Strain identifier

BacDive ID: 4142

Type strain: Yes

Species: Maridesulfovibrio hydrothermalis

Strain Designation: AM13, AM13cf, H7

Strain history: CIP <- 2001, JL Garcia, IRD, Marseille, France: strain H7 <- D. Alazard: strain AM13

NCBI tax ID(s): 191026 (species)

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

@ref: 5513

BacDive-ID: 4142

DSM-Number: 14728

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-negative

description: Maridesulfovibrio hydrothermalis AM13 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from deep-sea hydrothermal chimney wall-2600 m.

NCBI tax id

  • NCBI tax id: 191026
  • Matching level: species

strain history

@refhistory
5513<- J.-L. Garcia, Universités de Provence et de la Méditerranée, ESIL, Marseille, France; AM13cf <- D. Alazard {2000}
120012CIP <- 2001, JL Garcia, IRD, Marseille, France: strain H7 <- D. Alazard: strain AM13

doi: 10.13145/bacdive4142.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Deltaproteobacteria
  • order: Desulfovibrionales
  • family: Desulfovibrionaceae
  • genus: Maridesulfovibrio
  • species: Maridesulfovibrio hydrothermalis
  • full scientific name: Maridesulfovibrio hydrothermalis (Alazard et al. 2003) Waite et al. 2020
  • synonyms

    • @ref: 20215
    • synonym: Desulfovibrio hydrothermalis

@ref: 5513

domain: Bacteria

phylum: Proteobacteria

class: Deltaproteobacteria

order: Desulfovibrionales

family: Desulfovibrionaceae

genus: Maridesulfovibrio

species: Maridesulfovibrio hydrothermalis

full scientific name: Maridesulfovibrio hydrothermalis (Alazard et al. 2003) Waite et al. 2020

strain designation: AM13, AM13cf, H7

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480negative99.994
120012negativerod-shapedno

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5513DESULFOBACTER SP. MEDIUM (LACTATE) (DSMZ Medium 195c)yeshttps://mediadive.dsmz.de/medium/195cName: 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 KCl 0.498504 g/l Na-acetate 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 MnCl2 x 4 H2O 9.97009e-05 g/l Pyridoxine hydrochloride 9.97009e-05 g/l ZnCl2 6.97906e-05 g/l Riboflavin 4.98504e-05 g/l Nicotinic acid 4.98504e-05 g/l (DL)-alpha-Lipoic acid 4.98504e-05 g/l Calcium D-(+)-pantothenate 4.98504e-05 g/l Thiamine HCl 4.98504e-05 g/l p-Aminobenzoic acid 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
35429MEDIUM 401 - for Desulfovibrio hydrothermalisyesDistilled water make up to (1000.000 ml);Sodium chloride (25.000 g);Potassium chloride (0.200 g);Magnesium chloride hexahydrate (3.000 g);Calcium chloride dihydrate(0.100 g);Sodium sulphate (3.160 g);Yeast extract (0.500 g);Potassium di-hydrogen phosphate
120012CIP Medium 401yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=401

culture temp

@refgrowthtypetemperaturerange
5513positivegrowth35mesophilic
35429positivegrowth30mesophilic
120012positivegrowth30mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
5513anaerobe
69480anaerobe100

spore formation

@refspore formationconfidence
69481no100
69480no99.921

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryisolation date
5513deep-sea hydrothermal chimney wall-2600 mPacific Ocean, 13°N East Pacific Rise
120012Environment, Hydrothermal ventPacific Ocean2001

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Hydrothermal vent
#Environmental#Aquatic#Marine
#Condition#Thermophilic (>45°C)

taxonmaps

  • @ref: 69479
  • File name: preview.99_3970.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_320;96_2018;97_2430;98_3006;99_3970&stattab=map
  • Last taxonomy: Maridesulfovibrio hydrothermalis subclade
  • 16S sequence: AF458778
  • Sequence Identity:
  • Total samples: 521
  • soil counts: 24
  • aquatic counts: 450
  • animal counts: 40
  • plant counts: 7

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
55131Risk group (German classification)
1200121Risk group (French classification)

Sequence information

16S sequences

  • @ref: 5513
  • description: Desulfovibrio hydrothermalis 16S ribosomal RNA gene, partial sequence
  • accession: AF458778
  • length: 1535
  • database: ena
  • NCBI tax ID: 1121451

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Maridesulfovibrio hydrothermalis AM13 = DSM 14728GCA_000331025chromosomencbi1121451
66792Maridesulfovibrio hydrothermalis AM13 = DSM 14728GCA_000425245scaffoldncbi1121451
66792Desulfovibrio hydrothermalis AM13 = DSM 147281121451.5wgspatric1121451
66792Desulfovibrio hydrothermalis AM13 = DSM 147281121451.9plasmidpatric1121451
66792Desulfovibrio hydrothermalis AM13 = DSM 147281121451.3completepatric1121451
66792Desulfovibrio hydrothermalis AM13, DSM 147282648501899draftimg1121451
66792Desulfovibrio hydrothermalis AM13, DSM 147282523533539draftimg1121451

GC content

  • @ref: 5513
  • GC-content: 47±0.5
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes90.482no
flagellatedyes62.289no
gram-positiveno99.3no
anaerobicyes99.268yes
aerobicno98.784yes
halophileno70.037no
spore-formingno93.585no
thermophileno94.173no
glucose-utilno55.96no
glucose-fermentno71.017no

External links

@ref: 5513

culture collection no.: DSM 14728, CIP 107303

straininfo link

  • @ref: 73645
  • straininfo: 100629

literature

  • topic: Phylogeny
  • Pubmed-ID: 12656169
  • title: Desulfovibrio hydrothermalis sp. nov., a novel sulfate-reducing bacterium isolated from hydrothermal vents.
  • authors: Alazard D, Dukan S, Urios A, Verhe F, Bouabida N, Morel F, Thomas P, Garcia JL, Ollivier B
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.02323-0
  • year: 2003
  • mesh: DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Desulfovibrio/*classification/genetics/*isolation & purification/metabolism, Hot Temperature, Hydrostatic Pressure, Molecular Sequence Data, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Seawater/microbiology
  • topic2: Stress

Reference

@idauthorscataloguedoi/urltitle
5513Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 14728)https://www.dsmz.de/collection/catalogue/details/culture/DSM-14728
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
35429Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/4723
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
73645Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID100629.1StrainInfo: A central database for resolving microbial strain identifiers
120012Curators of the CIPCollection of Institut Pasteur (CIP 107303)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107303