Strain identifier

BacDive ID: 1439

Type strain: Yes

Species: Geobacillus vulcani

Strain Designation: 3S-1

Strain history: CIP <- 1999, T. Maugeri, Messina Univ., Sicily, Italie: strain 3s-1

NCBI tax ID(s): 135517 (species)

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General

@ref: 4958

BacDive-ID: 1439

DSM-Number: 13174

keywords: 16S sequence, Bacteria, aerobe, spore-forming, thermophilic, Gram-positive, motile, rod-shaped

description: Geobacillus vulcani 3S-1 is an aerobe, spore-forming, thermophilic bacterium that was isolated from marine sediment.

NCBI tax id

  • NCBI tax id: 135517
  • Matching level: species

strain history

@refhistory
4958<- D. Caccamo, Univ. Messina, Italy; 3S-1
67770CIP 106305 <-- T. Maugeri 3s-1.
123887CIP <- 1999, T. Maugeri, Messina Univ., Sicily, Italie: strain 3s-1

doi: 10.13145/bacdive1439.20241212.9.2

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Bacillaceae
  • genus: Geobacillus
  • species: Geobacillus vulcani
  • full scientific name: Geobacillus vulcani (Caccamo et al. 2000) Nazina et al. 2004

  • synonyms

    • @ref: 20215
    • synonym: Bacillus vulcani

@ref: 4958

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Bacillaceae

genus: Geobacillus

species: Geobacillus vulcani

full scientific name: Geobacillus vulcani (Caccamo et al. 2000) Nazina et al. 2004

strain designation: 3S-1

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
23039positive4.0-7.0 µm0.6-0.8 µmrod-shapedyes
123887positiverod-shapedno

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4958BACTO 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
40287Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
123887CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperature
4958positivegrowth50
23039positivegrowth37.0-72.0
23039nogrowth75.0
23039positiveoptimum60.0
23039
40287positivegrowth55
67770positivegrowth55
123887positivegrowth45-55
123887nogrowth10
123887nogrowth22
123887nogrowth30
123887nogrowth37

culture pH

@refabilitytypepHPH range
23039positiveoptimum6.0
23039positivegrowth5.5-9.0alkaliphile
123887nogrowth6

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
23105aerobe
123887obligate aerobe

spore formation

@refspore descriptiontype of sporespore formation
23105oval,terminalendosporeyes
123887yes

halophily

@refsalttested relationconcentrationgrowth
23105NaCloptimum2.0 %
23105NaClgrowth0.0-3.0 %positive
23105NaClgrowth3.0 %positive
23105NaClgrowth5.0 %no
123887NaClgrowth0-2 %positive
123887NaClgrowth4 %no
123887NaClgrowth6 %no
123887NaClgrowth8 %no
123887NaClgrowth10 %no

