Strain identifier
BacDive ID: 4153
Type strain: 
Species: Halodesulfovibrio marinisediminis
Strain Designation: NMRC 101113, C/L 2
Strain history: S. Takii C/L2.
NCBI tax ID(s): 1121457 (strain), 458711 (species)
version 8.1 (current version)
General
@ref: 6996
BacDive-ID: 4153
DSM-Number: 17456
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, vibrio-shaped
description: Halodesulfovibrio marinisediminis NMRC 101113 is an anaerobe, mesophilic, vibrio-shaped bacterium that was isolated from anoxic coastal sediment, highly eutrophic area.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 458711 | species |
| 1121457 | strain |
strain history
| @ref | history |
|---|---|
| 6996 | <- Y. Uchino <- S. Takii; C/L2 |
| 67770 | S. Takii C/L2. |
doi: 10.13145/bacdive4153.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Deltaproteobacteria
- order: Desulfovibrionales
- family: Desulfovibrionaceae
- genus: Halodesulfovibrio
- species: Halodesulfovibrio marinisediminis
- full scientific name: Halodesulfovibrio marinisediminis (Takii et al. 2008) Shivani et al. 2017
synonyms
- @ref: 20215
- synonym: Desulfovibrio marinisediminis
@ref: 6996
domain: Bacteria
phylum: Proteobacteria
class: Deltaproteobacteria
order: Desulfovibrionales
family: Desulfovibrionaceae
genus: Halodesulfovibrio
species: Halodesulfovibrio marinisediminis
full scientific name: Halodesulfovibrio marinisediminis (Takii et al. 2008) Shivani et al. 2017
strain designation: NMRC 101113, C/L 2
type strain: yes
Morphology
cell morphology
| @ref | cell length | cell width | cell shape | gram stain | motility | confidence |
|---|---|---|---|---|---|---|
| 25150 | 1.0-3.5 µm | 0.7-0.1 µm | vibrio-shaped | |||
| 32597 | 1-3.5 µm | 0.7-1 µm | coccus-shaped | negative | yes | |
| 69480 | yes | 96.269 | ||||
| 69480 | negative | 99.994 |
pigmentation
- @ref: 32597
- production: yes
Culture and growth conditions
culture medium
- @ref: 6996
- 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 20.9372 g/l Na2SO4 2.99103 g/l MgCl2 x 6 H2O 2.99103 g/l Na-L-lactate 2.49252 g/l Na2CO3 1.49551 g/l Yeast extract 0.997009 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 Nicotinic acid 4.98504e-05 g/l (DL)-alpha-Lipoic acid 4.98504e-05 g/l Thiamine HCl 4.98504e-05 g/l Riboflavin 4.98504e-05 g/l p-Aminobenzoic acid 4.98504e-05 g/l Calcium D-(+)-pantothenate 4.98504e-05 g/l Na2MoO4 x 2 H2O 3.58923e-05 g/l NiCl2 x 6 H2O 2.39282e-05 g/l Folic acid 1.99402e-05 g/l Biotin 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 |
|---|---|---|---|---|
| 6996 | positive | growth | 37 | mesophilic |
| 25150 | positive | optimum | 37 | mesophilic |
| 25150 | positive | growth | 15.0-40.0 | |
| 32597 | positive | growth | 15-40 | |
| 32597 | positive | optimum | 37 | mesophilic |
| 67770 | positive | growth | 30 | mesophilic |
culture pH
| @ref | ability | type | pH | PH range |
|---|---|---|---|---|
| 25150 | positive | optimum | 7.5 | |
| 25150 | positive | growth | 6.3-8.6 | alkaliphile |
| 32597 | positive | growth | 6.3-8.6 | |
| 32597 | positive | optimum | 7.5 |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 6996 | anaerobe | |
| 25150 | obligate anaerobe | |
| 32597 | anaerobe | |
| 69480 | anaerobe | 99.998 |
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 32597 | no | |
| 69481 | no | 100 |
| 69480 | no | 99.993 |
halophily
| @ref | salt | growth | tested relation | concentration |
|---|---|---|---|---|
| 25150 | NaCl | positive | optimum | 1.5-3.5 %(w/v) |
| 25150 | NaCl | positive | growth | 0.05-3.5 %(w/v) |
observation
| @ref | observation |
|---|---|
| 32597 | aggregates in chains |
| 67770 | quinones: MK-6(H2) |
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 25150 | 16150 | benzoate | - | electron donor |
| 25150 | 15356 | cysteine | - | electron donor |
| 25150 | 5291 | gelatin | - | hydrolysis |
| 25150 | 27897 | tryptophan | - | energy source |
| 25150 | 30089 | acetate | + | electron donor |
| 25150 | 35391 | aspartate | + | electron donor |
| 25150 | 17754 | glycerol | + | electron donor |
| 25150 | 17822 | serine | + | electron donor |
| 25150 | 17359 | sulfite | + | electron acceptor |
| 32597 | 35391 | aspartate | + | carbon source |
| 32597 | 17754 | glycerol | + | carbon source |
| 32597 | 30031 | succinate | + | carbon source |
metabolite production
- @ref: 25150
- Chebi-ID: 35581
- metabolite: indole
- production: no
metabolite tests
- @ref: 25150
- Chebi-ID: 35581
- metabolite: indole
- indole test: -
