Strain identifier
BacDive ID: 23871
Type strain: 
Species: Rhodoferax antarcticus
Strain Designation: Ant.Br
Strain history: <- M. Madigan, Univ. Illinois; Ant.Br <- M. Madigan, Univ. Illinois; <- M. T. Madigan; {1994}
NCBI tax ID(s): 81479 (species)
version 9.3 (current version)
General
@ref: 20764
BacDive-ID: 23871
DSM-Number: 24876
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, psychrophilic, Gram-negative
description: Rhodoferax antarcticus Ant.Br is an anaerobe, psychrophilic, Gram-negative bacterium that was isolated from algal-bacterial mat.
NCBI tax id
- NCBI tax id: 81479
- Matching level: species
strain history
- @ref: 20764
- history: <- M. Madigan, Univ. Illinois; Ant.Br <- M. Madigan, Univ. Illinois; <- M. T. Madigan; {1994}
doi: 10.13145/bacdive23871.20250331.9.3
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 antarcticus
- full scientific name: Rhodoferax antarcticus Madigan et al. 2024
@ref: 20764
domain: Bacteria
phylum: Proteobacteria
class: Betaproteobacteria
order: Burkholderiales
family: Comamonadaceae
genus: Rhodoferax
species: Rhodoferax antarcticus
full scientific name: Rhodoferax antarcticus Madigan et al. 2001
strain designation: Ant.Br
type strain: yes
Morphology
cell morphology
| @ref | gram stain | confidence |
|---|---|---|
| 125438 | negative | 96.494 |
| 125439 | negative | 99.2 |
Culture and growth conditions
culture medium
- @ref: 20764
- name: RHODOSPIRILLACEAE MEDIUM (modified) (DSMZ Medium 27)
- growth: yes
- link: https://mediadive.dsmz.de/medium/27
- composition: Name: RHODOSPIRILLACEAE MEDIUM (modified) (DSMZ Medium 27; with strain-specific modifications) Composition: Na-malate 1.0 g/l Disodium succinate 1.0 g/l Ammonium acetate 0.5 g/l KH2PO4 0.5 g/l MgSO4 x 7 H2O 0.4 g/l NH4Cl 0.4 g/l NaCl 0.4 g/l Yeast extract 0.3 g/l L-Cysteine HCl 0.3 g/l CaCl2 x 2 H2O 0.05 g/l Resazurin 0.005 g/l Fe(III) citrate 0.005 g/l H3BO3 0.0003 g/l CoCl2 x 6 H2O 0.0002 g/l ZnSO4 x 7 H2O 0.0001 g/l Na2MoO4 x 2 H2O 3e-05 g/l MnCl2 x 4 H2O 3e-05 g/l NiCl2 x 6 H2O 2e-05 g/l CuCl2 x 2 H2O 1e-05 g/l Vitamin B12 Distilled water
culture temp
- @ref: 20764
- growth: positive
- type: growth
- temperature: 18
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 20764 | anaerobe | |
| 125439 | obligate aerobe | 97 |
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 125438 | no | 91.108 |
| 125439 | no | 99.3 |
Isolation, sampling and environmental information
isolation
- @ref: 20764
- sample type: algal-bacterial mat
- geographic location: Ross Island (77-78 °S), ponds in and around Cape Royds
- continent: Australia and Oceania
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Microbial community | #Microbial mat |
| #Host | #Algae | |
| #Host | #Microbial | #Bacteria |
taxonmaps
- @ref: 69479
- File name: preview.99_6498.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_1;96_269;97_3620;98_4793;99_6498&stattab=map
- Last taxonomy: Rhodoferax antarcticus subclade
- 16S sequence: GU233447
- Sequence Identity:
- Total samples: 85
- soil counts: 19
- aquatic counts: 58
- animal counts: 2
- plant counts: 6
Safety information
risk assessment
- @ref: 20764
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20764 | Rhodoferax antarcticus small subunit ribosomal RNA gene, complete sequence | AF084947 | 1484 | nuccore | 1111071 |
| 20764 | Rhodoferax antarcticus strain ANT.BR 16S ribosomal RNA gene, partial sequence | GU233447 | 1458 | nuccore | 1111071 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Rhodoferax antarcticus DSMZ24876 | GCA_001955735 | complete | ncbi | 81479 |
| 66792 | Rhodoferax antarcticus ANT.BR | GCA_001938565 | contig | ncbi | 1111071 |
| 66792 | Rhodoferax antarcticus ANT.BR | 1111071.4 | wgs | patric | 1111071 |
| 66792 | Rhodoferax antarcticus strain DSM 24876 | 81479.8 | complete | patric | 81479 |
| 66792 | Rhodoferax antarcticus strain DSM 24876 strain DSMZ24876 | 81479.11 | plasmid | patric | 81479 |
| 66792 | Rhodoferax antarcticus strain DSM 24876 strain DSMZ24876 | 81479.10 | plasmid | patric | 81479 |
| 66792 | Rhodoferax antarcticus DSM 24876 | 2751185768 | complete | img | 81479 |
GC content
- @ref: 20764
- GC-content: 61.5
- method: thermal denaturation, midpoint method (Tm)
Genome-based predictions
predictions
| @ref | model | trait | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 125439 | BacteriaNet | oxygen_tolerance | Oxygenic conditions needed for growth | obligate aerobe | 97 | |
| 125439 | BacteriaNet | gram_stain | Reaction to gram-staining | negative | 99.2 | |
| 125439 | BacteriaNet | motility | Ability to perform movement | yes | 83.8 | |
| 125439 | BacteriaNet | spore_formation | Ability to form endo- or exospores | no | 99.3 | |
| 125438 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 96.494 | no |
| 125438 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 56.446 | yes |
| 125438 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | no | 50.429 | yes |
| 125438 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 91.108 | no |
| 125438 | thermophile | thermophilic | Ability to grow at temperatures above or equal to 45°C | no | 94.359 | yes |
| 125438 | motile2+ | flagellated | Ability to perform flagellated movement | yes | 84.754 | no |
External links
@ref: 20764
culture collection no.: DSM 24876, ATCC 700587
straininfo link
- @ref: 87883
- straininfo: 44024
literature
- topic: Phylogeny
- Pubmed-ID: 28956356
- title: Rhodoferax koreense sp. nov, an obligately aerobic bacterium within the family Comamonadaceae, and emended description of the genus Rhodoferax.
- authors: Farh ME, Kim YJ, Singh P, Jung SY, Kang JP, Yang DC
- journal: J Microbiol
- DOI: 10.1007/s12275-017-7033-z
- year: 2017
- mesh: 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
- topic2: Transcriptome
Reference
| @id | authors | title | doi/url | catalogue |
|---|---|---|---|---|
| 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 | |
| 20764 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-24876 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 24876) | |
| 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 | |
| 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/ | |
| 87883 | 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-ID44024.1 | |
| 125438 | Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann | Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets | 10.1101/2024.08.12.607695 | |
| 125439 | Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy | deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 | https://github.com/GenomeNet/deepG |