Strain identifier
BacDive ID: 3845
Type strain: 
Species: Deferribacter autotrophicus
Strain Designation: SL50
Strain history: <- G. B. Slobodkina, Russian Academy of Sciences, Inst. of Microbiology, Moscow; SL50 <- G. B. Slobodkina and A. I. Slobodkin
NCBI tax ID(s): 500465 (species)
version 8.1 (current version)
General
@ref: 15765
BacDive-ID: 3845
DSM-Number: 21529
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, thermophilic, Gram-negative, motile, rod-shaped
description: Deferribacter autotrophicus SL50 is an anaerobe, thermophilic, Gram-negative bacterium that was isolated from fragment of hydrothermal structure.
NCBI tax id
- NCBI tax id: 500465
- Matching level: species
strain history
- @ref: 15765
- history: <- G. B. Slobodkina, Russian Academy of Sciences, Inst. of Microbiology, Moscow; SL50 <- G. B. Slobodkina and A. I. Slobodkin
doi: 10.13145/bacdive3845.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/deferribacterota
- domain: Bacteria
- phylum: Deferribacterota
- class: Deferribacteres
- order: Deferribacterales
- family: Deferribacteraceae
- genus: Deferribacter
- species: Deferribacter autotrophicus
- full scientific name: Deferribacter autotrophicus Slobodkina et al. 2009
@ref: 15765
domain: Bacteria
phylum: Deferribacteres
class: Deferribacteres
order: Deferribacterales
family: Deferribacteraceae
genus: Deferribacter
species: Deferribacter autotrophicus
full scientific name: Deferribacter autotrophicus Slobodkina et al. 2009
strain designation: SL50
type strain: yes
Morphology
cell morphology
- @ref: 29120
- gram stain: negative
- cell length: 3.25 µm
- cell width: 0.55 µm
- cell shape: rod-shaped
- motility: yes
pigmentation
- @ref: 29120
- production: yes
Culture and growth conditions
culture medium
- @ref: 15765
- name: DEFERRIBACTER AUTOTROPHICUS MEDIUM (DSMZ Medium 985)
- growth: yes
- link: https://mediadive.dsmz.de/medium/985
- composition: Name: DEFERRIBACTER AUTOTROPHICUS MEDIUM (DSMZ Medium 985) Composition: NaCl 17.9462 g/l MgCl2 x 6 H2O 3.98804 g/l Na-acetate 1.59521 g/l Na2CO3 1.49551 g/l KNO3 0.997009 g/l Na2S x 9 H2O 0.498504 g/l KCl 0.338983 g/l NH4Cl 0.249252 g/l Yeast extract 0.199402 g/l K2HPO4 0.179462 g/l CaCl2 0.109671 g/l Fe(NH4)2(SO4)2 x 7 H2O 0.0199402 g/l HCl 0.00249252 g/l FeCl2 x 4 H2O 0.00149551 g/l Sodium resazurin 0.000498504 g/l NaOH 0.000498504 g/l CoCl2 x 6 H2O 0.000189432 g/l Pyridoxine hydrochloride 9.97009e-05 g/l MnCl2 x 4 H2O 9.97009e-05 g/l ZnCl2 6.97906e-05 g/l (DL)-alpha-Lipoic acid 4.98504e-05 g/l Riboflavin 4.98504e-05 g/l Nicotinic acid 4.98504e-05 g/l Thiamine HCl 4.98504e-05 g/l p-Aminobenzoic acid 4.98504e-05 g/l Calcium D-(+)-pantothenate 4.98504e-05 g/l Na2MoO4 x 2 H2O 3.58923e-05 g/l NiCl2 x 6 H2O 2.39282e-05 g/l Folic acid 1.99402e-05 g/l Biotin 1.99402e-05 g/l H3BO3 5.98205e-06 g/l Na2WO4 x 2 H2O 3.98804e-06 g/l Na2SeO3 x 5 H2O 2.99103e-06 g/l CuCl2 x 2 H2O 1.99402e-06 g/l Vitamin B12 9.97009e-07 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 15765 | positive | growth | 60 | thermophilic |
| 29120 | positive | growth | 25-75 | |
| 29120 | positive | optimum | 60 | thermophilic |
culture pH
| @ref | ability | type | pH |
|---|---|---|---|
| 29120 | positive | growth | 5.0-7.5 |
| 29120 | positive | optimum | 6.5 |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance |
|---|---|
| 15765 | anaerobe |
| 29120 | anaerobe |
spore formation
- @ref: 29120
- spore formation: no
halophily
