Strain identifier
BacDive ID: 4157
Type strain: 
Species: Maridesulfovibrio frigidus
Strain Designation: 18
Strain history: V. Vandieken 18.
NCBI tax ID(s): 1121447 (strain), 340956 (species)
version 8.1 (current version)
General
@ref: 6711
BacDive-ID: 4157
DSM-Number: 17176
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, psychrophilic, Gram-negative, motile, rod-shaped
description: Maridesulfovibrio frigidus 18 is an anaerobe, psychrophilic, Gram-negative bacterium that was isolated from marine surface sediment.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 340956 | species |
| 1121447 | strain |
strain history
| @ref | history |
|---|---|
| 6711 | <- V. Vandieken, Max-Planck-Inst. Marine Microbiology, Bremen, Germany; 18 <- V. Vandieken {2003} |
| 67770 | V. Vandieken 18. |
doi: 10.13145/bacdive4157.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Deltaproteobacteria
- order: Desulfovibrionales
- family: Desulfovibrionaceae
- genus: Maridesulfovibrio
- species: Maridesulfovibrio frigidus
- full scientific name: Maridesulfovibrio frigidus (Vandieken et al. 2006) Waite et al. 2020
synonyms
- @ref: 20215
- synonym: Desulfovibrio frigidus
@ref: 6711
domain: Bacteria
phylum: Proteobacteria
class: Deltaproteobacteria
order: Desulfovibrionales
family: Desulfovibrionaceae
genus: Maridesulfovibrio
species: Maridesulfovibrio frigidus
full scientific name: Maridesulfovibrio frigidus (Vandieken et al. 2006) Waite et al. 2020
strain designation: 18
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell width | cell shape | motility | confidence |
|---|---|---|---|---|---|---|
| 31689 | negative | 02-05 µm | 0.7 µm | rod-shaped | yes | |
| 69480 | yes | 96.149 | ||||
| 69480 | negative | 99.981 |
pigmentation
- @ref: 31689
- production: yes
Culture and growth conditions
culture medium
- @ref: 6711
- name: MARINE DESULFOVIBRIO COMPLEX MEDIUM (DSMZ Medium 1040)
- growth: yes
- link: https://mediadive.dsmz.de/medium/1040
- composition: Name: MARIDESULFOVIBRIO MEDIUM (DSMZ Medium 1040) Composition: Sea Salt 34.9301 g/l Na-DL-lactate 2.49501 g/l Yeast extract 0.998004 g/l Na2CO3 0.998004 g/l Na2S x 9 H2O 0.299401 g/l MgSO4 x 7 H2O 0.0299401 g/l NaCl 0.00998004 g/l MnSO4 x H2O 0.00499002 g/l (NH4)2Ni(SO4)2 x 6 H2O 0.00279441 g/l CoCl2 x 6 H2O 0.00179641 g/l ZnSO4 x 7 H2O 0.00179641 g/l CaCl2 x 2 H2O 0.000998004 g/l FeSO4 x 7 H2O 0.000998004 g/l Sodium resazurin 0.000499002 g/l AlK(SO4)2 x 12 H2O 0.000179641 g/l CuSO4 x 5 H2O 9.98004e-05 g/l H3BO3 9.98004e-05 g/l Na2MoO4 x 2 H2O 9.98004e-05 g/l Na2WO4 x 2 H2O 9.98004e-05 g/l Na2SeO4 9.98004e-05 g/l Pyridoxine hydrochloride 9.98004e-05 g/l (DL)-alpha-Lipoic acid 4.99002e-05 g/l Calcium D-(+)-pantothenate 4.99002e-05 g/l Nicotinic acid 4.99002e-05 g/l Riboflavin 4.99002e-05 g/l Thiamine HCl 4.99002e-05 g/l p-Aminobenzoic acid 4.99002e-05 g/l Folic acid 1.99601e-05 g/l Biotin 1.99601e-05 g/l Vitamin B12 9.98004e-07 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 6711 | positive | growth | 20 | psychrophilic |
| 31689 | positive | optimum | 20-23 | psychrophilic |
| 67770 | positive | growth | 20 | psychrophilic |
culture pH
| @ref | ability | type | pH |
|---|---|---|---|
| 31689 | positive | growth | 7.1 |
| 31689 | positive | optimum | 6.9-7.5 |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 6711 | anaerobe | |
| 31689 | anaerobe | |
| 69480 | anaerobe | 99.558 |
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 31689 | no | |
| 69481 | no | 100 |
| 69480 | no | 99.977 |
halophily
