Strain identifier
BacDive ID: 24035
Type strain: 
Species: Chryseobacterium frigidisoli
Strain Designation: PB4
Strain history: <- D. Wagner, Alfred Wegener Inst. Polar and Marine Res. (AWI) in the Helmholtz Association, Res. Unit Potsdam, Germany; PB4 <- L. Padur, AWI Potsdam, Germany
NCBI tax ID(s): 1125876 (species)
version 8.1 (current version)
General
@ref: 20930
BacDive-ID: 24035
DSM-Number: 26000
keywords: genome sequence, 16S sequence, Bacteria, aerobe, psychrophilic, Gram-negative, rod-shaped
description: Chryseobacterium frigidisoli PB4 is an aerobe, psychrophilic, Gram-negative bacterium that was isolated from sandy dry permafrost from a glacier forefield.
NCBI tax id
- NCBI tax id: 1125876
- Matching level: species
strain history
- @ref: 20930
- history: <- D. Wagner, Alfred Wegener Inst. Polar and Marine Res. (AWI) in the Helmholtz Association, Res. Unit Potsdam, Germany; PB4 <- L. Padur, AWI Potsdam, Germany
doi: 10.13145/bacdive24035.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacteroidota
- domain: Bacteria
- phylum: Bacteroidota
- class: Flavobacteriia
- order: Flavobacteriales
- family: Weeksellaceae
- genus: Chryseobacterium
- species: Chryseobacterium frigidisoli
- full scientific name: Chryseobacterium frigidisoli Bajerski et al. 2013
synonyms
- @ref: 20215
- synonym: Halpernia frigidisoli
@ref: 20930
domain: Bacteria
phylum: Bacteroidetes
class: Flavobacteriia
order: Flavobacteriales
family: Weeksellaceae
genus: Chryseobacterium
species: Chryseobacterium frigidisoli
full scientific name: Chryseobacterium frigidisoli Bajerski et al. 2013
strain designation: PB4
type strain: yes
Morphology
cell morphology
- @ref: 30891
- gram stain: negative
- cell length: 2.75 µm
- cell width: 0.45 µm
- cell shape: rod-shaped
- motility: no
pigmentation
- @ref: 30891
- production: yes
Culture and growth conditions
culture medium
- @ref: 20930
- name: NUTRIENT AGAR (DSMZ Medium 1)
- growth: yes
- link: https://mediadive.dsmz.de/medium/1
- composition: Name: NUTRIENT AGAR (DSMZ Medium 1) 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 |
|---|---|---|---|---|
| 20930 | positive | growth | 20 | psychrophilic |
| 30891 | positive | growth | 0-25 | |
| 30891 | positive | optimum | 20 | psychrophilic |
culture pH
| @ref | ability | type | pH | PH range |
|---|---|---|---|---|
| 30891 | positive | growth | 5.5-8.5 | alkaliphile |
| 30891 | positive | optimum | 6.5 |
Physiology and metabolism
oxygen tolerance
- @ref: 30891
- oxygen tolerance: aerobe
spore formation
- @ref: 30891
- spore formation: no
halophily
| @ref | salt | growth | tested relation | concentration |
|---|---|---|---|---|
| 30891 | NaCl | positive | growth | 0-5 % |
| 30891 | NaCl | positive | optimum | 0.5 % |
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 30891 | 15963 | ribitol | + | carbon source |
| 30891 | 18403 | L-arabitol | + | carbon source |
| 30891 | 17057 | cellobiose | + | carbon source |
| 30891 | 28757 | fructose | + | carbon source |
| 30891 | 28260 | galactose | + | carbon source |
| 30891 | 17234 | glucose | + | carbon source |
| 30891 | 17754 | glycerol | + | carbon source |
| 30891 | 28087 | glycogen | + | carbon source |
| 30891 | 17716 | lactose | + | carbon source |
| 30891 | 17306 | maltose | + | carbon source |
| 30891 | 29864 | mannitol | + | carbon source |
| 30891 | 37684 | mannose | + | carbon source |
| 30891 | 28053 | melibiose | + | carbon source |
| 30891 | 506227 | N-acetylglucosamine | + | carbon source |
| 30891 | 16634 | raffinose | + | carbon source |
| 30891 | 26546 | rhamnose | + | carbon source |
| 30891 | 33942 | ribose | + | carbon source |
| 30891 | 17814 | salicin | + | carbon source |
| 30891 | 30911 | sorbitol | + | carbon source |
| 30891 | 17992 | sucrose | + | carbon source |
| 30891 | 27082 | trehalose | + | carbon source |
| 30891 | 17151 | xylitol | + | carbon source |
