Strain identifier
BacDive ID: 13163
Type strain: 
Species: Pseudomonas duriflava
Strain Designation: HR2
Strain history: <- H. Liu, Nanjing Agricultural University
NCBI tax ID(s): 459528 (species)
version 9.3 (current version)
General
@ref: 15695
BacDive-ID: 13163
DSM-Number: 21419
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, rod-shaped
description: Pseudomonas duriflava HR2 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from desert soil.
NCBI tax id
- NCBI tax id: 459528
- Matching level: species
strain history
- @ref: 15695
- history: <- H. Liu, Nanjing Agricultural University
doi: 10.13145/bacdive13163.20250331.9.3
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Pseudomonadales
- family: Pseudomonadaceae
- genus: Pseudomonas
- species: Pseudomonas duriflava
- full scientific name: Pseudomonas duriflava Liu et al. 2008
synonyms
- @ref: 20215
- synonym: Chryseomonas duriflava
@ref: 15695
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Pseudomonadales
family: Pseudomonadaceae
genus: Pseudomonas
species: Pseudomonas duriflava
full scientific name: Pseudomonas duriflava Liu et al. 2008
strain designation: HR2
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell width | cell shape | motility | confidence |
|---|---|---|---|---|---|---|
| 32574 | negative | 0.9 µm | 0.7 µm | rod-shaped | no | |
| 125438 | negative | 98.75 | ||||
| 125439 | negative | 99.5 |
pigmentation
- @ref: 32574
- production: no
Culture and growth conditions
culture medium
- @ref: 15695
- name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)
- growth: yes
- link: https://mediadive.dsmz.de/medium/535
- composition: Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
culture temp
| @ref | growth | type | temperature |
|---|---|---|---|
| 15695 | positive | growth | 28 |
| 32574 | positive | growth | 05-42 |
| 32574 | positive | optimum | 33.5 |
culture pH
| @ref | ability | type | pH | PH range |
|---|---|---|---|---|
| 32574 | positive | growth | 05-09 | alkaliphile |
| 32574 | positive | optimum | 7.5 |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 32574 | aerobe | |
| 125438 | aerobe | 91.184 |
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 32574 | no | |
| 125439 | no | 99.6 |
halophily
| @ref | salt | growth | tested relation | concentration |
|---|---|---|---|---|
| 32574 | NaCl | positive | growth | 0-2 % |
| 32574 | NaCl | positive | optimum | 0.5 % |
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 32574 | 22599 | arabinose | + | carbon source |
| 32574 | 17057 | cellobiose | + | carbon source |
| 32574 | 28260 | galactose | + | carbon source |
| 32574 | 28053 | melibiose | + | carbon source |
| 32574 | 33942 | ribose | + | carbon source |
| 32574 | 4853 | esculin | + | hydrolysis |
enzymes
- @ref: 32574
- value: catalase
- activity: +
- ec: 1.11.1.6
Isolation, sampling and environmental information
isolation
- @ref: 15695
- sample type: desert soil
- geographic location: Xinjiang Province
- country: China
- origin.country: CHN
- continent: Asia
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Terrestrial | #Desert |
| #Environmental | #Terrestrial | #Soil |
| #Condition | #Xerophilic |
Safety information
risk assessment
- @ref: 15695
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 15695
- description: Pseudomonas duriflava strain HR2 16S ribosomal RNA gene, partial sequence
- accession: EU046271
- length: 1404
- database: nuccore
- NCBI tax ID: 459528
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Pseudomonas duriflava CGMCC 1.6858 | GCA_007830155 | contig | ncbi | 459528 |
| 66792 | Pseudomonas duriflava strain CGMCC 1.6858 | 459528.3 | wgs | patric | 459528 |
| 66792 | Pseudomonas duriflava CGMCC 1.6858 | 2596583584 | draft | img | 459528 |
GC content
- @ref: 32574
- GC-content: 55.2
Genome-based predictions
predictions
| @ref | model | trait | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 125438 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 98.75 | yes |
| 125438 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 97.59 | yes |
| 125438 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 83.889 | no |
| 125438 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 91.184 | no |
| 125438 | thermophile | thermophilic | Ability to grow at temperatures above or equal to 45°C | no | 98.497 | yes |
| 125438 | motile2+ | flagellated | Ability to perform flagellated movement | yes | 85.916 | no |
| 125439 | BacteriaNet | spore_formation | Ability to form endo- or exospores | no | 99.6 | |
| 125439 | BacteriaNet | motility | Ability to perform movement | yes | 88.7 | |
| 125439 | BacteriaNet | gram_stain | Reaction to gram-staining | negative | 99.5 | |
| 125439 | BacteriaNet | oxygen_tolerance | Oxygenic conditions needed for growth | obligate aerobe | 86.8 |
External links
@ref: 15695
culture collection no.: DSM 21419, CGMCC 1.6858, KCTC 22129
straininfo link
- @ref: 82371
- straininfo: 408087
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
|---|---|---|---|---|---|---|
| 15695 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21419) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-21419 | |||
| 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 | |||
| 32574 | 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 | 28789 | 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) | |||
| 82371 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID408087.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
| 125438 | Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann | 10.1101/2024.08.12.607695 | Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets | |||
| 125439 | Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy | https://github.com/GenomeNet/deepG | deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 |