Strain identifier

BacDive ID: 1487

Type strain: Yes

Species: Virgibacillus arcticus

Strain history: L. Whyte Hal 1.

NCBI tax ID(s): 469869 (species)

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General

@ref: 8188

BacDive-ID: 1487

DSM-Number: 19574

keywords: 16S sequence, Bacteria, moderately halophilic, spore-forming, psychrophilic, Gram-positive, motile, rod-shaped, pigmented

description: Virgibacillus arcticus DSM 19574 is a moderately halophilic, spore-forming, psychrophilic bacterium that has a light pink pigmentation and was isolated from permafrost core of 9 m depth.

NCBI tax id

  • NCBI tax id: 469869
  • Matching level: species

strain history

@refhistory
8188<- T. D. Niederberger and L.G. Whyte, Department of Natural Resource Sciences, McGill University, Canada <- B. Steven; Hal1
67770L. Whyte Hal 1.

doi: 10.13145/bacdive1487.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Bacillaceae
  • genus: Virgibacillus
  • species: Virgibacillus arcticus
  • full scientific name: Virgibacillus arcticus Niederberger et al. 2009

@ref: 8188

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Bacillaceae

genus: Virgibacillus

species: Virgibacillus arcticus

full scientific name: Virgibacillus arcticus Niederberger et al. 2009

type strain: yes

Morphology

cell morphology

  • @ref: 23057
  • gram stain: positive
  • cell length: 2.0-5.0 µm
  • cell width: 0.5-0.8 µm
  • cell shape: rod-shaped
  • motility: yes

colony morphology

  • @ref: 23057
  • colony size: 2.0 mm
  • incubation period: 7 days
  • medium used: 1/4 HM plates

pigmentation

  • @ref: 23057
  • production: yes
  • color: light pink

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8188BACTO 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
230571/4 HM platesyes

culture temp

@refgrowthtypetemperaturerange
8188positivegrowth20psychrophilic
23057positivegrowth0.0-30.0
23057nogrowth-5.0psychrophilic
23057nogrowth37.0mesophilic
23057positiveoptimum25.0mesophilic
67770positivegrowth25mesophilic

culture pH

@refabilitytypepHPH range
23057positivegrowth4.4-9.1alkaliphile
23057positiveoptimum7.0
23057nogrowth10.0

Physiology and metabolism

spore formation

  • @ref: 23057
  • spore description: ellipsoidal,central or subterminal
  • type of spore: endospore
  • spore formation: yes

halophily

@refhalophily levelsaltgrowthtested relationconcentration
23057moderately halophilicNaClpositivegrowth0.0-20.0 %(w/v)
23057NaCloptimum5.0 %(w/v)
23057NaClnogrowth25.0 %

murein

@refmurein short keytype
8188A11A1alpha L-Lys-direct
23057A11A1alpha L-Lys-direct

observation

  • @ref: 67770
  • observation: quinones: MK-7

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2305727613amygdalin-builds acid from
2305717924D-sorbitol-builds acid from
2305717268myo-inositol-builds acid from
2305730849L-arabinose-builds acid from
2305762345L-rhamnose-builds acid from
2305716634raffinose-builds acid from
2305717992sucrose-builds acid from
2305718222xylose-builds acid from
2305716947citrate-carbon source
2305717057cellobiose-carbon source
2305717716lactose-carbon source
2305728053melibiose-carbon source
2305727082trehalose-carbon source
2305727897tryptophan-energy source
2305717057cellobiose-growth
2305717716lactose-growth
2305728053melibiose-growth
2305727082trehalose-growth
2305715824D-fructose+builds acid from
2305717634D-glucose+builds acid from
2305716899D-mannitol+builds acid from
2305716024D-mannose+builds acid from
2305717716lactose+builds acid from
2305717306maltose+builds acid from
2305728053melibiose+builds acid from
23057320061methyl alpha-D-glucopyranoside+builds acid from
2305727082trehalose+builds acid from
2305717151xylitol+builds acid from
2305717634D-glucose+growth
2305717992sucrose+growth
23057casein+hydrolysis
230575291gelatin+hydrolysis
2305717632nitrate+reduction

