Strain identifier
BacDive ID: 3832
Type strain: 
Species: Rhodonellum psychrophilum
Strain Designation: GCM71
Strain history: <- P. Stougaard, Denmark; GCM71 <- M. Schmidt
NCBI tax ID(s): 1123057 (strain), 336828 (species)
version 8.1 (current version)
General
@ref: 7226
BacDive-ID: 3832
DSM-Number: 17998
keywords: genome sequence, 16S sequence, Bacteria
description: Rhodonellum psychrophilum GCM71 is a bacterium that was isolated from Ikaite tufa columns.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 1123057 | strain |
| 336828 | species |
strain history
- @ref: 7226
- history: <- P. Stougaard, Denmark; GCM71 <- M. Schmidt
doi: 10.13145/bacdive3832.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacteroidota
- domain: Bacteria
- phylum: Bacteroidota
- class: Cytophagia
- order: Cytophagales
- family: Cyclobacteriaceae
- genus: Rhodonellum
- species: Rhodonellum psychrophilum
- full scientific name: Rhodonellum psychrophilum Schmidt et al. 2006
@ref: 7226
domain: Bacteria
phylum: Bacteroidetes
class: Cytophagia
order: Cytophagales
family: Cyclobacteriaceae
genus: Rhodonellum
species: Rhodonellum psychrophilum
full scientific name: Rhodonellum psychrophilum Schmidt et al. 2006 emend. Hahnke et al. 2016
strain designation: GCM71
type strain: yes
Morphology
cell morphology
| @ref | motility | confidence | gram stain |
|---|---|---|---|
| 69480 | no | 90.415 | |
| 69480 | 99.998 | negative |
multimedia
| @ref | multimedia content | caption | intellectual property rights |
|---|---|---|---|
| 66793 | EM_DSM_17998_1.jpg | electron microscopic image | © HZI/Manfred Rohde |
| 66793 | EM_DSM_17998_2.jpg | electron microscopic image | © HZI/Manfred Rohde |
| 66793 | EM_DSM_17998_3.jpg | electron microscopic image | © HZI/Manfred Rohde |
| 66793 | EM_DSM_17998_4.jpg | electron microscopic image | © HZI/Manfred Rohde |
| 66793 | EM_DSM_17998_5.jpg | electron microscopic image | © HZI/Manfred Rohde |
Culture and growth conditions
culture medium
- @ref: 7226
- name: R2A MEDIUM (DSMZ Medium 830)
- growth: yes
- link: https://mediadive.dsmz.de/medium/830
- composition: Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
culture temp
- @ref: 7226
- growth: positive
- type: growth
- temperature: 5-28
Physiology and metabolism
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 99.981 |
Isolation, sampling and environmental information
isolation
- @ref: 7226
- sample type: Ikaite tufa columns
- geographic location: Ikka Fjord
- country: Greenland
- origin.country: GRL
- continent: North America
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Marine |
| #Environmental | #Terrestrial | #Geologic |
taxonmaps
- @ref: 69479
- File name: preview.99_5353.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15774;96_2595;97_3178;98_3991;99_5353&stattab=map
- Last taxonomy: Rhodonellum
- 16S sequence: DQ112660
- Sequence Identity:
- Total samples: 984
- soil counts: 161
- aquatic counts: 641
- animal counts: 175
- plant counts: 7
Safety information
risk assessment
- @ref: 7226
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 7226
- description: Rhodonellum psychrophilum strain GCM71 16S ribosomal RNA gene, partial sequence
- accession: DQ112660
- length: 1350
- database: ena
- NCBI tax ID: 336828
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Rhodonellum psychrophilum GCM71 = DSM 17998 | GCA_000473765 | contig | ncbi | 1123057 |
| 66792 | Rhodonellum psychrophilum GCM71 = DSM 17998 | GCA_000381545 | scaffold | ncbi | 1123057 |
| 66792 | Rhodonellum psychrophilum DSM 17998 | 1123057.3 | wgs | patric | 1123057 |
| 66792 | Rhodonellum psychrophilum DSM 17998 strain GCM71 | 1123057.7 | wgs | patric | 1123057 |
| 66792 | Rhodonellum psychrophilum GCM71, DSM 17998 | 2517572081 | draft | img | 1123057 |
| 66792 | Rhodonellum psychrophilum DSM 17998 | 2519899653 | draft | img | 1123057 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 7226 | 44.2 | |
| 7226 | 41.8 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| motile | no | 90.486 | no |
| flagellated | no | 97.018 | no |
| gram-positive | no | 97.697 | no |
| anaerobic | no | 98.87 | no |
| aerobic | yes | 93.034 | no |
| halophile | no | 76.622 | no |
| spore-forming | no | 95.018 | no |
| thermophile | no | 99.23 | no |
| glucose-util | yes | 85.416 | no |
| glucose-ferment | no | 91.664 | no |
External links
@ref: 7226
culture collection no.: DSM 17998, LMG 23454
straininfo link
- @ref: 73342
- straininfo: 290291
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 17158993 | Rhodonellum psychrophilum gen. nov., sp. nov., a novel psychrophilic and alkaliphilic bacterium of the phylum Bacteroidetes isolated from Greenland. | Schmidt M, Prieme A, Stougaard P | Int J Syst Evol Microbiol | 10.1099/ijs.0.64450-0 | 2006 | *Alkalies, Bacterial Typing Techniques, *Calcium Carbonate, *Cold Temperature, Cytophagaceae/*classification/genetics/isolation & purification/physiology, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fresh Water/*microbiology, Genes, rRNA, Greenland, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA | Genetics |
| Genetics | 24309741 | Draft Genome Sequence of the Psychrophilic and Alkaliphilic Rhodonellum psychrophilum Strain GCM71T. | Hauptmann AL, Glaring MA, Hallin PF, Prieme A, Stougaard P | Genome Announc | 10.1128/genomeA.01014-13 | 2013 |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 7226 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17998) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-17998 | |||
| 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) | |||
| 66793 | Mukherjee et al. | 10.1038/nbt.3886 | GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life | 35: 676-683 2017 | 28604660 | |
| 66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | 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. | 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 | |||
| 73342 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID290291.1 | StrainInfo: A central database for resolving microbial strain identifiers |