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 25150 | catalase | + | 1.11.1.6 |
| 25150 | tryptophan deaminase | - | 4.1.99.1 |
| 32597 | catalase | + | 1.11.1.6 |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 6996 | anoxic coastal sediment, highly eutrophic area | Tokyo Bay | Japan | JPN | Asia |
| 67770 | Coastal marine sediment from the eutrophic Tokyo Bay | Japan | JPN | Asia |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Sediment |
| #Condition | #Anoxic (anaerobic) |
taxonmaps
- @ref: 69479
- File name: preview.99_5213.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15981;96_2533;97_3094;98_3886;99_5213&stattab=map
- Last taxonomy: Halodesulfovibrio
- 16S sequence: AB353727
- Sequence Identity:
- Total samples: 879
- soil counts: 30
- aquatic counts: 424
- animal counts: 382
- plant counts: 43
Safety information
risk assessment
- @ref: 6996
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 6996
- description: Desulfovibrio marinisediminis gene for 16S rRNA, partial sequence
- accession: AB353727
- length: 1533
- database: ena
- NCBI tax ID: 1121457
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Halodesulfovibrio marinisediminis DSM 17456 | 1121457.4 | wgs | patric | 1121457 |
| 66792 | Halodesulfovibrio marinisediminis DSM 17456 | 2585428071 | draft | img | 1121457 |
| 67770 | Halodesulfovibrio marinisediminis DSM 17456 | GCA_900129975 | scaffold | ncbi | 1121457 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 6996 | 46.2 | high performance liquid chromatography (HPLC) |
| 25150 | 45 | genome sequence analysis |
| 32597 | 46.2 | |
| 6996 | 45 | sequence analysis |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| motile | yes | 92.354 | no |
| flagellated | yes | 54.012 | no |
| gram-positive | no | 99.215 | no |
| anaerobic | yes | 98.925 | yes |
| aerobic | no | 98.658 | no |
| halophile | no | 66.013 | no |
| spore-forming | no | 95.044 | yes |
| thermophile | no | 98.653 | no |
| glucose-util | no | 52.865 | no |
| glucose-ferment | no | 72.615 | no |
External links
@ref: 6996
culture collection no.: DSM 17456, JCM 14577, NBRC 101113
straininfo link
- @ref: 73654
- straininfo: 401170
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 18842870 | Desulfovibrio marinisediminis sp. nov., a novel sulfate-reducing bacterium isolated from coastal marine sediment via enrichment with Casamino acids. | Takii S, Hanada S, Hase Y, Tamaki H, Uyeno Y, Sekiguchi Y, Matsuura K | Int J Syst Evol Microbiol | 10.1099/ijs.0.65750-0 | 2008 | Amino Acids/chemistry, Base Composition, DNA, Bacterial/genetics, Desulfovibrio/chemistry/*classification/*genetics/isolation & purification, Genes, Bacterial, Genes, rRNA, Geologic Sediments/*microbiology, Japan, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sulfates/metabolism, *Water Microbiology | Genetics |
| Phylogeny | 20012196 | Desulfovibrio oceani subsp. oceani sp. nov., subsp. nov. and Desulfovibrio oceani subsp. galateae subsp. nov., novel sulfate-reducing bacteria isolated from the oxygen minimum zone off the coast of Peru. | Finster KW, Kjeldsen KU | Antonie Van Leeuwenhoek | 10.1007/s10482-009-9403-y | 2009 | Bacterial Typing Techniques, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Desulfovibrio/*classification/isolation & purification/*metabolism, Fatty Acids/analysis, Hydrogen-Ion Concentration, Locomotion, Molecular Sequence Data, Nucleic Acid Hybridization, Oxidation-Reduction, Pacific Ocean, Peru, Phylogeny, Quinones/analysis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, RNA, Untranslated/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Sodium Chloride/metabolism, Sulfates/*metabolism, Temperature | Metabolism |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed | ID_cross_reference |
|---|---|---|---|---|---|---|---|
| 6996 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17456) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-17456 | ||||
| 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 | ||||
| 25150 | Y. S. Shivani, Y.,Sasikala, C.,Ramana, C. V. | 10.1099/ijsem.0.001574 | Halodesulfovibrio spirochaetisodalis gen. nov. sp. nov. and reclassification of four Desulfovibrio spp | IJSEM 67: 87-93 2017 | 27902290 | ||
| 32597 | 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 | 28776041 | 28810 | ||
| 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 | ||||
| 73654 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID401170.1 | StrainInfo: A central database for resolving microbial strain identifiers |