Strain identifier
BacDive ID: 24521
Type strain: 
Species: Poseidonocella sedimentorum
Strain Designation: Sd3-23
Strain history: N. Tanaka <-- L. A. Romanenko Sd3-23.
NCBI tax ID(s): 871652 (species)
version 8.1 (current version)
General
@ref: 21232
BacDive-ID: 24521
DSM-Number: 29315
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative
description: Poseidonocella sedimentorum Sd3-23 is a mesophilic, Gram-negative bacterium that was isolated from shallow sediment sample.
NCBI tax id
- NCBI tax id: 871652
- Matching level: species
strain history
| @ref | history |
|---|---|
| 21232 | <- JCM 17311 <- N. Tanaka <- L. A. Romanenko; Sd3-23 |
| 67770 | N. Tanaka <-- L. A. Romanenko Sd3-23. |
doi: 10.13145/bacdive24521.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Rhodobacterales
- family: Roseobacteraceae
- genus: Poseidonocella
- species: Poseidonocella sedimentorum
- full scientific name: Poseidonocella sedimentorum Romanenko et al. 2012
@ref: 21232
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhodobacterales
family: Rhodobacteraceae
genus: Poseidonocella
species: Poseidonocella sedimentorum
full scientific name: Poseidonocella sedimentorum Romanenko et al. 2012
strain designation: Sd3-23
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.99
colony morphology
- @ref: 21232
- incubation period: 2-3 days
Culture and growth conditions
culture medium
- @ref: 21232
- 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 |
|---|---|---|---|---|
| 21232 | positive | growth | 30 | mesophilic |
| 67770 | positive | growth | 25 | mesophilic |
Physiology and metabolism
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 99.99 |
observation
- @ref: 67770
- observation: quinones: Q-10
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 68369 | 25115 | malate | + | assimilation |
| 68369 | 17128 | adipate | - | assimilation |
| 68369 | 27689 | decanoate | - | assimilation |
| 68369 | 24265 | gluconate | - | assimilation |
| 68369 | 17306 | maltose | + | assimilation |
| 68369 | 59640 | N-acetylglucosamine | - | assimilation |
| 68369 | 16899 | D-mannitol | + | assimilation |
| 68369 | 16024 | D-mannose | + | assimilation |
| 68369 | 30849 | L-arabinose | - | assimilation |
| 68369 | 5291 | gelatin | - | hydrolysis |
| 68369 | 4853 | esculin | + | hydrolysis |
| 68369 | 16199 | urea | - | hydrolysis |
| 68369 | 29016 | arginine | - | hydrolysis |
| 68369 | 17634 | D-glucose | - | fermentation |
| 68369 | 27897 | tryptophan | - | energy source |
| 68369 | 17632 | nitrate | - | reduction |
metabolite production
- @ref: 68369
- Chebi-ID: 35581
- metabolite: indole
- production: no
metabolite tests
- @ref: 68369
- Chebi-ID: 35581
- metabolite: indole
- indole test: -
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 21232 | catalase | + | 1.11.1.6 |
| 21232 | cytochrome-c oxidase | + | 1.9.3.1 |
| 68369 | gelatinase | - | |
| 68369 | beta-glucosidase | + | 3.2.1.21 |
| 68369 | urease | - | 3.5.1.5 |
| 68369 | arginine dihydrolase | - | 3.5.3.6 |
API 20NE
| @ref | NO3 | TRP | GLU_ Ferm | ADH Arg | URE | ESC | GEL | PNPG | GLU_ Assim | ARA | MNE | MAN | NAG | MAL | GNT | CAP | ADI | MLT | CIT | PAC |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 21232 | - | - | - | - | - | + | - | + | +/- | - | + | + | - | + | - | - | - | + | - | - |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 21232 | shallow sediment sample | Peter the Great Bay (Sea of Japan) | Russia | RUS | Asia |
| 67770 | Shallow sediment sample collected from Peter the Great Bay | Sea of Japan | Russia | RUS |
isolation source categories
- Cat1: #Environmental
- Cat2: #Aquatic
- Cat3: #Sediment
Safety information
risk assessment
- @ref: 21232
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 21232
- description: Poseidonocella sedimentorum gene for 16S ribosomal RNA, partial sequence
- accession: AB576006
- length: 1435
- database: ena
- NCBI tax ID: 871652
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Poseidonocella sedimentorum strain KMM 9023,NRIC 0796,JCM 17311,KCTC 23692 | 871652.3 | wgs | patric | 871652 |
| 66792 | Poseidonocella sedimentorum DSM 29315 | 2634166304 | draft | img | 871652 |
| 67770 | Poseidonocella sedimentorum KMM 9023,NRIC 0796,JCM 17311,KCTC 23692 | GCA_900116005 | contig | ncbi | 871652 |
GC content
- @ref: 21232
- GC-content: 65.4
- method: thermal denaturation, midpoint method (Tm)
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| motile | no | 66.497 | no |
| flagellated | no | 79.949 | no |
| gram-positive | no | 98.124 | no |
| anaerobic | no | 98.199 | no |
| halophile | yes | 77.949 | no |
| spore-forming | no | 95.419 | no |
| thermophile | no | 95.848 | yes |
| glucose-util | yes | 81.735 | no |
| aerobic | yes | 90.305 | no |
| glucose-ferment | no | 90.542 | yes |
External links
@ref: 21232
culture collection no.: DSM 29315, JCM 17311, KCTC 23692, NRIC 0796, KMM 9023
straininfo link
- @ref: 88376
- straininfo: 402871
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 21800148 | Poseidonocella pacifica gen. nov., sp. nov. and Poseidonocella sedimentorum sp. nov., novel alphaproteobacteria from the shallow sandy sediments of the Sea of Japan. | Romanenko LA, Tanaka N, Svetashev VI, Kalinovskaya NI | Arch Microbiol | 10.1007/s00203-011-0736-3 | 2011 | Alphaproteobacteria/chemistry/*classification/genetics/isolation & purification, Base Composition, DNA, Ribosomal/genetics, Fatty Acids/analysis, Geologic Sediments/*microbiology, Japan, Lipids/analysis, Molecular Sequence Data, Oceans and Seas, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Homology, Nucleic Acid, Species Specificity | Genetics |
| Pathogenicity | 30286988 | Sulfated O-polysaccharide with anticancer activity from the marine bacterium Poseidonocella sedimentorum KMM 9023(T). | Kokoulin MS, Kuzmich AS, Romanenko LA, Menchinskaya ES, Mikhailov VV, Chernikov OV | Carbohydr Polym | 10.1016/j.carbpol.2018.08.107 | 2018 | Alphaproteobacteria/*chemistry, Antineoplastic Agents/chemistry/isolation & purification/*pharmacology, Carbohydrate Conformation, Cell Proliferation/drug effects, Cell Survival/drug effects, Drug Screening Assays, Antitumor, Humans, O Antigens/chemistry/isolation & purification/*pharmacology, Sulfates/chemistry/isolation & purification/*pharmacology, Tumor Cells, Cultured | Enzymology |
Reference
| @id | authors | title | doi/url | catalogue | journal | 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 | |||
| 21232 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-29315 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 29315) | |||
| 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 | |||
| 66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | 10.1093/nar/gkaa1025 | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
| 68369 | Automatically annotated from API 20NE | |||||
| 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 | |||
| 88376 | 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-ID402871.1 |