Strain identifier

BacDive ID: 1387

Type strain: Yes

Species: Pontibacillus marinus

Strain Designation: BH030004, 10.101

Strain history: <- CJ Kim, KRIBB

NCBI tax ID(s): 1385511 (strain), 273164 (species)

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General

@ref: 6456

BacDive-ID: 1387

DSM-Number: 16465

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, moderately halophilic, spore-forming, mesophilic, Gram-positive, motile, rod-shaped, colony-forming

description: Pontibacillus marinus BH030004 is an obligate aerobe, moderately halophilic, spore-forming bacterium that forms circular colonies and was isolated from solar saltern soil.

NCBI tax id

NCBI tax idMatching level
273164species
1385511strain

strain history

@refhistory
6456<- C.-J. Kim, KRIBB, Korea <- J.-M. Lim; BH030004
67771<- CJ Kim, KRIBB

doi: 10.13145/bacdive1387.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Bacillaceae
  • genus: Pontibacillus
  • species: Pontibacillus marinus
  • full scientific name: Pontibacillus marinus Lim et al. 2005

@ref: 6456

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Bacillaceae

genus: Pontibacillus

species: Pontibacillus marinus

full scientific name: Pontibacillus marinus Lim et al. 2005

strain designation: BH030004, 10.101

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangementconfidence
23018positive3.3-4.0 µm0.4-0.9 µmrod-shapedyesperitrichous
67771positive
69480yes98.133
69480positive100

colony morphology

  • @ref: 23018
  • colony color: cream
  • colony shape: circular
  • medium used: MA

pigmentation

  • @ref: 23018
  • production: yes
  • color: cream

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6456BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)yeshttps://mediadive.dsmz.de/medium/514Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514; with strain-specific modifications) 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 MnSO4 0.01 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
23018Marine agar (MA)yes

culture temp

@refgrowthtypetemperaturerange
6456positivegrowth30mesophilic
23018positivegrowth15.0-40.0
23018positiveoptimum30.0mesophilic
67771positivegrowth34mesophilic

culture pH

@refabilitytypepHPH range
23018positivegrowth6.0-9.0alkaliphile
23018positiveoptimum7.0-7.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
23018obligate aerobe
67771aerobe

spore formation

@refspore descriptiontype of sporespore formationconfidence
23018spherical,terminal,in swollen sporangiaendosporeyes
69481yes100
69480yes100

halophily

@refhalophily levelsaltgrowthtested relationconcentration
23018moderately halophilic
23018NaClpositivegrowth1.0-9.0 %(w/v)
23018NaCloptimum2.0-5.0 %

murein

  • @ref: 23018
  • murein short key: A31
  • type: A1gamma m-Dpm-direct

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2301815963ribitol-builds acid from
2301836219alpha-lactose-builds acid from
2301817634D-glucose-builds acid from
2301816899D-mannitol-builds acid from
2301816024D-mannose-builds acid from
2301865327D-xylose-builds acid from
2301817754glycerol-builds acid from
2301817268myo-inositol-builds acid from
2301830849L-arabinose-builds acid from
2301862345L-rhamnose-builds acid from
23018casein-hydrolysis
230185291gelatin-hydrolysis
2301817368hypoxanthine-hydrolysis
2301817895L-tyrosine-hydrolysis
2301828017starch-hydrolysis
2301816199urea-hydrolysis
2301815318xanthine-hydrolysis
2301815824D-fructose+builds acid from
2301828053melibiose+builds acid from
2301816634raffinose+builds acid from
2301816988D-ribose+builds acid from
2301816551D-trehalose+builds acid from
2301817306maltose+builds acid from
2301817992sucrose+builds acid from
230184853esculin+hydrolysis
2301853426tween 80+hydrolysis
2301817632nitrate+reduction

enzymes

@refvalueactivityec
23018catalase+1.11.1.6
23018cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic locationenrichment cultureenrichment culture durationenrichment culture temperature
6456solar saltern soilRepublic of KoreaKORAsia
23018solar salternYellow Seamarine agar 2216 (MA) (Difco) supplemented with 5 % (w/v) NaCl3 days35.0
67771From soilRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Condition#Saline

taxonmaps

  • @ref: 69479
  • File name: preview.99_3089.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_1612;97_1929;98_2372;99_3089&stattab=map
  • Last taxonomy: Pontibacillus
  • 16S sequence: AY603977
  • Sequence Identity:
  • Total samples: 163
  • soil counts: 90
  • aquatic counts: 53
  • animal counts: 20

