Strain identifier
BacDive ID: 4149
Type strain: 
Species: Paucidesulfovibrio gracilis
Strain Designation: SRL6146
Strain history: <- M. Magot, Université de Pau et des Pays de l'Adour, IBEAS, Pau, France; SRL6146 <- M. Magot {1991}
NCBI tax ID(s): 1121449 (strain), 47158 (species)
version 8.1 (current version)
General
@ref: 6279
BacDive-ID: 4149
DSM-Number: 16080
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, moderately halophilic, mesophilic, rod-shaped
description: Paucidesulfovibrio gracilis SRL6146 is an anaerobe, moderately halophilic, mesophilic bacterium that was isolated from oil pipeline water.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 1121449 | strain |
| 47158 | species |
strain history
- @ref: 6279
- history: <- M. Magot, Université de Pau et des Pays de l'Adour, IBEAS, Pau, France; SRL6146 <- M. Magot {1991}
doi: 10.13145/bacdive4149.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Deltaproteobacteria
- order: Desulfovibrionales
- family: Desulfovibrionaceae
- genus: Paucidesulfovibrio
- species: Paucidesulfovibrio gracilis
- full scientific name: Paucidesulfovibrio gracilis (Magot et al. 2004) Waite et al. 2020
synonyms
- @ref: 20215
- synonym: Desulfovibrio gracilis
@ref: 6279
domain: Bacteria
phylum: Proteobacteria
class: Deltaproteobacteria
order: Desulfovibrionales
family: Desulfovibrionaceae
genus: Paucidesulfovibrio
species: Paucidesulfovibrio gracilis
full scientific name: Paucidesulfovibrio gracilis (Magot et al. 2004) Waite et al. 2020
strain designation: SRL6146
type strain: yes
Morphology
cell morphology
| @ref | cell shape | gram stain | cell length | cell width | motility | flagellum arrangement | confidence |
|---|---|---|---|---|---|---|---|
| 23373 | rod-shaped | ||||||
| 23373 | vibrio-shaped | ||||||
| 23373 | curved-shaped | negative | 4.5-9.0 µm | 0.3 µm | yes | polar | |
| 69480 | yes | 94.546 | |||||
| 69480 | negative | 99.996 |
colony morphology
- @ref: 23373
- colony color: grey to dark grey
Culture and growth conditions
culture medium
- @ref: 6279
- name: DESULFOVIBRIO HALOPHILUS MEDIUM (DSMZ Medium 496)
- growth: yes
- link: https://mediadive.dsmz.de/medium/496
- composition: Name: PSEUDODESULFOVIBRIO MEDIUM (DSMZ Medium 496) Composition: NaCl 69.7907 g/l Na2SO4 2.99102 g/l MgCl2 x 6 H2O 2.99102 g/l Na-L-lactate 2.49252 g/l Na2CO3 0.997009 g/l KCl 0.498505 g/l Na2S x 9 H2O 0.398804 g/l NH4Cl 0.299102 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 Sodium resazurin 0.000498505 g/l NaOH 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 (DL)-alpha-Lipoic acid 4.98504e-05 g/l p-Aminobenzoic acid 4.98504e-05 g/l Calcium D-(+)-pantothenate 4.98504e-05 g/l Nicotinic acid 4.98504e-05 g/l Riboflavin 4.98504e-05 g/l Thiamine HCl 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 | growth | type | temperature | range |
|---|---|---|---|---|
| 6279 | positive | growth | 37 | mesophilic |
| 23373 | positive | growth | 20-40 | |
| 23373 | positive | optimum | 37-40 |
culture pH
| @ref | ability | type | pH |
|---|---|---|---|
| 23373 | positive | growth | 5.4-8.4 |
| 23373 | positive | optimum | 6.8-7.2 |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 6279 | anaerobe | |
| 23373 | anaerobe | |
| 69480 | anaerobe | 99.999 |
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 23373 | no | |
| 69481 | no | 100 |
| 69480 | no | 98.806 |
halophily
| @ref | halophily level | salt | growth | tested relation | concentration |
|---|---|---|---|---|---|
| 23373 | moderately halophilic | NaCl | positive | growth | 20-120 g/L |
| 23373 | NaCl | positive | optimum | 50-60 g/L |
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 23373 | 17632 | nitrate | - | electron acceptor |
| 23373 | 15356 | cysteine | - | fermentation |
| 23373 | 28757 | fructose | - | fermentation |
| 23373 | 29806 | fumarate | - | fermentation |
| 23373 | 17234 | glucose | - | fermentation |
| 23373 | 17754 | glycerol | - | fermentation |
| 23373 | 24996 | lactate | - | fermentation |
| 23373 | 25115 | malate | - | fermentation |
| 23373 | 15361 | pyruvate | - | fermentation |
| 23373 | 30031 | succinate | - | fermentation |
| 23373 | 33403 | elemental sulfur | + | electron acceptor |
| 23373 | 29806 | fumarate | + | electron acceptor |
| 23373 | 16189 | sulfate | + | electron acceptor |
| 23373 | 17359 | sulfite | + | electron acceptor |
