Strain identifier

BacDive ID: 4034

Type strain: Yes

Species: Desulfonatronovibrio hydrogenovorans

Strain Designation: Z-7935

Strain history: <- T. Zhilina, Z-7935

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 3532

BacDive-ID: 4034

DSM-Number: 9292

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, lithoheterotroph, mesophilic, Gram-negative, motile, vibrio-shaped

description: Desulfonatronovibrio hydrogenovorans Z-7935 is an anaerobe, lithoheterotroph, mesophilic bacterium that was isolated from mud.

NCBI tax id

NCBI tax idMatching level
1121413strain
53245species

strain history

  • @ref: 3532
  • history: <- T. Zhilina, Z-7935

doi: 10.13145/bacdive4034.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Deltaproteobacteria
  • order: Desulfovibrionales
  • family: Desulfohalobiaceae
  • genus: Desulfonatronovibrio
  • species: Desulfonatronovibrio hydrogenovorans
  • full scientific name: Desulfonatronovibrio hydrogenovorans Zhilina et al. 1997

@ref: 3532

domain: Bacteria

phylum: Proteobacteria

class: Deltaproteobacteria

order: Desulfovibrionales

family: Desulfohalobiaceae

genus: Desulfonatronovibrio

species: Desulfonatronovibrio hydrogenovorans

full scientific name: Desulfonatronovibrio hydrogenovorans Zhilina et al. 1997

strain designation: Z-7935

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangementconfidence
23206negative1.5-2.0 µm0.5 µmvibrio-shapedyespolar
69480yes97.198
69480negative99.991

Culture and growth conditions

culture medium

  • @ref: 3532
  • name: DESULFONATRONOVIBRIO MEDIUM (DSMZ Medium 742)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/742
  • composition: Name: DESULFONATRONOVIBRIO MEDIUM (DSMZ Medium 742) Composition: NaHCO3 14.8368 g/l Na2CO3 9.8912 g/l Na-formate 4.9456 g/l Na2SO4 2.96736 g/l Yeast extract 1.48368 g/l NH4Cl 0.98912 g/l Na2S x 9 H2O 0.98912 g/l Na2HPO4 0.197824 g/l KCl 0.197824 g/l MgSO4 x 7 H2O 0.0296736 g/l Nitrilotriacetic acid 0.0148368 g/l NaCl 0.0098912 g/l MnSO4 x H2O 0.0049456 g/l ZnSO4 x 7 H2O 0.00178042 g/l CoSO4 x 7 H2O 0.00178042 g/l FeSO4 x 7 H2O 0.00098912 g/l CaCl2 x 2 H2O 0.00098912 g/l Sodium resazurin 0.00049456 g/l NiCl2 x 6 H2O 0.000296736 g/l AlK(SO4)2 x 12 H2O 0.000197824 g/l H3BO3 9.8912e-05 g/l Na2MoO4 x 2 H2O 9.8912e-05 g/l CuSO4 x 5 H2O 9.8912e-05 g/l Pyridoxine hydrochloride 9.8912e-05 g/l (DL)-alpha-Lipoic acid 4.9456e-05 g/l p-Aminobenzoic acid 4.9456e-05 g/l Riboflavin 4.9456e-05 g/l Nicotinic acid 4.9456e-05 g/l Calcium D-(+)-pantothenate 4.9456e-05 g/l Thiamine HCl 4.9456e-05 g/l Biotin 1.97824e-05 g/l Folic acid 1.97824e-05 g/l Na2WO4 x 2 H2O 3.95648e-06 g/l Na2SeO3 x 5 H2O 2.96736e-06 g/l Vitamin B12 9.8912e-07 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
3532positivegrowth30mesophilic
23206positivegrowth15-43
23206positiveoptimum37mesophilic

culture pH

@refabilitytypepHPH range
23206positivemaximum10.2alkaliphile
23206positiveoptimum9.5-9.7
23206nogrowth7.0

