Strain identifier
BacDive ID: 132959
Type strain: 
Species: Polymorphobacter fuscus
Strain Designation: D40P
Strain history: J. Lv D40P.
NCBI tax ID(s): 1439888 (species)
version 8.1 (current version)
General
@ref: 24747
BacDive-ID: 132959
DSM-Number: 105347
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative
description: Polymorphobacter fuscus D40P is a mesophilic, Gram-negative bacterium that was isolated from permafrost soil.
NCBI tax id
- NCBI tax id: 1439888
- Matching level: species
strain history
| @ref | history |
|---|---|
| 24747 | <- JCM <- J. Lv, Beijing University of Chemical Technology, Beijing, PR China |
| 67770 | J. Lv D40P. |
doi: 10.13145/bacdive132959.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Sphingomonadales
- family: Sphingosinicellaceae
- genus: Polymorphobacter
- species: Polymorphobacter fuscus
- full scientific name: Polymorphobacter fuscus Jia et al. 2015
@ref: 24747
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Pseudomonadales
family: Sphingosinicellaceae
genus: Polymorphobacter
species: Polymorphobacter fuscus
full scientific name: Polymorphobacter fuscus Jia et al. 2015
strain designation: D40P
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.976
multimedia
- @ref: 24747
- multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_105347.jpg
- intellectual property rights: © Leibniz-Institut DSMZ
Culture and growth conditions
culture medium
- @ref: 24747
- 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 |
|---|---|---|---|---|
| 24747 | positive | growth | 28 | mesophilic |
| 67770 | positive | growth | 25 | mesophilic |
Physiology and metabolism
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 99.991 |
observation
- @ref: 67770
- observation: quinones: Q-10, Q-9
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent | latitude | longitude |
|---|---|---|---|---|---|---|---|
| 24747 | permafrost soil | Kunlun Pass Basin, Qinghai-Tibet Plateau | China | CHN | Asia | 35.6667 | 94.05 |
| 67770 | Permafrost soil of Kunlun Mountains Gap | Qinghai-Tibet Plateau | China | CHN | Asia |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Terrestrial | #Permafrost |
| #Environmental | #Terrestrial | #Soil |
taxonmaps
- @ref: 69479
- File name: preview.99_22388.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_20;96_1995;97_2398;98_16878;99_22388&stattab=map
- Last taxonomy: Polymorphobacter
- 16S sequence: KF737330
- Sequence Identity:
- Total samples: 16848
- soil counts: 2630
- aquatic counts: 12147
- animal counts: 1756
- plant counts: 315
Safety information
risk assessment
- @ref: 24747
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 24747
- description: Polymorphobacter fuscus strain D40P 16S ribosomal RNA gene, partial sequence
- accession: KF737330
- length: 1452
- database: ena
- NCBI tax ID: 1439888
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Polymorphobacter fuscus D40P | GCA_009372075 | scaffold | ncbi | 1439888 |
| 66792 | Polymorphobacter fuscus D40P | GCA_009607675 | scaffold | ncbi | 1439888 |
| 66792 | Polymorphobacter fuscus strain DSM 105347 | 1439888.6 | wgs | patric | 1439888 |
| 66792 | Polymorphobacter fuscus DSM 105347 | 2830037985 | draft | img | 1439888 |
| 67770 | Polymorphobacter fuscus DSM 105347 | GCA_011927825 | contig | ncbi | 1439888 |
GC content
- @ref: 67770
- GC-content: 67.4
- method: thermal denaturation, midpoint method (Tm)
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| motile | yes | 55.83 | no |
| flagellated | no | 90.552 | no |
| gram-positive | no | 97.278 | no |
| anaerobic | no | 98.88 | no |
| aerobic | yes | 95.363 | no |
| halophile | no | 90.146 | no |
| spore-forming | no | 95.371 | no |
| thermophile | no | 97.619 | yes |
| glucose-util | yes | 83.29 | no |
| glucose-ferment | no | 92.112 | no |
External links
@ref: 24747
culture collection no.: DSM 105347, CGMCC 1.12714, JCM 19740
straininfo link
- @ref: 91236
- straininfo: 404984
literature
- topic: Phylogeny
- Pubmed-ID: 26246176
- title: Polymorphobacter fuscus sp. nov., isolated from permafrost soil, and emended description of the genus Polymorphobacter.
- authors: Jia L, Feng X, Zheng Z, Han L, Hou X, Lu Z, Lv J
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijsem.0.000514
- year: 2015
Reference
| @id | authors | title | doi/url | catalogue |
|---|---|---|---|---|
| 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 | |
| 24747 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-105347 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 105347) | |
| 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 | |
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||
| 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/ | |
| 69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |
| 69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | Predictions based on the model GenomeNet Sporulation v. 1 | 10.21203/rs.3.rs-2527258/v1 | |
| 91236 | 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-ID404984.1 |