Strain identifier

BacDive ID: 14251

Type strain: Yes

Species: Sphingomonas aestuarii

Strain Designation: K4

Strain history: CIP <- 2009, DSMZ <- Jin-Woo Bae, Kyung Hee Univ., Seoul, South Korea: strain K4

NCBI tax ID(s): 1123266 (strain), 453846 (species)

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General

@ref: 8107

BacDive-ID: 14251

DSM-Number: 19475

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

description: Sphingomonas aestuarii K4 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from tidal flat sediment.

NCBI tax id

NCBI tax idMatching level
453846species
1123266strain

strain history

@refhistory
8107<- S. W. Roh, Korea Res. Inst. Biosci. & Biotechnol. (KRIBB), Taejon
67771<- SW Roh, KRIBB
116098CIP <- 2009, DSMZ <- Jin-Woo Bae, Kyung Hee Univ., Seoul, South Korea: strain K4

doi: 10.13145/bacdive14251.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Sphingomonadales
  • family: Sphingomonadaceae
  • genus: Sphingomonas
  • species: Sphingomonas aestuarii
  • full scientific name: Sphingomonas aestuarii Roh et al. 2009

@ref: 8107

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Sphingomonadales

family: Sphingomonadaceae

genus: Sphingomonas

species: Sphingomonas aestuarii

full scientific name: Sphingomonas aestuarii Roh et al. 2009

strain designation: K4

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotility
32462negativerod-shapedno
67771negative
116098negativerod-shapedno

multimedia

  • @ref: 8107
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_19475.jpg
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8107R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
37297MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
116098CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
116098CIP Medium 566yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=566

culture temp

@refgrowthtypetemperaturerange
8107positivegrowth28mesophilic
32462positivegrowth20-35
32462positiveoptimum30mesophilic
37297positivegrowth30mesophilic
67771positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
67771aerobe
116098obligate aerobe

spore formation

  • @ref: 32462
  • spore formation: no

halophily

  • @ref: 32462
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-5 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3246217057cellobiose+carbon source
3246228757fructose+carbon source
3246217234glucose+carbon source
3246217306maltose+carbon source
3246237684mannose+carbon source
324624853esculin+hydrolysis
11609817632nitrate-reduction
11609816301nitrite-reduction

metabolite production

  • @ref: 116098
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
32462acid phosphatase+3.1.3.2
32462alkaline phosphatase+3.1.3.1
32462catalase+1.11.1.6
32462cytochrome oxidase+1.9.3.1
116098oxidase+
116098catalase+1.11.1.6
116098urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382cystine arylamidase+3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase-
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase-3.2.1.20
68382beta-glucosidase+3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
116098-+++-+++--+-----+---

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudeisolation date
8107tidal flat sedimentYeosu (34° 47' 26" N 127° 34' 01" E)Republic of KoreaKORAsia34.7906127.567
67771From flat tidalRepublic of KoreaKORAsia
116098Environment, Sediment, tidal flatYeosuRepublic of KoreaKORAsia2009

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Tidal flat
#Environmental#Terrestrial#Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_67185.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_20;96_348;97_4738;98_6089;99_67185&stattab=map
  • Last taxonomy: Sphingomonas
  • 16S sequence: EF660755
  • Sequence Identity:
  • Total samples: 709
  • soil counts: 79
  • aquatic counts: 98
  • animal counts: 523
  • plant counts: 9

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
81071Risk group (German classification)
1160981Risk group (French classification)

Sequence information

16S sequences

  • @ref: 8107
  • description: Sphingomonas aestuarii strain K4 16S ribosomal RNA gene, partial sequence
  • accession: EF660755
  • length: 1344
  • database: ena
  • NCBI tax ID: 453846

Genome sequences

  • @ref: 66792
  • description: Sphingomonas aestuarii DSM 19475
  • accession: 2576861403
  • assembly level: draft
  • database: img
  • NCBI tax ID: 1123266

External links

@ref: 8107

culture collection no.: DSM 19475, KCTC 22050, CIP 110056

straininfo link

  • @ref: 83410
  • straininfo: 362851

literature

  • topic: Phylogeny
  • Pubmed-ID: 19502316
  • title: Sphingomonas aestuarii sp. nov., isolated from tidal flat sediment.
  • authors: Roh SW, Kim KH, Nam YD, Chang HW, Kim MS, Oh HM, Bae JW
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.65528-0
  • year: 2009
  • mesh: Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genotype, Geologic Sediments/*microbiology, Korea, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species Specificity, Sphingomonas/*classification/genetics/isolation & purification/physiology
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
8107Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19475)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19475
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
32462Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2868428776041
37297Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7871
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)
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68382Automatically annotated from API zym
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
83410Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID362851.1StrainInfo: A central database for resolving microbial strain identifiers
116098Curators of the CIPCollection of Institut Pasteur (CIP 110056)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110056