Strain identifier
BacDive ID: 3841
Type strain: 
Species: Deferribacter desulfuricans
Strain Designation: SSM1
Strain history: K. Takai SSM1.
NCBI tax ID(s): 197162 (species)
version 8.1 (current version)
General
@ref: 5537
BacDive-ID: 3841
DSM-Number: 14783
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, heterotroph, thermophilic, Gram-negative, rod-shaped
description: Deferribacter desulfuricans SSM1 is an anaerobe, heterotroph, thermophilic bacterium that was isolated from black smoker chimney, 1385 m depth.
NCBI tax id
- NCBI tax id: 197162
- Matching level: species
strain history
| @ref | history |
|---|---|
| 5537 | <- K. Takai, Subground Animalcule Retrieval (SUGAR) Program, Japan Agency for Marine-Earth Science and Technology (JAMSTEC); SSM1 <- K. Takai {2000} |
| 67770 | K. Takai SSM1. |
doi: 10.13145/bacdive3841.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/deferribacterota
- domain: Bacteria
- phylum: Deferribacterota
- class: Deferribacteres
- order: Deferribacterales
- family: Deferribacteraceae
- genus: Deferribacter
- species: Deferribacter desulfuricans
- full scientific name: Deferribacter desulfuricans Takai et al. 2003
@ref: 5537
domain: Bacteria
phylum: Deferribacteres
class: Deferribacteres
order: Deferribacterales
family: Deferribacteraceae
genus: Deferribacter
species: Deferribacter desulfuricans
full scientific name: Deferribacter desulfuricans Takai et al. 2003
strain designation: SSM1
type strain: yes
Morphology
cell morphology
- @ref: 23104
- gram stain: negative
- cell length: 1.5-2.5 µm
- cell width: 0.3-0.7 µm
- cell shape: rod-shaped
- motility: no
Culture and growth conditions
culture medium
- @ref: 5537
- name: DEFERRIBACTER DESULFURICANS MEDIUM (DSMZ Medium 935a)
- growth: yes
- link: https://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium935a.pdf
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 5537 | positive | growth | 62 | thermophilic |
| 23104 | positive | growth | 40.0-70.0 | thermophilic |
| 23104 | positive | optimum | 60.0-65.0 | thermophilic |
| 67770 | positive | growth | 62 | thermophilic |
culture pH
| @ref | ability | type | pH |
|---|---|---|---|
| 23104 | positive | growth | 5.0-7.5 |
| 23104 | positive | optimum | 6.5 |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance |
|---|---|
| 5537 | anaerobe |
| 23104 | obligate anaerobe |
nutrition type
- @ref: 23104
- type: heterotroph
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent | latitude | longitude | enrichment culture | enrichment culture composition |
|---|---|---|---|---|---|---|---|---|---|
| 5537 | black smoker chimney, 1385 m depth | Suiyo Seamount, Izu-Bonin Arc | Japan | JPN | Asia | 28.5667 | 140.633 | ||
| 23104 | deep-sea hydrothermal vent chimney at the Suiyo Seamount | Izu-Bonin Arc | Japan | JPN | Asia | 28.5714 | 140.644 | MJNS medium | supplemented with 0.1 % (w/v) yeast extract and 0.1 % (w/v) tryptone |
| 67770 | Deep-sea hydrothermal vent chimney at the Suiyo Seamount in the Izu-Bonin Arc | Japan | JPN | Asia |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Hydrothermal vent |
| #Condition | #Thermophilic (>45°C) |
taxonmaps
- @ref: 69479
- File name: preview.99_5380.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_16611;96_2608;97_3193;98_4010;99_5380&stattab=map
- Last taxonomy: Deferribacter
- 16S sequence: JQ346740
- Sequence Identity:
- Total samples: 539
- soil counts: 134
- aquatic counts: 280
- animal counts: 123
- plant counts: 2
Safety information
risk assessment
- @ref: 5537
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | Deferribacter desulfuricans SSM1 16S ribosomal RNA gene, partial sequence | JQ346740 | 1410 | ena | 639282 |
| 5537 | Deferribacter desulfuricans gene for 16S rRNA, partial sequence | AB086060 | 1446 | ena | 639282 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Deferribacter desulfuricans SSM1 | GCA_000010985 | complete | ncbi | 639282 |
| 66792 | Deferribacter desulfuricans SSM1 | 639282.3 | complete | patric | 639282 |
| 66792 | Deferribacter desulfuricans SSM1 | 639282.12 | plasmid | patric | 639282 |
| 66792 | Deferribacter desulfuricans SSM1 | 646564525 | complete | img | 639282 |
GC content
- @ref: 5537
- GC-content: 38.6
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| motile | yes | 82.58 | yes |
| flagellated | no | 89.7 | yes |
| gram-positive | no | 99.581 | no |
| anaerobic | yes | 99.695 | yes |
| halophile | no | 73.338 | no |
| spore-forming | no | 93.803 | no |
| glucose-util | no | 56.176 | no |
| aerobic | no | 99.328 | yes |
| thermophile | yes | 99.628 | no |
| glucose-ferment | no | 86.395 | no |
External links
@ref: 5537
culture collection no.: DSM 14783, JCM 11476, NBRC 101012
straininfo link
- @ref: 73351
- straininfo: 88606
literature
- topic: Phylogeny
- Pubmed-ID: 12807210
- title: Deferribacter desulfuricans sp. nov., a novel sulfur-, nitrate- and arsenate-reducing thermophile isolated from a deep-sea hydrothermal vent.
- authors: Takai K, Kobayashi H, Nealson KH, Horikoshi K
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.02479-0
- year: 2003
- mesh: Arsenates/*metabolism, Base Composition, DNA, Ribosomal, Electron Transport, Fatty Acids/analysis, Gram-Negative Anaerobic Bacteria/*classification/genetics/growth & development/isolation & purification, Hot Temperature, Japan, Molecular Sequence Data, Nitrates/*metabolism, Nucleic Acid Hybridization, Oxidation-Reduction, Phylogeny, RNA, Ribosomal, 16S, Seawater/*microbiology, Sequence Analysis, DNA, Sulfur/*metabolism
- topic2: Metabolism
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 5537 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 14783) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-14783 | |||
| 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 | |
| 23104 | Ken Takai,Hideki Kobayashi,Kenneth H. Nealson,Koki Horikoshi | 10.1099/ijs.0.02479-0 | Deferribacter desulfuricans sp. nov., a novel sulfur-, nitrate- and arsenate-reducing thermophile isolated from a deep-sea hydrothermal vent | IJSEM 53: 839-846 2003 | 12807210 | |
| 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) | |||
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
| 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 | |||
| 73351 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID88606.1 | StrainInfo: A central database for resolving microbial strain identifiers |