Strain identifier
BacDive ID: 22961
Type strain: 
Species: Thiocapsa imhoffii
Strain history: <- M. T. Madigan, Dept. Microbiology, Southern Illinois Univ., Carbondale, USA; SC5 <- M. Asao
NCBI tax ID(s): 382777 (species)
version 8.1 (current version)
General
@ref: 19174
BacDive-ID: 22961
DSM-Number: 21303
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-negative
description: Thiocapsa imhoffii DSM 21303 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from Soap Lake.
NCBI tax id
- NCBI tax id: 382777
- Matching level: species
strain history
- @ref: 19174
- history: <- M. T. Madigan, Dept. Microbiology, Southern Illinois Univ., Carbondale, USA; SC5 <- M. Asao
doi: 10.13145/bacdive22961.20230509.8.1
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 imhoffii
- full scientific name: Thiocapsa imhoffii Asao et al. 2007
@ref: 19174
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Chromatiales
family: Chromatiaceae
genus: Thiocapsa
species: Thiocapsa imhoffii
full scientific name: Thiocapsa imhoffii Asao et al. 2007
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.998
multimedia
| @ref | multimedia content | caption | intellectual property rights |
|---|---|---|---|
| 66793 | EM_DSM_21303_1.jpg | electron microscopic image | © HZI/Manfred Rohde |
| 66793 | EM_DSM_21303_2.jpg | electron microscopic image | © HZI/Manfred Rohde |
| 66793 | EM_DSM_21303_3.jpg | electron microscopic image | © HZI/Manfred Rohde |
| 66793 | EM_DSM_21303_4.jpg | electron microscopic image | © HZI/Manfred Rohde |
| 66793 | EM_DSM_21303_5.jpg | electron microscopic image | © HZI/Manfred Rohde |
Culture and growth conditions
culture medium
- @ref: 19174
- name: 1/2 S° HELIORESTIS MEDIUM (DSMZ Medium 1381)
- growth: yes
- link: https://mediadive.dsmz.de/medium/1381
- composition: Name: ½ S° HELIORESTIS MEDIUM (DSMZ Medium 1381) Composition: Na2CO3 2.5 g/l NaHCO3 2.5 g/l Bicine 1.63 g/l Na-acetate 1.0 g/l Na-pyruvate 1.0 g/l KH2PO4 0.5 g/l NH4Cl 0.5 g/l Na2S2O3 x 5 H2O 0.5 g/l Na2S x 9 H2O 0.5 g/l MgSO4 x 7 H2O 0.2 g/l Yeast extract 0.1 g/l CaCl2 0.075 g/l EDTA 0.0052 g/l FeCl2 x 4 H2O 0.0015 g/l CoCl2 x 6 H2O 0.00019 g/l Na2MoO4 x 2 H2O 0.000188 g/l MnCl2 x 4 H2O 0.0001 g/l ZnCl2 7e-05 g/l VOSO4 x 2 H2O 3e-05 g/l NiCl2 x 6 H2O 2.5e-05 g/l Vitamin B12 2e-05 g/l CuCl2 x 2 H2O 1.7e-05 g/l H3BO3 6e-06 g/l NaHSeO3 2e-06 g/l Na2WO4 x 2 H2O 2e-06 g/l Distilled water
culture temp
- @ref: 19174
- growth: positive
- type: growth
- temperature: 28
- range: mesophilic
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 19174 | anaerobe | |
| 69480 | anaerobe | 97.776 |
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 99.988 |
Isolation, sampling and environmental information
isolation
- @ref: 19174
- sample type: Soap Lake
- geographic location: Central Washington State
- country: USA
- origin.country: USA
- continent: North America
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Lake (large) |
| #Condition | #Alkaline |
taxonmaps
- @ref: 69479
- File name: preview.99_119477.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_169;96_3627;97_60610;98_80552;99_119477&stattab=map
- Last taxonomy: Thiocapsa imhoffii subclade
- 16S sequence: DQ498828
- Sequence Identity:
- Total samples: 10
- soil counts: 2
- aquatic counts: 8
Sequence information
16S sequences
- @ref: 19174
- description: Thiocapsa imhoffii strain SC5 16S ribosomal RNA gene, partial sequence
- accession: DQ498828
- length: 1527
- database: ena
- NCBI tax ID: 382777
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Thiocapsa imhoffii DSM 21303 | GCA_016583985 | contig | ncbi | 382777 |
| 66792 | Thiocapsa imhoffii strain DSM 21303 | 382777.4 | wgs | patric | 382777 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| gram-positive | no | 99.011 | no |
| anaerobic | yes | 96.302 | yes |
| halophile | no | 74.428 | no |
| spore-forming | no | 92.814 | no |
| glucose-util | yes | 73.184 | no |
| aerobic | no | 94.335 | yes |
| motile | no | 84.706 | no |
| flagellated | no | 93.402 | no |
| thermophile | no | 98.795 | yes |
| glucose-ferment | no | 82.921 | no |
External links
@ref: 19174
culture collection no.: DSM 21303, SC 5
literature
- topic: Phylogeny
- Pubmed-ID: 17661016
- title: Thiocapsa imhoffii, sp. nov., an alkaliphilic purple sulfur bacterium of the family Chromatiaceae from Soap Lake, Washington (USA).
- authors: Asao M, Takaichi S, Madigan MT
- journal: Arch Microbiol
- DOI: 10.1007/s00203-007-0287-9
- year: 2007
- mesh: Adaptation, Physiological, Autotrophic Processes, Bacterial Typing Techniques, Ecosystem, Hydrogen-Ion Concentration, Phototrophic Processes, Phylogeny, RNA, Ribosomal, 16S/genetics, Thiocapsa/*classification/genetics/isolation & purification/physiology, Washington, Water Microbiology
- topic2: Enzymology
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 19174 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21303) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-21303 | |||
| 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) | |||
| 66793 | Mukherjee et al. | 10.1038/nbt.3886 | GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life | 35: 676-683 2017 | 28604660 | |
| 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 |