Strain identifier
BacDive ID: 23872
Type strain: 
Species: Rhodoferax saidenbachensis
Strain Designation: ED16, ED16I
Strain history: <- R. Kaden, Forschungszentrum Karlsruhe, Institute Functional Interfaces (IFG), Germany; ED16I (the accession form gives the strain designation as ED16I, but at the time of valid publication the strain designation is given as ED16)
NCBI tax ID(s): 1484693 (species)
version 8.1 (current version)
General
@ref: 20765
BacDive-ID: 23872
DSM-Number: 22694
keywords: genome sequence, 16S sequence, Bacteria, aerobe, psychrophilic, motile
description: Rhodoferax saidenbachensis ED16 is an aerobe, psychrophilic, motile bacterium that was isolated from sediment of a drinking water reservoir.
NCBI tax id
- NCBI tax id: 1484693
- Matching level: species
strain history
- @ref: 20765
- history: <- R. Kaden, Forschungszentrum Karlsruhe, Institute Functional Interfaces (IFG), Germany; ED16I (the accession form gives the strain designation as ED16I, but at the time of valid publication the strain designation is given as ED16)
doi: 10.13145/bacdive23872.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Betaproteobacteria
- order: Burkholderiales
- family: Comamonadaceae
- genus: Rhodoferax
- species: Rhodoferax saidenbachensis
- full scientific name: Rhodoferax saidenbachensis Kaden et al. 2014
@ref: 20765
domain: Bacteria
phylum: Proteobacteria
class: Betaproteobacteria
order: Burkholderiales
family: Comamonadaceae
genus: Rhodoferax
species: Rhodoferax saidenbachensis
full scientific name: Rhodoferax saidenbachensis Kaden et al. 2014
strain designation: ED16, ED16I
type strain: yes
Morphology
cell morphology
| @ref | motility | confidence | gram stain |
|---|---|---|---|
| 69480 | yes | 92.817 | |
| 69480 | 99.998 | negative |
colony morphology
- @ref: 61428
- incubation period: 3 days
Culture and growth conditions
culture medium
- @ref: 20765
- name: R2A MEDIUM (DSMZ Medium 830)
- growth: yes
- link: https://mediadive.dsmz.de/medium/830
- composition: Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 20765 | positive | growth | 20 | psychrophilic |
| 61428 | positive | growth | 30 | mesophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 61428
- oxygen tolerance: aerobe
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 99.998 |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent | latitude | longitude | sampling date |
|---|---|---|---|---|---|---|---|---|
| 20765 | sediment of a drinking water reservoir | Saxony, Saidenbach reservoir (50° 44' 9'' N 13° 14' 3'' E) | Germany | DEU | Europe | 50.7358 | 13.2342 | |
| 61428 | Water,drinking reservoir | Saxony,Saidenbach reservoir | Germany | DEU | Europe | 2006-06-01 |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Engineered | #Built environment | #Water reservoir (Aquarium/pool) |
| #Environmental | #Aquatic | #Freshwater |
| #Environmental | #Aquatic | #Sediment |
taxonmaps
- @ref: 69479
- File name: preview.99_4734.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_1;96_269;97_297;98_3550;99_4734&stattab=map
- Last taxonomy: Rhodoferax saidenbachensis
- 16S sequence: FJ755906
- Sequence Identity:
- Total samples: 4
- soil counts: 1
- aquatic counts: 3
Safety information
risk assessment
- @ref: 20765
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 20765
- description: Rhodoferax saidenbachensis ED16 16S ribosomal RNA gene, partial sequence
- accession: FJ755906
- length: 1499
- database: ena
- NCBI tax ID: 614083
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Rhodoferax saidenbachensis ED16 | GCA_000498435 | contig | ncbi | 614083 |
| 66792 | Rhodoferax saidenbachensis DSM 22694 | GCA_001955715 | complete | ncbi | 1484693 |
| 66792 | Rhodoferax saidenbachensis strain DSM 22694 | 1484693.3 | complete | patric | 1484693 |
| 66792 | Rhodoferax saidenbachensis ED16 | 2582581024 | draft | img | 614083 |
| 66792 | Rhodoferax saidenbachensis DSM 22694 | 2773857796 | complete | img | 1484693 |
GC content
- @ref: 20765
- GC-content: 60.3
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| flagellated | yes | 76.128 | no |
| gram-positive | no | 98.58 | no |
| anaerobic | no | 98.339 | yes |
| halophile | no | 95.39 | no |
| spore-forming | no | 96.025 | no |
| glucose-util | yes | 60.736 | no |
| aerobic | yes | 96.309 | yes |
| thermophile | no | 98.878 | no |
| motile | yes | 85.712 | no |
| glucose-ferment | no | 89.948 | no |
External links
@ref: 20765
culture collection no.: DSM 22694, ATCC BAA 1852, CCUG 57711
straininfo link
- @ref: 87884
- straininfo: 406225
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 24408525 | Rhodoferax saidenbachensis sp. nov., a psychrotolerant, very slowly growing bacterium within the family Comamonadaceae, proposal of appropriate taxonomic position of Albidiferax ferrireducens strain T118T in the genus Rhodoferax and emended description of the genus Rhodoferax. | Kaden R, Sproer C, Beyer D, Krolla-Sidenstein P | Int J Syst Evol Microbiol | 10.1099/ijs.0.054031-0 | 2014 | Bacterial Typing Techniques, Base Composition, Cold Temperature, Comamonadaceae/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Drinking Water/*microbiology, Fatty Acids/chemistry, Genes, Bacterial, Geologic Sediments/microbiology, Germany, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Ubiquinone/chemistry, Water Supply | Genetics |
| Phylogeny | 28956356 | Rhodoferax koreense sp. nov, an obligately aerobic bacterium within the family Comamonadaceae, and emended description of the genus Rhodoferax. | Farh ME, Kim YJ, Singh P, Jung SY, Kang JP, Yang DC | J Microbiol | 10.1007/s12275-017-7033-z | 2017 | Bacterial Typing Techniques, Base Composition, Comamonadaceae/*classification/*genetics/*isolation & purification/physiology, DNA, Bacterial/genetics, Fatty Acids/analysis, Genes, Bacterial/genetics, Nucleic Acid Hybridization, Phosphatidylethanolamines/analysis, Phospholipids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Sewage/microbiology, Ubiquinone/analysis | Transcriptome |
Reference
| @id | authors | title | doi/url | catalogue | journal | pubmed |
|---|---|---|---|---|---|---|
| 20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | 10.1099/ijsem.0.004332 | |||
| 20765 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-22694 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22694) | |||
| 61428 | Curators of the CCUG | https://www.ccug.se/strain?id=57711 | Culture Collection University of Gothenburg (CCUG) (CCUG 57711) | |||
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |||
| 66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | 10.1093/nar/gkaa1025 | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
| 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. | MicrobeAtlas 1.0 beta | https://microbeatlas.org/ | |||
| 69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |||
| 69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | Predictions based on the model GenomeNet Sporulation v. 1 | 10.21203/rs.3.rs-2527258/v1 | |||
| 87884 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | StrainInfo: A central database for resolving microbial strain identifiers | 10.60712/SI-ID406225.1 |