Strain identifier
BacDive ID: 4126
Type strain:
Species: Halodesulfovibrio aestuarii
Strain Designation: W218
Strain history: <- M. J. E. C. van der Maarel, Univ. Groningen, The Netherlands; W218 <- M. J. E. C. van der Maarel {1994}
NCBI tax ID(s): 1121434 (strain), 126333 (species)
General
@ref: 3818
BacDive-ID: 4126
DSM-Number: 10141
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, motile
description: Halodesulfovibrio aestuarii W218 is an anaerobe, mesophilic, motile bacterium that was isolated from marine sediment.
NCBI tax id
NCBI tax id | Matching level |
---|---|
1121434 | strain |
126333 | species |
strain history
- @ref: 3818
- history: <- M. J. E. C. van der Maarel, Univ. Groningen, The Netherlands; W218 <- M. J. E. C. van der Maarel {1994}
doi: 10.13145/bacdive4126.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Deltaproteobacteria
- order: Desulfovibrionales
- family: Desulfovibrionaceae
- genus: Halodesulfovibrio
- species: Halodesulfovibrio aestuarii
- full scientific name: Halodesulfovibrio aestuarii (Postgate and Campbell 1966) Shivani et al. 2017
synonyms
@ref synonym 20215 Desulfovibrio desulfuricans subsp. aestuarii 20215 Desulfovibrio acrylicus
@ref: 3818
domain: Bacteria
phylum: Proteobacteria
class: Deltaproteobacteria
order: Desulfovibrionales
family: Desulfovibrionaceae
genus: Halodesulfovibrio
species: Halodesulfovibrio aestuarii
full scientific name: Halodesulfovibrio aestuarii (Postgate and Campbell 1966) Shivani et al. 2017
strain designation: W218
type strain: no
Morphology
cell morphology
@ref | motility | confidence | gram stain |
---|---|---|---|
69480 | yes | 94.856 | |
69480 | 99.997 | negative |
Culture and growth conditions
culture medium
- @ref: 3818
- name: DESULFOBACTER SP. MEDIUM (LACTATE) (DSMZ Medium 195c)
- growth: yes
- link: https://mediadive.dsmz.de/medium/195c
- composition: Name: DESULFOBACTER SP. MEDIUM (LACTATE) (DSMZ Medium 195c; with strain-specific modifications) Composition: NaCl 20.9372 g/l Na2SO4 2.99103 g/l MgCl2 x 6 H2O 2.99103 g/l Na-L-lactate 2.49252 g/l Na2CO3 1.49551 g/l Yeast extract 0.997009 g/l KCl 0.498504 g/l Na2S x 9 H2O 0.398804 g/l NH4Cl 0.299103 g/l KH2PO4 0.199402 g/l CaCl2 x 2 H2O 0.149551 g/l HCl 0.00249252 g/l FeCl2 x 4 H2O 0.00149551 g/l NaOH 0.000498504 g/l Sodium resazurin 0.000498504 g/l CoCl2 x 6 H2O 0.000189432 g/l Pyridoxine hydrochloride 9.97009e-05 g/l MnCl2 x 4 H2O 9.97009e-05 g/l ZnCl2 6.97906e-05 g/l Nicotinic acid 4.98504e-05 g/l (DL)-alpha-Lipoic acid 4.98504e-05 g/l Thiamine HCl 4.98504e-05 g/l Riboflavin 4.98504e-05 g/l p-Aminobenzoic acid 4.98504e-05 g/l Calcium D-(+)-pantothenate 4.98504e-05 g/l Na2MoO4 x 2 H2O 3.58923e-05 g/l NiCl2 x 6 H2O 2.39282e-05 g/l Folic acid 1.99402e-05 g/l Biotin 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
- @ref: 3818
- growth: positive
- type: growth
- temperature: 30
- range: mesophilic
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance | confidence |
---|---|---|
3818 | anaerobe | |
69480 | anaerobe | 99.999 |
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.985 |
Isolation, sampling and environmental information
isolation
- @ref: 3818
- sample type: marine sediment
- geographic location: Wadden Sea near Westernieland
- country: Netherlands
- origin.country: NLD
- continent: Europe
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Aquatic | #Marine |
#Environmental | #Aquatic | #Sediment |
taxonmaps
- @ref: 69479
- File name: preview.99_72810.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15981;96_2533;97_3094;98_3886;99_72810&stattab=map
- Last taxonomy: Halodesulfovibrio
- 16S sequence: U32578
- Sequence Identity:
- Total samples: 30
- soil counts: 2
- aquatic counts: 28
