Strain identifier

BacDive ID: 4019

Type strain: Yes

Species: Desulfocapsa sulfexigens

Strain Designation: SB164P1

Strain history: <- K. Finster, University of Aarhus, Department of Microbial Ecology, Denmark; SB164P1 <- K. Finster {1995}

For citation purpose refer to the digital object identifier (doi) of the current version.
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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 idMatching level
65555species
1167006strain

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

@refoxygen toleranceconfidence
3963anaerobe
69480anaerobe99.999

spore formation

@refspore formationconfidence
69481no100
69480no99.849

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

Cat1Cat2Cat3
#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

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Desulfocapsa sulfexigens DSM 10523GCA_000341395completencbi1167006
66792Desulfocapsa sulfexigens DSM 105231167006.5completepatric1167006
66792Desulfocapsa sulfexigens DSM 105231167006.13plasmidpatric1167006
66792Desulfocapsa sulfexigens DSM 105232561511172completeimg1167006

GC content

  • @ref: 3963
  • GC-content: 47.2
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes75.276no
flagellatedno74.343no
gram-positiveno99.245no
anaerobicyes98.676yes
aerobicno98.084yes
halophileno86.001no
spore-formingno93.819no
glucose-utilno67.715no
thermophileno97.171yes
glucose-fermentno86.015no

External links

@ref: 3963

culture collection no.: DSM 10523

straininfo link

  • @ref: 73524
  • straininfo: 48846

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Metabolism9435068Elemental sulfur and thiosulfate disproportionation by Desulfocapsa sulfoexigens sp. nov., a new anaerobic bacterium isolated from marine surface sediment.Finster K, Liesack W, Thamdrup BAppl Environ Microbiol10.1128/AEM.64.1.119-125.19981998Base 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/*metabolismPhylogeny
Genetics23961312Complete 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 LStand Genomic Sci10.4056/sigs.37774122013

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
3963Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 10523)https://www.dsmz.de/collection/catalogue/details/culture/DSM-10523
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
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
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
73524Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID48846.1StrainInfo: A central database for resolving microbial strain identifiers