Strain identifier
BacDive ID: 132624
Type strain:
Species: Varunaivibrio sulfuroxidans
Strain history: C. Vetriani; Rutgers Univ., USA; TC8.
NCBI tax ID(s): 1773489 (species)
General
@ref: 24413
BacDive-ID: 132624
DSM-Number: 101688
keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, chemoautotroph, mesophilic, Gram-negative, motile, vibrio-shaped
description: Varunaivibrio sulfuroxidans DSM 101688 is a facultative anaerobe, chemoautotroph, mesophilic bacterium that was isolated from sediment from a submarine coastal gas vent.
NCBI tax id
- NCBI tax id: 1773489
- Matching level: species
strain history
@ref | history |
---|---|
24413 | <- C. Vetriani, Rutgers, State Univ. New Jersey, New Brunswick, USA; TC8 <- S. Patwardhan {2014} |
67770 | C. Vetriani; Rutgers Univ., USA; TC8. |
doi: 10.13145/bacdive132624.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Rhodospirillales
- family: Thalassospiraceae
- genus: Varunaivibrio
- species: Varunaivibrio sulfuroxidans
- full scientific name: Varunaivibrio sulfuroxidans Patwardhan and Vetriani 2016
@ref: 24413
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhodospirillales
family: Thalassospiraceae
genus: Varunaivibrio
species: Varunaivibrio sulfuroxidans
full scientific name: Varunaivibrio sulfuroxidans Patwardhan and Vetriani 2016
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
43161 | negative | 1-1.5 µm | 0.6 µm | vibrio-shaped | yes | |
69480 | negative | 99.999 | ||||
69480 | yes | 92.817 |
Culture and growth conditions
culture medium
- @ref: 24413
- name: SULFURIMONAS MJ MEDIUM (DSMZ Medium 1011)
- growth: yes
- link: https://mediadive.dsmz.de/medium/1011
- composition: Name: SULFURIMONAS MJ MEDIUM (DSMZ Medium 1011; with strain-specific modifications) Composition: MgCl2 x 6 H2O 4.13452 g/l KNO3 1.97824 g/l NaHCO3 1.48368 g/l Na2S2O3 x 5 H2O 1.48368 g/l KCl 0.326409 g/l NH4Cl 0.24728 g/l K2HPO4 0.138477 g/l MgSO4 x 7 H2O 0.0296736 g/l Nitrilotriacetic acid 0.0148368 g/l Fe(NH4)2(SO4)2 x 6 H2O 0.0098912 g/l NaCl 0.0098912 g/l MnSO4 x H2O 0.0049456 g/l CoSO4 x 7 H2O 0.00178042 g/l ZnSO4 x 7 H2O 0.00178042 g/l CaCl2 x 2 H2O 0.00098912 g/l FeSO4 x 7 H2O 0.00098912 g/l NiCl2 x 6 H2O 0.000296736 g/l AlK(SO4)2 x 12 H2O 0.000197824 g/l CuSO4 x 5 H2O 9.8912e-05 g/l Pyridoxine hydrochloride 9.8912e-05 g/l Na2MoO4 x 2 H2O 9.8912e-05 g/l H3BO3 9.8912e-05 g/l p-Aminobenzoic acid 4.9456e-05 g/l (DL)-alpha-Lipoic acid 4.9456e-05 g/l Calcium D-(+)-pantothenate 4.9456e-05 g/l Nicotinic acid 4.9456e-05 g/l Riboflavin 4.9456e-05 g/l Thiamine HCl 4.9456e-05 g/l Folic acid 1.97824e-05 g/l Biotin 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 |
---|---|---|---|---|
43161 | positive | optimum | 30 | mesophilic |
43161 | positive | growth | 20-35 | |
24413 | positive | growth | 30 | mesophilic |
67770 | positive | growth | 30 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
43161 | positive | growth | 4.5-8.5 | alkaliphile |
43161 | positive | optimum | 6.0-7.0 |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
43161 | facultative anaerobe |
43161 | microaerophile |
nutrition type
@ref | type |
---|---|
43161 | chemoautotroph |
43161 | chemoheterotroph |
43161 | chemoorganoheterotroph |
43161 | chemolithoheterotroph |
spore formation
@ref | type of spore | spore formation | confidence |
---|---|---|---|
43161 | spore | no | |
69481 | no | 100 | |
69480 | no | 99.996 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
43161 | NaCl | positive | growth | 5-45 g/L |
43161 | NaCl | positive | optimum | 15-20 g/L |
observation
- @ref: 67770
- observation: quinones: Q-9, Q-8
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
43161 | 16094 | thiosulfate | + | electron donor |
43161 | 33403 | elemental sulfur | + | electron donor |
43161 | 16526 | carbon dioxide | + | carbon source |
43161 | 17632 | nitrate | + | electron acceptor |
43161 | 15379 | dioxygen | + | electron acceptor |
43161 | 29034 | ferric iron | + | electron acceptor |
43161 | 24996 | lactate | + | carbon source |
43161 | peptone | + | carbon source | |
43161 | tryptone | + | carbon source | |
43161 | casamino acids | + | carbon source | |
43161 | yeast extract | + | carbon source | |
43161 | 16947 | citrate | + | carbon source |
43161 | 15361 | pyruvate | + | carbon source |
43161 | 18050 | L-glutamine | + | carbon source |
antibiotic resistance
@ref | ChEBI | metabolite | is antibiotic | is sensitive | sensitivity conc. |
---|---|---|---|---|---|