| 30891 | 18222 | xylose | + | carbon source |
metabolite production
- @ref: 30891
- Chebi-ID: 35581
- metabolite: indole
- production: yes
metabolite tests
- @ref: 30891
- Chebi-ID: 35581
- metabolite: indole
- indole test: +
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 30891 | catalase | + | 1.11.1.6 |
| 30891 | gelatinase | + | |
| 30891 | cytochrome oxidase | + | 1.9.3.1 |
Isolation, sampling and environmental information
isolation
- @ref: 20930
- sample type: sandy dry permafrost from a glacier forefield
- geographic location: Larsemann Hills (S 69°24', E 76°20')
- continent: Australia and Oceania
- latitude: -69.4
- longitude: 76.3333
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Terrestrial | #Glacier |
| #Environmental | #Terrestrial | #Permafrost |
| #Environmental | #Terrestrial | #Sandy |
taxonmaps
- @ref: 69479
- File name: preview.99_68125.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_76;96_19049;97_23613;98_47976;99_68125&stattab=map
- Last taxonomy: Chryseobacterium frigidisoli subclade
- 16S sequence: JN390676
- Sequence Identity:
- Total samples: 444
- soil counts: 68
- aquatic counts: 153
- animal counts: 200
- plant counts: 23
Safety information
risk assessment
- @ref: 20930
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 20930
- description: Chryseobacterium frigidisoli strain PB4 16S ribosomal RNA gene, partial sequence
- accession: JN390676
- length: 1301
- database: ena
- NCBI tax ID: 1125876
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Halpernia frigidisoli DSM 26000 | GCA_900113805 | contig | ncbi | 1125876 |
| 66792 | Chryseobacterium frigidisoli strain DSM 26000 | 1125876.4 | wgs | patric | 1125876 |
| 66792 | Chryseobacterium frigidisoli DSM 26000 | 2684622856 | draft | img | 1125876 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 20930 | 33.7 | high performance liquid chromatography (HPLC) |
| 30891 | 33.7 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| motile | no | 91.206 | yes |
| flagellated | no | 96.797 | no |
| gram-positive | no | 97.964 | yes |
| anaerobic | no | 99.545 | yes |
| aerobic | yes | 91.528 | yes |
| halophile | no | 91.606 | yes |
| spore-forming | no | 96.423 | yes |
| thermophile | no | 99.652 | yes |
| glucose-util | yes | 86.282 | yes |
| glucose-ferment | no | 92.923 | no |
External links
@ref: 20930
culture collection no.: DSM 26000, LMG 27025
straininfo link
- @ref: 88008
- straininfo: 380503
literature
- topic: Phylogeny
- Pubmed-ID: 23291884
- title: Chryseobacterium frigidisoli sp. nov., a psychrotolerant species of the family Flavobacteriaceae isolated from sandy permafrost from a glacier forefield.
- authors: Bajerski F, Ganzert L, Mangelsdorf K, Padur L, Lipski A, Wagner D
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.046904-0
- year: 2013
- mesh: Antarctic Regions, Bacterial Typing Techniques, Chryseobacterium/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/analysis, Ice Cover/*microbiology, Molecular Sequence Data, *Phylogeny, Polyamines/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/analysis
- topic2: Genetics
Reference
| @id | authors | title | doi/url | catalogue | ID_cross_reference | pubmed | journal |
|---|---|---|---|---|---|---|---|
| 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 | ||||
| 20930 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-26000 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 26000) | ||||
| 30891 | 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 | 27221 | 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 | ||||
| 66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | 10.1093/nar/gkaa1025 | 33211880 | Nucleic Acids Res. 49: D498-D508 2020 | ||
| 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. | MicrobeAtlas 1.0 beta | https://microbeatlas.org/ | ||||
| 88008 | 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-ID380503.1 |