Strain identifier
BacDive ID: 4019
Type strain:
Species: Desulfocapsa sulfexigens
Strain Designation: SB164P1
Strain history: <- K. Finster, University of Aarhus, Department of Microbial Ecology, Denmark; SB164P1 <- K. Finster {1995}
NCBI tax ID(s): 1167006 (strain), 65555 (species)
General
@ref: 3963
BacDive-ID: 4019
DSM-Number: 10523
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-negative
description: Desulfocapsa sulfexigens SB164P1 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from oxidized surface sediment from eel grass mud flat.
NCBI tax id
NCBI tax id | Matching level |
---|---|
65555 | species |
1167006 | strain |
strain history
- @ref: 3963
- history: <- K. Finster, University of Aarhus, Department of Microbial Ecology, Denmark; SB164P1 <- K. Finster {1995}
doi: 10.13145/bacdive4019.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Deltaproteobacteria
- order: Desulfobacterales
- family: Desulfobulbaceae
- genus: Desulfocapsa
- species: Desulfocapsa sulfexigens
- full scientific name: Desulfocapsa sulfexigens corrig. Finster et al. 2000
synonyms
- @ref: 20215
- synonym: Desulfocapsa sulfoexigens
@ref: 3963
domain: Bacteria
phylum: Proteobacteria
class: Deltaproteobacteria
order: Desulfobacterales
family: Desulfobulbaceae
genus: Desulfocapsa
species: Desulfocapsa sulfexigens
full scientific name: Desulfocapsa sulfexigens Finster et al. 2000
strain designation: SB164P1
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.994
colony morphology
- @ref: 3963
- incubation period: >14 days
Culture and growth conditions
culture medium
- @ref: 3963
- name: DESULFOCAPSA SULFOEXIGENS MEDIUM (DSMZ Medium 196)
- growth: yes
- link: https://mediadive.dsmz.de/medium/196
- composition: Name: DESULFOCAPSA SULFEXIGENS MEDIUM (DSMZ Medium 196) Composition: NaCl 20.979 g/l Na2SO4 2.997 g/l MgCl2 x 6 H2O 2.997 g/l FeCl3 x 6 H2O 2.6973 g/l Na2S2O3 x 5 H2O 2.4975 g/l Na2CO3 1.4985 g/l KCl 0.4995 g/l NH4Cl 0.2997 g/l KH2PO4 0.199801 g/l CaCl2 x 2 H2O 0.14985 g/l HCl 0.0024975 g/l FeCl2 x 4 H2O 0.0014985 g/l CoCl2 x 6 H2O 0.00018981 g/l MnCl2 x 4 H2O 9.99001e-05 g/l ZnCl2 6.99301e-05 g/l Na2MoO4 x 2 H2O 3.5964e-05 g/l NiCl2 x 6 H2O 2.3976e-05 g/l H3BO3 5.99401e-06 g/l CuCl2 x 2 H2O 1.998e-06 g/l Distilled water
culture temp
- @ref: 3963
- growth: positive
- type: growth
- temperature: 25
- range: mesophilic
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance | confidence |
---|---|---|
3963 | anaerobe | |
69480 | anaerobe | 99.999 |
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.849 |
Isolation, sampling and environmental information
isolation
- @ref: 3963
- sample type: oxidized surface sediment from eel grass (Zostera noltii) mud flat
- host species: Zostera noltii
- geographic location: Arcachon basin
- country: France
- origin.country: FRA
- continent: Europe
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Terrestrial | #Mud (Sludge) |
#Environmental | #Aquatic | #Sediment |
#Host | #Algae |
Safety information
risk assessment
- @ref: 3963
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 3963
- description: Desulfocapsa sulfoexigens 16S rRNA gene, partial
- accession: Y13672
- length: 1482
- database: ena
- NCBI tax ID: 1167006
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Desulfocapsa sulfexigens DSM 10523 | GCA_000341395 | complete | ncbi | 1167006 |
66792 | Desulfocapsa sulfexigens DSM 10523 | 1167006.5 | complete | patric | 1167006 |
66792 | Desulfocapsa sulfexigens DSM 10523 | 1167006.13 | plasmid | patric | 1167006 |
66792 | Desulfocapsa sulfexigens DSM 10523 | 2561511172 | complete | img | 1167006 |
GC content
- @ref: 3963
- GC-content: 47.2
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | yes | 75.276 | no |
flagellated | no | 74.343 | no |
gram-positive | no | 99.245 | no |
anaerobic | yes | 98.676 | yes |
aerobic | no | 98.084 | yes |
halophile | no | 86.001 | no |
spore-forming | no | 93.819 | no |
glucose-util | no | 67.715 | no |
thermophile | no | 97.171 | yes |
glucose-ferment | no | 86.015 | no |
External links
@ref: 3963
culture collection no.: DSM 10523
straininfo link
- @ref: 73524
- straininfo: 48846
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Metabolism | 9435068 | Elemental sulfur and thiosulfate disproportionation by Desulfocapsa sulfoexigens sp. nov., a new anaerobic bacterium isolated from marine surface sediment. | Finster K, Liesack W, Thamdrup B | Appl Environ Microbiol | 10.1128/AEM.64.1.119-125.1998 | 1998 | Base Composition, DNA, Bacterial/analysis/genetics, Ferric Compounds, Ferritins/metabolism, Formates/metabolism, Geologic Sediments/*microbiology, Gram-Negative Anaerobic Bacteria/classification/genetics/*metabolism, Hydrogen Sulfide/metabolism, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sulfates/metabolism, Sulfides/metabolism, Sulfites/metabolism, Sulfur/*metabolism, Thiosulfates/*metabolism | Phylogeny |
Genetics | 23961312 | Complete genome sequence of Desulfocapsa sulfexigens, a marine deltaproteobacterium specialized in disproportionating inorganic sulfur compounds. | Finster KW, Kjeldsen KU, Kube M, Reinhardt R, Mussmann M, Amann R, Schreiber L | Stand Genomic Sci | 10.4056/sigs.3777412 | 2013 |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
3963 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 10523) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-10523 | |||
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 | |||
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 | |
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 | |||
73524 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID48846.1 | StrainInfo: A central database for resolving microbial strain identifiers |