Strain identifier
BacDive ID: 4139
Type strain: 
Species: Desulfovibrio zosterae
Strain Designation: lac
Strain history: <- J. T. Nielsen, University of Aarhus, Department of Microbial Ecology, Denmark; lac <- J. T. Nielsen {1996}
NCBI tax ID(s): 82171 (species)
version 8.1 (current version)
General
@ref: 4563
BacDive-ID: 4139
DSM-Number: 11974
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, motile
description: Desulfovibrio zosterae lac is an anaerobe, mesophilic, motile bacterium that was isolated from rhizosphere of eel grass Zostera marina.
NCBI tax id
- NCBI tax id: 82171
- Matching level: species
strain history
- @ref: 4563
- history: <- J. T. Nielsen, University of Aarhus, Department of Microbial Ecology, Denmark; lac <- J. T. Nielsen {1996}
doi: 10.13145/bacdive4139.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Deltaproteobacteria
- order: Desulfovibrionales
- family: Desulfovibrionaceae
- genus: Desulfovibrio
- species: Desulfovibrio zosterae
- full scientific name: Desulfovibrio zosterae Nielsen et al. 1999
synonyms
- @ref: 20215
- synonym: Maridesulfovibrio zosterae
@ref: 4563
domain: Bacteria
phylum: Proteobacteria
class: Deltaproteobacteria
order: Desulfovibrionales
family: Desulfovibrionaceae
genus: Desulfovibrio
species: Desulfovibrio zosterae
full scientific name: Desulfovibrio zosterae Nielsen et al. 1999
strain designation: lac
type strain: yes
Morphology
cell morphology
| @ref | motility | confidence | gram stain |
|---|---|---|---|
| 69480 | yes | 94.71 | |
| 69480 | 99.992 | negative |
Culture and growth conditions
culture medium
- @ref: 4563
- name: DESULFOBACTER SP. MEDIUM (LACTATE) (DSMZ Medium 195c)
- growth: yes
- link: https://mediadive.dsmz.de/medium/195c
- composition: Name: DESULFOBACTER SP. MEDIUM (LACTATE) (DSMZ Medium 195c; with strain-specific modifications) Composition: NaCl 21.3631 g/l Na2SO4 3.05188 g/l MgCl2 x 6 H2O 3.05188 g/l Na-L-lactate 2.54324 g/l Na2CO3 1.52594 g/l KCl 0.508647 g/l Na2S x 9 H2O 0.406918 g/l NH4Cl 0.305188 g/l KH2PO4 0.203459 g/l CaCl2 x 2 H2O 0.152594 g/l HCl 0.00254323 g/l FeCl2 x 4 H2O 0.00152594 g/l NaOH 0.000508647 g/l Sodium resazurin 0.000478128 g/l Pyridoxine hydrochloride 0.000305188 g/l Nicotinic acid 0.000203459 g/l Thiamine-HCl x 2 H2O 0.000203459 g/l CoCl2 x 6 H2O 0.000193286 g/l MnCl2 x 4 H2O 0.000101729 g/l Calcium pantothenate 0.000101729 g/l Vitamin B12 0.000101729 g/l p-Aminobenzoic acid 8.13835e-05 g/l ZnCl2 7.12106e-05 g/l Riboflavin 5.08647e-05 g/l Calcium D-(+)-pantothenate 5.08647e-05 g/l (DL)-alpha-Lipoic acid 5.08647e-05 g/l Thiamine HCl 5.08647e-05 g/l Na2MoO4 x 2 H2O 3.66226e-05 g/l NiCl2 x 6 H2O 2.44151e-05 g/l D-(+)-biotin 2.03459e-05 g/l Folic acid 2.03459e-05 g/l Biotin 2.03459e-05 g/l H3BO3 6.10376e-06 g/l Na2WO4 x 2 H2O 4.06918e-06 g/l Na2SeO3 x 5 H2O 3.05188e-06 g/l CuCl2 x 2 H2O 2.03459e-06 g/l Distilled water
culture temp
- @ref: 4563
- growth: positive
- type: growth
- temperature: 25
- range: mesophilic
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 4563 | anaerobe | |
| 69480 | anaerobe | 99.691 |
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 99.93 |
Isolation, sampling and environmental information
isolation
- @ref: 4563
- sample type: rhizosphere of eel grass Zostera marina
- host species: Zostera marina
- geographic location: Limfjorden
- country: Denmark
- origin.country: DNK
- continent: Europe
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Host | #Plants | #Aquatic plant |
| #Host Body-Site | #Plant | #Rhizosphere |
Safety information
risk assessment
- @ref: 4563
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 4563
- description: Desulfovibrio zosterae 16S rRNA gene
- accession: Y18049
- length: 1477
- database: ena
- NCBI tax ID: 82171
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Maridesulfovibrio zosterae DSM 11974 | GCA_000425265 | scaffold | ncbi | 1121467 |
| 66792 | Desulfovibrio zosterae DSM 11974 | 1121467.3 | wgs | patric | 1121467 |
| 66792 | Desulfovibrio zosterae DSM 11974 | 2523533628 | draft | img | 1121467 |
GC content
- @ref: 4563
- GC-content: 41.8
- method: sequence analysis
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| motile | yes | 89.761 | no |
| flagellated | yes | 72.973 | no |
| gram-positive | no | 99.34 | no |
| anaerobic | yes | 98.387 | yes |
| aerobic | no | 98.272 | yes |
| halophile | no | 70.17 | no |
| spore-forming | no | 94.505 | no |
| thermophile | no | 98.159 | yes |
| glucose-util | no | 50 | no |
| glucose-ferment | no | 71.878 | no |
External links
@ref: 4563
culture collection no.: DSM 11974
straininfo link
- @ref: 73642
- straininfo: 49209
literature
- topic: Phylogeny
- Pubmed-ID: 10319511
- title: Desulfovibrio zosterae sp. nov., a new sulfate reducer isolated from surface-sterilized roots of the seagrass Zostera marina.
- authors: Nielsen JT, Liesack W, Finster K
- journal: Int J Syst Bacteriol
- DOI: 10.1099/00207713-49-2-859
- year: 1999
- mesh: Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Desulfovibrio/*classification/genetics/isolation & purification/physiology, Fatty Acids/analysis, Fructose/metabolism, Genes, rRNA, Molecular Sequence Data, Oxidation-Reduction, Phenotype, Phylogeny, Pigments, Biological/analysis, Plant Roots/*microbiology, *Poaceae, RNA, Ribosomal, 16S/genetics, Sulfates/*metabolism
- topic2: Metabolism
Reference
| @id | authors | catalogue | doi/url | title |
|---|---|---|---|---|
| 4563 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 11974) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-11974 | |
| 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) | |
| 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 | |
| 73642 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID49209.1 | StrainInfo: A central database for resolving microbial strain identifiers |