Strain identifier

BacDive ID: 130639

Type strain: Yes

Species: Marivita hallyeonensis

Strain Designation: DPG-28

Strain history: <- JH Yoon, KRIBB

NCBI tax ID(s): 996342 (species)

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General

@ref: 22070

BacDive-ID: 130639

DSM-Number: 29431

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

description: Marivita hallyeonensis DPG-28 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from seawater.

NCBI tax id

  • NCBI tax id: 996342
  • Matching level: species

strain history

@refhistory
22070<- KCTC <- J. H. Yoon, KRIBB; DPG-28
67771<- JH Yoon, KRIBB

doi: 10.13145/bacdive130639.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Rhodobacterales
  • family: Roseobacteraceae
  • genus: Marivita
  • species: Marivita hallyeonensis
  • full scientific name: Marivita hallyeonensis Yoon et al. 2012

@ref: 22070

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Marivita

species: Marivita hallyeonensis

full scientific name: Marivita hallyeonensis Yoon et al. 2012

strain designation: DPG-28

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
30268negative01-08 µm0.4-1.3 µmrod-shapedno
67771negative
69480negative99.997

colony morphology

@refincubation period
220702-3 days
623382 days

pigmentation

  • @ref: 30268
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 22070
  • 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
22070positivegrowth30mesophilic
30268positivegrowth10-40
30268positiveoptimum30mesophilic
62338positivegrowth30mesophilic
67771positivegrowth30mesophilic

culture pH

  • @ref: 30268
  • ability: positive
  • type: optimum
  • pH: 7-7.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
30268aerobe
62338aerobe
67771aerobe

spore formation

@refspore formationconfidence
30268no
69481no100
69480no99.991

halophily

@refsaltgrowthtested relationconcentration
30268NaClpositivegrowth0.5-8 %
30268NaClpositiveoptimum2 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3026853423tween 40+carbon source
3026853426tween 80+carbon source
302684853esculin+hydrolysis
3026817632nitrate+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

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

metabolite tests

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

enzymes

@refvalueactivityec
22070catalase+1.11.1.6
22070cytochrome-c oxidase+1.9.3.1
30268catalase+1.11.1.6
30268cytochrome oxidase+1.9.3.1
68369gelatinase-
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPAC
22070+----+/--+------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling date
22070seawaterGeoje-doRepublic of KoreaKORAsia
62338Seawater of a seaweed farmGeojedo,South SeaRepublic of KoreaKORAsia2009
67771From seawaterGeoje-doRepublic of KoreaKORAsia

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic
  • Cat3: #Marine

taxonmaps

  • @ref: 69479
  • File name: preview.99_6355.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_3019;97_3708;98_4698;99_6355&stattab=map
  • Last taxonomy: Marivita hallyeonensis
  • 16S sequence: JF260872
  • Sequence Identity:
  • Total samples: 180
  • soil counts: 12
  • aquatic counts: 153
  • animal counts: 7
  • plant counts: 8

Safety information

risk assessment

  • @ref: 22070
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 22070
  • description: Marivita hallyeonensis strain DPG-28 16S ribosomal RNA gene, partial sequence
  • accession: JF260872
  • length: 1384
  • database: ena
  • NCBI tax ID: 996342

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Marivita hallyeonensis DSM 29431GCA_900129875contigncbi996342
66792Marivita hallyeonensis strain DSM 29431996342.4wgspatric996342
66792Marivita hallyeonensis DSM 294312695421018draftimg996342

GC content

  • @ref: 30268
  • GC-content: 65.1

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno70.988no
flagellatedno93.433yes
gram-positiveno98.432yes
anaerobicno97.688yes
halophileyes82.489no
spore-formingno96.746yes
thermophileno95.689yes
glucose-utilyes68.246yes
aerobicyes87.634yes
glucose-fermentno90.13yes

External links

@ref: 22070

culture collection no.: DSM 29431, CCUG 60522, KCTC 23421

straininfo link

  • @ref: 89150
  • straininfo: 396898

literature

  • topic: Phylogeny
  • Pubmed-ID: 21602362
  • title: Marivita hallyeonensis sp. nov., isolated from seawater, reclassification of Gaetbulicola byunsanensis as Marivita byunsanensis comb. nov. and emended description of the genus Marivita Hwang et al. 2009.
  • authors: Yoon JH, Kang SJ, Lee SY, Jung YT, Lee JS, Oh TK
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.032086-0
  • year: 2011
  • mesh: Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Rhodobacteraceae/*classification/genetics/isolation & purification, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/analogs & derivatives/chemistry
  • topic2: Genetics

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
22070Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-29431Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 29431)
30268Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172660928776041
62338Curators of the CCUGhttps://www.ccug.se/strain?id=60522Culture Collection University of Gothenburg (CCUG) (CCUG 60522)
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
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68369Automatically annotated from API 20NE
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
89150Reimer, 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-ID396898.1