Strain identifier
BacDive ID: 23871
Type strain:
Species: Rhodoferax antarcticus
Strain Designation: Ant.Br
Strain history: <- M. Madigan, Department of Microbiology, University of Illinois; Ant.Br
NCBI tax ID(s): 81479 (species)
General
@ref: 20764
BacDive-ID: 23871
DSM-Number: 24876
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, psychrophilic, motile
description: Rhodoferax antarcticus Ant.Br is an anaerobe, psychrophilic, motile 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, Department of Microbiology, University of Illinois; Ant.Br
doi: 10.13145/bacdive23871.20230509.8.1
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 antarcticus
- full scientific name: Rhodoferax antarcticus Madigan et al. 2001
@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 | motility | confidence | gram stain |
---|---|---|---|
69480 | yes | 96.255 | |
69480 | 100 | negative |
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: 20
- range: psychrophilic
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance | confidence |
---|---|---|
20764 | anaerobe | |
69480 | anaerobe | 91.953 |
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.995 |
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 | ena | 1111071 |
20764 | Rhodoferax antarcticus strain ANT.BR 16S ribosomal RNA gene, partial sequence | GU233447 | 1458 | ena | 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
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
flagellated | yes | 84.383 | no |
gram-positive | no | 98.977 | no |
anaerobic | yes | 89.582 | yes |
aerobic | no | 82.206 | no |
halophile | no | 94.532 | no |
spore-forming | no | 95.05 | no |
glucose-util | no | 58.746 | no |
thermophile | no | 98.95 | no |
glucose-ferment | no | 85.722 | no |
motile | yes | 88.916 | 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/ | |
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 | |
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 |