Strain identifier

BacDive ID: 4159

Type strain: Yes

Species: Desulfohalovibrio alkalitolerans

Strain Designation: RT2

Strain history: K. Ingvorsen RT2.

NCBI tax ID(s): 1121439 (strain), 293256 (species)

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General

@ref: 6392

BacDive-ID: 4159

DSM-Number: 16529

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, thermophilic, motile, ovoid-shaped

description: Desulfohalovibrio alkalitolerans RT2 is an anaerobe, thermophilic, motile bacterium that was isolated from metal coupon in corrosion monitoring reactor in District Heating Plant.

NCBI tax id

NCBI tax idMatching level
293256species
1121439strain

strain history

@refhistory
6392<- K. Ingvorsen, University of Aarhus, Department of Microbiology, Institute of Biological Sciences, Denmark; RT2 <- M. B. Nielsen {2004}
67770K. Ingvorsen RT2.

doi: 10.13145/bacdive4159.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Deltaproteobacteria
  • order: Desulfovibrionales
  • family: Desulfovibrionaceae
  • genus: Desulfohalovibrio
  • species: Desulfohalovibrio alkalitolerans
  • full scientific name: Desulfohalovibrio alkalitolerans (Abildgaard et al. 2006) Spring et al. 2019

  • synonyms

    @refsynonym
    20215Desulfovibrio alkalitolerans
    20215Alkalidesulfovibrio alkalitolerans

@ref: 6392

domain: Bacteria

phylum: Proteobacteria

class: Deltaproteobacteria

order: Desulfovibrionales

family: Desulfovibrionaceae

genus: Desulfohalovibrio

species: Desulfohalovibrio alkalitolerans

full scientific name: Desulfohalovibrio alkalitolerans (Abildgaard et al. 2006) Spring et al. 2019

strain designation: RT2

type strain: yes

Morphology

cell morphology

@refcell lengthcell widthcell shapemotilitygram stainconfidence
316181.4-1.9 µm0.5-0.8 µmovoid-shapedyes
69480negative99.991
69480yes95.231

pigmentation

  • @ref: 31618
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 6392
  • name: DESULFOHALOTOMACULUM ALKALIPHILUM MEDIUM (DSMZ Medium 866)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/866
  • composition: Name: DESULFOFALX MEDIUM (DSMZ Medium 866; with strain-specific modifications) Composition: NaHCO3 7.98403 g/l NaCl 4.99002 g/l Na2SO4 4.99002 g/l Na-(L)-lactate 2.49501 g/l Yeast extract 1.49701 g/l NH4Cl 0.998004 g/l Na2CO3 0.499002 g/l Na2S x 9 H2O 0.499002 g/l KCl 0.199601 g/l KH2PO4 0.199601 g/l MgCl2 x 6 H2O 0.0998004 g/l HCl 0.00249501 g/l FeCl2 x 4 H2O 0.00149701 g/l Sodium resazurin 0.000499002 g/l CoCl2 x 6 H2O 0.000189621 g/l Pyridoxine hydrochloride 9.98004e-05 g/l MnCl2 x 4 H2O 9.98004e-05 g/l ZnCl2 6.98603e-05 g/l p-Aminobenzoic acid 4.99002e-05 g/l (DL)-alpha-Lipoic acid 4.99002e-05 g/l Riboflavin 4.99002e-05 g/l Calcium D-(+)-pantothenate 4.99002e-05 g/l Thiamine HCl 4.99002e-05 g/l Nicotinic acid 4.99002e-05 g/l Na2MoO4 x 2 H2O 3.59281e-05 g/l NiCl2 x 6 H2O 2.39521e-05 g/l Biotin 1.99601e-05 g/l Folic acid 1.99601e-05 g/l H3BO3 5.98802e-06 g/l CuCl2 x 2 H2O 1.99601e-06 g/l Vitamin B12 9.98004e-07 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
6392positivegrowth40thermophilic
31618positivegrowth16-47
31618positiveoptimum43thermophilic
67770positivegrowth40thermophilic

culture pH

@refabilitytypepHPH range
31618positivegrowth6.9-9.9alkaliphile
31618positiveoptimum9-9.4

