Strain identifier

BacDive ID: 11959

Type strain: Yes

Species: Planococcus antarcticus

Strain history: CIP <- 2002, S. Shivaji, CCMB, Hyderabad, India: strain CMS 26or

NCBI tax ID(s): 1185653 (strain), 161360 (species)

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General

@ref: 5380

BacDive-ID: 11959

DSM-Number: 14505

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, mesophilic, Gram-positive, motile, coccus-shaped, colony-forming

description: Planococcus antarcticus DSM 14505 is a facultative anaerobe, mesophilic, Gram-positive bacterium that forms circular colonies and was isolated from cyanobacterial mat sample.

NCBI tax id

NCBI tax idMatching level
1185653strain
161360species

strain history

@refhistory
5380<- S. Shivaji; CMS 26or
399392002, S. Shivaji, CCMB, Hyderabad, India: strain CMS 26or
116409CIP <- 2002, S. Shivaji, CCMB, Hyderabad, India: strain CMS 26or

doi: 10.13145/bacdive11959.20230509.8.1

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 antarcticus
  • full scientific name: Planococcus antarcticus Reddy et al. 2002

@ref: 5380

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Caryophanaceae

genus: Planococcus

species: Planococcus antarcticus

full scientific name: Planococcus antarcticus Reddy et al. 2002

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
43354positivecoccus-shapedyes
69480yes93.138
69480positive100
116409positivecoccus-shapedno

colony morphology

@refcolony sizecolony colorcolony shapemedium usedhemolysis ability
433541-2 mmorangecircularpeptone-yeast agar
1164091

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5380TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://mediadive.dsmz.de/medium/92Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water
39939MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
43354peptone-yeast agaryes
116409CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
5380positivegrowth25mesophilic
39939positivegrowth25mesophilic
43354positiveoptimum20psychrophilic
43354positivegrowth2-30
116409positivegrowth10-25psychrophilic
116409nogrowth30mesophilic
116409nogrowth37mesophilic
116409nogrowth41thermophilic
116409nogrowth45thermophilic

culture pH

  • @ref: 43354
  • ability: positive
  • type: growth
  • pH: 6-12
  • PH range: alkaliphile

Physiology and metabolism

oxygen tolerance

  • @ref: 116409
  • oxygen tolerance: facultative anaerobe

spore formation

@refspore formationconfidence
43354no
69481no94
69480no99.792

halophily

@refsaltgrowthtested relationconcentration
43354NaClpositivegrowth0-12 %(w/v)
116409NaClpositivegrowth0-4 %
116409NaClnogrowth6 %
116409NaClnogrowth8 %
116409NaClnogrowth10 %

murein

  • @ref: 5380
  • murein short key: A11.33
  • type: A4alpha L-Lys-D-Glu

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4335430089acetate+carbon source
4335415963ribitol-carbon source
4335422599arabinose-carbon source
4335429016arginine-carbon source
433548295beta-hydroxybutyrate-carbon source
4335417057cellobiose-carbon source
4335417057cellobiose-builds acid from
4335462968cellulose-carbon source
4335462968cellulose-degradation
4335416737creatinine-carbon source
4335423652dextrin-carbon source
4335416813galactitol-carbon source
433544853esculin-hydrolysis
4335428757fructose+carbon source
4335428260galactose-carbon source
433545417glucosamine-carbon source
4335417234glucose-fermentation
4335417234glucose+carbon source
4335417234glucose+builds acid from
4335429987glutamate+carbon source
4335428300glutamine-carbon source
4335417754glycerol+carbon source
4335415428glycine-carbon source
4335428087glycogen-carbon source
4335417268myo-inositol+carbon source
4335415443inulin-carbon source
43354L-alanine 4-nitroanilide-carbon source
4335424996lactate-carbon source
4335417716lactose-carbon source
4335417716lactose-builds acid from
4335425094lysine-carbon source
4335425094lysine+carbon source
4335417306maltose-carbon source
4335429864mannitol-carbon source
4335437684mannose-carbon source
4335428053melibiose+carbon source
4335416811methionine-carbon source
4335417632nitrate-reduction
4335428044phenylalanine-carbon source
4335446793polyethylene glycol-carbon source
4335415361pyruvate+carbon source
4335416634raffinose-carbon source
4335426546rhamnose+carbon source
4335433942ribose-carbon source
4335417822serine-carbon source
4335464243sodium L-glutamate-builds acid from
4335430911sorbitol-carbon source
4335427922sorbose-carbon source
4335428017starch-hydrolysis
4335430031succinate+carbon source
4335417992sucrose-carbon source
4335417992sucrose+builds acid from
4335447869thioglycolate-builds acid from
4335427082trehalose-carbon source
4335427897tryptophan-energy source
4335418186tyrosine-carbon source
4335418222xylose+carbon source
116409606565hippurate-hydrolysis
11640917632nitrate+reduction
11640916301nitrite-reduction

