Strain identifier
BacDive ID: 23823
Type strain: 
Species: Sulfurospirillum sp.
Strain Designation: JPD-1
Strain history: <- J. Pietari, Univ. of Washington, Seattle, USA; JPD-1 <- J. M. H. Pietari {2000}
NCBI tax ID(s): 2053622 (species)
version 8.1 (current version)
General
@ref: 20848
BacDive-ID: 23823
DSM-Number: 16452
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, psychrophilic, motile
description: Sulfurospirillum sp. JPD-1 is an anaerobe, psychrophilic, motile bacterium that was isolated from contaminated soil.
NCBI tax id
- NCBI tax id: 2053622
- Matching level: species
strain history
- @ref: 20848
- history: <- J. Pietari, Univ. of Washington, Seattle, USA; JPD-1 <- J. M. H. Pietari {2000}
doi: 10.13145/bacdive23823.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Epsilonproteobacteria
- order: Campylobacterales
- family: Campylobacteraceae
- genus: Sulfurospirillum
- species: Sulfurospirillum sp.
- full scientific name: Sulfurospirillum Schumacher et al. 1993
synonyms
- @ref: 20215
- synonym: Dehalospirillum
@ref: 20848
domain: Bacteria
phylum: Proteobacteria
class: Epsilonproteobacteria
order: Campylobacterales
family: Campylobacteraceae
genus: Sulfurospirillum
species: Sulfurospirillum sp.
full scientific name: Sulfurospirillum sp.
strain designation: JPD-1
type strain: no
Morphology
cell morphology
| @ref | motility | confidence | gram stain |
|---|---|---|---|
| 69480 | yes | 94.17 | |
| 69480 | 99.999 | negative |
colony morphology
- @ref: 20848
- incubation period: 2-3 days
Culture and growth conditions
culture medium
- @ref: 20848
- name: DESULFITOBACTERIUM (PCE II) MEDIUM (DSMZ Medium 1062)
- growth: yes
- link: https://mediadive.dsmz.de/medium/1062
- composition: Name: DESULFITOBACTERIUM (PCE II) MEDIUM (DSMZ Medium 1062) Composition: Na2-fumarate 6.42928 g/l Na-pyruvate 4.45104 g/l Yeast extract 1.97824 g/l Na2CO3 1.48368 g/l KCl 0.49456 g/l MgCl2 x 6 H2O 0.395648 g/l NH4Cl 0.24728 g/l KH2PO4 0.197824 g/l MgSO4 x 7 H2O 0.0296736 g/l FeSO4 x 7 H2O 0.0217606 g/l Nitrilotriacetic acid 0.0148368 g/l NaCl 0.0098912 g/l MnSO4 x H2O 0.0049456 g/l CoSO4 x 7 H2O 0.00178042 g/l ZnSO4 x 7 H2O 0.00178042 g/l CaCl2 x 2 H2O 0.00098912 g/l Sodium resazurin 0.00049456 g/l NiCl2 x 6 H2O 0.000296736 g/l Pyridoxine hydrochloride 0.000296736 g/l Thiamine-HCl x 2 H2O 0.000197824 g/l AlK(SO4)2 x 12 H2O 0.000197824 g/l Nicotinic acid 0.000197824 g/l CuSO4 x 5 H2O 9.8912e-05 g/l Calcium pantothenate 9.8912e-05 g/l Vitamin B12 9.8912e-05 g/l Na2MoO4 x 2 H2O 9.8912e-05 g/l H3BO3 9.8912e-05 g/l p-Aminobenzoic acid 7.91296e-05 g/l D-(+)-biotin 1.97824e-05 g/l Na2WO4 x 2 H2O 3.95648e-06 g/l Na2SeO3 x 5 H2O 2.96736e-06 g/l Distilled water
culture temp
- @ref: 20848
- growth: positive
- type: growth
- temperature: 20
- range: psychrophilic
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 20848 | anaerobe | |
| 69480 | anaerobe | 98.65 |
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 99.988 |
Isolation, sampling and environmental information
isolation
- @ref: 20848
- sample type: contaminated soil
- geographic location: Washington, Tacoma
- country: USA
- origin.country: USA
- continent: North America
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Engineered | #Contamination | |
| #Environmental | #Terrestrial | #Soil |
taxonmaps
- @ref: 69479
- File name: preview.99_73815.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_283;96_1116;97_1309;98_1939;99_73815&stattab=map
- Last taxonomy: Sulfurospirillum
- 16S sequence: AY189928
- Sequence Identity:
- Total samples: 274
- soil counts: 48
- aquatic counts: 203
- animal counts: 22
- plant counts: 1
Sequence information
16S sequences
- @ref: 20848
- description: Sulfurospirillum sp. JPD-1 16S ribosomal RNA gene, partial sequence
- accession: AY189928
- length: 1415
- database: ena
- NCBI tax ID: 220622
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Sulfurospirillum diekertiae JPD-1 | GCA_002309535 | complete | ncbi | 1854492 |
| 66792 | Sulfurospirillum sp. JPD-1 | 220622.7 | complete | patric | 220622 |
| 66792 | Sulfurospirillum sp. JPD-1 | 2775506916 | complete | img | 220622 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| flagellated | yes | 73.514 | no |
| gram-positive | no | 98.369 | no |
| anaerobic | yes | 93.851 | no |
| aerobic | no | 97.377 | yes |
| halophile | no | 93.264 | no |
| spore-forming | no | 93.097 | no |
| glucose-util | no | 77.292 | no |
| thermophile | no | 99.386 | yes |
| motile | yes | 87.667 | no |
| glucose-ferment | no | 84.54 | no |
External links
@ref: 20848
culture collection no.: DSM 16452, ATCC BAA 971
straininfo link
- @ref: 87849
- straininfo: 406411
Reference
| @id | authors | title | doi/url | catalogue |
|---|---|---|---|---|
| 20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | 10.1099/ijsem.0.004332 | |
| 20848 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-16452 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16452) | |
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |
| 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. | MicrobeAtlas 1.0 beta | https://microbeatlas.org/ | |
| 69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |
| 69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | Predictions based on the model GenomeNet Sporulation v. 1 | 10.21203/rs.3.rs-2527258/v1 | |
| 87849 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | StrainInfo: A central database for resolving microbial strain identifiers | 10.60712/SI-ID406411.1 |