Strain identifier

BacDive ID: 23871

Type strain: Yes

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)

For citation purpose refer to the digital object identifier (doi) of the current version.
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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

@refmotilityconfidencegram stain
69480yes96.255
69480100negative

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

@refoxygen toleranceconfidence
20764anaerobe
69480anaerobe91.953

spore formation

@refspore formationconfidence
69481no100
69480no99.995

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

Cat1Cat2Cat3
#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

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20764Rhodoferax antarcticus small subunit ribosomal RNA gene, complete sequenceAF0849471484ena1111071
20764Rhodoferax antarcticus strain ANT.BR 16S ribosomal RNA gene, partial sequenceGU2334471458ena1111071

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Rhodoferax antarcticus DSMZ24876GCA_001955735completencbi81479
66792Rhodoferax antarcticus ANT.BRGCA_001938565contigncbi1111071
66792Rhodoferax antarcticus ANT.BR1111071.4wgspatric1111071
66792Rhodoferax antarcticus strain DSM 2487681479.8completepatric81479
66792Rhodoferax antarcticus strain DSM 24876 strain DSMZ2487681479.11plasmidpatric81479
66792Rhodoferax antarcticus strain DSM 24876 strain DSMZ2487681479.10plasmidpatric81479
66792Rhodoferax antarcticus DSM 248762751185768completeimg81479

GC content

  • @ref: 20764
  • GC-content: 61.5
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedyes84.383no
gram-positiveno98.977no
anaerobicyes89.582yes
aerobicno82.206no
halophileno94.532no
spore-formingno95.05no
glucose-utilno58.746no
thermophileno98.95no
glucose-fermentno85.722no
motileyes88.916no

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

@idauthorstitledoi/urlcatalogue
20215Parte, 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 DSMZ10.1099/ijsem.0.004332
20764Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-24876Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 24876)
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69479João 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 betahttps://microbeatlas.org/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions 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
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
87883Reimer, 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 identifiers10.60712/SI-ID44024.1