Strain identifier
BacDive ID: 3968
Type strain: 
Species: Desulfocicer vacuolatum
Strain Designation: IbRM
Strain history: DSM 3385 <-- F. Widdel lbRM.
NCBI tax ID(s): 2298 (species)
version 8.1 (current version)
General
@ref: 1371
BacDive-ID: 3968
DSM-Number: 3385
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-negative
description: Desulfocicer vacuolatum IbRM is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from marine mud.
NCBI tax id
- NCBI tax id: 2298
- Matching level: species
strain history
| @ref | history |
|---|---|
| 1371 | <- F. Widdel, Universität Konstanz, Fakultät für Biologie, Konstanz, Germany; IbRM <- F. Widdel {1984} |
| 67770 | DSM 3385 <-- F. Widdel lbRM. |
doi: 10.13145/bacdive3968.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Deltaproteobacteria
- order: Desulfobacterales
- family: Desulfobacteraceae
- genus: Desulfocicer
- species: Desulfocicer vacuolatum
- full scientific name: Desulfocicer vacuolatum (Kuever et al. 2006) Galushko and Kuever 2021
synonyms
- @ref: 20215
- synonym: Desulfobacterium vacuolatum
@ref: 1371
domain: Bacteria
phylum: Pseudomonadota
class: Deltaproteobacteria
order: Desulfobacterales
family: Desulfobacteraceae
genus: Desulfocicer
species: Desulfocicer vacuolatum
full scientific name: Desulfocicer vacuolatum
strain designation: IbRM
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.993
Culture and growth conditions
culture medium
- @ref: 1371
- name: DESULFUROMUSA MEDIUM (DSMZ Medium 195a)
- growth: yes
- link: https://mediadive.dsmz.de/medium/195a
- composition: Name: DESULFUROMUSA MEDIUM (DSMZ Medium 195a) Composition: NaCl 20.9372 g/l Na2SO4 2.99103 g/l MgCl2 x 6 H2O 2.99103 g/l Na2-fumarate 2.49252 g/l Na2CO3 1.49551 g/l KCl 0.498504 g/l Na2S x 9 H2O 0.398804 g/l NH4Cl 0.299103 g/l KH2PO4 0.199402 g/l CaCl2 x 2 H2O 0.149551 g/l HCl 0.00249252 g/l FeCl2 x 4 H2O 0.00149551 g/l NaOH 0.000498504 g/l Sodium resazurin 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 p-Aminobenzoic acid 4.98504e-05 g/l (DL)-alpha-Lipoic acid 4.98504e-05 g/l Thiamine HCl 4.98504e-05 g/l Calcium D-(+)-pantothenate 4.98504e-05 g/l Riboflavin 4.98504e-05 g/l Nicotinic acid 4.98504e-05 g/l Na2MoO4 x 2 H2O 3.58923e-05 g/l NiCl2 x 6 H2O 2.39282e-05 g/l Biotin 1.99402e-05 g/l Folic acid 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 |
|---|---|---|---|---|
| 1371 | positive | growth | 30 | mesophilic |
| 67770 | positive | growth | 30 | mesophilic |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 1371 | anaerobe | |
| 69480 | anaerobe | 98.769 |
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 99.7 |
Isolation, sampling and environmental information
isolation
- @ref: 1371
- sample type: marine mud
- geographic location: Venice
- country: Italy
- origin.country: ITA
- continent: Europe
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Marine |
| #Environmental | #Terrestrial | #Mud (Sludge) |
| #Environmental | #Aquatic | #Sediment |
taxonmaps
- @ref: 69479
- File name: preview.99_6358.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_522;96_3021;97_3710;98_4701;99_6358&stattab=map
- Last taxonomy: Desulfobacterium vacuolatum subclade
- 16S sequence: AF418178
- Sequence Identity:
- Total samples: 644
- soil counts: 43
- aquatic counts: 456
- animal counts: 133
- plant counts: 12
Safety information
risk assessment
- @ref: 1371
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 1371 | Desulfobacterium vacuolatum DSM 3385 16S ribosomal RNA gene, partial sequence | AF418178 | 1553 | ena | 2298 |
| 67770 | D.vacuolatum 16S ribosomal rRNA | M34408 | 1383 | ena | 2298 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Desulfobacterium vacuolatum DSM 3385 strain DSM 3385 | 1121400.3 | wgs | patric | 1121400 |
| 66792 | Desulfobacterium vacuolatum DSM 3385 | 2681813565 | draft | img | 1121400 |
| 67770 | Desulfocicer vacuolatum DSM 3385 | GCA_900176365 | scaffold | ncbi | 1121400 |
| 66792 | Desulfocicer vacuolatum DSM 3385 MiH-14oct19-180 | GCA_945870015 | contig | ncbi | 1121400 |
| 66792 | Desulfocicer vacuolatum DSM 3385 strain MiH-14oct19-180 | 1121400.7 | wgs | patric | 1121400 |
GC content
- @ref: 1371
- GC-content: 45.0
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| motile | no | 79.93 | no |
| flagellated | no | 92.917 | no |
| gram-positive | no | 98.952 | no |
| anaerobic | yes | 98.444 | no |
| aerobic | no | 95.159 | yes |
| halophile | no | 50.568 | no |
| spore-forming | no | 90.098 | no |
| thermophile | no | 97.88 | yes |
| glucose-util | yes | 62.468 | no |
| glucose-ferment | no | 80.728 | no |
External links
@ref: 1371
culture collection no.: DSM 3385, JCM 12295
straininfo link
- @ref: 73476
- straininfo: 47719
literature
- topic: Metabolism
- Pubmed-ID: 8899985
- title: Demethylation of dimethylsulfoniopropionate to 3-S-methylmercaptopropionate by marine sulfate-reducing bacteria.
- authors: van der Maarel MJ, Jansen M, Haanstra R, Meijer WG, Hansen TA
- journal: Appl Environ Microbiol
- DOI: 10.1128/aem.62.11.3978-3984.1996
- year: 1996
- mesh: Base Sequence, Biodegradation, Environmental, DNA Primers/genetics, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Ecosystem, Fatty Acids/analysis, Kinetics, Marine Biology, Molecular Sequence Data, Phylogeny, Propionates/*metabolism, Sulfonium Compounds/*metabolism, Sulfur-Reducing Bacteria/chemistry/genetics/*metabolism, Water Microbiology
- topic2: Enzymology
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 1371 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 3385) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-3385 | |||
| 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) | |||
| 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 | |
| 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 | |||
| 73476 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID47719.1 | StrainInfo: A central database for resolving microbial strain identifiers |