| @ref | salt | growth | tested relation | concentration |
|---|---|---|---|---|
| 29120 | NaCl | positive | growth | 1.0-6.0 % |
| 29120 | NaCl | positive | optimum | 2.5 % |
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 29120 | 30089 | acetate | + | carbon source |
| 29120 | 15740 | formate | + | carbon source |
| 29120 | 24996 | lactate | + | carbon source |
| 29120 | 25115 | malate | + | carbon source |
| 29120 | 17306 | maltose | + | carbon source |
| 29120 | 17272 | propionate | + | carbon source |
| 29120 | 15361 | pyruvate | + | carbon source |
| 29120 | 30031 | succinate | + | carbon source |
Isolation, sampling and environmental information
isolation
- @ref: 15765
- sample type: fragment of hydrothermal structure
- geographic location: Mid-Atlantic Ridge
- country: International waters
- latitude: 12.9725
- longitude: -44.8631
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | |
| #Environmental | #Terrestrial | #Geologic |
Safety information
risk assessment
- @ref: 15765
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 15765
- description: Deferribacter autotrophicus strain SL50 16S ribosomal RNA gene, partial sequence
- accession: EU407777
- length: 1543
- database: ena
- NCBI tax ID: 500465
Genome sequences
- @ref: 66792
- description: Deferribacter autotrophicus SL50
- accession: GCA_008362905
- assembly level: contig
- database: ncbi
- NCBI tax ID: 500465
GC content
| @ref | GC-content | method |
|---|---|---|
| 15765 | 28.7 | thermal denaturation, midpoint method (Tm) |
| 29120 | 28.7 | |
| 15765 | 32.6 | sequence analysis |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| motile | yes | 89.842 | yes |
| flagellated | no | 84.878 | no |
| gram-positive | no | 99.654 | yes |
| anaerobic | yes | 99.679 | yes |
| aerobic | no | 99.383 | yes |
| halophile | no | 79.692 | no |
| spore-forming | no | 95.713 | yes |
| glucose-util | no | 56.427 | no |
| thermophile | yes | 100 | yes |
| glucose-ferment | no | 84.756 | no |
External links
@ref: 15765
culture collection no.: DSM 21529, VKPM B-10097
straininfo link
- @ref: 73355
- straininfo: 407321
literature
- topic: Phylogeny
- Pubmed-ID: 19502344
- title: Deferribacter autotrophicus sp. nov., an iron(III)-reducing bacterium from a deep-sea hydrothermal vent.
- authors: Slobodkina GB, Kolganova TV, Chernyh NA, Querellou J, Bonch-Osmolovskaya EA, Slobodkin AI
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.006767-0
- year: 2009
- mesh: Bacteria, Anaerobic/*classification/genetics/isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, *Chemoautotrophic Growth, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, *Hot Temperature, Iron/*metabolism, Molecular Sequence Data, Oxidation-Reduction, Phenotype, Phylogeny, Polymerase Chain Reaction/methods, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Species Specificity
- topic2: Stress
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
|---|---|---|---|---|---|---|
| 15765 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21529) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-21529 | |||
| 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 | |||
| 29120 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 25546 | 28776041 | |
| 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) | |||
| 73355 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID407321.1 | StrainInfo: A central database for resolving microbial strain identifiers |