Strain identifier
BacDive ID: 4129
Type strain:
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)
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
@ref | oxygen tolerance | confidence |
---|---|---|
4336 | anaerobe | |
69480 | anaerobe | 99.518 |
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.93 |
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
Cat1 | Cat2 | Cat3 |
---|---|---|
#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
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Desulfovibrio profundus DSM 11384 16S ribosomal RNA gene, partial sequence | AF418172 | 1547 | ena | 57320 |
20218 | Desulfovibrio profundus 16S ribosomal RNA gene, partial sequence | U90726 | 1366 | ena | 57320 |
4336 | Desulfovibrio profundus partial 16S rRNA gene, type strain DSM11384T | FR733706 | 1545 | ena | 57320 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Pseudodesulfovibrio profundus 500-1 | GCA_900217235 | complete | ncbi | 57320 |
66792 | Pseudodesulfovibrio profundus 500-1 | 2775506867 | complete | img | 57320 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
flagellated | yes | 55.514 | no |
gram-positive | no | 98.906 | no |
anaerobic | yes | 98.14 | yes |
aerobic | no | 97.564 | no |
halophile | no | 55.329 | no |
spore-forming | no | 94.412 | no |
thermophile | no | 92.392 | no |
glucose-util | no | 55.631 | no |
motile | yes | 90.194 | no |
glucose-ferment | no | 86.689 | no |
External links
@ref: 4336
culture collection no.: DSM 11384, MCCC 1A01905
straininfo link
- @ref: 73632
- straininfo: 49091
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 9103642 | Desulfovibrio 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 RJ | Int J Syst Bacteriol | 10.1099/00207713-47-2-515 | 1997 | Base 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/*metabolism | Metabolism |
Phylogeny | 27392787 | Pseudodesulfovibrio 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 K | Int J Syst Evol Microbiol | 10.1099/ijsem.0.001286 | 2016 | Bacterial 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 & purification | Enzymology |
Genetics | 29097459 | Genome 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 N | Genome Announc | 10.1128/genomeA.01181-17 | 2017 | Phylogeny |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
4336 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 11384) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-11384 | |||
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 | |||
20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
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) | |||
66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
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 | |||
73632 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID49091.1 | StrainInfo: A central database for resolving microbial strain identifiers |