| 23373 | 16094 | thiosulfate | + | electron acceptor |
| 23373 | 24996 | lactate | + | growth |
| 23373 | 15361 | pyruvate | + | growth |
| 23373 | 24996 | lactate | + | oxidation |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 6279 | oil pipeline water | Emeraude oilfield | Republic of the Congo | COG | Africa |
| 23373 | from oilfield production water collected at the E153 wellhead of Emeraude Oilfield |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Engineered | #Industrial | #Machines and devices |
| #Environmental | #Aquatic | |
| #Engineered | #Industrial | #Engineered product |
| #Engineered | #Industrial | #Oil reservoir |
taxonmaps
- @ref: 69479
- File name: preview.99_3858.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_428;96_1980;97_2381;98_2940;99_3858&stattab=map
- Last taxonomy: Desulfovibrio gracilis
- 16S sequence: U53464
- Sequence Identity:
- Total samples: 138
- soil counts: 13
- aquatic counts: 103
- animal counts: 21
- plant counts: 1
Safety information
risk assessment
- @ref: 6279
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 23373 | Desulfovibrio gracilis strain SEBR 6116 16S ribosomal RNA gene, complete sequence | U53464 | 1449 | nuccore | 47158 |
| 6279 | Zea mays cultivar PI221733 starch debranching enzyme I (sbe1) gene, upstream region | AY453464 | 339 | ena | 4577 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Paucidesulfovibrio gracilis DSM 16080 | GCA_900167125 | contig | ncbi | 1121449 |
| 66792 | Desulfovibrio gracilis DSM 16080 strain DSM 16080 | 1121449.4 | wgs | patric | 1121449 |
| 66792 | Desulfovibrio gracilis DSM 16080 | 2568526008 | draft | img | 1121449 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 6279 | 59 | high performance liquid chromatography (HPLC) |
| 23368 | 59.0 | |
| 23368 | 62.4 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| motile | yes | 92.166 | yes |
| flagellated | yes | 52.974 | no |
| gram-positive | no | 99.527 | yes |
| anaerobic | yes | 99.05 | yes |
| aerobic | no | 98.695 | yes |
| halophile | yes | 59.628 | yes |
| spore-forming | no | 94.729 | yes |
| thermophile | no | 69.159 | no |
| glucose-util | no | 66.382 | no |
| glucose-ferment | no | 90.186 | yes |
External links
@ref: 6279
culture collection no.: DSM 16080, ATCC BAA 904
straininfo link
- @ref: 73650
- straininfo: 134286
literature
- topic: Phylogeny
- Pubmed-ID: 15388730
- title: Desulfovibrio bastinii sp. nov. and Desulfovibrio gracilis sp. nov., moderately halophilic, sulfate-reducing bacteria isolated from deep subsurface oilfield water.
- authors: Magot M, Basso O, Tardy-Jacquenod C, Caumette P
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.02977-0
- year: 2004
- mesh: Anti-Bacterial Agents/pharmacology, Bacterial Typing Techniques, Congo, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Desulfovibrio/*classification/cytology/*isolation & purification/physiology, Genes, rRNA, Hydrogen-Ion Concentration, Microscopy, Phase-Contrast, Molecular Sequence Data, Movement, Nucleic Acid Hybridization, Oxidation-Reduction, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Saline Solution, Hypertonic/pharmacology, Sequence Analysis, DNA, Sulfates/*metabolism, Temperature, Water Microbiology
- topic2: Enzymology
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 6279 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16080) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-16080 | |||
| 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 | |||
| 23368 | Nurettin Sahin, Akio Tani, Recep Kotan, Ivo Sedlácek, Kazuhide Kimbara, Abdurrahman U. Tamer | 10.1099/ijs.0.026138-0 | Pandoraea oxalativorans sp. nov., Pandoraea faecigallinarum sp. nov. and Pandoraea vervacti sp. nov., isolated from oxalate-enriched culture | IJSEM 61: 2247-2253 2011 | 20952546 | |
| 23373 | Michel Magot, Odile Basso, Christèle Tardy-Jacquenod, Pierre Caumette | 10.1099/ijs.0.02977-0 | Desulfovibrio bastinii sp. nov. and Desulfovibrio gracilis sp. nov., moderately halophilic, sulfate-reducing bacteria isolated from deep subsurface oilfield water | IJSEM 54: 1693-1697 2004 | 15388730 | |
| 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 | |||
| 73650 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID134286.1 | StrainInfo: A central database for resolving microbial strain identifiers |