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
6392anaerobe
31618anaerobe
69480anaerobe100

spore formation

@refspore formationconfidence
31618no
69481no100
69480no99.944

halophily

@refsaltgrowthtested relationconcentration
31618NaClpositivegrowth0-13 %
31618NaClpositiveoptimum0-7 %

observation

@refobservation
31618aggregates in chains
67770quinones: MK-7

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3161815740formate+carbon source
3161824996lactate+carbon source
3161815361pyruvate+carbon source

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
6392metal coupon in corrosion monitoring reactor in District Heating PlantSkanderborgDenmarkDNKEurope
67770Metal coupon in corrosion monitoring reactor in a district heating plantJutlandDenmarkDNKEurope

isolation source categories

Cat1Cat2Cat3
#Engineered#Industrial#Engineered product
#Engineered#Industrial#Plant (Factory)

taxonmaps

  • @ref: 69479
  • File name: preview.99_5245.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_179;96_2548;97_3113;98_3910;99_5245&stattab=map
  • Last taxonomy: Desulfohalovibrio alkalitolerans subclade
  • 16S sequence: AY649785
  • Sequence Identity:
  • Total samples: 176
  • soil counts: 16
  • aquatic counts: 114
  • animal counts: 42
  • plant counts: 4

Safety information

risk assessment

  • @ref: 6392
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
6392Desulfovibrio alkalitolerans 16S ribosomal RNA gene, partial sequenceAY6497851517ena293256
67770Desulfohalovibrio alkalitolerans DSM 16529 ctg24, whole genome shotgun sequenceATHI010000165157ena1121439

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Desulfovibrio alkalitolerans DSM 165291121439.3wgspatric1121439
66792Desulfovibrio alkalitolerans DSM 165292571042912draftimg1121439
66792Desulfovibrio alkalitolerans DSM 165292619619068draftimg1121439
67770Desulfohalovibrio alkalitolerans DSM 16529GCA_000422245contigncbi1121439

GC content

  • @ref: 6392
  • GC-content: 64.7

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes87.364yes
flagellatedno65.595no
gram-positiveno99.146no
anaerobicyes99.4yes
aerobicno98.797yes
halophileno63.182no
spore-formingno93.525yes
thermophileno76.398yes
glucose-utilno71.552no
glucose-fermentno81.743no

External links

@ref: 6392

culture collection no.: DSM 16529, JCM 12612

straininfo link

  • @ref: 73660
  • straininfo: 132770

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Metabolism16627648Desulfovibrio alkalitolerans sp. nov., a novel alkalitolerant, sulphate-reducing bacterium isolated from district heating water.Abildgaard L, Nielsen MB, Kjeldsen KU, Ingvorsen KInt J Syst Evol Microbiol10.1099/ijs.0.63909-02006Acetic Acid/metabolism, Alkalies/*pharmacology, Anti-Bacterial Agents/pharmacology, Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Denmark, Desulfovibrio/*classification/*isolation & purification/metabolism/physiology, Formates/metabolism, Genes, rRNA, Hydrogen/metabolism, Hydrogen-Ion Concentration, Lactic Acid/metabolism, Molecular Sequence Data, Movement, Oxidation-Reduction, Phylogeny, Pyruvic Acid/metabolism, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sulfates/*metabolism, Sulfites/metabolism, Temperature, *Water MicrobiologyPhylogeny
Genetics23950126Draft genome sequences for three mercury-methylating, sulfate-reducing bacteria.Brown SD, Hurt RA Jr, Gilmour CC, Elias DAGenome Announc10.1128/genomeA.00618-132013

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
6392Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16529)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16529
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
31618Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2790528776041
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
73660Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID132770.1StrainInfo: A central database for resolving microbial strain identifiers