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitive
2305728971ampicillinyesyes
2305717698chloramphenicolyesyes
2305748923erythromycinyesyes
2305728077rifampicinyesyes
2305717076streptomycinyesyes

metabolite production

@refChebi-IDmetaboliteproduction
2305735581indoleno
2305716136hydrogen sulfideno
2305715688acetoinno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole testcitrate test
2305715688acetoin-
2305735581indole-
2305716947citrate-

enzymes

@refvalueactivityec
23057alkaline phosphatase-3.1.3.1
23057arginine dihydrolase-3.5.3.6
23057beta-galactosidase-3.2.1.23
23057catalase+1.11.1.6
23057cytochrome oxidase-1.9.3.1
23057gelatinase+
23057lysine decarboxylase-4.1.1.18
23057ornithine decarboxylase-4.1.1.17
23057tryptophan deaminase-4.1.99.1
23057urease-3.5.1.5

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentenrichment cultureenrichment culture compositionenrichment culture durationenrichment culture temperature
8188permafrost core of 9 m depthCanadian high Arctic, Ellesmere Island, EurekaCanadaCANNorth America
230571/4 HM mediumper litre: 178 g NaCl, 2 g KCl, 1 g MgSO4.7H2O, 0.36 g CaCl2.2H2O, 0.23 g NaBr, 0.06 g NaHCO3 , 0.01 g FeCl3 , 1.25 g proteose-peptone, 2.5 g yeast extract and 0.25 g glucose, adjusted to about pH 7.014 days23.0
230571/4 HM mediumper litre: 178 g NaCl, 2 g KCl, 1 g MgSO4.7H2O, 0.36 g CaCl2.2H2O, 0.23 g NaBr, 0.06 g NaHCO3 , 0.01 g FeCl3 , 1.25 g proteose-peptone, 2.5 g yeast extract and 0.25 g glucose, adjusted to about pH 7.030 days5.0
67770Permafrost core of 9 m in depth collected near EurekaEllesmere Island, in the Canadian high ArcticCanadaCANNorth America

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Core sample
#Environmental#Terrestrial#Permafrost

Safety information

risk assessment

  • @ref: 8188
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 8188
  • description: Virgibacillus arcticus strain Hal 1 16S ribosomal RNA gene, partial sequence
  • accession: EF675742
  • length: 1350
  • database: ena
  • NCBI tax ID: 469869

GC content

@refGC-contentmethod
818838.2fluorimetric
6777038.2thermal denaturation, midpoint method (Tm)

External links

@ref: 8188

culture collection no.: DSM 19574, JCM 14839, HAL Hal1, HAL 1

straininfo link

  • @ref: 71133
  • straininfo: 408292

literature

  • topic: Phylogeny
  • Pubmed-ID: 19605723
  • title: Virgibacillus arcticus sp. nov., a moderately halophilic, endospore-forming bacterium from permafrost in the Canadian high Arctic.
  • authors: Niederberger TD, Steven B, Charvet S, Barbier B, Whyte LG
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.002931-0
  • year: 2009
  • mesh: Arctic Regions, Bacillaceae/chemistry/*classification/genetics/*isolation & purification, Bacterial Typing Techniques, Base Composition, Canada, Cell Wall/chemistry, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/*metabolism, *Soil Microbiology, Spores, Bacterial/*cytology, Temperature
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8188Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19574)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19574
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
23057Thomas D. Niederberger,Blaire Steven,Sophie Charvet,Beatrice Barbier,Lyle G. Whyte10.1099/ijs.0.002931-0Virgibacillus arcticus sp. nov., a moderately halophilic, endospore-forming bacterium from permafrost in the Canadian high ArcticIJSEM 59: 2219-2225 200919605723
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
71133Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID408292.1StrainInfo: A central database for resolving microbial strain identifiers