Strain identifier

BacDive ID: 1112

Type strain: Yes

Species: Halalkalibacterium halodurans

Strain Designation: PN 80, B-3881

Strain history: CIP <- 1997, DSMZ <- NRRL: strain B-3881 <- E.W. Boyer: strain PN 80, Bacillus alcalophilus subsp. halodurans

NCBI tax ID(s): 86665 (species)

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General

@ref: 236

BacDive-ID: 1112

DSM-Number: 497

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, spore-forming, mesophilic, motile

description: Halalkalibacterium halodurans PN 80 is an obligate aerobe, spore-forming, mesophilic bacterium that was isolated from dried sewage sludge.

NCBI tax id

  • NCBI tax id: 86665
  • Matching level: species

strain history

@refhistory
236<- NRRL <- E.W. Boyer (Bacillus alcalophilus subsp. halodurans)
119803CIP <- 1997, DSMZ <- NRRL: strain B-3881 <- E.W. Boyer: strain PN 80, Bacillus alcalophilus subsp. halodurans

doi: 10.13145/bacdive1112.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Bacillaceae
  • genus: Halalkalibacterium
  • species: Halalkalibacterium halodurans
  • full scientific name: Halalkalibacterium halodurans (Nielsen et al. 1995 ex Boyer et al. 1973) Joshi et al. 2022

  • synonyms

    @refsynonym
    20215Bacillus alcalophilus subsp. halodurans
    20215Bacillus okuhidensis
    20215Bacillus halodurans
    20215Alkalihalobacillus halodurans
    20215Alkalihalobacillus okuhidensis

@ref: 236

domain: Bacteria

phylum: Bacillota

class: Bacilli

order: Caryophanales

family: Bacillaceae

genus: Halalkalibacterium

species: Halalkalibacterium halodurans

full scientific name: Halalkalibacterium halodurans (Nielsen et al. 1995) Joshi et al. 2022

strain designation: PN 80, B-3881

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes91.846
69480100positive
119803yespositiverod-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
236ALKALINE NUTRIENT AGAR (DSMZ Medium 31)yeshttps://mediadive.dsmz.de/medium/31Name: ALKALINE NUTRIENT AGAR (DSMZ Medium 31) Composition: Agar 15.0 g/l Na2CO3 anhydrous 5.3 g/l Peptone 5.0 g/l NaHCO3 4.2 g/l Meat extract 3.0 g/l Distilled water
38542MEDIUM 113 - for BacillusyesDistilled water make up to (900.000 ml);Columbia agar (39.000 g);Solution 1 - M00343 (100.000 ml)
119803CIP Medium 113yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=113

culture temp

@refgrowthtypetemperaturerange
236positivegrowth30mesophilic
38542positivegrowth30mesophilic
119803positivegrowth22-55
119803nogrowth10psychrophilic

culture pH

  • @ref: 119803
  • ability: no
  • type: growth
  • pH: 6

Physiology and metabolism

oxygen tolerance

  • @ref: 119803
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481yes100
69480yes100

compound production

  • @ref: 236
  • compound: ß amylase, alkaline

halophily

@refsaltgrowthtested relationconcentration
119803NaClpositivegrowth2-10 %
119803NaClnogrowth0 %

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose+builds acid from32528
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371glycogen+builds acid from28087
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose+builds acid from27082
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371maltose+builds acid from17306
68371cellobiose+builds acid from17057
68371salicin+builds acid from17814
68371esculin+builds acid from4853
68371arbutin-builds acid from18305
68371N-acetylglucosamine+builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol-builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose+builds acid from16024
68371D-fructose+builds acid from15824
68371D-glucose+builds acid from17634
68371D-galactose-builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371D-ribose+builds acid from16988
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol+builds acid from17754
119803citrate-carbon source16947
119803esculin-hydrolysis4853
119803hippurate-hydrolysis606565
119803nitrate-reduction17632
119803nitrite-reduction16301
119803nitrate-respiration17632

metabolite production

  • @ref: 119803
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11980315688acetoin-
11980317234glucose+

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase+3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase+3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase-3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase-3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase-3.1.3.1
119803oxidase-
119803beta-galactosidase+3.2.1.23
119803alcohol dehydrogenase-1.1.1.1
119803gelatinase+
119803amylase-
119803DNase-
119803caseinase-3.4.21.50
119803catalase+1.11.1.6
119803tween esterase-
119803gamma-glutamyltransferase-2.3.2.2
119803lysine decarboxylase-4.1.1.18
119803ornithine decarboxylase-4.1.1.17
119803urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
119803--++-------+-+-++---

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
119803+---+-----+++--------++/--++++--+/-+---+/-+--+------+/---

Isolation, sampling and environmental information

isolation

@refsample type
236dried sewage sludge
119803Environment, Dried sewage sludge

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Waste
  • Cat3: #Sewage sludge

taxonmaps

  • @ref: 69479
  • File name: preview.99_4299.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_2160;97_2613;98_3236;99_4299&stattab=map
  • Last taxonomy: Alkalihalobacillus halodurans
  • 16S sequence: AJ302709
  • Sequence Identity:
  • Total samples: 6986
  • soil counts: 1545
  • aquatic counts: 1519
  • animal counts: 3493
  • plant counts: 429

