Strain identifier
BacDive ID: 130831
Type strain: 
Species: Roseiarcus fermentans
Strain Designation: Pf56
Strain history: <- S. N. Dedysh, Winogradsky Inst. Microbiol., RAS, Moscow, Russia; Pf56 <- I. S. Kulichevskaya
NCBI tax ID(s): 1473586 (species)
version 8.1 (current version)
General
@ref: 22110
BacDive-ID: 130831
DSM-Number: 24875
keywords: genome sequence, 16S sequence, Bacteria, Gram-negative
description: Roseiarcus fermentans Pf56 is a Gram-negative bacterium that was isolated from acidic peat soil of a Spagnum peat bog.
NCBI tax id
- NCBI tax id: 1473586
- Matching level: species
strain history
- @ref: 22110
- history: <- S. N. Dedysh, Winogradsky Inst. Microbiol., RAS, Moscow, Russia; Pf56 <- I. S. Kulichevskaya
doi: 10.13145/bacdive130831.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Hyphomicrobiales
- family: Roseiarcaceae
- genus: Roseiarcus
- species: Roseiarcus fermentans
- full scientific name: Roseiarcus fermentans Kulichevskaya et al. 2014
@ref: 22110
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhizobiales
family: Roseiarcaceae
genus: Roseiarcus
species: Roseiarcus fermentans
full scientific name: Roseiarcus fermentans Kulichevskaya et al. 2014
strain designation: Pf56
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.992
Culture and growth conditions
culture medium
- @ref: 22110
- name: MP MEDIUM (DSMZ Medium 1382)
- growth: yes
- link: https://mediadive.dsmz.de/medium/1382
- composition: Name: MP MEDIUM (DSMZ Medium 1382) Composition: Glucose 0.5 g/l NH4Cl 0.2 g/l KH2PO4 0.1 g/l Yeast extract 0.1 g/l CaCl2 x 2 H2O 0.02 g/l FeCl2 x 4 H2O 0.0018 g/l H3BO3 0.0005 g/l CoCl2 x 6 H2O 0.00025 g/l ZnCl2 0.0001 g/l MnCl2 x 4 H2O 7e-05 g/l Na2MoO4 x 2 H2O 3e-05 g/l NiCl2 x 6 H2O 1e-05 g/l CuCl2 x 2 H2O 1e-05 g/l Na2SeO3 x 5 H2O 1e-05 g/l Distilled water
culture temp
- @ref: 22110
- growth: positive
- type: growth
- temperature: 22-28
Physiology and metabolism
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 97 |
| 69480 | no | 99.976 |
Isolation, sampling and environmental information
isolation
- @ref: 22110
- sample type: acidic peat soil of a Spagnum peat bog
- host species: Sphagnum
- geographic location: Tver region, Staroselsky moss (56° 34' N 32° 46' E)
- country: Russia
- origin.country: RUS
- continent: Europe
- latitude: 56.5667
- longitude: 32.7667
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Terrestrial | #Wetland (Swamp) |
| #Environmental | #Terrestrial | #Soil |
| #Condition | #Acidic |
taxonmaps
- @ref: 69479
- File name: preview.99_59578.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_86;96_9458;97_11378;98_42353;99_59578&stattab=map
- Last taxonomy: Roseiarcus fermentans subclade
- 16S sequence: KJ406703
- Sequence Identity:
- Total samples: 321
- soil counts: 238
- aquatic counts: 46
- animal counts: 29
- plant counts: 8
Safety information
risk assessment
- @ref: 22110
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 22110
- description: Roseiarcus fermentans strain Pf56 16S ribosomal RNA gene, partial sequence
- accession: KJ406703
- length: 1399
- database: ena
- NCBI tax ID: 1473586
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Roseiarcus fermentans DSM 24875 | GCA_003315135 | scaffold | ncbi | 1473586 |
| 66792 | Roseiarcus fermentans strain DSM 24875 | 1473586.4 | wgs | patric | 1473586 |
| 66792 | Roseiarcus fermentans DSM 24875 | 2770939636 | draft | img | 1473586 |
GC content
- @ref: 22110
- GC-content: 70.0
- method: thermal denaturation, midpoint method (Tm)
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 97 | no |
| motile | no | 79.483 | no |
| flagellated | no | 94.667 | no |
| gram-positive | no | 97.42 | no |
| anaerobic | no | 95.293 | no |
| aerobic | yes | 69.02 | no |
| halophile | no | 94.554 | no |
| spore-forming | no | 93.791 | no |
| glucose-util | yes | 84.668 | no |
| thermophile | no | 98.338 | no |
| glucose-ferment | no | 90.855 | no |
External links
@ref: 22110
culture collection no.: DSM 24875, VKM B-2876
straininfo link
- @ref: 89318
- straininfo: 401964
literature
- topic: Phylogeny
- Pubmed-ID: 24812364
- title: Descriptions of Roseiarcus fermentans gen. nov., sp. nov., a bacteriochlorophyll a-containing fermentative bacterium related phylogenetically to alphaproteobacterial methanotrophs, and of the family Roseiarcaceae fam. nov.
- authors: Kulichevskaya IS, Danilova OV, Tereshina VM, Kevbrin VV, Dedysh SN
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.064576-0
- year: 2014
- mesh: Alphaproteobacteria/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Bacteriochlorophyll A/chemistry, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Russia, Sequence Analysis, DNA, Sphagnopsida/*microbiology, Ubiquinone/chemistry, *Wetlands
- topic2: Genetics
Reference
| @id | authors | title | doi/url | catalogue | journal | pubmed |
|---|---|---|---|---|---|---|
| 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 | |||
| 22110 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-24875 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 24875) | |||
| 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 | |||
| 66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | 10.1093/nar/gkaa1025 | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
| 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 | |||
| 89318 | 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-ID401964.1 |