Strain identifier
BacDive ID: 14112
Type strain: 
Species: Pedobacter borealis
Strain Designation: G-1
Strain history: <- N. S. Gordon, Univ. Montana, Missoula, USA; G-1 <- J. L. Pollock {2005}
NCBI tax ID(s): 1454007 (strain), 475254 (species)
version 8.1 (current version)
General
@ref: 8218
BacDive-ID: 14112
DSM-Number: 19626
keywords: genome sequence, 16S sequence, Bacteria, aerobe, psychrophilic, Gram-negative, rod-shaped
description: Pedobacter borealis G-1 is an aerobe, psychrophilic, Gram-negative bacterium that was isolated from rhizosphere of a conifer forest.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 475254 | species |
| 1454007 | strain |
strain history
- @ref: 8218
- history: <- N. S. Gordon, Univ. Montana, Missoula, USA; G-1 <- J. L. Pollock {2005}
doi: 10.13145/bacdive14112.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacteroidota
- domain: Bacteria
- phylum: Bacteroidota
- class: Sphingobacteriia
- order: Sphingobacteriales
- family: Sphingobacteriaceae
- genus: Pedobacter
- species: Pedobacter borealis
- full scientific name: Pedobacter borealis Gordon et al. 2009
@ref: 8218
domain: Bacteria
phylum: Bacteroidetes
class: Sphingobacteriia
order: Sphingobacteriales
family: Sphingobacteriaceae
genus: Pedobacter
species: Pedobacter borealis
full scientific name: Pedobacter borealis Gordon et al. 2009
strain designation: G-1
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell width | cell shape | motility | confidence |
|---|---|---|---|---|---|---|
| 28921 | negative | 1.85 µm | 0.4 µm | rod-shaped | no | |
| 69480 | negative | 99.974 |
pigmentation
- @ref: 28921
- production: yes
Culture and growth conditions
culture medium
- @ref: 8218
- 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 |
|---|---|---|---|---|
| 8218 | positive | growth | 20 | psychrophilic |
| 28921 | positive | growth | 04-30 | |
| 28921 | positive | optimum | 17 | psychrophilic |
culture pH
| @ref | ability | type | pH |
|---|---|---|---|
| 28921 | positive | growth | 05-07 |
| 28921 | positive | optimum | 7 |
Physiology and metabolism
oxygen tolerance
- @ref: 28921
- oxygen tolerance: aerobe
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 28921 | no | |
| 69481 | no | 100 |
| 69480 | no | 99.978 |
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 28921 | 22599 | arabinose | + | carbon source |
| 28921 | 17057 | cellobiose | + | carbon source |
| 28921 | 28757 | fructose | + | carbon source |
| 28921 | 28260 | galactose | + | carbon source |
| 28921 | 17234 | glucose | + | carbon source |
| 28921 | 37684 | mannose | + | carbon source |
| 28921 | 28053 | melibiose | + | carbon source |
| 28921 | 506227 | N-acetylglucosamine | + | carbon source |
| 28921 | 16634 | raffinose | + | carbon source |
| 28921 | 26546 | rhamnose | + | carbon source |
| 28921 | 17814 | salicin | + | carbon source |
| 28921 | 17992 | sucrose | + | carbon source |
| 28921 | 27082 | trehalose | + | carbon source |
| 28921 | 18222 | xylose | + | carbon source |
| 28921 | 4853 | esculin | + | hydrolysis |
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 28921 | alkaline phosphatase | + | 3.1.3.1 |
| 28921 | alpha-galactosidase | + | 3.2.1.22 |
| 28921 | catalase | + | 1.11.1.6 |
| 28921 | cytochrome oxidase | + | 1.9.3.1 |
Isolation, sampling and environmental information
isolation
- @ref: 8218
- sample type: rhizosphere of a conifer forest
- geographic location: western Montana
- country: USA
- origin.country: USA
- continent: North America
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Terrestrial | #Forest |
| #Host | #Plants | #Tree |
| #Host Body-Site | #Plant | #Rhizosphere |
taxonmaps
- @ref: 69479
- File name: preview.99_4554.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_115;96_1456;97_1737;98_3423;99_4554&stattab=map
- Last taxonomy: Pedobacter borealis
- 16S sequence: EU030687
- Sequence Identity:
- Total samples: 204
- soil counts: 110
- aquatic counts: 15
- animal counts: 55
- plant counts: 24
Safety information
risk assessment
- @ref: 8218
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 8218
- description: Pedobacter borealis strain G-1 16S ribosomal RNA gene, partial sequence
- accession: EU030687
- length: 1412
- database: ena
- NCBI tax ID: 475254
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Pedobacter borealis DSM 19626 | GCA_000708285 | contig | ncbi | 1454007 |
| 66792 | Pedobacter borealis DSM 19626 | 1454007.3 | wgs | patric | 1454007 |
| 66792 | Pedobacter borealis DSM 19626 | 2585427687 | draft | img | 1454007 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 8218 | 35.5±0.5 | high performance liquid chromatography (HPLC) |
| 8218 | 39.7 | high performance liquid chromatography (HPLC) |
| 28921 | 35.5 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| motile | no | 91.225 | no |
| gram-positive | no | 96.899 | yes |
| anaerobic | no | 99.469 | yes |
| halophile | no | 96.636 | no |
| spore-forming | no | 93.383 | no |
| thermophile | no | 99.433 | yes |
| glucose-util | yes | 88.235 | yes |
| aerobic | yes | 85.867 | no |
| flagellated | no | 97.055 | yes |
| glucose-ferment | no | 90.23 | no |
External links
@ref: 8218
culture collection no.: DSM 19626, LMG 24259
straininfo link
- @ref: 83279
- straininfo: 309277
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 19542109 | Pedobacter nyackensis sp. nov., Pedobacter alluvionis sp. nov. and Pedobacter borealis sp. nov., isolated from Montana flood-plain sediment and forest soil. | Gordon NS, Valenzuela A, Adams SM, Ramsey PW, Pollock JL, Holben WE, Gannon JE | Int J Syst Evol Microbiol | 10.1099/ijs.0.000158-0 | 2009 | Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/isolation & purification/physiology, DNA, Bacterial/analysis, *Floods, Genes, rRNA, Genotype, Geologic Sediments/*microbiology, Molecular Sequence Data, Montana, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Species Specificity, Tracheophyta, *Trees | Genetics |
| Phylogeny | 27498823 | Pedobacterpsychrotolerans sp. nov., isolated from soil. | Manandhar P, Zhang G, Lama A, Hu Y, Gao F | Int J Syst Evol Microbiol | 10.1099/ijsem.0.001391 | 2016 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Pedobacter/*classification/genetics/isolation & purification, Phosphatidylethanolamines/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistry | Transcriptome |
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
|---|---|---|---|---|---|---|
| 8218 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19626) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-19626 | |||
| 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 | |||
| 28921 | 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 | 25360 | 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 | |||
| 83279 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID309277.1 | StrainInfo: A central database for resolving microbial strain identifiers |