Strain identifier
BacDive ID: 24271
Type strain: 
Species: Noviherbaspirillum psychrotolerans
Strain Designation: PB1
Strain history: <- D. Wagner, Helmholtz Centre Potsdam, GFZ German Res. Centre for Geosciences, Germany; PB1 <- L. Padur, AWI
NCBI tax ID(s): 1125875 (species)
version 8.1 (current version)
General
@ref: 20982
BacDive-ID: 24271
DSM-Number: 26001
keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, psychrophilic, Gram-negative, motile, rod-shaped
description: Noviherbaspirillum psychrotolerans PB1 is a facultative anaerobe, psychrophilic, Gram-negative bacterium that was isolated from soil.
NCBI tax id
- NCBI tax id: 1125875
- Matching level: species
strain history
- @ref: 20982
- history: <- D. Wagner, Helmholtz Centre Potsdam, GFZ German Res. Centre for Geosciences, Germany; PB1 <- L. Padur, AWI
doi: 10.13145/bacdive24271.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Betaproteobacteria
- order: Burkholderiales
- family: Oxalobacteraceae
- genus: Noviherbaspirillum
- species: Noviherbaspirillum psychrotolerans
- full scientific name: Noviherbaspirillum psychrotolerans (Bajerski et al. 2013) Lin et al. 2013
synonyms
- @ref: 20215
- synonym: Herbaspirillum psychrotolerans
@ref: 20982
domain: Bacteria
phylum: Proteobacteria
class: Betaproteobacteria
order: Burkholderiales
family: Oxalobacteraceae
genus: Noviherbaspirillum
species: Noviherbaspirillum psychrotolerans
full scientific name: Noviherbaspirillum psychrotolerans (Bajerski et al. 2013) Lin et al. 2013
strain designation: PB1
type strain: yes
Morphology
cell morphology
- @ref: 30892
- gram stain: negative
- cell length: 4 µm
- cell width: 1 µm
- cell shape: rod-shaped
- motility: yes
pigmentation
- @ref: 30892
- production: yes
Culture and growth conditions
culture medium
- @ref: 20982
- 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 |
|---|---|---|---|---|
| 20982 | positive | growth | 20 | psychrophilic |
| 30892 | positive | optimum | 17 | psychrophilic |
culture pH
| @ref | ability | type | pH |
|---|---|---|---|
| 30892 | positive | growth | 4.5-8.0 |
| 30892 | positive | optimum | 6.75 |
Physiology and metabolism
oxygen tolerance
- @ref: 30892
- oxygen tolerance: facultative anaerobe
spore formation
- @ref: 30892
- spore formation: no
halophily
| @ref | salt | growth | tested relation | concentration |
|---|---|---|---|---|
| 30892 | NaCl | positive | growth | 0-2.5 % |
| 30892 | NaCl | positive | optimum | 0.25 % |
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 30892 | 22599 | arabinose | + | carbon source |
| 30892 | 28757 | fructose | + | carbon source |
| 30892 | 33984 | fucose | + | carbon source |
| 30892 | 28260 | galactose | + | carbon source |
| 30892 | 24265 | gluconate | + | carbon source |
| 30892 | 17754 | glycerol | + | carbon source |
| 30892 | 18222 | xylose | + | carbon source |
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 30892 | catalase | + | 1.11.1.6 |
| 30892 | gelatinase | + | |
| 30892 | urease | + | 3.5.1.5 |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent | latitude | longitude |
|---|---|---|---|---|---|---|---|
| 30892 | soil | ||||||
| 20982 | surface soil of a glacier forefield | Larsemann Hills (69° 24' S 76°20' E) | Antarctica | ATA | Australia and Oceania | -69.4 | 76.3333 |
isolation source categories
- Cat1: #Environmental
- Cat2: #Terrestrial
- Cat3: #Soil
Safety information
risk assessment
- @ref: 20982
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 20982
- description: Noviherbaspirillum psychrotolerans strain PB1 16S ribosomal RNA gene, partial sequence
- accession: JN390675
- length: 1303
- database: ena
- NCBI tax ID: 1125875
Genome sequences
- @ref: 66792
- description: Noviherbaspirillum suwonense DSM 26001
- accession: 2706794918
- assembly level: draft
- database: img
- NCBI tax ID: 1224511
GC content
| @ref | GC-content | method |
|---|---|---|
| 20982 | 62.5 | high performance liquid chromatography (HPLC) |
| 30892 | 62.5 |
External links
@ref: 20982
culture collection no.: DSM 26001, LMG 27282
straininfo link
- @ref: 88212
- straininfo: 399837
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 23456802 | Herbaspirillum psychrotolerans sp. nov., a member of the family Oxalobacteraceae from a glacier forefield. | Bajerski F, Ganzert L, Mangelsdorf K, Lipski A, Busse HJ, Padur L, Wagner D | Int J Syst Evol Microbiol | 10.1099/ijs.0.046920-0 | 2013 | Antarctic Regions, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Herbaspirillum/*classification/genetics/isolation & purification, Ice Cover/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, Polyamines/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Ubiquinone/analysis | Genetics |
| Phylogeny | 23749276 | Description of Noviherbaspirillum malthae gen. nov., sp. nov., isolated from an oil-contaminated soil, and proposal to reclassify Herbaspirillum soli, Herbaspirillum aurantiacum, Herbaspirillum canariense and Herbaspirillum psychrotolerans as Noviherbaspirillum soli comb. nov., Noviherbaspirillum aurantiacum comb. nov., Noviherbaspirillum canariense comb. nov. and Noviherbaspirillum psychrotolerans comb. nov. based on polyphasic analysis. | Lin SY, Hameed A, Arun AB, Liu YC, Hsu YH, Lai WA, Rekha PD, Young CC | Int J Syst Evol Microbiol | 10.1099/ijs.0.048231-0 | 2013 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Herbaspirillum/*classification/genetics/isolation & purification, Molecular Sequence Data, Petroleum Pollution, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Soil Pollutants, Taiwan, Ubiquinone/chemistry | 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 | |||
| 20982 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-26001 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 26001) | |||
| 30892 | 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 | 27222 | 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 | |||
| 88212 | 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-ID399837.1 |