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
2361Risk group (German classification)
1198031Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Bacillus halodurans gene for 16S ribosomal RNAAB0211871508ena86665
20218Bacillus halodurans strain ATCC 27557 16S ribosomal RNA gene, partial sequenceKC884852501ena86665
20218Bacillus halodurans 16S rRNA gene, strain DSM 497TAJ3027091509ena86665

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Halalkalibacterium halodurans DSM 497GCA_004376175scaffoldncbi86665
66792Bacillus halodurans strain DSM 49786665.8wgspatric86665

GC content

  • @ref: 236
  • GC-content: 42.5

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileyes89.369no
flagellatedyes81.891no
gram-positiveyes85.442no
anaerobicno97.833no
aerobicyes82.74no
halophileyes71.292no
spore-formingyes95.012no
glucose-utilyes90.458no
thermophileno92.512yes
glucose-fermentno92.457no

External links

@ref: 236

culture collection no.: DSM 497, ATCC 27557, NRRL B-3881, CIP 105296

straininfo link

  • @ref: 70784
  • straininfo: 1092

literature

topicPubmed-IDtitleauthorsjournalyearmeshtopic2DOI
Phylogeny9331963Identification of Bacillus sp. FTU strain and the study of the caa3-type oxidase homology.Grinkevich VA, Lysenko AM, Muntyan MS, Skripnikova EV, Afrikyan EKBiochemistry (Mosc)1997Amino Acid Sequence, Bacillus/classification/*enzymology/*genetics, DNA, Bacterial/genetics, Electron Transport Complex IV/chemistry/*genetics, Molecular Sequence Data, Protein Conformation, Sequence Homology, Amino Acid, Species SpecificityGenetics
Phylogeny10591021Reidentification of the keratinase-producing facultatively alkaliphilic Bacillus sp. AH-101 as Bacillus halodurans.Takami H, Nogi Y, Horikoshi KExtremophiles1999Bacillus/*classification/enzymology/*genetics, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Hydrogen-Ion Concentration, Peptide Hydrolases/*genetics/metabolism, *Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/geneticsEnzymology10.1007/s007920050130
Phylogeny12382115Revision of the taxonomic position of the xylanolytic Bacillus sp. MIR32 reidentified as Bacillus halodurans and plasmid-mediated transformation of B. halodurans.Martinez MA, Delgado OD, Breccia JD, Baigori MD, Sineriz FExtremophiles2002Bacillus/*classification/genetics/metabolism, Base Composition, DNA, Bacterial/genetics, DNA, Intergenic/genetics, DNA, Ribosomal/genetics, Hydrogen-Ion Concentration, Nucleic Acid Hybridization, Plasmids/genetics, RNA, Ribosomal, 16S/genetics, RNA, Ribosomal, 23S/genetics, RNA, Transfer/genetics, Species Specificity, Transformation, Bacterial, Xylans/*metabolismMetabolism10.1007/s00792-002-0269-4
Phylogeny15269555Starch hydrolysing Bacillus halodurans isolates from a Kenyan soda lake.Hashim SO, Delgado O, Hatti-Kaul R, Mulaa FJ, Mattiasson BBiotechnol Lett2004Amylases/genetics/*metabolism, Bacillus/classification/genetics/*isolation & purification/*metabolism, Fresh Water/*microbiology, Hydrolysis, Kenya, Species Specificity, Starch/*metabolism, Temperature, Water MicrobiologyMetabolism10.1023/b:bile.0000025885.19910.d7
Phylogeny24554634Bacillus ligniniphilus sp. nov., an alkaliphilic and halotolerant bacterium isolated from sediments of the South China Sea.Zhu D, Tanabe SH, Xie C, Honda D, Sun J, Ai LInt J Syst Evol Microbiol2014Bacillus/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry, *Water MicrobiologyGenetics10.1099/ijs.0.058610-0
Phylogeny26887220Bacterial treatment of alkaline cement kiln dust using Bacillus halodurans strain KG1.Kunal, Rajor A, Siddique RBraz J Microbiol2016Bacillus/classification/*growth & development/isolation & purification/*metabolism, Bacterial Typing Techniques, Biotechnology/*methods, Cluster Analysis, Construction Materials, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Hydrogen-Ion Concentration, *Industrial Waste, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/metabolism, Temperature, Waste Management/*methodsMetabolism10.1016/j.bjm.2015.11.001
Phylogeny31436524Genome-based reclassification of Bacillus okuhidensis as a later heterotypic synonym of Bacillus halodurans.Liu GH, Narsing Rao MP, Dong ZY, Wang JP, Che JM, Chen QQ, Sengonca C, Liu B, Li WJInt J Syst Evol Microbiol2019Bacillus/*classification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Genome, Bacterial, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics10.1099/ijsem.0.003666

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
236Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 497)https://www.dsmz.de/collection/catalogue/details/culture/DSM-497
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
38542Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17299
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)
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
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
70784Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID1092.1StrainInfo: A central database for resolving microbial strain identifiers
119803Curators of the CIPCollection of Institut Pasteur (CIP 105296)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105296