Strain identifier

BacDive ID: 131313

Type strain: Yes

Species: Novosphingobium marinum

Strain Designation: LA53

Strain history: Y.-Y. Huo; Second Inst. of Oceanogr., State Oceanic Admin., China; LA53.

NCBI tax ID(s): 1514948 (species)

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General

@ref: 22540

BacDive-ID: 131313

DSM-Number: 29043

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

description: Novosphingobium marinum LA53 is a mesophilic, Gram-negative bacterium that was isolated from sea water.

NCBI tax id

  • NCBI tax id: 1514948
  • Matching level: species

strain history

@refhistory
22540<- Y.-Y. Huo, Second Inst. Oceanography, State Oceanic Admin., Hangzhou, China; LA53
67770Y.-Y. Huo; Second Inst. of Oceanogr., State Oceanic Admin., China; LA53.

doi: 10.13145/bacdive131313.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Sphingomonadales
  • family: Erythrobacteraceae
  • genus: Novosphingobium
  • species: Novosphingobium marinum
  • full scientific name: Novosphingobium marinum Huo et al. 2015

@ref: 22540

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Pseudomonadales

family: Erythrobacteraceae

genus: Novosphingobium

species: Novosphingobium marinum

full scientific name: Novosphingobium marinum Huo et al. 2015

strain designation: LA53

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: negative
  • confidence: 99.965

colony morphology

  • @ref: 22540
  • incubation period: 3-7 days

multimedia

  • @ref: 22540
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_29043.jpg
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

  • @ref: 22540
  • name: REACTIVATION WITH LIQUID MEDIUM 514 (DSMZ Medium 514c)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/514c
  • composition: Name: REACTIVATION WITH LIQUID MEDIUM 514 (DSMZ Medium 514c) Composition: NaCl 19.45 g/l Agar 18.0 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 Na2CO3 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
22540positivegrowth28mesophilic
67770positivegrowth30mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.964

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
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
68369cytochrome 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_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
22540+-------+-----+-+---+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationlatitudelongitude
22540sea watereastern part (144° 59' W 7° 30' N at a depth of 800 m)7.5-144.983
67770Seawater collected from the eastern Pacific Ocean

isolation source categories

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

Safety information

risk assessment

  • @ref: 22540
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 22540
  • description: Novosphingobium marinum strain LA53 16S ribosomal RNA gene, partial sequence
  • accession: KJ708552
  • length: 1411
  • database: ena
  • NCBI tax ID: 1514948

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Novosphingobium marinum CGMCC 1.12918GCA_014640055contigncbi1514948
66792Novosphingobium marinum strain CGMCC 1.129181514948.4wgspatric1514948
66792Novosphingobium marinum strain DSM 290431514948.3wgspatric1514948
66792Novosphingobium marinum DSM 290432828405992draftimg1514948
67770Novosphingobium marinum DSM 29043GCA_013408095contigncbi1514948

GC content

  • @ref: 22540
  • GC-content: 57.7
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes60.531no
gram-positiveno95.811no
anaerobicno98.781no
aerobicyes92.925no
halophileno89.765no
spore-formingno92.428no
thermophileno96.506yes
glucose-utilyes85.615yes
flagellatedno90.087no
glucose-fermentno93.584yes

External links

@ref: 22540

culture collection no.: DSM 29043, CGMCC 1.12918, JCM 30307

straininfo link

  • @ref: 89754
  • straininfo: 408264

literature

  • topic: Phylogeny
  • Pubmed-ID: 25424486
  • title: Novosphingobium marinum sp. nov., isolated from seawater.
  • authors: Huo YY, You H, Li ZY, Wang CS, Xu XW
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.070433-0
  • year: 2014
  • mesh: Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Pacific Ocean, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Sphingomonadaceae/*classification/genetics/isolation & purification, Ubiquinone/chemistry
  • topic2: Genetics

Reference

@idauthorstitledoi/urlcatalogue
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
22540Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-29043Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 29043)
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/
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
89754Reimer, 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-ID408264.1