Strain identifier

BacDive ID: 130606

Type strain: Yes

Species: Yoonia rosea

Strain Designation: Fg36

Strain history: CIP <- 2003, E. Ivanova, Swinburne Inst, Victoria, Autralia: strain Fg 36, Sulfitobacter sp. <- N. Gorshkova

NCBI tax ID(s): 287098 (species)

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General

@ref: 21633

BacDive-ID: 130606

DSM-Number: 29591

keywords: genome sequence, 16S sequence, Bacteria, aerobe, spore-forming, mesophilic, Gram-negative, rod-shaped

description: Yoonia rosea Fg36 is an aerobe, spore-forming, mesophilic bacterium that was isolated from sediments.

NCBI tax id

  • NCBI tax id: 287098
  • Matching level: species

strain history

@refhistory
21633<- LMG <- E. Ivanova, Swinburne Univ. of Technol., IRIS, Australia
366602003, E. Ivanova, Swinburne Inst., Victoria, Australia, Ruegeria sp.: strain R10SW5
122255CIP <- 2003, E. Ivanova, Swinburne Inst, Victoria, Autralia: strain Fg 36, Sulfitobacter sp. <- N. Gorshkova

doi: 10.13145/bacdive130606.20230509.8.1

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 rosea
  • full scientific name: Yoonia rosea (Ivanova et al. 2005) Wirth and Whitman 2018

  • synonyms

    • @ref: 20215
    • synonym: Loktanella rosea

@ref: 21633

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Yoonia

species: Yoonia rosea

full scientific name: Yoonia rosea (Ivanova et al. 2005) Wirth and Whitman 2018

strain designation: Fg36

type strain: yes

Morphology

cell morphology

@refgram staincell widthcell shapemotilityconfidence
31393negative0.8 µmrod-shapedno
69480negative99.997
122255negativerod-shapedno

colony morphology

  • @ref: 21633
  • incubation period: 1-2 days

pigmentation

  • @ref: 31393
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
21633BACTO 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
36653Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
36660Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
122255CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
21633positivegrowth30mesophilic
31393positivegrowth04-35
31393positiveoptimum25mesophilic
36653positivegrowth25mesophilic
36660positivegrowth25mesophilic
122255positivegrowth15-35
122255nogrowth5psychrophilic
122255nogrowth41thermophilic
122255nogrowth45thermophilic

culture pH

@refabilitytypepHPH range
31393positivegrowth6.0-10.0alkaliphile
31393positiveoptimum7.75

Physiology and metabolism

oxygen tolerance

  • @ref: 31393
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
31393yes
69481yes92
69480no99.987

halophily

@refsaltgrowthtested relationconcentration
31393NaClpositivegrowth01-12 %
31393NaClpositiveoptimum6.5 %
122255NaClpositivegrowth0 %
122255NaClnogrowth2 %
122255NaClnogrowth4 %
122255NaClnogrowth6 %
122255NaClnogrowth8 %
122255NaClnogrowth10 %

observation

  • @ref: 31393
  • observation: aggregates in clumps

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3139321217L-alaninamide+carbon source
3139332323glucuronamide+carbon source
3139315428glycine+carbon source
3139353426tween 80+carbon source
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate-assimilation
6836917306maltose-assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol+assimilation
6836916024D-mannose-assimilation
6836930849L-arabinose-assimilation
683695291gelatin-hydrolysis
683694853esculin+hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction
12225516947citrate-carbon source
1222554853esculin+hydrolysis
122255606565hippurate-hydrolysis
12225517632nitrate-builds gas from
12225517632nitrate-reduction
12225516301nitrite-builds gas from
12225516301nitrite-reduction
12225515792malonate-assimilation
12225517234glucose-degradation

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
12225535581indoleno

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-testmethylred-test
6836935581indole-
12225515688acetoin-
12225517234glucose-

enzymes

@refvalueactivityec
21633catalase+1.11.1.6
21633cytochrome-c oxidase+1.9.3.1
31393catalase+1.11.1.6
68369gelatinase-
68369beta-glucosidase+3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
122255oxidase+
122255beta-galactosidase+3.2.1.23
122255alcohol dehydrogenase-1.1.1.1
122255gelatinase+/-
122255amylase-
122255caseinase-3.4.21.50
122255catalase+1.11.1.6
122255tween esterase+
122255gamma-glutamyltransferase-2.3.2.2
122255lecithinase-
122255lipase-
122255lysine decarboxylase-4.1.1.18
122255ornithine decarboxylase-4.1.1.17
122255phenylalanine ammonia-lyase-4.3.1.24
122255protease+
122255tryptophan deaminase-
122255urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase+3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase-3.2.1.20
68382beta-glucosidase+3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
122255-+++-+----++-+--+---

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPAC
21633-----+-++/---+-----+/---

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
21633sedimentsPacific Ocean, Sea of Japan, Chazma BayJapanJPNAsia
122255Environment, Sediment sampleJapanJPNAsia2002

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_1165.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_683;97_791;98_916;99_1165&stattab=map
  • Last taxonomy: Yoonia
  • 16S sequence: AY682199
  • Sequence Identity:
  • Total samples: 392
  • soil counts: 11
  • aquatic counts: 352
  • animal counts: 21
  • plant counts: 8

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
216331Risk group (German classification)
1222551Risk group (French classification)

Sequence information

16S sequences

  • @ref: 21633
  • description: Loktanella rosea 16S ribosomal RNA gene, partial sequence
  • accession: AY682199
  • length: 1398
  • database: ena
  • NCBI tax ID: 287098

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Yoonia rosea DSM 29591GCA_900156505contigncbi287098
66792Loktanella rosea strain DSM 29591287098.3wgspatric287098
66792Yoonia rosea DSM 295912681812930draftimg287098

GC content

  • @ref: 31393
  • GC-content: 60.5-61.8

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes92no
gram-positiveno98.265yes
anaerobicno97.196yes
halophileyes84.689yes
spore-formingno93.347yes
glucose-utilyes72.705no
motileno59.267yes
flagellatedno83.269yes
aerobicyes92.709yes
thermophileno96.54yes
glucose-fermentno88.757no

External links

@ref: 21633

culture collection no.: DSM 29591, CIP 107851, KMM 6003, LMG 22534

straininfo link

  • @ref: 89120
  • straininfo: 131997

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16166733Loktanella agnita sp. nov. and Loktanella rosea sp. nov., from the north-west Pacific Ocean.Ivanova EP, Zhukova NV, Lysenko AM, Gorshkova NM, Sergeev AF, Mikhailov VV, Bowman JPInt J Syst Evol Microbiol10.1099/ijs.0.63461-02005DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Genotype, Geologic Sediments/*microbiology, Molecular Sequence Data, Pacific Ocean, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/chemistry/*classification/genetics/isolation & purification, Seawater/*microbiology, Sequence Analysis, DNA, Species SpecificityGenetics
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

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
21633Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-29591Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 29591)
31393Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172770428776041
36653Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5408
36660Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5443
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
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/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions 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
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
89120Reimer, 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-ID131997.1
122255Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107851Collection of Institut Pasteur (CIP 107851)