Strain identifier
BacDive ID: 11909
Type strain: 
Species: Sulfurivirga caldicuralii
Strain Designation: MM1
Strain history: K. Takai MM1.
NCBI tax ID(s): 364032 (species)
version 8.1 (current version)
General
@ref: 6928
BacDive-ID: 11909
DSM-Number: 17737
keywords: genome sequence, 16S sequence, Bacteria, microaerophile, thermophilic, Gram-negative, motile, rod-shaped
description: Sulfurivirga caldicuralii MM1 is a microaerophile, thermophilic, Gram-negative bacterium that was isolated from shallow marine hydrothermal system occurring in coral reefs off Taketomi Island.
NCBI tax id
- NCBI tax id: 364032
- Matching level: species
strain history
| @ref | history |
|---|---|
| 6928 | <- K. Takai, Subground Animalcule Retrieval (SUGAR) Program, Japan Agency for Marine-Earth Science and Technology (JAMSTEC); MM1 <- K. Takai et al. |
| 67770 | K. Takai MM1. |
doi: 10.13145/bacdive11909.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Beggiatoales
- family: Piscirickettsiaceae
- genus: Sulfurivirga
- species: Sulfurivirga caldicuralii
- full scientific name: Sulfurivirga caldicuralii Takai et al. 2006
@ref: 6928
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Thiotrichales
family: Piscirickettsiaceae
genus: Sulfurivirga
species: Sulfurivirga caldicuralii
full scientific name: Sulfurivirga caldicuralii Takai et al. 2006
strain designation: MM1
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell width | cell shape | motility | confidence |
|---|---|---|---|---|---|---|
| 31795 | negative | 01-03 µm | 0.3-0.6 µm | rod-shaped | yes | |
| 69480 | negative | 99.999 |
pigmentation
- @ref: 31795
- production: yes
Culture and growth conditions
culture medium
- @ref: 6928
- name: MMJS MEDIUM (MODIFIED) (DSMZ Medium 1121)
- growth: yes
- link: https://mediadive.dsmz.de/medium/1121
- composition: Name: MMJS MEDIUM (modified) (DSMZ Medium 1121) Composition: NaCl 20.0 g/l MgSO4 x 7 H2O 4.0 g/l Sulfur 3.0 g/l MgCl2 x 6 H2O 3.0 g/l Na2S2O3 x 5 H2O 3.0 g/l NaHCO3 2.0 g/l NH4Cl 1.25 g/l CaCl2 x 2 H2O 0.8 g/l KCl 0.33 g/l K2HPO4 0.09 g/l KH2PO4 0.07 g/l Nitrilotriacetic acid 0.015 g/l Fe(III) citrate 0.01 g/l FeSO4 x 7 H2O 0.01 g/l Fe2(SO4)3 x n H2O 0.01 g/l CoSO4 x 7 H2O 0.005 g/l MnSO4 x n H2O 0.005 g/l ZnSO4 x 7 H2O 0.0018 g/l H2WO4 0.001 g/l Na2SeO3 x 5 H2O 0.001 g/l NiCl2 x 6 H2O 0.001 g/l AlK(SO4)2 x 12 H2O 0.0002 g/l CuSO4 x 5 H2O 0.0001 g/l KI 0.0001 g/l NaBr 0.0001 g/l SrCl2 x 6 H2O 0.0001 g/l H3BO3 0.0001 g/l Pyridoxine hydrochloride 1e-05 g/l Na2MoO4 x 2 H2O 1e-05 g/l Lipoic acid 5e-06 g/l p-Aminobenzoic acid 5e-06 g/l D-Calcium pantothenate 5e-06 g/l Nicotinic acid 5e-06 g/l Riboflavin 5e-06 g/l Thiamine-HCl x 2 H2O 5e-06 g/l Folic acid 2e-06 g/l Biotin 2e-06 g/l Vitamin B12 1e-07 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 6928 | positive | growth | 55 | thermophilic |
| 31795 | positive | growth | 30-60 | |
| 31795 | positive | optimum | 50-55 | thermophilic |
| 67770 | positive | growth | 55 | thermophilic |
culture pH
| @ref | ability | type | pH |
|---|---|---|---|
| 31795 | positive | growth | 5.5-7.1 |
| 31795 | positive | optimum | 6 |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance |
|---|---|
| 6928 | microaerophile |
| 31795 | microaerophile |
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 31795 | no | |
| 69481 | no | 98 |
| 69480 | no | 99.996 |
observation
- @ref: 31795
- observation: aggregates in chains
Isolation, sampling and environmental information
isolation
| @ref | sample type | country | origin.country | continent | geographic location |
|---|---|---|---|---|---|
