Strain identifier
BacDive ID: 2481
Type strain: 
Species: Thiocapsa marina
Strain Designation: 5811
Strain history: <- N. Pfennig, 5811 (Thiocapsa roseopersicina f. purpurea)
NCBI tax ID(s): 244573 (species)
version 9.1 (current version)
General
@ref: 2147
BacDive-ID: 2481
DSM-Number: 5653
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, Gram-negative, coccus-shaped
description: Thiocapsa marina 5811 is an anaerobe, Gram-negative, coccus-shaped bacterium that was isolated from marine sediment.
NCBI tax id
- NCBI tax id: 244573
- Matching level: species
strain history
- @ref: 2147
- history: <- N. Pfennig, 5811 (Thiocapsa roseopersicina f. purpurea)
doi: 10.13145/bacdive2481.20240916.9.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Chromatiales
- family: Chromatiaceae
- genus: Thiocapsa
- species: Thiocapsa marina
- full scientific name: Thiocapsa marina Caumette et al. 2004
@ref: 2147
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Chromatiales
family: Chromatiaceae
genus: Thiocapsa
species: Thiocapsa marina
full scientific name: Thiocapsa marina Caumette et al. 2004
strain designation: 5811
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell shape | motility | confidence |
|---|---|---|---|---|---|
| 30120 | negative | 2.3 µm | coccus-shaped | no | |
| 69480 | negative | 98 |
pigmentation
- @ref: 30120
- production: yes
Culture and growth conditions
culture medium
- @ref: 2147
- name: PFENNIG'S MEDIUM I (modified 1988, for purple sulfur bacteria) (DSMZ Medium 28)
- growth: yes
- link: https://mediadive.dsmz.de/medium/28
- composition: Name: PFENNIG'S MEDIUM I (DSMZ Medium 28) Composition: NaHCO3 1.5 g/l Na2S x 9 H2O 0.592592 g/l MgSO4 x 7 H2O 0.500001 g/l KCl 0.349999 g/l KH2PO4 0.349999 g/l Ammonium chloride 0.349999 g/l Pyruvic acid sodium salt 0.25 g/l Dextrose 0.25 g/l CaCl2 x 2 H2O 0.25 g/l Yeast extract 0.25 g/l Ammonium acetate 0.25 g/l Na2-EDTA 0.003 g/l Resazurin 0.00225 g/l FeSO4 x 7 H2O 0.0011 g/l Vitamin B12 0.001 g/l H3BO3 0.0003 g/l CoCl2 x 6 H2O 0.00019 g/l MnCl2 x 2 H2O 5e-05 g/l ZnCl2 4.2e-05 g/l NiCl2 x 6 H2O 2.4e-05 g/l Na2MoO4 x 2 H2O 1.8e-05 g/l CuCl2 x 2 H2O 2e-06 g/l Distilled water
culture temp
| @ref | growth | type | temperature |
|---|---|---|---|
| 2147 | positive | growth | 25 |
| 30120 | positive | optimum | 32.5 |
culture pH
- @ref: 30120
- ability: positive
- type: optimum
- pH: 7.3
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance |
|---|---|
| 2147 | anaerobe |
| 30120 | aerobe |
spore formation
- @ref: 69481
- spore formation: no
- confidence: 100
halophily
| @ref | salt | growth | tested relation | concentration |
|---|---|---|---|---|
| 30120 | NaCl | positive | growth | 0.0-8.0 % |
| 30120 | NaCl | positive | optimum | 1.5 % |
observation
- @ref: 30120
- observation: aggregates in chains
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 30120 | 30089 | acetate | + | carbon source |
| 30120 | 15740 | formate | + | carbon source |
| 30120 | 28757 | fructose | + | carbon source |
| 30120 | 17754 | glycerol | + | carbon source |
| 30120 | 24996 | lactate | + | carbon source |
| 30120 | 25115 | malate | + | carbon source |
| 30120 | 17272 | propionate | + | carbon source |
| 30120 | 15361 | pyruvate | + | carbon source |
| 30120 | 30031 | succinate | + | carbon source |
Isolation, sampling and environmental information
isolation
- @ref: 30120
- sample type: marine sediment
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Marine |
| #Environmental | #Aquatic | #Sediment |
taxonmaps
- @ref: 69479
- File name: preview.99_7824.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_169;96_3627;97_4456;98_5717;99_7824&stattab=map
- Last taxonomy: Thiocapsa
- 16S sequence: FM178270
- Sequence Identity:
- Total samples: 150
- soil counts: 33
- aquatic counts: 108
- animal counts: 6
- plant counts: 3
Safety information
risk assessment
- @ref: 2147
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | Thiocapsa marina partial 16S rRNA gene, type strain DSM 5653T | FM178270 | 1426 | nuccore | 244573 |
| 30120 | Thiocapsa marina 16S rRNA gene, strain 5811 | Y12301 | 1530 | nuccore | 768671 |
| 2147 | Thiocapsa marina 5811 16S ribosomal RNA gene, partial sequence | AF112998 | 1494 | nuccore | 768671 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Thiocapsa marina 5811 | GCA_000223985 | contig | ncbi | 768671 |
| 66792 | Thiocapsa marina 5811 | 768671.3 | wgs | patric | 768671 |
| 66792 | Thiocapsa marina 5811, DSM 5653 | 2508501107 | draft | img | 768671 |
GC content
- @ref: 30120
- GC-content: 62.7
Genome-based predictions
predictions
| @ref | trait | model | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 69481 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 100 | no |
| 69480 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 98 | yes |
| 69480 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | yes | 60.237 | no |
| 69480 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | no | 63.461 | no |
| 69480 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 87.444 | no |
| 69480 | thermophilic | thermophile | Ability to grow at temperatures above or equal to 45°C | no | 95.327 | no |
| 69480 | flagellated | motile2+ | Ability to perform flagellated movement | no | 61.264 | yes |
External links
@ref: 2147
culture collection no.: DSM 5653
straininfo link
- @ref: 72023
- straininfo: 41690
literature
- topic: Phylogeny
- Pubmed-ID: 15280266
- title: Thiocapsa marina sp. nov., a novel, okenone-containing, purple sulfur bacterium isolated from brackish coastal and marine environments.
- authors: Caumette P, Guyoneaud R, Imhoff JF, Suling J, Gorlenko V
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.02964-0
- year: 2004
- mesh: Anaerobiosis, Bacteriochlorophyll A/analysis, Base Composition, Carbon Dioxide/metabolism, Carotenoids/analysis, DNA, Bacterial/chemistry, DNA, Ribosomal/chemistry, Genes, rRNA, Geologic Sediments/microbiology, Hydrogen/metabolism, Hydrogen Sulfide/metabolism, Molecular Sequence Data, Movement, Nucleic Acid Hybridization, Organic Chemicals/metabolism, Phylogeny, Pigments, Biological/biosynthesis/physiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sulfur/metabolism, Thiocapsa/*classification/cytology/isolation & purification/physiology, Thiosulfates/metabolism, Water Microbiology
- topic2: Metabolism
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed | ID_cross_reference |
|---|---|---|---|---|---|---|---|
| 2147 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 5653) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-5653 | ||||
| 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 | ||
| 30120 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 28776041 | 26474 | ||
| 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) | ||||
| 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 | ||||
| 72023 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID41690.1 | StrainInfo: A central database for resolving microbial strain identifiers |