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Strain identifier

BacDive ID: 132960

Type strain: Yes

Species: Actibacterium naphthalenivorans

Strain Designation: NS6

Strain history: C. O. Jeon; Chung-Ang Univ., South Korea; NS6.

NCBI tax ID(s): 1614693 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 24748

BacDive-ID: 132960

DSM-Number: 105040

keywords: genome sequence, 16S sequence, Bacteria, mesophilic

description: Actibacterium naphthalenivorans NS6 is a mesophilic bacterium that was isolated from sea-tidal-flat sediment, crude-oil contaminated.

NCBI tax id

  • NCBI tax id: 1614693
  • Matching level: species

strain history

doi: 10.13145/bacdive132960.20221219.7.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Rhodobacterales
  • family: Rhodobacteraceae
  • genus: Actibacterium
  • species: Actibacterium naphthalenivorans
  • full scientific name: Actibacterium naphthalenivorans (Jeong et al. 2015) Hördt et al. 2020
  • synonyms

    • @ref: 20215
    • synonym: Confluentimicrobium naphthalenivorans

@ref: 24748

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Actibacterium

species: Actibacterium naphthalenivorans

full scientific name: Actibacterium naphthalenivorans (Jeong et al. 2015) Hördt et al. 2020

strain designation: NS6

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: negative
  • confidence: 99.569

Culture and growth conditions

culture medium

  • @ref: 24748
  • 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
24748positivegrowth30mesophilic
67770positivegrowth30mesophilic

Physiology and metabolism

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 98.199

halophily

  • @ref: 69480
  • halophily level: non-halophilic
  • confidence: 90.307

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
24748--------+--------+--+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitude
24748sea-tidal-flat sediment, crude-oil contaminatedYeosu coastel areaRepublic of KoreaKORAsia34.8092127.724
67770Sea-tidal-flat sedimentSouth SeaRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Contamination#Oil (Fuel)
#Environmental#Aquatic#Marine
#Environmental#Aquatic#Sediment
#Environmental#Terrestrial#Tidal flat

taxonmaps

  • @ref: 69479
  • File name: preview.99_517.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_330;97_368;98_420;99_517&stattab=map
  • Last taxonomy: Actibacterium naphthalenivorans subclade
  • 16S sequence: KP272155
  • Sequence Identity:
  • Total samples: 3295
  • soil counts: 100
  • aquatic counts: 3015
  • animal counts: 171
  • plant counts: 9

Safety information

risk assessment

  • @ref: 24748
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 24748
  • description: Confluentimicrobium naphthalenivorans strain NS6 16S ribosomal RNA gene, partial sequence
  • accession: KP272155
  • length: 1453
  • database: ena
  • NCBI tax ID: 1614693

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Actibacterium naphthalenivorans DSM 105040GCA_014196965contigncbi1614693
66792Confluentimicrobium naphthalenivorans strain DSM 1050401614693.4wgspatric1614693
66792Actibacterium naphthalenivorans DSM 1050402830026743draftimg1614693
66792Butyrivibrio sp. L3_072_000M1_dasL3_072_000M1_metabat.metabat.123GCA_018376655contigpatric28121

GC content

@refGC-contentmethod
2474864.5
6777064.5high performance liquid chromatography (HPLC)

External links

@ref: 24748

culture collection no.: DSM 105040, JCM 30828, KCTC 18418

literature

  • topic: Phylogeny
  • Pubmed-ID: 26311461
  • title: Confluentimicrobium naphthalenivorans sp. nov., a naphthalene-degrading bacterium isolated from sea-tidal-flat sediment, and emended description of the genus Confluentimicrobium Park et al. 2015.
  • authors: Jeong HI, Jin HM, Jeon CO
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.000561
  • year: 2015
  • mesh: Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Naphthalenes/*metabolism, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/chemistry
  • topic2: Transcriptome

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
24748Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-105040Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 105040)
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
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