Strain identifier

BacDive ID: 133091

Type strain: Yes

Species: Planococcus versutus

Strain Designation: L10.15

Strain history: <- W. S. See-Too, Univ. of Malaya, Kuala Lumpur, Malaysia; L10.15

NCBI tax ID(s): 1302659 (species)

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General

@ref: 24879

BacDive-ID: 133091

DSM-Number: 101994

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

description: Planococcus versutus L10.15 is an aerobe, Gram-positive, motile bacterium that forms circular colonies and was isolated from soil from an elephant seal wallow.

NCBI tax id

  • NCBI tax id: 1302659
  • Matching level: species

strain history

  • @ref: 24879
  • history: <- W. S. See-Too, Univ. of Malaya, Kuala Lumpur, Malaysia; L10.15

doi: 10.13145/bacdive133091.20230509.8.1

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 versutus
  • full scientific name: Planococcus versutus See-Too et al. 2017

@ref: 24879

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Caryophanaceae

genus: Planococcus

species: Planococcus versutus

full scientific name: Planococcus versutus See-Too et al. 2017

strain designation: L10.15

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
25288positive1.0-1.5 µm1.0-1.5 µmcoccus-shapedyes
69480yes93.702
69480positive100

colony morphology

  • @ref: 25288
  • colony size: 1-2 mm
  • colony color: orange
  • colony shape: circular
  • incubation period: 2 days
  • medium used: LB agar

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
25288LB (Luria-Bertani) MEDIUMyes
24879BACTO 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

culture temp

@refgrowthtypetemperaturerange
25288positivegrowth4-30
25288positiveoptimum25mesophilic
24879positivegrowth15psychrophilic

culture pH

@refabilitytypepHPH range
25288positivegrowth6.0-11.0alkaliphile
25288positiveoptimum7.0-8.0

Physiology and metabolism

oxygen tolerance

  • @ref: 25288
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
25288no
69480no96.679

halophily

@refsaltgrowthtested relationconcentration
25288NaClpositivegrowth0.0-14.0 %(w/v)
25288NaCloptimum6 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
25288645522-hydroxybutyrate-assimilation
25288167632-oxobutanoate-assimilation
25288739183-O-methyl-D-glucose-assimilation
25288181014-hydroxyphenylacetic acid-assimilation
2528836219alpha-lactose-assimilation
2528873706bromosuccinate-assimilation
2528817057cellobiose-assimilation
2528816947citrate-assimilation
2528818333D-arabitol-assimilation
2528829990D-aspartate-assimilation
2528828847D-fucose-assimilation
2528812936D-galactose-assimilation
2528816024D-mannose-assimilation
2528816523D-serine-assimilation
2528817924D-sorbitol-assimilation
2528816865gamma-aminobutyric acid-assimilation
252885291gelatin-assimilation
2528828066gentiobiose-assimilation
2528817268myo-inositol-assimilation
2528816467L-arginine-assimilation
2528818287L-fucose-assimilation
2528815971L-histidine-assimilation
2528816651(S)-lactate-assimilation
2528862345L-rhamnose-assimilation
2528817306maltose-assimilation
2528828053melibiose-assimilation
25288320055methyl beta-D-glucopyranoside-assimilation
2528851850methyl pyruvate-assimilation
2528828037n-acetyl-D-galactosamine-assimilation
2528863153N-acetyl-D-mannosamine-assimilation
2528817272propionate-assimilation
2528826490quinate-assimilation
2528816634raffinose-assimilation
2528817814salicin-assimilation
2528817164stachyose-assimilation
2528817992sucrose-assimilation
2528827082trehalose-assimilation
2528832528turanose-assimilation
25288309162-oxoglutarate+assimilation
2528830089acetate+assimilation
2528813705acetoacetate+assimilation
2528817925alpha-D-glucose+assimilation
252888295beta-hydroxybutyrate+assimilation
2528815824D-fructose+assimilation
2528878697D-fructose 6-phosphate+assimilation
2528818024D-galacturonic acid+assimilation
2528830612D-glucarate+assimilation
252888391D-gluconate+assimilation
2528814314D-glucose 6-phosphate+assimilation
2528815748D-glucuronate+assimilation
25288D-lactic acid methyl ester+assimilation
2528815588D-malate+assimilation
2528816899D-mannitol+assimilation
2528823652dextrin+assimilation
2528815740formate+assimilation
2528816537galactarate+assimilation
2528832323glucuronamide+assimilation
2528817754glycerol+assimilation
2528870744glycine-proline+assimilation
2528817596inosine+assimilation
2528816977L-alanine+assimilation
2528829991L-aspartate+assimilation
2528817464L-galactonic acid gamma-lactone+assimilation
2528829985L-glutamate+assimilation
2528815589L-malate+assimilation
2528818183L-pyroglutamic acid+assimilation
2528817115L-serine+assimilation
252888006N-acetyl-D-glucosamine+assimilation
2528835418n-acetylneuraminate+assimilation
2528817309pectin+assimilation
2528853423tween 40+assimilation

antibiotic resistance

  • @ref: 25288
  • ChEBI: 8006
  • metabolite: N-acetyl-D-glucosamine
  • is antibiotic: yes

enzymes

@refvalueactivityec
25288alkaline phosphatase-3.1.3.1
25288alpha-chymotrypsin+3.4.21.1
25288amylase-
25288beta-galactosidase-3.2.1.23
25288beta-glucosidase-3.2.1.21
25288catalase+1.11.1.6
25288cystine arylamidase+3.4.11.3
25288esterase-
25288leucine arylamidase+3.4.11.1
25288valine arylamidase-

