Strain identifier

BacDive ID: 11872

Type strain: Yes

Species: Nitratireductor kimnyeongensis

Strain history: S. D. Lee KY101.

NCBI tax ID(s): 1231184 (strain), 430679 (species)

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General

@ref: 7957

BacDive-ID: 11872

DSM-Number: 19185

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

description: Nitratireductor kimnyeongensis DSM 19185 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from dried seaweed.

NCBI tax id

NCBI tax idMatching level
430679species
1231184strain

strain history

@refhistory
7957<- S. D. Lee, Cheju National Univ., Rep. of Korea; Ky 101
67770S. D. Lee KY101.

doi: 10.13145/bacdive11872.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Hyphomicrobiales
  • family: Phyllobacteriaceae
  • genus: Nitratireductor
  • species: Nitratireductor kimnyeongensis
  • full scientific name: Nitratireductor kimnyeongensis Kang et al. 2009

@ref: 7957

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Phyllobacteriaceae

genus: Nitratireductor

species: Nitratireductor kimnyeongensis

full scientific name: Nitratireductor kimnyeongensis Kang et al. 2009

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
32588negative1.95 µm0.45 µmrod-shapedyes
69480negative99.982

pigmentation

  • @ref: 32588
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 7957
  • name: TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/545
  • composition: Name: TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545) Composition: Casein peptone 17.0 g/l NaCl 5.0 g/l Soy peptone 3.0 g/l D(+)-Glucose 2.5 g/l K2HPO4 2.5 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
7957positivegrowth28mesophilic
32588positivegrowth10-40
32588positiveoptimum30mesophilic
67770positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
32588positivegrowth6.1-12.1alkaliphile
32588positiveoptimum9.1

Physiology and metabolism

oxygen tolerance

  • @ref: 32588
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.994

halophily

  • @ref: 32588
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: <7 %

observation

  • @ref: 32588
  • observation: aggregates in clumps

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
32588581435-dehydro-D-gluconate+carbon source
3258818403L-arabitol+carbon source
3258828757fructose+carbon source
3258833984fucose+carbon source
3258817234glucose+carbon source
3258829864mannitol+carbon source
3258833942ribose+carbon source
3258817992sucrose+carbon source
3258827082trehalose+carbon source
325884853esculin+hydrolysis

enzymes

@refvalueactivityec
32588acid phosphatase+3.1.3.2
32588alkaline phosphatase+3.1.3.1
32588catalase+1.11.1.6
32588cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
7957dried seaweedJejuRepublic of KoreaKORAsia
67770Dried seaweed sample collected from Kimnyeong Beach in JejuRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2
#Host#Algae
#Engineered#Food production
#Condition#Xerophilic

taxonmaps

  • @ref: 69479
  • File name: preview.99_5008.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_5;96_2450;97_2989;98_3744;99_5008&stattab=map
  • Last taxonomy: Nitratireductor
  • 16S sequence: AM498744
  • Sequence Identity:
  • Total samples: 1522
  • soil counts: 144
  • aquatic counts: 1046
  • animal counts: 279
  • plant counts: 53

Safety information

risk assessment

  • @ref: 7957
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 7957
  • description: Nitratireductor kimnyeongensis partial 16S rRNA gene, type strain KY 101T
  • accession: AM498744
  • length: 1371
  • database: ena
  • NCBI tax ID: 1231184

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nitratireductor kimnyeongensis KACC 11904GCA_019891395completencbi430679
66792Nitratireductor kimnyeongensis strain KACC 11904430679.3completepatric430679
66792Nitratireductor kimnyeongensis strain KACC 11904430679.6completepatric430679
66792Nitratireductor kimnyeongensis strain KACC 11904430679.5completepatric430679
66792Nitratireductor kimnyeongensis strain KACC 11904430679.4completepatric430679

GC content

  • @ref: 7957
  • GC-content: 60.4

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno66.087no
gram-positiveno98.412yes
anaerobicno97.987yes
aerobicyes92.576yes
halophileyes63.128yes
spore-formingno97.314no
motileyes88.554yes
thermophileno88.28yes
glucose-utilyes92.499yes
glucose-fermentno91.449no

External links

@ref: 7957

culture collection no.: DSM 19185, JCM 14851, KACC 11904, Ky 101, NBRC 106418

straininfo link

  • @ref: 81090
  • straininfo: 402247

literature

  • topic: Phylogeny
  • Pubmed-ID: 19406788
  • title: Nitratireductor kimnyeongensis sp. nov., isolated from seaweed.
  • authors: Kang HS, Yang HL, Lee SD
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.65734-0
  • year: 2009
  • mesh: Alphaproteobacteria/*classification/genetics/isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, Catalase/metabolism, DNA, Bacterial/analysis/genetics, Genes, rRNA, Korea, Molecular Sequence Data, Nucleic Acid Hybridization, Oxidoreductases/metabolism, Phenotype, RNA, Ribosomal, 16S/genetics, Seaweed/*microbiology, Sequence Analysis, DNA, Species Specificity
  • topic2: Enzymology

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
7957Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19185)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19185
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
32588Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2880228776041
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
81090Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID402247.1StrainInfo: A central database for resolving microbial strain identifiers