43161 | 28971 | ampicillin | yes | yes | 100000 µg/mL |
43161 | 17698 | chloramphenicol | yes | yes | 100000 µg/mL |
43161 | 6104 | kanamycin | yes | yes | 100000 µg/mL |
43161 | 17076 | streptomycin | yes | yes | 100000 µg/mL |
enzymes
- @ref: 43161
- value: catalase
- activity: -
- ec: 1.11.1.6
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent | latitude | longitude | sampling date |
---|---|---|---|---|---|---|---|---|
24413 | sediment from a submarine coastal gas vent | Tyrrhenian Sea, Tor Caldara | Italy | ITA | Europe | 41.4858 | 12.5897 | |
43161 | surface sediment of an active shallow-water gas vent | Tor Caldara in the Tyrrhenian Sea, Italy | Italy | ITA | Europe | 41 | 12 | 2013-08 |
67770 | Sulfidic shallow-water marine gas vent located at Tor Caldara in the Tyrrhenian Sea | Italy | ITA | Europe |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Aquatic | #Marine |
#Environmental | #Aquatic | #Sediment |
#Environmental | #Terrestrial | #Coast |
taxonmaps
- @ref: 69479
- File name: preview.99_131186.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_430;96_51027;97_65734;98_87770;99_131186&stattab=map
- Last taxonomy: Varunaivibrio sulfuroxidans subclade
- 16S sequence: KU294728
- Sequence Identity:
- Total samples: 133
- soil counts: 11
- aquatic counts: 108
- animal counts: 10
- plant counts: 4
Safety information
risk assessment
- @ref: 24413
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 24413
- description: Varunaivibrio sulfuroxidans strain TC8 16S ribosomal RNA gene, partial sequence
- accession: KU294728
- length: 1360
- database: ena
- NCBI tax ID: 1773489
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Varunaivibrio sulfuroxidans strain DSM 101688 | 1773489.15 | wgs | patric | 1773489 |
66792 | Varunaivibrio sulfuroxidans DSM 101688 | 2784746782 | draft | img | 1773489 |
67770 | Varunaivibrio sulfuroxidans DSM 101688 | GCA_004341725 | contig | ncbi | 1773489 |
GC content
- @ref: 24413
- GC-content: 59.9
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | yes | 92.667 | yes |
gram-positive | no | 99.207 | no |
anaerobic | no | 93.336 | yes |
aerobic | no | 88.051 | yes |
halophile | no | 68.735 | no |
spore-forming | no | 93.528 | yes |
thermophile | yes | 60.562 | no |
glucose-util | yes | 61.615 | no |
flagellated | yes | 60.628 | no |
glucose-ferment | no | 89.664 | no |
External links
@ref: 24413
culture collection no.: DSM 101688, JCM 31027, TC 8
straininfo link
- @ref: 90938
- straininfo: 405343
literature
- topic: Phylogeny
- Pubmed-ID: 27298285
- title: Varunaivibrio sulfuroxidans gen. nov., sp. nov., a facultatively chemolithoautotrophic, mesophilic alphaproteobacterium from a shallow-water gas vent at Tor Caldara, Tyrrhenian Sea.
- authors: Patwardhan S, Vetriani C
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijsem.0.001235
- year: 2016
- mesh: Alphaproteobacteria/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Chemoautotrophic Growth, DNA, Bacterial/genetics, Hydrothermal Vents/*microbiology, Italy, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA
- topic2: Transcriptome
Reference
@id | authors | title | doi/url | catalogue | journal | pubmed |
---|---|---|---|---|---|---|
20215 | Parte, 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 DSMZ | 10.1099/ijsem.0.004332 | |||
24413 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-101688 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 101688) | |||
43161 | Sushmita Patwardhan and Costantino Vetriani | Varunaivibrio sulfuroxidans gen. nov., sp. nov., a facultatively chemolithoautotrophic, mesophilic alphaproteobacterium from a shallow-water gas vent at Tor Caldara, Tyrrhenian Sea | 10.1099/ijsem.0.001235 | IJSEM 66: 3579-3584 2016 | 27298285 | |
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |||
66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | 10.1093/nar/gkaa1025 | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
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. | MicrobeAtlas 1.0 beta | https://microbeatlas.org/ | |||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Predictions 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 | |||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | Predictions based on the model GenomeNet Sporulation v. 1 | 10.21203/rs.3.rs-2527258/v1 | |||
90938 | Reimer, 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 identifiers | 10.60712/SI-ID405343.1 |