Strain identifier

BacDive ID: 4129

Type strain: Yes

Species: Pseudodesulfovibrio profundus

Strain Designation: 500-1

Strain history: <- R. J. Parkes, University of Bristol, Department of Geology, United Kingdom; 500-1 <- S. J. Bale {1989}

NCBI tax ID(s): 57320 (species)

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

@ref: 4336

BacDive-ID: 4129

DSM-Number: 11384

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

description: Pseudodesulfovibrio profundus 500-1 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from marine sediment, 500 m below sea floor.

NCBI tax id

  • NCBI tax id: 57320
  • Matching level: species

strain history

  • @ref: 4336
  • history: <- R. J. Parkes, University of Bristol, Department of Geology, United Kingdom; 500-1 <- S. J. Bale {1989}

doi: 10.13145/bacdive4129.20230509.8.1

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 profundus
  • full scientific name: Pseudodesulfovibrio profundus (Bale et al. 1997) Cao et al. 2016
  • synonyms

    • @ref: 20215
    • synonym: Desulfovibrio profundus

@ref: 4336

domain: Bacteria

phylum: Proteobacteria

class: Deltaproteobacteria

order: Desulfovibrionales

family: Desulfovibrionaceae

genus: Pseudodesulfovibrio

species: Pseudodesulfovibrio profundus

full scientific name: Pseudodesulfovibrio profundus (Bale et al. 1997) Cao et al. 2016

strain designation: 500-1

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: negative
  • confidence: 99.99

Culture and growth conditions

culture medium

  • @ref: 4336
  • 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) 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 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 p-Aminobenzoic acid 4.98504e-05 g/l (DL)-alpha-Lipoic acid 4.98504e-05 g/l Thiamine HCl 4.98504e-05 g/l Calcium D-(+)-pantothenate 4.98504e-05 g/l Riboflavin 4.98504e-05 g/l Nicotinic acid 4.98504e-05 g/l Na2MoO4 x 2 H2O 3.58923e-05 g/l NiCl2 x 6 H2O 2.39282e-05 g/l Biotin 1.99402e-05 g/l Folic acid 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: 4336
  • growth: positive
  • type: growth
  • temperature: 30
  • range: mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
4336anaerobe
69480anaerobe99.518

spore formation

@refspore formationconfidence
69481no100
69480no99.93

Isolation, sampling and environmental information

isolation

  • @ref: 4336
  • sample type: marine sediment, 500 m below sea floor
  • geographic location: Japan Sea, ocean drilling program site 798B
  • country: Japan
  • origin.country: JPN
  • continent: Asia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Environmental#Aquatic#Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_114849.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_320;96_32694;97_41403;98_54028;99_114849&stattab=map
  • Last taxonomy: Pseudodesulfovibrio profundus subclade
  • 16S sequence: U90726
  • Sequence Identity:
  • Total samples: 278
  • soil counts: 10
  • aquatic counts: 239
  • animal counts: 29

Safety information

risk assessment

  • @ref: 4336
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Desulfovibrio profundus DSM 11384 16S ribosomal RNA gene, partial sequenceAF4181721547ena57320
20218Desulfovibrio profundus 16S ribosomal RNA gene, partial sequenceU907261366ena57320
4336Desulfovibrio profundus partial 16S rRNA gene, type strain DSM11384TFR7337061545ena57320

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudodesulfovibrio profundus 500-1GCA_900217235completencbi57320
66792Pseudodesulfovibrio profundus 500-12775506867completeimg57320

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedyes55.514no
gram-positiveno98.906no
anaerobicyes98.14yes
aerobicno97.564no
halophileno55.329no
spore-formingno94.412no
thermophileno92.392no
glucose-utilno55.631no
motileyes90.194no
glucose-fermentno86.689no

External links

@ref: 4336

culture collection no.: DSM 11384, MCCC 1A01905

straininfo link

  • @ref: 73632
  • straininfo: 49091

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny9103642Desulfovibrio profundus sp. nov., a novel barophilic sulfate-reducing bacterium from deep sediment layers in the Japan Sea.Bale SJ, Goodman K, Rochelle PA, Marchesi JR, Fry JC, Weightman AJ, Parkes RJInt J Syst Bacteriol10.1099/00207713-47-2-5151997Base Sequence, DNA Primers/genetics, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Desulfovibrio/*classification/genetics/*metabolism, Genes, Bacterial, Japan, Microscopy, Electron, Scanning, Molecular Sequence Data, Oxidation-Reduction, Phylogeny, Pressure, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Seawater/microbiology, Species Specificity, Sulfates/*metabolismMetabolism
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
Genetics29097459Genome Sequence of Piezophilic Bacterium Desulfovibrio profundus Strain 500-1, Isolated from a Deep Sediment Layer in the Japan Sea.Fouteau S, Guerin T, Magdelenat G, Roumagnac M, Bartoli M, Ollivier B, Dolla A, Barbe V, Pradel NGenome Announc10.1128/genomeA.01181-172017Phylogeny

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
4336Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 11384)https://www.dsmz.de/collection/catalogue/details/culture/DSM-11384
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
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
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
73632Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID49091.1StrainInfo: A central database for resolving microbial strain identifiers