Strain identifier
BacDive ID: 6237
Type strain: 
Species: Pseudidiomarina sediminum
Strain Designation: c121
Strain history: <- LMG <- Z.-Y. Hu, Ocean Univ. China, Qingdao, P. R. China; c121
NCBI tax ID(s): 1122124 (strain), 431675 (species)
version 8.1 (current version)
General
@ref: 15901
BacDive-ID: 6237
DSM-Number: 21906
keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, mesophilic, Gram-negative, rod-shaped
description: Pseudidiomarina sediminum c121 is a facultative anaerobe, mesophilic, Gram-negative bacterium that was isolated from coastal sediment.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 1122124 | strain |
| 431675 | species |
strain history
- @ref: 15901
- history: <- LMG <- Z.-Y. Hu, Ocean Univ. China, Qingdao, P. R. China; c121
doi: 10.13145/bacdive6237.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Alteromonadales
- family: Idiomarinaceae
- genus: Pseudidiomarina
- species: Pseudidiomarina sediminum
- full scientific name: Pseudidiomarina sediminum Hu and Li 2007
synonyms
- @ref: 20215
- synonym: Idiomarina sediminum
@ref: 15901
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Alteromonadales
family: Idiomarinaceae
genus: Pseudidiomarina
species: Pseudidiomarina sediminum
full scientific name: Pseudidiomarina sediminum Hu and Li 2007 emend. Liu et al. 2018
strain designation: c121
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell width | cell shape | motility | confidence |
|---|---|---|---|---|---|---|
| 32253 | negative | 1.5 µm | 0.3 µm | rod-shaped | no | |
| 69480 | negative | 99.936 |
pigmentation
- @ref: 32253
- production: no
Culture and growth conditions
culture medium
- @ref: 15901
- name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)
- growth: yes
- link: https://mediadive.dsmz.de/medium/514
- composition: Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 15901 | positive | growth | 28 | mesophilic |
| 32253 | positive | growth | 13-42 | |
| 32253 | positive | optimum | 35 | mesophilic |
culture pH
| @ref | ability | type | pH | PH range |
|---|---|---|---|---|
| 32253 | positive | growth | 6.3-10.5 | alkaliphile |
| 32253 | positive | optimum | 8.5 |
Physiology and metabolism
oxygen tolerance
- @ref: 32253
- oxygen tolerance: facultative anaerobe
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 32253 | no | |
| 69481 | no | 100 |
| 69480 | no | 99.993 |
halophily
| @ref | salt | growth | tested relation | concentration |
|---|---|---|---|---|
| 32253 | NaCl | positive | growth | 0.5-15 % |
| 32253 | NaCl | positive | optimum | 4.5 % |
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 32253 | 5291 | gelatin | + | carbon source |
| 32253 | 17306 | maltose | + | carbon source |
| 32253 | 53426 | tween 80 | + | carbon source |
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 32253 | gelatinase | + | |
| 32253 | cytochrome oxidase | + | 1.9.3.1 |
Isolation, sampling and environmental information
isolation
- @ref: 15901
- sample type: coastal sediment
- geographic location: Luoyuan Bay, Fujian Province
- country: China
- origin.country: CHN
- continent: Asia
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Sediment |
| #Environmental | #Terrestrial | #Coast |
taxonmaps
- @ref: 69479
- File name: preview.99_45100.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_197;96_3743;97_25784;98_32708;99_45100&stattab=map
- Last taxonomy: Pseudidiomarina sediminum subclade
- 16S sequence: EF212001
- Sequence Identity:
- Total samples: 92
- soil counts: 3
- aquatic counts: 57
- animal counts: 32
Safety information
risk assessment
- @ref: 15901
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 15901
- description: Pseudidiomarina sediminum strain c121 16S ribosomal RNA gene, partial sequence
- accession: EF212001
- length: 1455
- database: ena
- NCBI tax ID: 1122124
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Pseudidiomarina sediminum c121 | GCA_003987265 | contig | ncbi | 431675 |
| 66792 | Pseudidiomarina sediminum DSM 21906 | GCA_000423165 | scaffold | ncbi | 1122124 |
| 66792 | Idiomarina sediminum DSM 21906 | 1122124.3 | wgs | patric | 1122124 |
| 66792 | Idiomarina sediminum DSM 21906 | 2524614571 | draft | img | 1122124 |
GC content
| @ref | GC-content |
|---|---|
| 15901 | 50.0 |
| 32253 | 50 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| motile | no | 65.96 | no |
| flagellated | no | 95.378 | no |
| gram-positive | no | 98.959 | no |
| anaerobic | no | 98.029 | yes |
| aerobic | yes | 83.067 | yes |
| halophile | yes | 54.619 | no |
| spore-forming | no | 97.482 | yes |
| glucose-util | yes | 80.003 | no |
| thermophile | no | 99.711 | yes |
| glucose-ferment | no | 80.854 | no |
External links
@ref: 15901
culture collection no.: DSM 21906, CICC 10319, LMG 24046
straininfo link
- @ref: 75716
- straininfo: 298148
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 17978220 | Pseudidiomarina sediminum sp. nov., a marine bacterium isolated from coastal sediments of Luoyuan Bay in China. | Hu ZY, Li Y | Int J Syst Evol Microbiol | 10.1099/ijs.0.65199-0 | 2007 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial, DNA, Ribosomal, Fatty Acids/analysis, Gammaproteobacteria/chemistry/*classification/genetics/*isolation & purification, Genes, rRNA, Geologic Sediments/*microbiology, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Species Specificity | Genetics |
| Phylogeny | 19502309 | Pseudidiomarina donghaiensis sp. nov. and Pseudidiomarina maritima sp. nov., isolated from the East China Sea. | Wu YH, Shen YQ, Xu XW, Wang CS, Oren A, Wu M | Int J Syst Evol Microbiol | 10.1099/ijs.0.005702-0 | 2009 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Gammaproteobacteria/*classification/genetics/isolation & purification/physiology, Genotype, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Species Specificity | Genetics |
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
|---|---|---|---|---|---|---|
| 15901 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21906) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-21906 | |||
| 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 | |||
| 32253 | 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 | 28494 | 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 | |||
| 75716 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID298148.1 | StrainInfo: A central database for resolving microbial strain identifiers |