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2303915963ribitol-builds acid from
2303917268myo-inositol-builds acid from
2303930849L-arabinose-builds acid from
2303926546rhamnose-builds acid from
2303930911sorbitol-builds acid from
2310529864mannitol-builds acid from
2310527922sorbose-builds acid from
2303917234glucose-builds gas from
2303917632nitrate-builds gas from
2303917234glucose-fermentation
23105casein-hydrolysis
2310553426tween 80-hydrolysis
2310516199urea-hydrolysis
2310517632nitrate-reduction
2310527613amygdalin+builds acid from
2310518305arbutin+builds acid from
2310517057cellobiose+builds acid from
2310532528turanose+builds acid from
2310565327D-xylose+builds acid from
231054853esculin+builds acid from
2310528757fructose+builds acid from
2310528260galactose+builds acid from
2310528066gentiobiose+builds acid from
2310524265gluconate+builds acid from
2310517234glucose+builds acid from
2310517754glycerol+builds acid from
2310528087glycogen+builds acid from
2310517716lactose+builds acid from
2310517306maltose+builds acid from
2310537684mannose+builds acid from
2310528053melibiose+builds acid from
2310516634raffinose+builds acid from
2310533942ribose+builds acid from
2310517814salicin+builds acid from
2310528017starch+builds acid from
2310517992sucrose+builds acid from
2310527082trehalose+builds acid from
2310517128adipate+carbon source
2310517057cellobiose+carbon source
2310516947citrate+carbon source
2310528757fructose+carbon source
2310528260galactose+carbon source
2310524265gluconate+carbon source
2310517234glucose+carbon source
2310517716lactose+carbon source
2310525115malate+carbon source
2310517306maltose+carbon source
2310529864mannitol+carbon source
2310537684mannose+carbon source
2310518401phenylacetate+carbon source
2310517992sucrose+carbon source
2310527082trehalose+carbon source
231054853esculin+hydrolysis
231055291gelatin+hydrolysis
2310528017starch+hydrolysis
2310553424tween 20+hydrolysis
12388716947citrate-carbon source
1238874853esculin+hydrolysis
123887606565hippurate-hydrolysis
12388717632nitrate+reduction
12388716301nitrite+reduction
68371Potassium 5-ketogluconate+builds acid from
6837159640N-acetylglucosamine+builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837117634D-glucose+builds acid from
6837112936D-galactose+builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose+builds acid from
6837128066gentiobiose+builds acid from
6837117151xylitol-builds acid from
6837128087glycogen+builds acid from
6837128017starch+builds acid from
6837116634raffinose+builds acid from
683716731melezitose+builds acid from
6837115443inulin-builds acid from
6837127082trehalose+builds acid from
6837117992sucrose+builds acid from
6837128053melibiose+builds acid from
6837117716lactose-builds acid from
6837117306maltose+builds acid from
6837117057cellobiose+builds acid from
6837117814salicin+builds acid from
683714853esculin+builds acid from
6837118305arbutin+builds acid from
6837127613amygdalin-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol+builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose+builds acid from
6837115824D-fructose+builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose+builds acid from
6837116988D-ribose+builds acid from
6837130849L-arabinose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol+builds acid from

antibiotic resistance

  • @ref: 23105
  • ChEBI: 8309
  • metabolite: polymyxin b
  • is antibiotic: yes
  • is resistant: yes

metabolite production

@refChebi-IDmetaboliteproduction
2310535581indoleno
2310516136hydrogen sulfideno
2303915688acetoinno
2310515688acetoinyes
12388735581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
2303915688acetoin-
2303917234glucose-
12388715688acetoin-
12388717234glucose-

enzymes

@refvalueactivityec
23039alkaline phosphatase-3.1.3.1
23039alpha-glucosidase-3.2.1.20
23039catalase+1.11.1.6
23039cytochrome oxidase-1.9.3.1
23039esterase (C 4)-
23039esterase lipase (C 8)-
23039urease-3.5.1.5
68382alpha-fucosidase-3.2.1.51
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase-3.2.1.21
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-galactosidase+3.2.1.22
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-chymotrypsin+3.4.21.1
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382valine arylamidase-
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382esterase lipase (C 8)+
68382esterase (C 4)-
68382alkaline phosphatase+3.1.3.1
123887oxidase+
123887beta-galactosidase-3.2.1.23
123887alcohol dehydrogenase-1.1.1.1
123887gelatinase-
123887amylase+
123887DNase-
123887caseinase-3.4.21.50
123887catalase-1.11.1.6
123887tween esterase-
123887gamma-glutamyltransferase-2.3.2.2
123887lecithinase-
123887lipase-
123887lysine decarboxylase-4.1.1.18
123887ornithine decarboxylase-4.1.1.17
123887protease-
123887urease-3.5.1.5
68382alpha-mannosidase-3.2.1.24

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
123887-+-+-+---++++--+----

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
123887+---++---++++----+---+-+++++-+++-++++-++-+/-------+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationlatitudelongitudeenrichment cultureenrichment culture durationenrichment culture temperaturecountryorigin.countrycontinentisolation date
4958marine sedimentEolian Islands 14°58' E, 38°25' N, Mediterranean Sea, Volcano-La Roya38.416714.9667
23105shallow marine hydrothermal ventBacto Marine Broth 2216 (Difco) and Medium D3 days65
67770Sediment of a shallow hydrothermal vent at Vulcano IslandItalyITAEurope
123887Environment, Environmental strainSicilyItalyITAEurope1996