metabolite production

@refChebi-IDmetaboliteproduction
4335415688acetoinno
4335435581indoleno
11640935581indoleno

metabolite tests

@refChebi-IDmetabolitemethylred-testvoges-proskauer-testindole test
4335417234glucose-
4335415688acetoin-
4335435581indole-
11640915688acetoin-

enzymes

@refvalueactivityec
43354catalase+1.11.1.6
43354lipase+
43354gelatinase+
43354beta-galactosidase+3.2.1.23
43354arginine dihydrolase+3.5.3.6
43354cytochrome oxidase-1.9.3.1
43354urease-3.5.1.5
43354phosphatase-
43354tryptophan deaminase-4.1.99.1
116409oxidase-
116409beta-galactosidase+3.2.1.23
116409alcohol dehydrogenase-1.1.1.1
116409gelatinase-
116409amylase-
116409DNase-
116409caseinase-3.4.21.50
116409catalase+1.11.1.6
116409tween esterase-
116409gamma-glutamyltransferase-2.3.2.2
116409lecithinase-
116409lysine decarboxylase-4.1.1.18
116409ornithine decarboxylase-4.1.1.17
116409phenylalanine ammonia-lyase-4.3.1.24
116409tryptophan deaminase-
116409urease-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
116409--++-------+-+-+----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcontinentcountryorigin.country
5380cyanobacterial mat sampleAntarctica, McMurdo Dry ValleysAustralia and Oceania
43354cyanobacterial mat sample from Mcmurdo Dry ValleysAntarcticaAustralia and OceaniaAntarcticaATA
116409Cyanobacterial materialAntarcticaAntarcticaATA

isolation source categories

Cat1Cat2Cat3
#Environmental#Microbial community#Microbial mat
#Host#Microbial#Bacteria

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
53801Risk group (German classification)
1164091Risk group (French classification)

Sequence information

16S sequences

  • @ref: 5380
  • description: Planococcus southpolaris partial 16S rRNA gene, strain CMS 26or
  • accession: AJ314745
  • length: 1479
  • database: ena
  • NCBI tax ID: 1185653

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Planococcus antarcticus DSM 14505GCA_001687565completencbi1185653
66792Planococcus antarcticus DSM 14505GCA_000264415contigncbi1185653
66792Planococcus antarcticus DSM 145051185653.11plasmidpatric1185653
66792Planococcus antarcticus DSM 145051185653.6completepatric1185653
66792Planococcus antarcticus DSM 145051185653.10plasmidpatric1185653
66792Planococcus antarcticus DSM 145051185653.3wgspatric1185653
66792Planococcus antarcticus DSM 145052534682145draftimg1185653
66792Planococcus antarcticus DSM 145052700988610completeimg1185653

GC content

@refGC-contentmethod
538041.5
4335441.5high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno94no
flagellatedno54.37no
flagellatedno54.37no
gram-positiveyes91.591yes
gram-positiveyes91.591yes
anaerobicno98.979no
anaerobicno98.979no
aerobicyes96.771no
aerobicyes96.771no
halophileyes83.914no
halophileyes83.914no
spore-formingno51.453no
spore-formingno51.453no
glucose-utilyes90.942yes
glucose-utilyes90.942yes
thermophileno99.304yes
thermophileno99.304yes
motileyes77.208yes
glucose-fermentno85.902yes
glucose-fermentno85.902yes
motileyes77.208yes

