Strain identifier
BacDive ID: 3028
Type strain: 
Species: Albidiferax ferrireducens
Strain Designation: T118
Strain history: <- D. R. Lovely; T118 <- UMass, Amherst Microbiology Dept. <- K. T. Finneran
NCBI tax ID(s): 192843 (species)
version 9.2 (current version)
General
@ref: 5775
BacDive-ID: 3028
DSM-Number: 15236
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative
description: Albidiferax ferrireducens T118 is a mesophilic, Gram-negative bacterium that was isolated from coastal aquifer sediment.
NCBI tax id
- NCBI tax id: 192843
- Matching level: species
strain history
- @ref: 5775
- history: <- D. R. Lovely; T118 <- UMass, Amherst Microbiology Dept. <- K. T. Finneran
doi: 10.13145/bacdive3028.20241212.9.2
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Betaproteobacteria
- order: Burkholderiales
- family: Comamonadaceae
- genus: Albidiferax
- species: Albidiferax ferrireducens
- full scientific name: Albidiferax ferrireducens corrig. (Finneran et al. 2003) Ramana and Sasikala 2009
synonyms
@ref synonym 20215 Rhodoferax ferrireducens 20215 Albidoferax ferrireducens
@ref: 5775
domain: Bacteria
phylum: Proteobacteria
class: Betaproteobacteria
order: Burkholderiales
family: Comamonadaceae
genus: Albidiferax
species: Albidiferax ferrireducens
full scientific name: Albidiferax ferrireducens (Finneran et al. 2003) Ramana and Sasikala 2009
strain designation: T118
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 98
Culture and growth conditions
culture medium
- @ref: 5775
- name: BASAL MEDIUM (DSMZ Medium 1001)
- growth: yes
- link: https://mediadive.dsmz.de/medium/1001
- composition: Name: BASAL MEDIUM (DSMZ Medium 1001) Composition: NaHCO3 2.5 g/l NaH2PO4 x H2O 0.6 g/l NH4Cl 0.25 g/l KCl 0.1 g/l MgSO4 0.03 g/l NTA 0.015 g/l NaCl 0.01 g/l MnSO4 x H2O 0.005 g/l ZnCl2 0.0013 g/l FeSO4 x 7 H2O 0.001 g/l CaCl2 x 2 H2O 0.001 g/l CoCl2 x 6 H2O 0.001 g/l Na2MoO4 0.00025 g/l Na2WO4 x 2 H2O 0.00025 g/l NiCl2 x 6 H2O 0.00024 g/l H3BO3 0.0001 g/l AlK(SO4)2 x 12 H2O 0.0001 g/l CuSO4 x 5 H2O 0.0001 g/l Pyridoxine hydrochloride 0.0001 g/l p-Aminobenzoic acid 5e-05 g/l Thioctic acid 5e-05 g/l Riboflavin 5e-05 g/l Thiamine 5e-05 g/l Nicotinic acid 5e-05 g/l Pantothenic acid 5e-05 g/l Biotin 2e-05 g/l Folic acid 2e-05 g/l Vitamin B12 1e-06 g/l Distilled water
culture temp
- @ref: 5775
- growth: positive
- type: growth
- temperature: 25
Physiology and metabolism
spore formation
- @ref: 69481
- spore formation: no
- confidence: 100
Isolation, sampling and environmental information
isolation
- @ref: 5775
- sample type: coastal aquifer sediment
- geographic location: VA, Oyster Bay
- country: USA
- origin.country: USA
- continent: North America
isolation source categories
- Cat1: #Environmental
- Cat2: #Aquatic
- Cat3: #Sediment
taxonmaps
- @ref: 69479
- File name: preview.99_5621.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_1;96_269;97_297;98_4189;99_5621&stattab=map
- Last taxonomy: Rhodoferax ferrireducens subclade
- 16S sequence: AF435948
- Sequence Identity:
- Total samples: 18
- aquatic counts: 16
- animal counts: 1
- plant counts: 1
Safety information
risk assessment
- @ref: 5775
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 5775
- description: Rhodoferax ferrireducens 16S ribosomal RNA gene, partial sequence
- accession: AF435948
- length: 1470
- database: nuccore
- NCBI tax ID: 338969
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Rhodoferax ferrireducens T118 DSM 15236 | GCA_000013605 | complete | ncbi | 338969 |
| 66792 | Rhodoferax ferrireducens T118 strain DSM 15236 | 338969.25 | plasmid | patric | 338969 |
Genome-based predictions
predictions
| @ref | trait | model | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 69481 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 100 | no |
| 69480 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 98 | no |
| 69480 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 83.152 | no |
| 69480 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 68.107 | no |
| 69480 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 89.634 | no |
| 69480 | thermophilic | thermophile | Ability to grow at temperatures above or equal to 45°C | no | 94.956 | yes |
| 69480 | flagellated | motile2+ | Ability to perform flagellated movement | yes | 85.894 | no |
External links
@ref: 5775
culture collection no.: DSM 15236, ATCC BAA-621
straininfo link
- @ref: 72548
- straininfo: 100908
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 12807184 | Rhodoferax ferrireducens sp. nov., a psychrotolerant, facultatively anaerobic bacterium that oxidizes acetate with the reduction of Fe(III). | Finneran KT, Johnsen CV, Lovley DR | Int J Syst Evol Microbiol | 10.1099/ijs.0.02298-0 | 2003 | Acetates/*metabolism, Anaerobiosis, Bacterial Typing Techniques, Betaproteobacteria/*classification/genetics/*growth & development/metabolism, *Cold Temperature, Culture Media, DNA, Ribosomal/analysis, Electron Transport, Ferric Compounds/*metabolism, Fresh Water/microbiology, Molecular Sequence Data, Oxidation-Reduction, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA | Metabolism |
| 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 | catalogue | doi/url | title |
|---|---|---|---|---|
| 5775 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15236) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-15236 | |
| 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 | |
| 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) | |
| 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 | |
| 69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |
| 69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |
| 72548 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID100908.1 | StrainInfo: A central database for resolving microbial strain identifiers |