Strain identifier
BacDive ID: 134244
Type strain: 
Species: Psychromonas hadalis
Strain Designation: K41G
Strain history: Y. Nogi K41G.
NCBI tax ID(s): 1278302 (strain), 211669 (species)
version 9.1 (current version)
General
@ref: 32081
BacDive-ID: 134244
keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, Gram-negative, motile, rod-shaped
description: Psychromonas hadalis K41G is a facultative anaerobe, Gram-negative, motile bacterium that was isolated from bottom of Japan Trench.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 211669 | species |
| 1278302 | strain |
strain history
- @ref: 67770
- history: Y. Nogi K41G.
doi: 10.13145/bacdive134244.20240916.9.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Alteromonadales
- family: Psychromonadaceae
- genus: Psychromonas
- species: Psychromonas hadalis
- full scientific name: Psychromonas hadalis Nogi et al. 2007
@ref: 32081
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Alteromonadales
family: Psychromonadaceae
genus: Psychromonas
species: Psychromonas hadalis
strain designation: K41G
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell width | cell shape | motility | confidence |
|---|---|---|---|---|---|---|
| 32081 | negative | 1.5-2 µm | 0.8-1 µm | rod-shaped | yes | |
| 69480 | negative | 99.5 |
Culture and growth conditions
culture temp
| @ref | growth | type | temperature |
|---|---|---|---|
| 32081 | positive | growth | 02-12 |
| 32081 | positive | optimum | 6 |
| 67770 | positive | growth | 10 |
Physiology and metabolism
oxygen tolerance
- @ref: 32081
- oxygen tolerance: facultative anaerobe
halophily
- @ref: 32081
- salt: NaCl
- growth: positive
- tested relation: optimum
- concentration: 3 %
observation
- @ref: 67770
- observation: quinones: Q-8
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 32081 | 28260 | galactose | + | carbon source |
| 32081 | 17754 | glycerol | + | carbon source |
| 32081 | 37684 | mannose | + | carbon source |
| 32081 | 27082 | trehalose | + | carbon source |
| 32081 | 17632 | nitrate | + | reduction |
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 32081 | catalase | + | 1.11.1.6 |
| 32081 | cytochrome oxidase | + | 1.9.3.1 |
Isolation, sampling and environmental information
isolation
| @ref | sample type |
|---|---|
| 32081 | bottom of Japan Trench |
| 67770 | Sediment collected from the bottom of the Japan Trench at a depth of 7,542 m |
isolation source categories
- Cat1: #Environmental
- Cat2: #Aquatic
- Cat3: #Marine
Sequence information
16S sequences
- @ref: 32081
- description: Psychromonas hadalis gene for 16S rRNA, partial sequence, strain:K41G
- accession: AB094413
- length: 1451
- database: nuccore
- NCBI tax ID: 211669
Genome sequences
- @ref: 67770
- description: Psychromonas hadalis ATCC BAA-638 ATCC BAA-638
- accession: GCA_000420245
- assembly level: contig
- database: ncbi
- NCBI tax ID: 1278302
GC content
- @ref: 67770
- GC-content: 39.1
Genome-based predictions
predictions
| @ref | trait | model | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 69480 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 99.5 | yes |
| 69480 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 90.525 | yes |
| 69480 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | no | 65.819 | yes |
| 69480 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 89.721 | no |
| 69480 | thermophilic | thermophile | Ability to grow at temperatures above or equal to 45°C | no | 93.458 | no |
| 69480 | flagellated | motile2+ | Ability to perform flagellated movement | yes | 82.336 | no |
External links
@ref: 32081
culture collection no.: JCM 11830, ATCC BAA-638
straininfo link
- @ref: 91837
- straininfo: 309498
literature
- topic: Phylogeny
- Pubmed-ID: 17551059
- title: Psychromonas hadalis sp. nov., a novel piezophilic bacterium isolated from the bottom of the Japan Trench.
- authors: Nogi Y, Hosoya S, Kato C, Horikoshi K
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.64933-0
- year: 2007
- mesh: Bacterial Typing Techniques, Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Gammaproteobacteria/*classification/genetics/*isolation & purification/physiology, Genes, rRNA, Geologic Sediments/*microbiology, Hydrostatic Pressure, Japan, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Temperature
- topic2: Genetics
Reference
| @id | authors | title | doi/url | 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 | ||
| 32081 | 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 | 28327 | 28776041 |
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | |||
| 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 | ||
| 91837 | 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-ID309498.1 |