| 6928 | shallow marine hydrothermal system occurring in coral reefs off Taketomi Island | Japan | JPN | Asia | |
| 67770 | Microbial mat sample from a shallow hydrothermal system occurring in coral reefs off Taketomi Island | Japan | JPN | Asia | Okinawa |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Coral reef |
| #Environmental | #Aquatic | #Marine |
| #Condition | #Thermophilic (>45°C) |
taxonmaps
- @ref: 69479
- File name: preview.99_2263.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_16361;96_1223;97_1449;98_1767;99_2263&stattab=map
- Last taxonomy: Sulfurivirga caldicuralii subclade
- 16S sequence: AB245479
- Sequence Identity:
- Total samples: 346
- soil counts: 35
- aquatic counts: 143
- animal counts: 154
- plant counts: 14
Safety information
risk assessment
- @ref: 6928
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 6928
- description: Sulfurivirga caldicuralii gene for 16S rRNA, partial sequence, strain: MM1
- accession: AB245479
- length: 1457
- database: ena
- NCBI tax ID: 364032
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Sulfurivirga caldicuralii strain DSM 17737 | 364032.3 | wgs | patric | 364032 |
| 66792 | Sulfurivirga caldicuralii DSM 17737 | 2695421043 | draft | img | 364032 |
| 67770 | Sulfurivirga caldicuralii DSM 17737 | GCA_900141795 | contig | ncbi | 364032 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 6928 | 50.0 | |
| 31795 | 49.5 | |
| 67770 | 49.5 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 98 | no |
| gram-positive | no | 99.264 | yes |
| anaerobic | no | 95.587 | yes |
| halophile | yes | 51.064 | no |
| spore-forming | no | 97.572 | yes |
| glucose-util | no | 60.673 | no |
| aerobic | no | 96.21 | yes |
| motile | yes | 91.362 | no |
| flagellated | yes | 71.55 | no |
| thermophile | yes | 90.315 | yes |
| glucose-ferment | no | 79.425 | no |
External links
@ref: 6928
culture collection no.: DSM 17737, JCM 13439
straininfo link
- @ref: 81123
- straininfo: 297343
literature
- topic: Phylogeny
- Pubmed-ID: 16902032
- title: Sulfurivirga caldicuralii gen. nov., sp. nov., a novel microaerobic, thermophilic, thiosulfate-oxidizing chemolithoautotroph, isolated from a shallow marine hydrothermal system occurring in a coral reef, Japan.
- authors: Takai K, Miyazaki M, Nunoura T, Hirayama H, Oida H, Furushima Y, Yamamoto H, Horikoshi K
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.64297-0
- year: 2006
- mesh: Animals, Anthozoa, Base Composition, Culture Media, DNA, Bacterial/genetics, Fatty Acids/analysis, Hydrogen-Ion Concentration, Japan, *Marine Biology, Molecular Sequence Data, Oxidation-Reduction, Phylogeny, Proteobacteria/chemistry/*classification/isolation & purification/physiology, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Homology, Nucleic Acid, Species Specificity, Temperature, Thiosulfates/metabolism, *Water Microbiology
- topic2: Cultivation
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed | journal |
|---|---|---|---|---|---|---|---|
| 6928 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17737) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-17737 | ||||
| 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 | ||||
| 31795 | 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 | 28066 | 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) | ||||
| 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 | 33211880 | Nucleic Acids Res. 49: D498-D508 2020 | ||
| 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 | ||||
| 81123 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID297343.1 | StrainInfo: A central database for resolving microbial strain identifiers |