Strain identifier

BacDive ID: 4177

Type strain: Yes

Species: Pseudodesulfovibrio piezophilus

Strain Designation: C1TLV30

Strain history: M.-L. Fardeau C1TLV30.

For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 15709

BacDive-ID: 4177

DSM-Number: 21447

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic

description: Pseudodesulfovibrio piezophilus C1TLV30 is an anaerobe, mesophilic bacterium that was isolated from wood falls on deep-sea sediments at a depth of 1693 m.

NCBI tax id

NCBI tax idMatching level
879567species
1322246strain

strain history

@refhistory
15709<- M. L. Fardeau, IRD/ESIL, Marseille, France; CITLV30
67770M.-L. Fardeau C1TLV30.

doi: 10.13145/bacdive4177.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Deltaproteobacteria
  • order: Desulfovibrionales
  • family: Desulfovibrionaceae
  • genus: Pseudodesulfovibrio
  • species: Pseudodesulfovibrio piezophilus
  • full scientific name: Pseudodesulfovibrio piezophilus (Khelaifia et al. 2011) Cao et al. 2016
  • synonyms

    • @ref: 20215
    • synonym: Desulfovibrio piezophilus

@ref: 15709

domain: Bacteria

phylum: Proteobacteria

class: Deltaproteobacteria

order: Desulfovibrionales

family: Desulfovibrionaceae

genus: Pseudodesulfovibrio

species: Pseudodesulfovibrio piezophilus

full scientific name: Pseudodesulfovibrio piezophilus (Khelaifia et al. 2011) Cao et al. 2016

strain designation: C1TLV30

type strain: yes

Culture and growth conditions

culture medium

  • @ref: 15709
  • name: MARINE DESULFOVIBRIO COMPLEX MEDIUM (DSMZ Medium 1040)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/1040
  • composition: Name: MARIDESULFOVIBRIO MEDIUM (DSMZ Medium 1040) Composition: Sea Salt 34.9301 g/l Na-DL-lactate 2.49501 g/l Yeast extract 0.998004 g/l Na2CO3 0.998004 g/l Na2S x 9 H2O 0.299401 g/l MgSO4 x 7 H2O 0.0299401 g/l NaCl 0.00998004 g/l MnSO4 x H2O 0.00499002 g/l (NH4)2Ni(SO4)2 x 6 H2O 0.00279441 g/l CoCl2 x 6 H2O 0.00179641 g/l ZnSO4 x 7 H2O 0.00179641 g/l CaCl2 x 2 H2O 0.000998004 g/l FeSO4 x 7 H2O 0.000998004 g/l Sodium resazurin 0.000499002 g/l AlK(SO4)2 x 12 H2O 0.000179641 g/l CuSO4 x 5 H2O 9.98004e-05 g/l H3BO3 9.98004e-05 g/l Na2MoO4 x 2 H2O 9.98004e-05 g/l Na2WO4 x 2 H2O 9.98004e-05 g/l Na2SeO4 9.98004e-05 g/l Pyridoxine hydrochloride 9.98004e-05 g/l (DL)-alpha-Lipoic acid 4.99002e-05 g/l Calcium D-(+)-pantothenate 4.99002e-05 g/l Nicotinic acid 4.99002e-05 g/l Riboflavin 4.99002e-05 g/l Thiamine HCl 4.99002e-05 g/l p-Aminobenzoic acid 4.99002e-05 g/l Folic acid 1.99601e-05 g/l Biotin 1.99601e-05 g/l Vitamin B12 9.98004e-07 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
15709positivegrowth28mesophilic
67770positivegrowth30mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 15709
  • oxygen tolerance: anaerobe

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitude
15709wood falls on deep-sea sediments at a depth of 1693 mMediterranean SeaEgyptEGYAfrica32.543630.355
67770Wood falls at a depth of 1,693 m in the Mediterranean SeaMediterranean Sea

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Environmental#Aquatic#Sediment
#Host Body Product#Plant#Timber

taxonmaps

  • @ref: 69479
  • File name: preview.99_7284.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_320;96_3407;97_4182;98_5343;99_7284&stattab=map
  • Last taxonomy: Pseudodesulfovibrio piezophilus subclade
  • 16S sequence: HM852532
  • Sequence Identity:
  • Total samples: 130
  • soil counts: 25
  • aquatic counts: 103
  • plant counts: 2

Safety information

risk assessment

  • @ref: 15709
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 15709
  • description: Desulfovibrio piezophilus strain C1TLV30 16S ribosomal RNA gene, partial sequence
  • accession: HM852532
  • length: 1539
  • database: ena
  • NCBI tax ID: 1322246

