Strain identifier
BacDive ID: 24490
Type strain:
Species: Yoonia maricola
Strain Designation: DSW-18
Strain history: CIP <- 2007, JCM <- 2006, Y.H. Yoon, KRIBB, Taejon, Korea: strain DSW-18
NCBI tax ID(s): 420999 (species)
General
@ref: 20630
BacDive-ID: 24490
DSM-Number: 29128
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, rod-shaped
description: Yoonia maricola DSW-18 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from seawater.
NCBI tax id
- NCBI tax id: 420999
- Matching level: species
strain history
@ref | history |
---|---|
20630 | <- JCM <- J. H. Yoon, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea; DSW-18 |
67770 | Y.-H. Yoon DSW-18. |
67771 | <- JH Yoon, KRIBB |
120791 | CIP <- 2007, JCM <- 2006, Y.H. Yoon, KRIBB, Taejon, Korea: strain DSW-18 |
doi: 10.13145/bacdive24490.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Rhodobacterales
- family: Roseobacteraceae
- genus: Yoonia
- species: Yoonia maricola
- full scientific name: Yoonia maricola (Yoon et al. 2007) Wirth and Whitman 2018
synonyms
- @ref: 20215
- synonym: Loktanella maricola
@ref: 20630
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhodobacterales
family: Rhodobacteraceae
genus: Yoonia
species: Yoonia maricola
full scientific name: Yoonia maricola (Yoon et al. 2007) Wirth and Whitman 2018
strain designation: DSW-18
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
32157 | negative | 1.9 µm | 0.5 µm | rod-shaped | no | |
67771 | negative | |||||
69480 | negative | 99.962 | ||||
120791 | negative | rod-shaped | no |
colony morphology
- @ref: 20630
- incubation period: 2-3 days
pigmentation
- @ref: 32157
- production: no
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
20630 | BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) | yes | https://mediadive.dsmz.de/medium/514 | 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 |
37383 | Marine agar (MA) | yes | Distilled water make up to (1000.000 ml);Marine agar (55.100 g) | |
120791 | CIP Medium 13 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
20630 | positive | growth | 25 | mesophilic |
32157 | positive | growth | 04-34 | |
32157 | positive | optimum | 25 | mesophilic |
37383 | positive | growth | 25 | mesophilic |
67770 | positive | growth | 25 | mesophilic |
67771 | positive | growth | 25 | mesophilic |
culture pH
@ref | ability | type | pH |
---|---|---|---|
32157 | positive | growth | >5.5 |
32157 | positive | optimum | 7.5 |
Physiology and metabolism
oxygen tolerance
- @ref: 67771
- oxygen tolerance: aerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.997 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
32157 | NaCl | positive | growth | 01-07 % |
32157 | NaCl | positive | optimum | 2 % |
observation
- @ref: 67770
- observation: quinones: Q-10
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
32157 | 30089 | acetate | + | carbon source |
32157 | 17057 | cellobiose | + | carbon source |
32157 | 16947 | citrate | + | carbon source |
32157 | 28757 | fructose | + | carbon source |
32157 | 28260 | galactose | + | carbon source |
32157 | 17234 | glucose | + | carbon source |
32157 | 25115 | malate | + | carbon source |
32157 | 15361 | pyruvate | + | carbon source |
32157 | 30031 | succinate | + | carbon source |
32157 | 53424 | tween 20 | + | carbon source |
32157 | 53423 | tween 40 | + | carbon source |
32157 | 53425 | tween 60 | + | carbon source |
32157 | 53426 | tween 80 | + | carbon source |
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 | 17634 | D-glucose | - | assimilation |
68369 | 5291 | gelatin | - | hydrolysis |
68369 | 16199 | urea | - | hydrolysis |
68369 | 29016 | arginine | - | hydrolysis |
68369 | 17634 | D-glucose | - | fermentation |
68369 | 27897 | tryptophan | - | energy source |
68369 | 17632 | nitrate | - | reduction |
120791 | 17632 | nitrate | - | reduction |
120791 | 16301 | nitrite | - | reduction |
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
68369 | 35581 | indole | no |
120791 | 35581 | indole | no |
metabolite tests
- @ref: 68369
- Chebi-ID: 35581
- metabolite: indole
- indole test: -
enzymes
@ref | value | activity | ec |
---|---|---|---|
20630 | catalase | + | 1.11.1.6 |
20630 | cytochrome-c oxidase | + | 1.9.3.1 |
32157 | acid phosphatase | + | 3.1.3.2 |
32157 | alkaline phosphatase | + | 3.1.3.1 |
32157 | catalase | + | 1.11.1.6 |
32157 | cytochrome oxidase | + | 1.9.3.1 |
68369 | gelatinase | - | |
68369 | urease | - | 3.5.1.5 |
68369 | arginine dihydrolase | - | 3.5.3.6 |
120791 | oxidase | + | |
120791 | catalase | + | 1.11.1.6 |
120791 | urease | - | 3.5.1.5 |
68382 | alkaline phosphatase | + | 3.1.3.1 |
68382 | esterase (C 4) | + | |
68382 | esterase lipase (C 8) | + | |
68382 | lipase (C 14) | - | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | valine arylamidase | - | |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | trypsin | - | 3.4.21.4 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | naphthol-AS-BI-phosphohydrolase | - | |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | beta-galactosidase | - | 3.2.1.23 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | alpha-glucosidase | - | 3.2.1.20 |
68382 | beta-glucosidase | + | 3.2.1.21 |
68382 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | alpha-fucosidase | - | 3.2.1.51 |
API zym