Safety information
risk assessment
- @ref: 3818
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 3818
- description: Desulfovibrio acrylicus 16S ribosomal RNA gene
- accession: U32578
- length: 1354
- database: ena
- NCBI tax ID: 1121434
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Halodesulfovibrio aestuarii DSM 10141 | GCA_000422525 | scaffold | ncbi | 1121434 |
66792 | Desulfovibrio acrylicus DSM 10141 | 1121434.3 | wgs | patric | 1121434 |
66792 | Halodesulfovibrio aestuarii DSM 10141 | 2524614816 | draft | img | 1121434 |
GC content
- @ref: 3818
- GC-content: 45.1
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | yes | 90.36 | no |
flagellated | yes | 58.939 | no |
gram-positive | no | 99.393 | no |
anaerobic | yes | 99.288 | no |
aerobic | no | 98.655 | yes |
halophile | no | 54.937 | no |
spore-forming | no | 95.166 | no |
glucose-util | no | 51.318 | no |
thermophile | no | 97.501 | yes |
glucose-ferment | no | 73.712 | no |
External links
@ref: 3818
culture collection no.: DSM 10141
straininfo link
- @ref: 73629
- straininfo: 48761
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 18398176 | Desulfovibrio psychrotolerans sp. nov., a psychrotolerant and moderately alkaliphilic sulfate-reducing deltaproteobacterium from the Himalayas. | Sasi Jyothsna TS, Sasikala Ch, Ramana ChV | Int J Syst Evol Microbiol | 10.1099/ijs.0.65402-0 | 2008 | Base Composition, DNA, Bacterial/chemistry/genetics, Desulfovibrio/classification/genetics/*isolation & purification/*metabolism, Fresh Water/microbiology, Genes, Bacterial, India, Molecular Sequence Data, Oxidation-Reduction, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sodium Chloride/metabolism, Species Specificity, Sulfates/metabolism, Terminology as Topic | Metabolism |
Phylogeny | 18842870 | Desulfovibrio marinisediminis sp. nov., a novel sulfate-reducing bacterium isolated from coastal marine sediment via enrichment with Casamino acids. | Takii S, Hanada S, Hase Y, Tamaki H, Uyeno Y, Sekiguchi Y, Matsuura K | Int J Syst Evol Microbiol | 10.1099/ijs.0.65750-0 | 2008 | Amino Acids/chemistry, Base Composition, DNA, Bacterial/genetics, Desulfovibrio/chemistry/*classification/*genetics/isolation & purification, Genes, Bacterial, Genes, rRNA, Geologic Sediments/*microbiology, Japan, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sulfates/metabolism, *Water Microbiology | Genetics |
Phylogeny | 20012196 | Desulfovibrio oceani subsp. oceani sp. nov., subsp. nov. and Desulfovibrio oceani subsp. galateae subsp. nov., novel sulfate-reducing bacteria isolated from the oxygen minimum zone off the coast of Peru. | Finster KW, Kjeldsen KU | Antonie Van Leeuwenhoek | 10.1007/s10482-009-9403-y | 2009 | Bacterial Typing Techniques, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Desulfovibrio/*classification/isolation & purification/*metabolism, Fatty Acids/analysis, Hydrogen-Ion Concentration, Locomotion, Molecular Sequence Data, Nucleic Acid Hybridization, Oxidation-Reduction, Pacific Ocean, Peru, Phylogeny, Quinones/analysis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, RNA, Untranslated/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Sodium Chloride/metabolism, Sulfates/*metabolism, Temperature | Metabolism |
Reference
@id | authors | catalogue | doi/url | title |
---|---|---|---|---|
3818 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 10141) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-10141 | |
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 | |
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 | |
73629 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID48761.1 | StrainInfo: A central database for resolving microbial strain identifiers |