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Environmental#Aquatic#Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_1030.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_79;96_191;97_207;98_231;99_1030&stattab=map
  • Last taxonomy: Geobacillus
  • 16S sequence: AJ293805
  • Sequence Identity:
  • Total samples: 3714
  • soil counts: 485
  • aquatic counts: 635
  • animal counts: 2412
  • plant counts: 182

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
49581Risk group (German classification)
1238871Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Geobacillus vulcani strain BCRC 17563 16S ribosomal RNA gene, partial sequenceEU4843491532nuccore135517
20218Geobacillus vulcani strain DSM 13174 16S-23S ribosomal RNA intergenic spacer and tRNA-Ile gene, partial sequence; and tRNA-Ala gene, complete sequenceEU157958516nuccore135517
23105Bacillus vulcani 16S rRNA gene, strain 3S-1AJ2938051532nuccore135517

GC content

@refGC-contentmethod
495853
2303953.0high performance liquid chromatography (HPLC)

External links

@ref: 4958

culture collection no.: DSM 13174, CIP 106305, JCM 12214, KCTC 3847

straininfo link

  • @ref: 71089
  • straininfo: 49428

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny11155974Bacillus vulcani sp. nov., a novel thermophilic species isolated from a shallow marine hydrothermal vent.Caccamo D, Gugliandolo C, Stackebrandt E, Maugeri TLInt J Syst Evol Microbiol10.1099/00207713-50-6-20092000Bacillus/chemistry/*classification/genetics/isolation & purification, Bacterial Typing Techniques, DNA, Ribosomal/analysis, Italy, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, TemperatureGenetics
Phylogeny15545427Geobacillus gargensis sp. nov., a novel thermophile from a hot spring, and the reclassification of Bacillus vulcani as Geobacillus vulcani comb. nov.Nazina TN, Lebedeva EV, Poltaraus AB, Tourova TP, Grigoryan AA, Sokolova DS, Lysenko AM, Osipov GAInt J Syst Evol Microbiol10.1099/ijs.0.02932-02004Aerobiosis, Bacillaceae/*classification/cytology/*isolation & purification/physiology, Bacterial Typing Techniques, Carbohydrate Metabolism, Carboxylic Acids/metabolism, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Fatty Acids/analysis/isolation & purification, Genes, rRNA, Gentian Violet, Glycerol/metabolism, Hot Springs/*microbiology, Hot Temperature, Hydrocarbons/metabolism, Lactose/metabolism, Molecular Sequence Data, Nucleic Acid Hybridization, Phenazines, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Ribose/metabolism, Russia, Sequence Analysis, DNA, Temperature, *Water MicrobiologyMetabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
4958Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 13174)https://www.dsmz.de/collection/catalogue/details/culture/DSM-13174
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
23039Tamara N. Nazina,Elena V. Lebedeva,Andrei B. Poltaraus,Tatyana P. Tourova,Alexandre A. Grigoryan,Diyana Sh. Sokolova,Anatoliy M. Lysenko,George A. Osipov10.1099/ijs.0.02932-0Geobacillus gargensis sp. nov., a novel thermophile from a hot spring, and the reclassification of Bacillus vulcani as Geobacillus vulcani comb. nov.IJSEM 54: 2019-2024 200415545427
23105D. Caccamo,C. Gugliandolo,E. Stackebrandt,T. L. Maugeri10.1099/00207713-50-6-2009Bacillus vulcani sp. nov., a novel thermophilic species isolated from a shallow marine hydrothermal vent.IJSEM 50: 2009-2012 200011155974
40287Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18420
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
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
71089Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID49428.1StrainInfo: A central database for resolving microbial strain identifiers
123887Curators of the CIPCollection of Institut Pasteur (CIP 106305)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106305