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudodesulfovibrio piezophilus C1TLV302540341170completeimg1322246
67770Pseudodesulfovibrio piezophilus C1TLV30 type strain: C1TLV30GCA_000341895chromosomencbi1322246

GC content

  • @ref: 15709
  • GC-content: 49.6
  • method: high performance liquid chromatography (HPLC)

External links

@ref: 15709

culture collection no.: DSM 21447, JCM 15486

straininfo link

  • @ref: 73677
  • straininfo: 63233

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny21169465Desulfovibrio piezophilus sp. nov., a piezophilic, sulfate-reducing bacterium isolated from wood falls in the Mediterranean Sea.Khelaifia S, Fardeau ML, Pradel N, Aussignargues C, Garel M, Tamburini C, Cayol JL, Gaudron S, Gaill F, Ollivier BInt J Syst Evol Microbiol10.1099/ijs.0.028670-02010Base Composition, Desulfovibrio/chemistry/*classification/genetics/*isolation & purification, Fatty Acids/metabolism, Geologic Sediments/*microbiology, Mediterranean Sea, Molecular Sequence Data, Oxidation-Reduction, Phylogeny, Seawater/*microbiology, Sodium Chloride/metabolism, Sulfates/*metabolismMetabolism
Metabolism23383081The first genomic and proteomic characterization of a deep-sea sulfate reducer: insights into the piezophilic lifestyle of Desulfovibrio piezophilus.Pradel N, Ji B, Gimenez G, Talla E, Lenoble P, Garel M, Tamburini C, Fourquet P, Lebrun R, Bertin P, Denis Y, Pophillat M, Barbe V, Ollivier B, Dolla APLoS One10.1371/journal.pone.00551302013Adaptation, Physiological/genetics, Amino Acids/metabolism, Atmospheric Pressure, Desulfovibrio/genetics/metabolism/*physiology, Energy Metabolism/genetics, Hydrostatic Pressure, Lipids/biosynthesis, Multigene Family/genetics, *Oceans and Seas, Oxidation-Reduction, *Pressure, *Proteomics, Species Specificity, Sulfates/*metabolismPhylogeny
Metabolism27264199Deciphering the adaptation strategies of Desulfovibrio piezophilus to hydrostatic pressure through metabolic and transcriptional analyses.Amrani A, van Helden J, Bergon A, Aouane A, Ben Hania W, Tamburini C, Loriod B, Imbert J, Ollivier B, Pradel N, Dolla AEnviron Microbiol Rep10.1111/1758-2229.124272016Acetyl Coenzyme A/metabolism, *Adaptation, Physiological, Desulfovibrio/*physiology, Energy Metabolism, Formates/metabolism, Gene Expression Profiling, Glutamic Acid/metabolism, Hydrogen/metabolism, *Hydrostatic Pressure, Lactates/metabolism, Mediterranean Sea, Metabolomics, Oxidation-Reduction, *Stress, Physiological
Phylogeny27392787Pseudodesulfovibrio indicus gen. nov., sp. nov., a piezophilic sulfate-reducing bacterium from the Indian Ocean and reclassification of four species of the genus Desulfovibrio.Cao J, Gayet N, Zeng X, Shao Z, Jebbar M, Alain KInt J Syst Evol Microbiol10.1099/ijsem.0.0012862016Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Desulfovibrio/*classification/genetics/isolation & purification, Fatty Acids/chemistry, Indian Ocean, Oxidation-Reduction, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sulfur-Reducing Bacteria/*classification/genetics/isolation & purificationEnzymology
Metabolism31655199Genome insights of mercury methylation among Desulfovibrio and Pseudodesulfovibrio strains.Goni-Urriza M, Klopp C, Ranchou-Peyruse M, Ranchou-Peyruse A, Monperrus M, Khalfaoui-Hassani B, Guyoneaud RRes Microbiol10.1016/j.resmic.2019.10.0032019Bacterial Proteins/genetics/metabolism, Desulfovibrio/classification/genetics/*metabolism, Desulfovibrionaceae/classification/genetics/*metabolism, Gene Expression Regulation, Bacterial, *Genome, Bacterial, Mercury/*metabolism, Methylation, PhylogenyPhylogeny

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
15709Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21447)https://www.dsmz.de/collection/catalogue/details/culture/DSM-21447
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
73677Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID63233.1StrainInfo: A central database for resolving microbial strain identifiers