Strain identifier
BacDive ID: 4034
Type strain:
Species: Desulfonatronovibrio hydrogenovorans
Strain Designation: Z-7935
Strain history: <- T. Zhilina, Z-7935
NCBI tax ID(s): 1121413 (strain), 53245 (species)
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 id | Matching level |
---|---|
1121413 | strain |
53245 | species |
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
@ref | gram stain | cell length | cell width | cell shape | motility | flagellum arrangement | confidence |
---|---|---|---|---|---|---|---|
23206 | negative | 1.5-2.0 µm | 0.5 µm | vibrio-shaped | yes | polar | |
69480 | yes | 97.198 | |||||
69480 | negative | 99.991 |
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
@ref | growth | type | temperature | range |
---|---|---|---|---|
3532 | positive | growth | 30 | mesophilic |
23206 | positive | growth | 15-43 | |
23206 | positive | optimum | 37 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
23206 | positive | maximum | 10.2 | alkaliphile |
23206 | positive | optimum | 9.5-9.7 | |
23206 | no | growth | 7.0 |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance | confidence |
---|---|---|
3532 | anaerobe | |
23206 | anaerobe | |
69480 | anaerobe | 100 |
nutrition type
- @ref: 23206
- type: lithoheterotroph
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.778 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
23206 | NaCl | no | growth | <1 %(w/v) |
23206 | NaCl | no | growth | >12 %(w/v) |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
23206 | 33403 | elemental sulfur | - | electron acceptor |
23206 | 16236 | ethanol | - | electron donor |
23206 | 29806 | fumarate | - | electron donor |
23206 | 17754 | glycerol | - | electron donor |
23206 | 24996 | lactate | - | electron donor |
23206 | 25115 | malate | - | electron donor |
23206 | 17272 | propionate | - | electron donor |
23206 | 15361 | pyruvate | - | electron donor |
23206 | 17822 | serine | - | electron donor |
23206 | 30089 | acetate | + | carbon source |
23206 | yeast extract | + | carbon source | |
23206 | 16189 | sulfate | + | electron acceptor |
23206 | 17359 | sulfite | + | electron acceptor |
23206 | 16094 | thiosulfate | + | electron acceptor |
23206 | 30089 | acetate | + | electron donor |
23206 | 15740 | formate | + | electron donor |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
3532 | mud | Lake Magadi | Kenya | KEN | Africa |
23206 | sediments of an equatorial soda lake |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#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
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Desulfonatronovibrio hydrogenovorans DSM 9292 | GCA_000686525 | scaffold | ncbi | 1121413 |
66792 | Desulfonatronovibrio hydrogenovorans DSM 9292 | 1121413.3 | wgs | patric | 1121413 |
66792 | Desulfonatronovibrio hydrogenovorans DSM 9292 | 2563366506 | draft | img | 1121413 |
GC content
- @ref: 23206
- GC-content: 48.6
- method: Thermal denaturation, fluorometry
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | yes | 86.897 | no |
flagellated | no | 68.732 | no |
gram-positive | no | 99.216 | yes |
anaerobic | yes | 99.622 | no |
halophile | no | 53.512 | no |
spore-forming | no | 93.809 | no |
glucose-util | no | 68.121 | no |
aerobic | no | 98.82 | no |
thermophile | no | 54.235 | no |
glucose-ferment | no | 79.983 | no |
External links
@ref: 3532
culture collection no.: DSM 9292
straininfo link
- @ref: 73539
- straininfo: 48611
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Metabolism | 8995816 | Desulfonatronovibrio hydrogenovorans gen. nov., sp. nov., an alkaliphilic, sulfate-reducing bacterium. | Zhilina TN, Zavarzin GA, Rainey FA, Pikuta EN, Osipov GA, Kostrikina NA | Int J Syst Bacteriol | 10.1099/00207713-47-1-144 | 1997 | Bacteriological 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/metabolism | Phylogeny |
Metabolism | 11882721 | Bioenergetics of the alkaliphilic sulfate-reducing bacterium Desulfonatronovibrio hydrogenovorans. | Sydow U, Wohland P, Wolke I, Cypionka H | Microbiology (Reading) | 10.1099/00221287-148-3-853 | 2002 | Culture Media, Deltaproteobacteria/growth & development/*metabolism, *Energy Metabolism, Hydrogen-Ion Concentration, Oxidation-Reduction, Protons, Sodium/metabolism, Sodium-Hydrogen Exchangers/metabolism, Sulfates/metabolism, Sulfites/metabolism, Sulfur/*metabolism | Cultivation |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
3532 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 9292) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-9292 | |||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
23206 | T. N. ZHILINA, G. A. ZAVARZIN, F. A. RAINEY, E. N. PIKUTA, G. A. OSIPOV, N. A. KOSTRIKINA | 10.1099/00207713-47-1-144 | Desulfonatronovibrio hydrogenovorans gen. nov., sp. nov., an Alkaliphilic, Sulfate-Reducing Bacterium | IJSEM 47: 144-149 1997 | 8995816 | |
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
69479 | João 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 | |||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
73539 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID48611.1 | StrainInfo: A central database for resolving microbial strain identifiers |