| @ref | salt | growth | tested relation | concentration |
|---|---|---|---|---|
| 31689 | NaCl | positive | growth | 2-3.5 % |
| 31689 | NaCl | positive | optimum | 02-03 % |
observation
- @ref: 31689
- observation: aggregates in chains
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 31689 | 16449 | alanine | + | carbon source |
| 31689 | 16236 | ethanol | + | carbon source |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 6711 | marine surface sediment | Svalbard | Norway | NOR | Europe |
| 67770 | Arctic fjord sediment at the west coast of Svalbard |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Marine |
| #Environmental | #Aquatic | #Sediment |
taxonmaps
- @ref: 69479
- File name: preview.99_7582.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_320;96_1303;97_4338;98_5553;99_7582&stattab=map
- Last taxonomy: Maridesulfovibrio frigidus subclade
- 16S sequence: DQ148943
- Sequence Identity:
- Total samples: 797
- soil counts: 5
- aquatic counts: 706
- animal counts: 65
- plant counts: 21
Safety information
risk assessment
- @ref: 6711
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 6711
- description: Desulfovibrio frigidus strain 18 16S ribosomal RNA gene, partial sequence
- accession: DQ148943
- length: 1514
- database: ena
- NCBI tax ID: 340956
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Desulfovibrio frigidus DSM 17176 | 1121447.3 | wgs | patric | 1121447 |
| 66792 | Desulfovibrio frigidus DSM 17176 | 2565956520 | draft | img | 1121447 |
| 67770 | Maridesulfovibrio frigidus DSM 17176 | GCA_000711735 | scaffold | ncbi | 1121447 |
GC content
- @ref: 6711
- GC-content: 43.3
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| motile | yes | 91.593 | yes |
| flagellated | yes | 67.537 | no |
| gram-positive | no | 99.203 | yes |
| anaerobic | yes | 98.577 | yes |
| aerobic | no | 97.042 | yes |
| halophile | no | 64.532 | no |
| spore-forming | no | 92.74 | yes |
| thermophile | no | 99.523 | yes |
| glucose-util | no | 56.13 | no |
| glucose-ferment | no | 78.043 | no |
External links
@ref: 6711
culture collection no.: DSM 17176, JCM 12924
straininfo link
- @ref: 73658
- straininfo: 290970
literature
- topic: Phylogeny
- Pubmed-ID: 16585676
- title: Desulfovibrio frigidus sp. nov. and Desulfovibrio ferrireducens sp. nov., psychrotolerant bacteria isolated from Arctic fjord sediments (Svalbard) with the ability to reduce Fe(III).
- authors: Vandieken V, Knoblauch C, Jorgensen BB
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.64057-0
- year: 2006
- mesh: Arctic Regions, Cold Temperature, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Desulfovibrio/*classification/cytology/isolation & purification/physiology, Ferric Compounds/*metabolism, Genes, rRNA, Geologic Sediments/*microbiology, Molecular Sequence Data, RNA, Ribosomal, 16S/analysis/genetics
- topic2: Genetics
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
|---|---|---|---|---|---|---|
| 6711 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17176) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-17176 | |||
| 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 | |||
| 31689 | 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 | 27966 | 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) | |||
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
| 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 | |||
| 73658 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID290970.1 | StrainInfo: A central database for resolving microbial strain identifiers |