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
3532anaerobe
23206anaerobe
69480anaerobe100

nutrition type

  • @ref: 23206
  • type: lithoheterotroph

spore formation

@refspore formationconfidence
69481no100
69480no99.778

halophily

@refsaltgrowthtested relationconcentration
23206NaClnogrowth<1 %(w/v)
23206NaClnogrowth>12 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2320633403elemental sulfur-electron acceptor
2320616236ethanol-electron donor
2320629806fumarate-electron donor
2320617754glycerol-electron donor
2320624996lactate-electron donor
2320625115malate-electron donor
2320617272propionate-electron donor
2320615361pyruvate-electron donor
2320617822serine-electron donor
2320630089acetate+carbon source
23206yeast extract+carbon source
2320616189sulfate+electron acceptor
2320617359sulfite+electron acceptor
2320616094thiosulfate+electron acceptor
2320630089acetate+electron donor
2320615740formate+electron donor

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
3532mudLake MagadiKenyaKENAfrica
23206sediments of an equatorial soda lake

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Lake (large)
#Environmental#Aquatic#Sediment
#Condition#Alkaline

taxonmaps

  • @ref: 69479
  • File name: preview.99_7079.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_389;96_1711;97_4072;98_5205;99_7079&stattab=map
  • Last taxonomy: Desulfonatronovibrio hydrogenovorans subclade
  • 16S sequence: X99234
  • Sequence Identity:
  • Total samples: 20
  • soil counts: 1
  • aquatic counts: 19

Safety information

risk assessment

  • @ref: 3532
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 3532
  • description: D.hydrogenovorans 16S rRNA gene
  • accession: X99234
  • length: 1503
  • database: ena
  • NCBI tax ID: 53245

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Desulfonatronovibrio hydrogenovorans DSM 9292GCA_000686525scaffoldncbi1121413
66792Desulfonatronovibrio hydrogenovorans DSM 92921121413.3wgspatric1121413
66792Desulfonatronovibrio hydrogenovorans DSM 92922563366506draftimg1121413

GC content

  • @ref: 23206
  • GC-content: 48.6
  • method: Thermal denaturation, fluorometry

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes86.897no
flagellatedno68.732no
gram-positiveno99.216yes
anaerobicyes99.622no
halophileno53.512no
spore-formingno93.809no
glucose-utilno68.121no
aerobicno98.82no
thermophileno54.235no
glucose-fermentno79.983no

External links

@ref: 3532

culture collection no.: DSM 9292

straininfo link

  • @ref: 73539
  • straininfo: 48611

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Metabolism8995816Desulfonatronovibrio hydrogenovorans gen. nov., sp. nov., an alkaliphilic, sulfate-reducing bacterium.Zhilina TN, Zavarzin GA, Rainey FA, Pikuta EN, Osipov GA, Kostrikina NAInt J Syst Bacteriol10.1099/00207713-47-1-1441997Bacteriological Techniques, Base Composition, Carbonates/metabolism, Culture Media/metabolism, Desulfovibrio/*classification/genetics/growth & development/metabolism, Formates/metabolism, Hydrogen/metabolism, Hydrogen-Ion Concentration, Lipids/analysis, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Homology, Nucleic Acid, Sodium Chloride/metabolism, Sulfates/metabolism, Sulfites/metabolism, Thiosulfates/metabolismPhylogeny
Metabolism11882721Bioenergetics of the alkaliphilic sulfate-reducing bacterium Desulfonatronovibrio hydrogenovorans.Sydow U, Wohland P, Wolke I, Cypionka HMicrobiology (Reading)10.1099/00221287-148-3-8532002Culture Media, Deltaproteobacteria/growth & development/*metabolism, *Energy Metabolism, Hydrogen-Ion Concentration, Oxidation-Reduction, Protons, Sodium/metabolism, Sodium-Hydrogen Exchangers/metabolism, Sulfates/metabolism, Sulfites/metabolism, Sulfur/*metabolismCultivation

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
3532Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 9292)https://www.dsmz.de/collection/catalogue/details/culture/DSM-9292
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
23206T. N. ZHILINA, G. A. ZAVARZIN, F. A. RAINEY, E. N. PIKUTA, G. A. OSIPOV, N. A. KOSTRIKINA10.1099/00207713-47-1-144Desulfonatronovibrio hydrogenovorans gen. nov., sp. nov., an Alkaliphilic, Sulfate-Reducing BacteriumIJSEM 47: 144-149 19978995816
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)
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
73539Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID48611.1StrainInfo: A central database for resolving microbial strain identifiers