Strain identifier

BacDive ID: 11968

Type strain: Yes

Species: Planococcus mcmeekinii

Strain Designation: S23F2

Strain history: CIP <- 1998, K. Junge, School Oceanography, Washington Univ., Seattle, Washington, USA: strain S23F2

NCBI tax ID(s): 71546 (species)

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General

@ref: 5198

BacDive-ID: 11968

DSM-Number: 13963

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

description: Planococcus mcmeekinii S23F2 is an obligate aerobe, mesophilic, Gram-positive bacterium that was isolated from antarctic sea ice brine.

NCBI tax id

  • NCBI tax id: 71546
  • Matching level: species

strain history

@refhistory
5198<- J. Dodsworth, Dept. of Microbiol., Univ. of Washington
385691998, K. Junge, School Oceanography, Univ. Washington, Seattle, USA: strain S23F2
120865CIP <- 1998, K. Junge, School Oceanography, Washington Univ., Seattle, Washington, USA: strain S23F2

doi: 10.13145/bacdive11968.20230509.8.1

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 mcmeekinii
  • full scientific name: Planococcus mcmeekinii Junge et al. 1998

  • synonyms

    • @ref: 20215
    • synonym: Planomicrobium mcmeekinii

@ref: 5198

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Caryophanaceae

genus: Planococcus

species: Planococcus mcmeekinii

full scientific name: Planococcus mcmeekinii Junge et al. 1998

strain designation: S23F2

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480positive100
120865positiverod-shapedyes

colony morphology

  • @ref: 120865

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5198BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)yeshttps://mediadive.dsmz.de/medium/514Name: 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
38569Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
120865CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
5198positivegrowth28mesophilic
38569positivegrowth22psychrophilic
120865positivegrowth10-37
120865nogrowth41thermophilic
120865nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 120865
  • oxygen tolerance: obligate aerobe

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 93.622

halophily

  • @ref: 120865
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1208654853esculin-hydrolysis
120865606565hippurate-hydrolysis
12086517632nitrate+reduction
12086516301nitrite-reduction

metabolite production

  • @ref: 120865
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12086515688acetoin-
12086517234glucose-

enzymes

@refvalueactivityec
120865oxidase-
120865beta-galactosidase-3.2.1.23
120865alcohol dehydrogenase-1.1.1.1
120865gelatinase-
120865amylase-
120865DNase+
120865caseinase-3.4.21.50
120865catalase+1.11.1.6
120865tween esterase-
120865gamma-glutamyltransferase-2.3.2.2
120865lecithinase-
120865lipase-
120865lysine decarboxylase-4.1.1.18
120865ornithine decarboxylase-4.1.1.17
120865phenylalanine ammonia-lyase-4.3.1.24
120865tryptophan deaminase-
120865urease-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
120865-+++------++---+----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
5198antarctic sea ice brine2.5 km west from McMurdo Station
120865Environment, Antarctic sea ice brineMcMurdo soundAntarcticaATAAntarctica1992

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Ice
#Environmental#Aquatic#Marine
#Condition#Saline
#Climate#Cold#Polar

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
51981Risk group (German classification)
1208651Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Planococcus mcmeekinii 16S ribosomal RNA gene, partial sequenceAF0417911481ena71546
20218Planococcus mcmeekinii 16S-23S rRNA intergenic spacer region, partial sequenceAF228699221ena71546

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Planomicrobium mcmeekinii strain DSM 1396371546.3wgspatric71546
66792Planomicrobium mcmeekinii DSM 139632913357338draftimg71546

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes84no
gram-positiveyes93.013no
anaerobicno98.97no
halophileyes85.747no
spore-formingyes68.68no
glucose-utilyes86.882no
thermophileno99.785yes
flagellatedno65.992no
motileyes72.608no
aerobicyes92.908no
glucose-fermentno87.025no

External links

@ref: 5198

culture collection no.: DSM 13963, ATCC 700539, CIP 105673

straininfo link

  • @ref: 81179
  • straininfo: 43990

literature

  • topic: Phylogeny
  • Pubmed-ID: 24854007
  • title: Planomicrobium soli sp. nov., isolated from soil.
  • authors: Luo X, Zhang J, Li D, Xin Y, Xin D, Fan L
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.055426-0
  • year: 2014
  • mesh: Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, Pigmentation, Planococcaceae/*classification/genetics/isolation & purification, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistry
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
5198Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 13963)https://www.dsmz.de/collection/catalogue/details/culture/DSM-13963
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
38569Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17718
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)
68382Automatically annotated from API zym
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)
81179Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID43990.1StrainInfo: A central database for resolving microbial strain identifiers
120865Curators of the CIPCollection of Institut Pasteur (CIP 105673)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105673