Strain identifier

BacDive ID: 11960

Type strain: Yes

Species: Planococcus salinarum

Strain Designation: ISL-16

Strain history: <- JH Yoon, KRIBB

NCBI tax ID(s): 622695 (species)

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General

@ref: 17388

BacDive-ID: 11960

DSM-Number: 23820

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

description: Planococcus salinarum ISL-16 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from sediment from marine solar saltern.

NCBI tax id

  • NCBI tax id: 622695
  • Matching level: species

strain history

@refhistory
17388<- CCUG <- J. H. Yoon, KRIBB, Taejon, South Korea
67771<- JH Yoon, KRIBB

doi: 10.13145/bacdive11960.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Caryophanaceae
  • genus: Planococcus
  • species: Planococcus salinarum
  • full scientific name: Planococcus salinarum Yoon et al. 2010

@ref: 17388

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Caryophanaceae

genus: Planococcus

species: Planococcus salinarum

full scientific name: Planococcus salinarum Yoon et al. 2010

strain designation: ISL-16

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
29437positive2.9 µm0.6 µmrod-shapedno
67771rod-shapedno
67771coccus-shaped
67771positive
69480yes90.595
69480positive100

colony morphology

  • @ref: 61441
  • incubation period: 3 days

pigmentation

  • @ref: 29437
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 17388
  • 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
17388positivegrowth28mesophilic
29437positivegrowth04-38
61441positivegrowth30mesophilic
67771positivegrowth30mesophilic

culture pH

@refabilitytypepH
29437positivegrowth6-7.5
29437positiveoptimum7.25

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
29437aerobe
61441aerobe
67771aerobe

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.639

halophily

@refsaltgrowthtested relationconcentration
29437NaClpositivegrowth0-13 %
29437NaClpositiveoptimum2 %

observation

  • @ref: 67771
  • observation: quinones: MK-8, MK-7

metabolite utilization

  • @ref: 29437
  • Chebi-ID: 28757
  • metabolite: fructose
  • utilization activity: +
  • kind of utilization tested: carbon source

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling date
17388sediment from marine solar salternYellow SeaRepublic of KoreaKORAsia
61441Sediment from marine solar salternYellow SeaRepublic of KoreaKORAsia2007
67771From marine solar saltern of the Yellow SeaByunsanRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Environmental#Aquatic#Sediment
#Condition#Saline

taxonmaps

  • @ref: 69479
  • File name: preview.99_2903.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_67;97_70;98_75;99_2903&stattab=map
  • Last taxonomy: Planococcus salinarum
  • 16S sequence: FJ765415
  • Sequence Identity:
  • Total samples: 331
  • soil counts: 72
  • aquatic counts: 84
  • animal counts: 148
  • plant counts: 27

Safety information

risk assessment

  • @ref: 17388
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 17388
  • description: Planococcus salinarum strain ISL-16 16S ribosomal RNA gene, partial sequence
  • accession: FJ765415
  • length: 1506
  • database: ena
  • NCBI tax ID: 622695

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Planococcus salinarum ISL-16GCA_003428865contigncbi622695
66792Planococcus salinarum KCTC 13584GCA_007004625scaffoldncbi622695
66792Planococcus salinarum DSM 23820GCA_001856085contigncbi622695
66792Planococcus salinarum strain DSM 23820622695.3wgspatric622695
66792Planococcus salinarum strain KCTC 13584622695.5wgspatric622695
66792Planococcus salinarum DSM 238202837105295draftimg622695
66792Planococcus salinarum ISL-162840865273draftimg622695

GC content

@refGC-contentmethod
1738848.3high performance liquid chromatography (HPLC)
2943748.3

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes88no
motileyes72.783yes
flagellatedno63.532yes
gram-positiveyes92.531yes
anaerobicno99.263yes
aerobicyes95.187yes
halophileyes84.939no
spore-formingyes62.207no
thermophileno99.673no
glucose-utilyes83.766no
glucose-fermentno87.797no

External links

@ref: 17388

culture collection no.: DSM 23820, CCUG 57753, KCTC 13584

straininfo link

  • @ref: 81173
  • straininfo: 400238

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19656937Planococcus salinarum sp. nov., isolated from a marine solar saltern, and emended description of the genus Planococcus.Yoon JH, Kang SJ, Lee SY, Oh KH, Oh TKInt J Syst Evol Microbiol10.1099/ijs.0.013136-02009Bacillales/chemistry/*classification/genetics/*isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Ribosomal/analysis/genetics, Fatty Acids/analysis, Genes, rRNA, Geologic Sediments/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seawater/*microbiology, Sequence Analysis, DNA, Species SpecificityGenetics
Phylogeny29300160Planococcus salinus sp. nov., a moderately halophilic bacterium isolated from a saline-alkali soil.Gan L, Zhang H, Tian J, Li X, Long X, Zhang Y, Dai Y, Tian YInt J Syst Evol Microbiol10.1099/ijsem.0.0025482018Alkalies, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Planococcus Bacteria/*classification/genetics/isolation & purification, RNA, Ribosomal, 16S/genetics, Salinity, Sequence Analysis, DNA, Soil/chemistry, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
17388Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23820)https://www.dsmz.de/collection/catalogue/details/culture/DSM-23820
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
29437Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2584328776041
61441Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 57753)https://www.ccug.se/strain?id=57753
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
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)
81173Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID400238.1StrainInfo: A central database for resolving microbial strain identifiers