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    25288C13:0 anteiso0.6
    25288C15:0 anteiso46.2
    25288C17:0 anteiso10.7
    25288C14:00.6
    25288C15:01.2
    25288C16:04
    25288C16:1ω11c alcohol5.6
    25288C16:1ω7c / C16:10.6
    25288C16:1ω7c alcohol6.5
    25288C17:00.7
    25288C17:1ω7c0.8
    25288C18:01
    25288C18:1ω9c0.7
    25288C14:0 iso3.4
    25288C15:0 iso1.9
    25288C16:0 iso5.5
    25288C17:0 iso1.9
    25288iso-C17:1 / anteiso-C17:16
    25288C17:1 iso ω10c1.3
    25288C18:0 iso0.7
  • type of FA analysis: whole cell analysis
  • incubation medium: LB
  • agar/liquid: agar
  • incubation temperature: 26
  • incubation time: 1
  • software version: Sherlock 6.0
  • library/peak naming table: RTSBA 6
  • system: MIS MIDI
  • instrument: Agilent 6890N

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudeenrichment cultureenrichment culture durationenrichment culture temperature
24879soil from an elephant seal wallowLagoon IslandAntarcticaATAAustralia and Oceania
25288Antarctic soil sample from elephant seal wallowLagoon IslandAntarcticaATAAustralia and Oceania-6768QQ bacteria enrichment medium1 week4

isolation source categories

Cat1Cat2Cat3
#Condition#Psychrophilic (<10°C)
#Climate#Cold#Polar
#Environmental#Terrestrial#Soil
#Host#Mammals

taxonmaps

  • @ref: 69479
  • File name: preview.99_2783.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_67;97_70;98_134;99_2783&stattab=map
  • Last taxonomy: Planococcus
  • 16S sequence: KX516729
  • Sequence Identity:
  • Total samples: 548
  • soil counts: 184
  • aquatic counts: 87
  • animal counts: 244
  • plant counts: 33

Safety information

risk assessment

  • @ref: 24879
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 24879
  • description: Planococcus versutus strain L10.15 16S ribosomal RNA gene, partial sequence
  • accession: KX516729
  • length: 1538
  • database: ena
  • NCBI tax ID: 1302659

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Planococcus versutus L10.15GCA_001186155completencbi1302659
66792Planococcus versutus L10.152788500496completeimg1302659
66792Planococcus versutus L10.152700988609completeimg1302659

GC content

  • @ref: 24879
  • GC-content: 39.4
  • method: sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno72no
motileyes72.313yes
motileyes72.313yes
motileyes72.313yes
flagellatedno73.015no
flagellatedno73.015no
flagellatedno73.015no
gram-positiveyes89.992yes
gram-positiveyes89.992yes
gram-positiveyes89.992yes
anaerobicno99.329no
anaerobicno99.329no
anaerobicno99.329no
aerobicyes94.747yes
aerobicyes94.747yes
aerobicyes94.747yes
halophileyes87.73no
halophileyes87.73no
halophileyes87.73no
spore-formingyes51.701yes
spore-formingyes51.701yes
spore-formingyes51.701yes
glucose-utilyes84.445no
glucose-utilyes84.445no
glucose-utilyes84.445no
thermophileno99.649no
thermophileno99.649no
thermophileno99.649no
glucose-fermentno87.16no
glucose-fermentno87.16no
glucose-fermentno87.16no

External links

@ref: 24879

culture collection no.: DSM 101994, KACC 18918

straininfo link

  • @ref: 91356
  • straininfo: 406612

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
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
Phylogeny28225085AidP, a novel N-Acyl homoserine lactonase gene from Antarctic Planococcus sp.See-Too WS, Ee R, Lim YL, Convey P, Pearce DA, Yin WF, Chan KGSci Rep10.1038/srep4296820174-Butyrolactone/analogs & derivatives/analysis/metabolism, Amino Acid Sequence, Bacterial Proteins/classification/*genetics, Carboxylic Ester Hydrolases/classification/*genetics, Escherichia coli/metabolism, Phylogeny, Planococcus Bacteria/*enzymology/isolation & purification, Quorum Sensing, Sequence AlignmentMetabolism
Metabolism30445965Characterization of a novel N-acylhomoserine lactonase, AidP, from Antarctic Planococcus sp.See-Too WS, Convey P, Pearce DA, Chan KGMicrob Cell Fact10.1186/s12934-018-1024-620184-Butyrolactone/analogs & derivatives/metabolism, Amino Acid Sequence, Antarctic Regions, Bacterial Proteins/chemistry/isolation & purification/*metabolism, Carboxylic Ester Hydrolases/chemistry/isolation & purification/*metabolism, Models, Molecular, Pectins/metabolism, Pectobacterium carotovorum/metabolism, Planococcus Bacteria/*enzymology, Quorum Sensing, Sequence Analysis, Protein, Substrate SpecificityEnzymology

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
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
24879Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-101994Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 101994)
25288W. S. E. See-Too, R.,Madhaiyan, M.,Kwon, S. W.,Tan, J. Y.,Lim, Y. L.,Convey, P.,Pearce, D. A.,Yin, W. F.,Chan, K. G.Planococcus versutus sp. nov., isolated from soil10.1099/ijsem.0.001721IJSEM 67: 944-950 201727959786
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
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
91356Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID406612.1