Strain identifier

BacDive ID: 4126

Type strain: No

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}

For citation purpose refer to the digital object identifier (doi) of the current version.
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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 idMatching level
1121434strain
126333species

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

    @refsynonym
    20215Desulfovibrio desulfuricans subsp. aestuarii
    20215Desulfovibrio 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

@refmotilityconfidencegram stain
69480yes94.856
6948099.997negative

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

@refoxygen toleranceconfidence
3818anaerobe
69480anaerobe99.999

spore formation

@refspore formationconfidence
69481no100
69480no99.985

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

Cat1Cat2Cat3
#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

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Halodesulfovibrio aestuarii DSM 10141GCA_000422525scaffoldncbi1121434
66792Desulfovibrio acrylicus DSM 101411121434.3wgspatric1121434
66792Halodesulfovibrio aestuarii DSM 101412524614816draftimg1121434

GC content

  • @ref: 3818
  • GC-content: 45.1
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes90.36no
flagellatedyes58.939no
gram-positiveno99.393no
anaerobicyes99.288no
aerobicno98.655yes
halophileno54.937no
spore-formingno95.166no
glucose-utilno51.318no
thermophileno97.501yes
glucose-fermentno73.712no

External links

@ref: 3818

culture collection no.: DSM 10141

straininfo link

  • @ref: 73629
  • straininfo: 48761

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny18398176Desulfovibrio psychrotolerans sp. nov., a psychrotolerant and moderately alkaliphilic sulfate-reducing deltaproteobacterium from the Himalayas.Sasi Jyothsna TS, Sasikala Ch, Ramana ChVInt J Syst Evol Microbiol10.1099/ijs.0.65402-02008Base 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 TopicMetabolism
Phylogeny18842870Desulfovibrio 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 KInt J Syst Evol Microbiol10.1099/ijs.0.65750-02008Amino 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 MicrobiologyGenetics
Phylogeny20012196Desulfovibrio 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 KUAntonie Van Leeuwenhoek10.1007/s10482-009-9403-y2009Bacterial 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, TemperatureMetabolism

Reference

@idauthorscataloguedoi/urltitle
3818Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 10141)https://www.dsmz.de/collection/catalogue/details/culture/DSM-10141
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
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
73629Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID48761.1StrainInfo: A central database for resolving microbial strain identifiers