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Strain identifier

BacDive ID: 130610

Type strain: Yes

Species: Limimaricola soesokkakensis

Strain Designation: DSSK1-5

Strain history: <- CECT <- J. H. Yoon, Sungkyunkwan Univ., Suwon, Republic of Korea

NCBI tax ID(s): 1343159 (species)

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

@ref: 21637

BacDive-ID: 130610

DSM-Number: 29956

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

description: Limimaricola soesokkakensis DSSK1-5 is a mesophilic bacterium that was isolated from water collected from the junction between the ocean and a freshwater spring.

NCBI tax id

  • NCBI tax id: 1343159
  • Matching level: species

strain history: <- CECT <- J. H. Yoon, Sungkyunkwan Univ., Suwon, Republic of Korea

doi: 10.13145/bacdive130610.20221219.7.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Rhodobacterales
  • family: Rhodobacteraceae
  • genus: Limimaricola
  • species: Limimaricola soesokkakensis
  • full scientific name: Limimaricola soesokkakensis (Park et al. 2014) Wirth and Whitman 2018
  • synonyms

    • @ref: 20215
    • synonym: Loktanella soesokkakensis

@ref: 21637

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Limimaricola

species: Limimaricola soesokkakensis

full scientific name: Limimaricola soesokkakensis (Park et al. 2014) Wirth and Whitman 2018

strain designation: DSSK1-5

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: negative
  • confidence: 99.294

colony morphology

  • @ref: 21637
  • incubation period: 1-2 days

Culture and growth conditions

culture medium

  • @ref: 21637
  • 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

  • @ref: 21637
  • growth: positive
  • type: growth
  • temperature: 30
  • range: mesophilic

Physiology and metabolism

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 95.883

halophily

  • @ref: 69480
  • halophily level: non-halophilic
  • confidence: 84.634

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836925115malate-assimilation
6836927689decanoate-assimilation
6836917306maltose-assimilation
6836959640N-acetylglucosamine-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
21637catalase+1.11.1.6
21637cytochrome-c 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_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPAC
21637-----+-+---+/---+/--+/----

Isolation, sampling and environmental information

isolation

  • @ref: 21637
  • sample type: water collected from the junction between the ocean and a freshwater spring
  • geographic location: Wando
  • country: Republic of Korea
  • origin.country: KOR
  • continent: Asia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Freshwater
#Environmental#Aquatic#Marine
#Environmental#Aquatic#Spring

taxonmaps

  • @ref: 69479
  • File name: preview.99_5744.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_59;97_62;98_67;99_5744&stattab=map
  • Last taxonomy: Limimaricola
  • 16S sequence: KC987356
  • Sequence Identity:
  • Total samples: 3727
  • soil counts: 214
  • aquatic counts: 3059
  • animal counts: 378
  • plant counts: 76

Safety information

risk assessment

  • @ref: 21637
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 21637
  • description: Loktanella soesokkakensis strain DSSK1-5 from South Korea 16S ribosomal RNA gene, partial sequence
  • accession: KC987356
  • length: 1385
  • database: ena
  • NCBI tax ID: 1343159

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Limimaricola soesokkakensis DSM 29956GCA_003014435contigncbi1343159
66792Limimaricola soesokkakensis CECT 8367GCA_900172345contigncbi1343159
66792Loktanella soesokkakensis strain CECT 83671343159.4wgspatric1343159
66792Loktanella soesokkakensis strain DSM 299561343159.8wgspatric1343159
66792Limimaricola soesokkakensis DSM 299562728369479draftimg1343159
66792Salmonella enterica subsp. enterica serovar Saintpaul CFSAN004175GCA_001952995completepatric90105
66792Staphylococcus aureus 278GCA_020389025completepatric1280

GC content

  • @ref: 21637
  • GC-content: 67.6

External links

@ref: 21637

culture collection no.: DSM 29956, CECT 8367, KCTC 32425

straininfo link

@refpassport
20218http://www.straininfo.net/strains/893217
20218http://www.straininfo.net/strains/893216

literature

  • topic: Phylogeny
  • Pubmed-ID: 23824249
  • title: Loktanella soesokkakensis sp. nov., isolated from the junction between the North Pacific Ocean and a freshwater spring.
  • authors: Park S, Lee JS, Lee KC, Yoon JH
  • journal: Antonie Van Leeuwenhoek
  • DOI: 10.1007/s10482-013-9962-9
  • year: 2013
  • mesh: Bacteria, Aerobic/*classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Fresh Water, Hydrogen-Ion Concentration, Korea, Molecular Sequence Data, Nucleic Acid Hybridization, Pacific Ocean, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/*isolation & purification/physiology, Sequence Analysis, DNA, Sodium Chloride/metabolism, Temperature, Ubiquinone/analysis, *Water Microbiology
  • topic2: Enzymology

Reference

@idauthorstitledoi/urljournalpubmedcatalogue
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.StrainInfo introduces electronic passports for microorganisms.10.1016/j.syapm.2013.11.002Syst Appl Microbiol. 37: 42-50 201424321274
21637Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-29956Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 29956)
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/gkaa1025Nucleic Acids Res. 49: D498-D508 202033211880
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