@ref | Control | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Acid phosphatase | Naphthol-AS-BI-phosphohydrolase | alpha- Galactosidase | beta- Galactosidase | beta- Glucuronidase | alpha- Glucosidase | beta- Glucosidase | N-acetyl-beta- glucosaminidase | alpha- Mannosidase | alpha- Fucosidase |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
120791 | - | + | + | + | - | + | - | - | - | - | + | - | - | - | - | - | + | - | - | - |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
20630 | - | - | - | - | - | + | - | + | - | - | - | - | - | - | - | - | - | - | - | - |
20630 | - | - | - | - | - | +/- | - | + | - | - | - | - | - | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
20630 | seawater | East Sea | Republic of Korea | KOR | Asia |
67770 | Seawater | ||||
67771 | From seawater | East Sea | Republic of Korea | KOR | Asia |
120791 | Environment, Seawater | From seawater off Dokdo in the East Sea | Republic of Korea | KOR | Asia |
isolation source categories
- Cat1: #Environmental
- Cat2: #Aquatic
- Cat3: #Marine
taxonmaps
- @ref: 69479
- File name: preview.99_21896.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_683;97_791;98_916;99_21896&stattab=map
- Last taxonomy: Yoonia maricola
- 16S sequence: EF202613
- Sequence Identity:
- Total samples: 236
- soil counts: 4
- aquatic counts: 215
- animal counts: 17
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
20630 | 1 | Risk group (German classification) |
120791 | 1 | Risk group (French classification) |
Sequence information
16S sequences
- @ref: 20630
- description: Loktanella maricola strain DSW-18 16S ribosomal RNA gene, partial sequence
- accession: EF202613
- length: 1419
- database: ena
- NCBI tax ID: 420999
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Yoonia maricola DSM 29128 | GCA_002797915 | contig | ncbi | 420999 |
66792 | Loktanella maricola strain DSM 29128 | 420999.3 | wgs | patric | 420999 |
66792 | Yoonia maricola DSM 29128 | 2695420968 | draft | img | 420999 |
GC content
@ref | GC-content | method |
---|---|---|
32157 | 56.8 | |
67770 | 56.8 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
gram-positive | no | 98.432 | yes |
anaerobic | no | 97.841 | no |
halophile | yes | 84.579 | no |
spore-forming | no | 94.318 | no |
glucose-util | yes | 72.741 | no |
aerobic | yes | 89.817 | yes |
flagellated | no | 77.958 | yes |
thermophile | no | 97.099 | yes |
motile | yes | 61.78 | no |
glucose-ferment | no | 87.928 | yes |
External links
@ref: 20630
culture collection no.: DSM 29128, JCM 14564, KCTC 12863, CIP 109730
straininfo link
- @ref: 88350
- straininfo: 309463
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 17684260 | Loktanella maricola sp. nov., isolated from seawater of the East Sea in Korea. | Yoon JH, Kang SJ, Lee SY, Oh TK | Int J Syst Evol Microbiol | 10.1099/ijs.0.65050-0 | 2007 | DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Korea, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/chemistry/classification/genetics/*isolation & purification, Seawater/*microbiology | Genetics |
Phylogeny | 21515703 | Loktanella tamlensis sp. nov., isolated from seawater. | Lee SD | Int J Syst Evol Microbiol | 10.1099/ijs.0.029462-0 | 2011 | Aerobiosis, Bacterial Typing Techniques, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Hydrogen-Ion Concentration, Locomotion, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Rhodobacteraceae/*classification/genetics/*isolation & purification/physiology, Seawater/*microbiology, Sequence Analysis, DNA, Temperature, Ubiquinone/analysis | Genetics |
Phylogeny | 23749279 | Loktanella sediminilitoris sp. nov., isolated from tidal flat sediment. | Park S, Jung YT, Yoon JH | Int J Syst Evol Microbiol | 10.1099/ijs.0.049841-0 | 2013 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Rhodobacteraceae/*classification/genetics/isolation & purification, Seawater/microbiology, Ubiquinone/analogs & derivatives/chemistry | Genetics |
Phylogeny | 24744019 | Loktanella maritima sp. nov. isolated from shallow marine sediments. | Tanaka N, Romanenko LA, Kurilenko VV, Svetashev VI, Kalinovskaya NI, Mikhailov VV | Int J Syst Evol Microbiol | 10.1099/ijs.0.061747-0 | 2014 | DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Japan, Molecular Sequence Data, Nucleic Acid Hybridization, Oceans and Seas, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/isolation & purification, Seawater/*microbiology, Ubiquinone/chemistry | Genetics |
Reference
@id | authors | title | doi/url | catalogue | 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 | |||
20630 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-29128 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 29128) | |||
32157 | 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 | 28400 | 28776041 | |
37383 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/7506 | ||||
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/ | ||||
67771 | Curators of the KCTC | https://kctc.kribb.re.kr/En/Kctc | ||||
68369 | Automatically annotated from API 20NE | |||||
68382 | Automatically annotated from API zym | |||||
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 | |||
88350 | 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-ID309463.1 | |||
120791 | Curators of the CIP | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109730 | Collection of Institut Pasteur (CIP 109730) |