Strain identifier
BacDive ID: 17908
Type strain:
Species: Dasania marina
Strain Designation: SE12
Strain history: <- HK Lee, KOPRI
NCBI tax ID(s): 1121374 (strain), 471499 (species)
General
@ref: 16027
BacDive-ID: 17908
DSM-Number: 21967
keywords: genome sequence, 16S sequence, Bacteria, aerobe, psychrophilic, Gram-negative
description: Dasania marina SE12 is an aerobe, psychrophilic, Gram-negative bacterium that was isolated from marine sediment.
NCBI tax id
NCBI tax id | Matching level |
---|---|
1121374 | strain |
471499 | species |
strain history
@ref | history |
---|---|
16027 | <- KCTC <- Y. K. Lee, Korea Polar Research Institute, Incheon |
67770 | H. K. Lee KOPRI 20902 <-- H. H. Cho <-- Y. K. Lee. |
67771 | <- HK Lee, KOPRI |
doi: 10.13145/bacdive17908.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Cellvibrionales
- family: Spongiibacteraceae
- genus: Dasania
- species: Dasania marina
- full scientific name: Dasania marina Lee et al. 2008
@ref: 16027
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Pseudomonadales
family: Spongiibacteraceae
genus: Dasania
species: Dasania marina
full scientific name: Dasania marina Lee et al. 2008
strain designation: SE12
type strain: yes
Morphology
cell morphology
@ref | gram stain | motility | confidence |
---|---|---|---|
67771 | negative | ||
69480 | yes | 92.809 | |
69480 | negative | 99.997 |
multimedia
@ref | multimedia content | caption | intellectual property rights |
---|---|---|---|
66793 | EM_DSM_21967_1.jpg | electron microscopic image | © HZI/Manfred Rohde |
66793 | EM_DSM_21967_2.jpg | electron microscopic image | © HZI/Manfred Rohde |
66793 | EM_DSM_21967_3.jpg | electron microscopic image | © HZI/Manfred Rohde |
66793 | EM_DSM_21967_4.jpg | electron microscopic image | © HZI/Manfred Rohde |
66793 | EM_DSM_21967_5.jpg | electron microscopic image | © HZI/Manfred Rohde |
Culture and growth conditions
culture medium
- @ref: 16027
- 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 |
---|---|---|---|---|
16027 | positive | growth | 20 | psychrophilic |
67770 | positive | growth | 20 | psychrophilic |
67771 | positive | growth | 10-20 | psychrophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 67771
- oxygen tolerance: aerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.986 |
observation
- @ref: 67770
- observation: quinones: Q-8
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
16027 | marine sediment | Ny-Alesund, Spitsbergen | Norway | NOR | Europe |
67770 | Marine sediment sample from Ny-Ålesund | Spitsbergen Islands | Norway | NOR | Europe |
67771 | From Kings bay Sediment | Republic of Korea | KOR | Asia |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Aquatic | #Marine |
#Environmental | #Aquatic | #Sediment |
taxonmaps
- @ref: 69479
- File name: preview.99_7245.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_305;96_3384;97_4155;98_5316;99_7245&stattab=map
- Last taxonomy: Dasania marina subclade
- 16S sequence: AY771747
- Sequence Identity:
- Total samples: 1799
- soil counts: 46
- aquatic counts: 1679
- animal counts: 65
- plant counts: 9
Safety information
risk assessment
- @ref: 16027
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 16027
- description: Dasania marina strain KOPRI 20902 16S ribosomal RNA gene, partial sequence
- accession: AY771747
- length: 1486
- database: ena
- NCBI tax ID: 1121374
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Dasania marina DSM 21967 | 1121374.3 | wgs | patric | 1121374 |
66792 | Dasania marina DSM 21967 | 2515154073 | draft | img | 1121374 |
67770 | Dasania marina DSM 21967 | GCA_000373485 | scaffold | ncbi | 1121374 |
GC content
- @ref: 67770
- GC-content: 37
- method: thermal denaturation, midpoint method (Tm)
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | yes | 84.522 | no |
flagellated | yes | 65.34 | no |
gram-positive | no | 98.95 | yes |
anaerobic | no | 98.765 | yes |
aerobic | yes | 92.253 | yes |
halophile | yes | 70.33 | no |
spore-forming | no | 96.395 | no |
thermophile | no | 99.145 | yes |
glucose-util | yes | 55.913 | no |
glucose-ferment | no | 91.327 | no |
External links
@ref: 16027
culture collection no.: DSM 21967, JCM 13441, KCTC 12566, KOPRI 20902
straininfo link
- @ref: 86897
- straininfo: 397584
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 18176532 | Dasania marina gen. nov., sp. nov., of the order Pseudomonadales, isolated from Arctic marine sediment. | Lee YK, Hong SG, Cho HH, Cho KH, Lee HK | J Microbiol | 2644 | 2007 | Arctic Regions, Gammaproteobacteria/classification/genetics/*isolation & purification, Geologic Sediments/*microbiology, Norway, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology | Enzymology |
Phylogeny | 21538243 | Oceanicoccus sagamiensis gen. nov., sp. nov., a gammaproteobacterium isolated from sea water of Sagami Bay in Japan. | Park S, Yoshizawa S, Kogure K, Yokota A | J Microbiol | 10.1007/s12275-011-0368-y | 2011 | Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Gammaproteobacteria/*classification/genetics/*isolation & purification/physiology, Japan, Locomotion, Molecular Sequence Data, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA | Genetics |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
16027 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21967) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-21967 | |||
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 | |||
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) | |||
66793 | Mukherjee et al. | 10.1038/nbt.3886 | GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life | 35: 676-683 2017 | 28604660 | |
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
67771 | Curators of the KCTC | https://kctc.kribb.re.kr/En/Kctc | ||||
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 | |||
86897 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID397584.1 | StrainInfo: A central database for resolving microbial strain identifiers |