Safety information

risk assessment

  • @ref: 6456
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Pontibacillus marinus strain KCTC 3917 16S ribosomal RNA gene, partial sequenceFJ8086131430ena273164
6456Pontibacillus marinus strain BH030004 16S ribosomal RNA gene, partial sequenceAY6039771376ena273164
67771RPCI-24-247N19.TJ RPCI-24 Mus musculus genomic clone RPCI-24-247N19, genomic survey sequenceBH030004472ena10090

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pontibacillus marinus BH030004 = DSM 16465GCA_000775605contigncbi1385511
66792Pontibacillus marinus BH030004 = DSM 16465GCA_000425225scaffoldncbi1385511
66792Pontibacillus marinus BH030004 = DSM 164651385511.3wgspatric1385511
66792Pontibacillus marinus DSM 164651122965.4wgspatric1385511
66792Pontibacillus marinus BH0300042630968890draftimg1385511
66792Pontibacillus marinus BH030004, DSM 164652524023192draftimg1385511

GC content

@refGC-contentmethod
645642.0
2301842.0high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileyes90.89yes
flagellatedyes88.665yes
gram-positiveyes87.58yes
anaerobicno97.901yes
aerobicyes94.034no
halophileyes85.506no
spore-formingyes93.802no
thermophileno95.823yes
glucose-utilyes87.608no
glucose-fermentno89.83no

External links

@ref: 6456

culture collection no.: DSM 16465, KCTC 3917

straininfo link

  • @ref: 71038
  • straininfo: 139010

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15879229Pontibacillus marinus sp. nov., a moderately halophilic bacterium from a solar saltern, and emended description of the genus Pontibacillus.Lim JM, Jeon CO, Park DJ, Kim HR, Yoon BJ, Kim CJInt J Syst Evol Microbiol10.1099/ijs.0.63489-02005Bacillaceae/*classification/cytology/*isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, Cyanoacrylates/analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis/chemistry, Fatty Acids/analysis, Flagella, Genes, rRNA, Gentian Violet, Korea, Molecular Sequence Data, Nucleic Acid Hybridization, Phenazines, Phylogeny, Quinones/analysis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Sodium Chloride/pharmacology, Spores, Bacterial/cytology, Water MicrobiologyGenetics
Phylogeny19542115Pontibacillus halophilus sp. nov., a moderately halophilic bacterium isolated from a sea urchin.Chen YG, Zhang YQ, Xiao HD, Liu ZX, Yi LB, Shi JX, Zhi XY, Cui XL, Li WJInt J Syst Evol Microbiol10.1099/ijs.0.002469-02009Animals, Bacillaceae/*classification/genetics/isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/analysis, Fatty Acids/analysis, Genes, rRNA, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sea Urchins/*microbiology, Sequence Analysis, DNA, *Sodium Chloride, Species SpecificityGenetics
Phylogeny19654352Pontibacillus litoralis sp. nov., a facultatively anaerobic bacterium isolated from a sea anemone, and emended description of the genus Pontibacillus.Chen YG, Zhang YQ, Yi LB, Li ZY, Wang YX, Xiao HD, Chen QH, Cui XL, Li WJInt J Syst Evol Microbiol10.1099/ijs.0.009910-02009Anaerobiosis, Anemone/*microbiology, Animals, Bacillaceae/*classification/genetics/*isolation & purification/metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiologyMetabolism
Phylogeny20833883Pontibacillus yanchengensis sp. nov., a moderately halophilic bacterium isolated from salt field soil.Yang Y, Zou Z, He M, Wang GInt J Syst Evol Microbiol10.1099/ijs.0.023911-02010Bacillaceae/*classification/genetics/*isolation & purification/metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Sodium Chloride/*metabolism, *Soil MicrobiologyMetabolism
Phylogeny25368138Pontibacillus salicampi sp. nov., a moderately halophilic bacterium isolated from saltern soil.Lee JC, Kim YS, Yun BS, Whang KSInt J Syst Evol Microbiol10.1099/ijs.0.066423-02014Bacillaceae/*classification/genetics/isolation & purification, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Salinity, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryGenetics
Phylogeny27381178Pontibacillus salipaludis sp. nov., a slightly halophilic bacterium isolated from a salt pan.Sultanpuram VR, Mothe T, Mohammed F, Chintalapati S, Chintalapati VRInt J Syst Evol Microbiol10.1099/ijsem.0.0012812016Bacillaceae/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, India, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Salinity, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
6456Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16465)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16465
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
23018Jee-Min Lim,Che Ok Jeon,Dong-Jin Park,Hye-Ryoung Kim,Byoung-Jun Yoon,Chang-Jin Kim10.1099/ijs.0.63489-0Pontibacillus marinus sp. nov., a moderately halophilic bacterium from a solar saltern, and emended description of the genus PontibacillusIJSEM 55: 1027-1031 200515879229
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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
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
71038Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID139010.1StrainInfo: A central database for resolving microbial strain identifiers