Strain identifier

BacDive ID: 24490

Type strain: Yes

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)

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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

@refhistory
20630<- JCM <- J. H. Yoon, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea; DSW-18
67770Y.-H. Yoon DSW-18.
67771<- JH Yoon, KRIBB
120791CIP <- 2007, JCM <- 2006, Y.H. Yoon, KRIBB, Taejon, Korea: strain DSW-18

doi: 10.13145/bacdive24490.20250331.9.3

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

@refgram staincell lengthcell widthcell shapemotilityconfidence
32157negative1.9 µm0.5 µmrod-shapedno
67771negative
125438negative98.333
125439negative96
120791negativerod-shapedno

colony morphology

  • @ref: 20630
  • incubation period: 2-3 days

pigmentation

  • @ref: 32157
  • production: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
20630BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)yeshttps://mediadive.dsmz.de/medium/514Name: 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
37383Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
120791CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperature
20630positivegrowth25
32157positivegrowth04-34
32157positiveoptimum25
37383positivegrowth25
67770positivegrowth25
67771positivegrowth25

culture pH

@refabilitytypepH
32157positivegrowth>5.5
32157positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
67771aerobe
125439obligate aerobe96.9

spore formation

  • @ref: 125439
  • spore formation: no
  • confidence: 97.3

halophily

@refsaltgrowthtested relationconcentration
32157NaClpositivegrowth01-07 %
32157NaClpositiveoptimum2 %

observation

  • @ref: 67770
  • observation: quinones: Q-10

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3215730089acetate+carbon source
3215717057cellobiose+carbon source
3215716947citrate+carbon source
3215728757fructose+carbon source
3215728260galactose+carbon source
3215717234glucose+carbon source
3215725115malate+carbon source
3215715361pyruvate+carbon source
3215730031succinate+carbon source
3215753424tween 20+carbon source
3215753423tween 40+carbon source
3215753425tween 60+carbon source
3215753426tween 80+carbon source
12079117632nitrate-reduction
12079116301nitrite-reduction
6836925115malate-assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate-assimilation
6836917306maltose-assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol-assimilation
6836916024D-mannose-assimilation
6836930849L-arabinose-assimilation
6836917634D-glucose-assimilation
683695291gelatin-hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
12079135581indoleno

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
20630catalase+1.11.1.6
20630cytochrome-c oxidase+1.9.3.1
32157acid phosphatase+3.1.3.2
32157alkaline phosphatase+3.1.3.1
32157catalase+1.11.1.6
32157cytochrome oxidase+1.9.3.1
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382naphthol-AS-BI-phosphohydrolase-
68382alpha-galactosidase-3.2.1.22
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382leucine arylamidase+3.4.11.1
68382valine arylamidase-
68382lipase (C 14)-
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
120791oxidase+
120791catalase+1.11.1.6
120791urease-3.5.1.5
68369urease-3.5.1.5
68382beta-glucosidase+3.2.1.21
68382alpha-glucosidase-3.2.1.20
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382esterase lipase (C 8)+
68369gelatinase-
68369arginine dihydrolase-3.5.3.6

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
120791-+++-+----+-----+---

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPAC
20630-----+-+------------
20630-----+/--+------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
20630seawaterEast SeaRepublic of KoreaKORAsia
67770Seawater
67771From seawaterEast SeaRepublic of KoreaKORAsia
120791Environment, SeawaterFrom seawater off Dokdo in the East SeaRepublic of KoreaKORAsia

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

@refbiosafety levelbiosafety level comment
206301Risk group (German classification)
1207911Risk 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: nuccore
  • NCBI tax ID: 420999

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Yoonia maricola DSM 29128GCA_002797915contigncbi420999
66792Loktanella maricola strain DSM 29128420999.3wgspatric420999
66792Yoonia maricola DSM 291282695420968draftimg420999

GC content

@refGC-contentmethod
3215756.8
6777056.8high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno98.333no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no91.271yes
125438spore-formingspore-formingAbility to form endo- or exosporesno84.813no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes84.342no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno96.95yes
125438motile2+flagellatedAbility to perform flagellated movementyes61.403no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno97.3
125439BacteriaNetmotilityAbility to perform movementyes62.4
125439BacteriaNetgram_stainReaction to gram-stainingnegative96
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe96.9

External links

@ref: 20630

culture collection no.: DSM 29128, JCM 14564, KCTC 12863, CIP 109730

straininfo link

  • @ref: 88350
  • straininfo: 309463

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17684260Loktanella maricola sp. nov., isolated from seawater of the East Sea in Korea.Yoon JH, Kang SJ, Lee SY, Oh TKInt J Syst Evol Microbiol10.1099/ijs.0.65050-02007DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Korea, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/chemistry/classification/genetics/*isolation & purification, Seawater/*microbiologyGenetics
Phylogeny21515703Loktanella tamlensis sp. nov., isolated from seawater.Lee SDInt J Syst Evol Microbiol10.1099/ijs.0.029462-02011Aerobiosis, 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/analysisGenetics
Phylogeny23749279Loktanella sediminilitoris sp. nov., isolated from tidal flat sediment.Park S, Jung YT, Yoon JHInt J Syst Evol Microbiol10.1099/ijs.0.049841-02013Bacterial 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/chemistryGenetics
Phylogeny24744019Loktanella maritima sp. nov. isolated from shallow marine sediments.Tanaka N, Romanenko LA, Kurilenko VV, Svetashev VI, Kalinovskaya NI, Mikhailov VVInt J Syst Evol Microbiol10.1099/ijs.0.061747-02014DNA, 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/chemistryGenetics

Reference

@idauthorstitledoi/urlcatalogueID_cross_referencepubmed
20215Parte, 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 DSMZ10.1099/ijsem.0.004332
20630Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-29128Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 29128)
32157Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172840028776041
37383Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7506
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68369Automatically annotated from API 20NE
68382Automatically annotated from API zym
69479João 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 betahttps://microbeatlas.org/
88350Reimer, 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 identifiers10.60712/SI-ID309463.1
120791Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109730Collection of Institut Pasteur (CIP 109730)
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg OvermannPredicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets10.1101/2024.08.12.607695
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardydeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1https://github.com/GenomeNet/deepG