbi | 653931 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 16384 | 64.1 | high performance liquid chromatography (HPLC) |
| 30431 | 64.1 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| flagellated | no | 87.025 | no |
| gram-positive | no | 96.675 | yes |
| anaerobic | no | 99.662 | yes |
| aerobic | yes | 91.387 | no |
| halophile | no | 93.68 | yes |
| spore-forming | no | 92.745 | no |
| thermophile | no | 98.983 | yes |
| glucose-util | yes | 90.317 | yes |
| motile | yes | 79.067 | yes |
| glucose-ferment | no | 90.901 | no |
External links
@ref: 16384
culture collection no.: DSM 22537, LMG 26055
straininfo link
- @ref: 83426
- straininfo: 370924
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 21856979 | Sphingomonas alpina sp. nov., a psychrophilic bacterium isolated from alpine soil. | Margesin R, Zhang DC, Busse HJ | Int J Syst Evol Microbiol | 10.1099/ijs.0.035964-0 | 2011 | Aerobiosis, Bacterial Typing Techniques, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, Polyamines/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Sphingomonas/*classification/genetics/*isolation & purification/physiology, Ubiquinone/analysis | Genetics |
| Phylogeny | 26363994 | Sphingomonas fonticola sp. nov., isolated from spring water. | Sheu SY, Chen YL, Chen WM | Int J Syst Evol Microbiol | 10.1099/ijsem.0.000602 | 2015 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Fresh Water/*microbiology, Hydroxybutyrates/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Polyamines/chemistry, Polyesters/chemistry, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sphingomonas/*classification/genetics/isolation & purification, Taiwan, Ubiquinone/analogs & derivatives/chemistry, *Water Microbiology | Genetics |
| Phylogeny | 26676296 | Sphingomonas qilianensis sp. nov., Isolated from Surface Soil in the Permafrost Region of Qilian Mountains, China. | Piao AL, Feng XM, Nogi Y, Han L, Li Y, Lv J | Curr Microbiol | 10.1007/s00284-015-0957-9 | 2015 | Base Composition, China, *Environment, Permafrost/*microbiology, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Sphingomonas/chemistry/*classification/genetics/isolation & purification | Transcriptome |
| Phylogeny | 34435946 | Sphingomonas aliaeris sp. nov., a new species isolated from pork steak packed under modified atmosphere. | Heidler von Heilborn D, Reinmuller J, Holzl G, Meier-Kolthoff JP, Woehle C, Marek M, Huttel B, Lipski A | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004973 | 2021 | Animals, Atmosphere, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Food Microbiology, Germany, Phospholipids/chemistry, *Phylogeny, Pigmentation, *Pork Meat/microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Sphingomonas/classification/isolation & purification, Swine | Biotechnology |
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
|---|---|---|---|---|---|---|
| 16384 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22537) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-22537 | |||
| 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 | |||
| 30431 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 26767 | 28776041 | |
| 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 | |||
| 83426 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID370924.1 | StrainInfo: A central database for resolving microbial strain identifiers |