External links

@ref: 5380

culture collection no.: DSM 14505, MTCC 3854, CMS 26or, CIP 107767

straininfo link

  • @ref: 81172
  • straininfo: 100451

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny12072961Planococcus antarcticus and Planococcus psychrophilus spp. nov. isolated from cyanobacterial mat samples collected from ponds in Antarctica.Reddy GS, Prakash JS, Vairamani M, Prabhakar S, Matsumoto GI, Shivaji SExtremophiles10.1007/s00792-001-0250-72002Antarctic Regions, Bacteria/classification/genetics/*isolation & purification, Base Sequence, Cyanobacteria/*isolation & purification, DNA Primers, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, *Water MicrobiologyEnzymology
Phylogeny14657138Planococcus maritimus sp. nov., isolated from sea water of a tidal flat in Korea.Yoon JH, Weiss N, Kang KH, Oh TK, Park YHInt J Syst Evol Microbiol10.1099/ijs.0.02557-02003DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Gram-Positive Bacteria/*classification/genetics/growth & development/isolation & purification, Korea, Molecular Sequence Data, *Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Seawater/microbiologyGenetics
Phylogeny15653859Planococcus stackebrandtii sp. nov., isolated from a cold desert of the Himalayas, India.Mayilraj S, Prasad GS, Suresh K, Saini HS, Shivaji S, Chakrabarti TInt J Syst Evol Microbiol10.1099/ijs.0.63290-02005Bacterial Typing Techniques, *Cold Temperature, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, *Desert Climate, Gram-Positive Cocci/*classification/genetics/growth & development/isolation & purification, India, Molecular Sequence Data, Nucleic Acid Hybridization, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil MicrobiologyGenetics
Phylogeny17978233Planococcus donghaensis sp. nov., a starch-degrading bacterium isolated from the East Sea, South Korea.Choi JH, Im WT, Liu QM, Yoo JS, Shin JH, Rhee SK, Roh DHInt J Syst Evol Microbiol10.1099/ijs.0.65036-02007Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Genotype, Geologic Sediments/*microbiology, Gram-Positive Cocci/*classification/genetics/*isolation & purification/physiology, Korea, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Species Specificity, Starch/*metabolismGenetics
Phylogeny22003043Planococcus halocryophilus sp. nov., an extreme sub-zero species from high Arctic permafrost.Mykytczuk NCS, Wilhelm RC, Whyte LGInt J Syst Evol Microbiol10.1099/ijs.0.035782-02011Arctic Regions, Bacterial Typing Techniques, Base Composition, Canada, DNA, Bacterial/genetics, Fatty Acids/analysis, Gram-Positive Bacteria/*classification/genetics/isolation & purification, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil/analysis, *Soil Microbiology, Vitamin K 2/analysisGenetics
Genetics22843594Genome sequence of the Antarctic psychrophile bacterium Planococcus antarcticus DSM 14505.Margolles A, Gueimonde M, Sanchez BJ Bacteriol10.1128/JB.00888-122012Antarctic Regions, DNA, Bacterial/*chemistry/*genetics, Enzymes/metabolism, *Genome, Bacterial, Geologic Sediments/microbiology, Molecular Sequence Data, Pigments, Biological/metabolism, Planococcaceae/*genetics/growth & development/isolation & purification/physiology, *Sequence Analysis, DNA, TemperatureEnzymology
Phylogeny26297353Planococcus faecalis sp. nov., a carotenoid-producing species isolated from stools of Antarctic penguins.Kim JH, Kang HJ, Yu BJ, Kim SC, Lee PCInt J Syst Evol Microbiol10.1099/ijsem.0.0004232015Animals, Antarctic Regions, Bacterial Typing Techniques, Base Composition, Carotenoids/chemistry, DNA, Bacterial/genetics, Fatty Acids/chemistry, Feces/microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phosphatidylglycerols/chemistry, *Phylogeny, Pigmentation, Planococcus Bacteria/*classification/genetics/isolation & purification, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Spheniscidae/*microbiology, Vitamin K 2/analogs & derivatives/chemistryGenetics
Phylogeny27959786Planococcus versutus sp. nov., isolated from soil.See-Too WS, Ee R, Madhaiyan M, Kwon SW, Tan JY, Lim YL, Convey P, Pearce DA, Yin WF, Chan KGInt J Syst Evol Microbiol10.1099/ijsem.0.0017212017Antarctic Regions, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids, *Phylogeny, Planococcus Bacteria/*classification/genetics/isolation & purification, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/chemistry, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny28809140Planococcus ruber sp. nov., isolated from a polluted farmland soil sample.Wang X, Wang Z, Zhao X, Huang X, Zhou Y, Li WJInt J Syst Evol Microbiol10.1099/ijsem.0.0019602017Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, *Farms, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Pigmentation, Planococcus Bacteria/*classification/genetics/isolation & purification, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, *Soil Pollutants, Vitamin K 2/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
5380Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 14505)https://www.dsmz.de/collection/catalogue/details/culture/DSM-14505
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
39939Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5239
43354G.S.N. Reddy, J.S.S. Prakash, M. Vairamani, S. Prabhakar, G.I. Matsumoto, S. Shivaji10.1007/s00792-001-0250-7Planococcus antarcticus and Planococcus psychrophilus spp. nov. isolated from cyanobacterial mat samples collected from ponds in AntarcticaExtremophiles 6: 253-261 200212072961
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)
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
81172Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID100451.1StrainInfo: A central database for resolving microbial strain identifiers
116409Curators of the CIPCollection of Institut Pasteur (CIP 107767)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107767