Strain identifier

BacDive ID: 24523

Type strain: Yes

Species: Epibacterium ulvae

Strain Designation: U95

Strain history: <- S. Egan, University of New South Wales; U95 <- A. Penesyan

NCBI tax ID(s): 1156985 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 21250

BacDive-ID: 24523

DSM-Number: 24752

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

description: Epibacterium ulvae U95 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from surface of the marine green alga Ulva australis collected from a rocky intertidal zone.

NCBI tax id

  • NCBI tax id: 1156985
  • Matching level: species

strain history

  • @ref: 21250
  • history: <- S. Egan, University of New South Wales; U95 <- A. Penesyan

doi: 10.13145/bacdive24523.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Rhodobacterales
  • family: Roseobacteraceae
  • genus: Epibacterium
  • species: Epibacterium ulvae
  • full scientific name: Epibacterium ulvae Penesyan et al. 2013
  • synonyms

    • @ref: 20215
    • synonym: Tritonibacter ulvae

@ref: 21250

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Not assigned to order

family: Rhodobacteraceae

genus: Epibacterium

species: Epibacterium ulvae

full scientific name: Epibacterium ulvae Penesyan et al. 2013

strain designation: U95

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
30714negative2.5 µm0.5 µmrod-shapedyes
69480negative99.996

colony morphology

  • @ref: 21250
  • incubation period: 3-7 days

pigmentation

  • @ref: 30714
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 21250
  • 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

@refgrowthtypetemperaturerange
21250positivegrowth25mesophilic
30714positivegrowth12-34
30714positiveoptimum25mesophilic

culture pH

@refabilitytypepHPH range
30714positivegrowth06-09alkaliphile
30714positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

  • @ref: 30714
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.998

halophily

@refsaltgrowthtested relationconcentration
30714NaClpositivegrowth01-06 %
30714NaClpositiveoptimum2.5 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3071416947citrate+carbon source
3071428757fructose+carbon source
3071428260galactose+carbon source
3071417234glucose+carbon source
3071417754glycerol+carbon source
3071424996lactate+carbon source
3071417306maltose+carbon source
3071429864mannitol+carbon source
3071437684mannose+carbon source
3071417272propionate+carbon source
3071430031succinate+carbon source
3071417992sucrose+carbon source
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
683694853esculin-hydrolysis
6836916199urea+hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction

metabolite production

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

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

enzymes

@refvalueactivityec
21250catalase+1.11.1.6
21250cytochrome-c oxidase+1.9.3.1
30714catalase+1.11.1.6
30714cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369urease+3.5.1.5
68369arginine dihydrolase-3.5.3.6

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPAC
21250----+--+------------

Isolation, sampling and environmental information

isolation

  • @ref: 21250
  • sample type: surface of the marine green alga Ulva australis collected from a rocky intertidal zone
  • host species: Ulva australis
  • geographic location: near Sydney (33° 51'09''S, 151° 16'00''E), Clovelly, Sharks Point
  • country: Australia
  • origin.country: AUS
  • continent: Australia and Oceania
  • latitude: 33.8525
  • longitude: 151.267

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Environmental#Terrestrial#Tidal flat
#Host#Algae#Green algae

Safety information

risk assessment

  • @ref: 21250
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 21250
  • description: Epibacterium ulvae strain U95 16S ribosomal RNA gene, partial sequence
  • accession: JN935021
  • length: 1326
  • database: ena
  • NCBI tax ID: 1156985

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Epibacterium ulvae U95GCA_002796795scaffoldncbi1156985
66792Epibacterium ulvae U95GCA_900102795contigncbi1156985
66792Epibacterium ulvae U952622736501draftimg1156985

GC content

@refGC-contentmethod
2125052.6high performance liquid chromatography (HPLC)
3071452.6

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno60.441no
gram-positiveno98.367yes
anaerobicno98.871yes
aerobicyes87.005yes
halophileyes62.683no
spore-formingno92.853no
thermophileno97.638yes
glucose-utilyes82.16no
motileyes77.657yes
glucose-fermentno89.073yes

External links

@ref: 21250

culture collection no.: DSM 24752, LMG 26464

straininfo link

  • @ref: 88378
  • straininfo: 377580

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny22904216Epibacterium ulvae gen. nov., sp. nov., epibiotic bacteria isolated from the surface of a marine alga.Penesyan A, Breider S, Schumann P, Tindall BJ, Egan S, Brinkhoff TInt J Syst Evol Microbiol10.1099/ijs.0.042838-02012Australia, Bacterial Typing Techniques, Bacteriochlorophyll A/analysis, Base Composition, DNA, Bacterial/genetics, DNA, Ribosomal Spacer/genetics, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Roseobacter/*classification/genetics/isolation & purification, Seawater, Sequence Analysis, DNA, Ubiquinone/analysis, Ulva/*microbiology, Water MicrobiologyGenetics
Genetics33902719Genome sequence of Epibacterium ulvae strain DSM 24752(T), an indigoidine-producing, macroalga-associated member of the marine Roseobacter group.Breider S, Sehar S, Berger M, Thomas T, Brinkhoff T, Egan SEnviron Microbiome10.1186/s40793-019-0343-52019

Reference

@idauthorstitledoi/urlcatalogueID_cross_referencepubmedjournal
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
21250Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-24752Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 24752)
30714Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172704528776041
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
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa102533211880Nucleic Acids Res. 49: D498-D508 2020
68369Automatically annotated from API 20NE
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
88378Reimer, 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-ID377580.1