Strain identifier

BacDive ID: 132643

Type strain: Yes

Species: Tepidibacillus decaturensis

Strain Designation: Z9

Strain history: B. W. Fouke; Univ. of Illinois Urbana-Champaign, USA; Z9.

NCBI tax ID(s): 1413211 (species)

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General

@ref: 24432

BacDive-ID: 132643

DSM-Number: 103037

keywords: genome sequence, 16S sequence, Bacteria, microaerophile, spore-forming, Gram-negative, motile, rod-shaped, colony-forming

description: Tepidibacillus decaturensis Z9 is a microaerophile, spore-forming, Gram-negative bacterium that forms circular colonies and was isolated from deep subsurface groundwater.

NCBI tax id

  • NCBI tax id: 1413211
  • Matching level: species

strain history

@refhistory
24432<- Y. Dong, Univ. Illinois, Urbana, USA; Z9 <- Y. Dong {2012}
67770B. W. Fouke; Univ. of Illinois Urbana-Champaign, USA; Z9.

doi: 10.13145/bacdive132643.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Bacillaceae
  • genus: Tepidibacillus
  • species: Tepidibacillus decaturensis
  • full scientific name: Tepidibacillus decaturensis Dong et al. 2016

@ref: 24432

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Bacillaceae

genus: Tepidibacillus

species: Tepidibacillus decaturensis

full scientific name: Tepidibacillus decaturensis Dong et al. 2016

strain designation: Z9

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangementconfidence
24926negative1.0-10.0 µm0.3 µmrod-shapedyesmonotrichous, polar
69480yes96.166
69480positive100

colony morphology

  • @ref: 24926
  • colony size: 0.5-1.0 mm
  • colony color: beige
  • colony shape: circular
  • incubation period: 7 days

Culture and growth conditions

culture medium

  • @ref: 24432
  • name: DEFERRISOMA MEDIUM (DSMZ Medium 1451)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/1451
  • composition: Name: DEFERRISOMA MEDIUM (DSMZ Medium 1451; with strain-specific modifications) Composition: NaCl 17.9462 g/l MgCl2 x 6 H2O 3.98804 g/l Fe(III) citrate 2.49252 g/l D-Glucose 0.997009 g/l Na2CO3 0.498504 g/l Na-acetate 0.408774 g/l Na-formate 0.338983 g/l KH2PO4 0.329013 g/l CaCl2 x 2 H2O 0.329013 g/l KCl 0.329013 g/l NH4Cl 0.329013 g/l Yeast extract 0.199402 g/l Na2S x 9 H2O 0.0997009 g/l HCl 0.00249252 g/l FeCl2 x 4 H2O 0.00149551 g/l NaOH 0.000498504 g/l CoCl2 x 6 H2O 0.000189432 g/l MnCl2 x 4 H2O 9.97009e-05 g/l Pyridoxine hydrochloride 9.97009e-05 g/l ZnCl2 6.97906e-05 g/l (DL)-alpha-Lipoic acid 4.98504e-05 g/l Thiamine HCl 4.98504e-05 g/l Nicotinic acid 4.98504e-05 g/l Calcium D-(+)-pantothenate 4.98504e-05 g/l p-Aminobenzoic acid 4.98504e-05 g/l Riboflavin 4.98504e-05 g/l Na2MoO4 x 2 H2O 3.58923e-05 g/l NiCl2 x 6 H2O 2.39282e-05 g/l Biotin 1.99402e-05 g/l Folic acid 1.99402e-05 g/l H3BO3 5.98205e-06 g/l Na2WO4 x 2 H2O 3.98804e-06 g/l Na2SeO3 x 5 H2O 2.99103e-06 g/l CuCl2 x 2 H2O 1.99402e-06 g/l Vitamin B12 9.97009e-07 g/l Distilled water

culture temp

@refgrowthtypetemperaturerangeconfidence
24926positivegrowth20.0-60.0
24926positiveoptimum30.0-40.0
24432positivegrowth37mesophilic
67770positivegrowth37mesophilic
69480thermophilic100

