Strain identifier

BacDive ID: 13673

Type strain: Yes

Species: Yoonia vestfoldensis

Strain Designation: R-9477

Strain history: CIP <- 2004, S. Van Trappen, Ghent Univ., Ghent, Belgium <- J. Mergaert, Ghent Univ., Ghent, Belgium: strain R-9477

NCBI tax ID(s): 1122181 (strain), 245188 (species)

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General

@ref: 6328

BacDive-ID: 13673

DSM-Number: 16212

keywords: genome sequence, 16S sequence, Bacteria, aerobe, psychrophilic, Gram-negative, rod-shaped

description: Yoonia vestfoldensis R-9477 is an aerobe, psychrophilic, Gram-negative bacterium that was isolated from microbial mat.

NCBI tax id

NCBI tax idMatching level
1122181strain
245188species

strain history

@refhistory
6328<- D. Janssens, LMG <- J. Mergaert, Univ. Ghent, Belgium; R-9477
67770IAM 15182 <-- LMG 22003 <-- J. Mergaert R-9477.
123829CIP <- 2004, S. Van Trappen, Ghent Univ., Ghent, Belgium <- J. Mergaert, Ghent Univ., Ghent, Belgium: strain R-9477

doi: 10.13145/bacdive13673.20230509.8.1

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 vestfoldensis
  • full scientific name: Yoonia vestfoldensis (Van Trappen et al. 2004) Wirth and Whitman 2018

  • synonyms

    • @ref: 20215
    • synonym: Loktanella vestfoldensis

@ref: 6328

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Yoonia

species: Yoonia vestfoldensis

full scientific name: Yoonia vestfoldensis (Van Trappen et al. 2004) Wirth and Whitman 2018

strain designation: R-9477

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
30155negative3.5 µm1 µmrod-shapedno
123829negativerod-shapedno

colony morphology

  • @ref: 6328
  • incubation period: 3-7 days

pigmentation

  • @ref: 30155
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6328BACTO 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
37380Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
123829CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
6328positivegrowth20psychrophilic
30155positivegrowth5.0-37
30155positiveoptimum25mesophilic
37380positivegrowth25mesophilic
67770positivegrowth25mesophilic
123829positivegrowth15-30
123829nogrowth5psychrophilic
123829nogrowth37mesophilic
123829nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 30155
  • oxygen tolerance: aerobe

spore formation

  • @ref: 30155
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
30155NaClpositivegrowth0.0-10 %
30155NaClpositiveoptimum5 %
123829NaClnogrowth0 %
123829NaClnogrowth2 %
123829NaClnogrowth4 %
123829NaClnogrowth6 %
123829NaClnogrowth8 %
123829NaClnogrowth10 %

observation

  • @ref: 30155
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3015553426tween 80+carbon source
301554853esculin+hydrolysis
6836925115malate+assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate-assimilation
6836917306maltose+assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol+assimilation
6836930849L-arabinose-assimilation
683695291gelatin-hydrolysis
683694853esculin-hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction
12382916947citrate-carbon source
1238294853esculin+hydrolysis
12382917632nitrate-reduction
12382916301nitrite-reduction
123829132112sodium thiosulfate-builds gas from
12382917234glucose-degradation

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
12382935581indoleno

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-testmethylred-test
6836935581indole-
12382915688acetoin-
12382917234glucose-

enzymes

@refvalueactivityec
6328catalase+1.11.1.6
6328cytochrome-c oxidase+1.9.3.1
30155acid phosphatase+3.1.3.2
30155alkaline phosphatase+3.1.3.1
30155catalase+1.11.1.6
30155cytochrome oxidase+1.9.3.1
30155urease+3.5.1.5
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
123829oxidase+
123829beta-galactosidase+3.2.1.23
123829alcohol dehydrogenase-1.1.1.1
123829gelatinase-
123829amylase-
123829caseinase-3.4.21.50
123829catalase+1.11.1.6
123829tween esterase+
123829gamma-glutamyltransferase+2.3.2.2
123829lecithinase-
123829lipase-
123829lysine decarboxylase-4.1.1.18
123829ornithine decarboxylase-4.1.1.17
123829phenylalanine ammonia-lyase-4.3.1.24
123829protease-
123829tryptophan deaminase-
123829urease+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
123829-+++-+--+-++-+-+----

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPAC
6328-------++/--+/-+-+---+--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcontinentcountryorigin.countryisolation date
6328microbial matLake Ace, Vestfold HillsAustralia and Oceania
67770Microbial mat from Ace Lake in the Vestfold HillsAntarcticaAntarcticaATA
123829Microbial materialAce lake, Vestfold hillsAntarcticaAntarcticaATA1999

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Microbial community
  • Cat3: #Microbial mat

taxonmaps

  • @ref: 69479
  • File name: preview.99_5578.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_2693;97_3307;98_4163;99_5578&stattab=map
  • Last taxonomy: Yoonia vestfoldensis subclade
  • 16S sequence: AJ582226
  • Sequence Identity:
  • Total samples: 22849
  • soil counts: 1689
  • aquatic counts: 18624
  • animal counts: 2367
  • plant counts: 169

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
63281Risk group (German classification)
1238291Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Loktanella vestfoldensis strain LMG22003 16S ribosomal RNA gene, partial sequenceDQ9156111306ena245188
20218Loktanella vestfoldensis gene for 16S rRNA, partial sequence, strain: NBRC 102487AB6818261388ena245188
6328Loktanella vestfoldensis 16S rRNA gene, type strain LMG 22003TAJ5822261449ena245188

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Loktanella vestfoldensis DSM 162121122181.3wgspatric1122181
66792Loktanella vestfoldensis DSM 162122521172635draftimg1122181
67770Yoonia vestfoldensis DSM 16212GCA_000382265scaffoldncbi1122181

GC content

@refGC-contentmethod
3015562.6
6777062.1high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno51.957no
flagellatedno82.098no
gram-positiveno97.844no
anaerobicno97.719yes
aerobicyes86.92yes
halophileyes64.747no
spore-formingno96.264yes
thermophileno97.895yes
glucose-utilyes78.918no
glucose-fermentno91.947no

External links

@ref: 6328

culture collection no.: DSM 16212, LMG 22003, JCM 21637, CIP 108321, IAM 15182, NBRC 102487

straininfo link

  • @ref: 82856
  • straininfo: 23227

literature

  • topic: Phylogeny
  • Pubmed-ID: 15280301
  • title: Loktanella salsilacus gen. nov., sp. nov., Loktanella fryxellensis sp. nov. and Loktanella vestfoldensis sp. nov., new members of the Rhodobacter group, isolated from microbial mats in Antarctic lakes.
  • authors: Van Trappen S, Mergaert J, Swings J
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.03006-0
  • year: 2004
  • mesh: Antarctic Regions, Bacterial Typing Techniques, Base Composition, DNA Fingerprinting, DNA, Bacterial/chemistry, DNA, Ribosomal/chemistry, Fatty Acids/analysis, Fresh Water/*microbiology, Genes, rRNA, Gentian Violet, Geologic Sediments/microbiology, Molecular Sequence Data, Movement, Nucleic Acid Hybridization, Phenazines, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Repetitive Sequences, Nucleic Acid, Rhodobacteraceae/*classification/cytology/*isolation & purification/physiology, Sequence Analysis, DNA, Sequence Homology, Water Microbiology
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
6328Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16212)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16212
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
30155Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604126506
37380Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5931
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
82856Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID23227.1StrainInfo: A central database for resolving microbial strain identifiers
123829Curators of the CIPCollection of Institut Pasteur (CIP 108321)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108321