culture pH

@refabilitytypepH
24926positivegrowth5.0-8.0
24926positiveoptimum5.2-5.8

Physiology and metabolism

oxygen tolerance

  • @ref: 24926
  • oxygen tolerance: microaerophile

spore formation

@reftype of sporespore formationconfidence
24926endosporeyes
69481yes100
69480yes100

halophily

@refsaltgrowthtested relationconcentration
24926NaClpositivegrowth1.0-5.0 %(w/v)
24926NaCloptimum2.5 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2492617750betaine-fermentation
2492633403elemental sulfur-electron acceptor
2492616301nitrite-electron acceptor
2492616189sulfate-electron acceptor
2492616094thiosulfate-electron acceptor
2492631605ferric citrate+electron acceptor
24926ferrihydrite+electron acceptor
2492628757fructose+fermentation
2492628260galactose+fermentation
249265417glucosamine+fermentation
2492617234glucose+fermentation
2492617754glycerol+fermentation
2492615428glycine+fermentation
2492617716lactose+fermentation
2492617306maltose+fermentation
2492629864mannitol+fermentation
2492637684mannose+fermentation
2492617632nitrate+electron acceptor
24926peptone+fermentation
2492628017starch+fermentation
2492617992sucrose+fermentation
2492627082trehalose+fermentation
2492618139trimethylamine+fermentation

enzymes

@refvalueactivityec
24926catalase-1.11.1.6
24926cytochrome oxidase-1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentenrichment cultureenrichment culture compositionenrichment culture duration
24432deep subsurface groundwaterIllinois, DecaturUSAUSANorth America
249261.7 km depth groundwateriron-reducing enrichment culture10 mM Fe(III)-citrate as the electron acceptor and a mixture of fatty acids (5 mM each of acetate, lactate, pyruvate and formate) plus H2 (5 ml per 25 ml serum tube) as electron donors>180 days
67770Groundwater at a depth of 1.7 km from the Mt. Simon Sandstone of the Illinois BasinILUSAUSANorth America

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic
  • Cat3: #Groundwater

Safety information

risk assessment

  • @ref: 24432
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
24926Orenia metallireducens strain Z6 16S ribosomal RNA gene, partial sequenceKP8987321495nuccore1413210
24432Tepidibacillus decaturensis strain Z9 16S ribosomal RNA gene, partial sequenceKP8987331512ena1413211

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Tepidibacillus decaturensis Z92675903671draftimg1413211
67770Tepidibacillus decaturensis Z9GCA_001561915scaffoldncbi1413211

GC content

@refGC-contentmethod
2492636.1
2443236.1sequence analysis
6777036.1genome sequence analysis

Genome-based predictions

predictions

  • trait: spore-forming
  • prediction: yes
  • confidence: 100
  • training_data: no

External links

@ref: 24432

culture collection no.: DSM 103037, ATCC BAA 2644, JCM 31418

straininfo link

  • @ref: 90956
  • straininfo: 405822

literature

  • topic: Phylogeny
  • Pubmed-ID: 27406851
  • title: Tepidibacillus decaturensis sp. nov., a microaerophilic, moderately thermophilic iron-reducing bacterium isolated from 1.7 km depth groundwater.
  • authors: Dong Y, Sanford RA, Boyanov MI, Kemner KM, Flynn TM, O'Loughlin EJ, Locke RA, Weber JR, Egan SM, Fouke BW
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.001295
  • year: 2016
  • mesh: Bacillaceae/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Groundwater/*microbiology, Illinois, Iron/*metabolism, Oxidation-Reduction, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA
  • topic2: Transcriptome

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
24432Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-103037Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 103037)
24926Y. S. Dong, Robert A.,Boyanov, Maxim I.,Kemner, Kenneth M.,Flynn, Theodore M.,O'Loughlin, Edward J.,Locke, Randall A.,Weber, Joseph R.,Egan, Sheila M.,Fouke, Bruce W.Tepidibacillus decaturensis sp. nov., a microaerophilic, moderately thermophilic iron-reducing bacterium isolated from 1.7 km depth groundwater10.1099/ijsem.0.001295IJSEM 66: 3964-3971 201627406851
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
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
90956Reimer, 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-ID405822.1