Strain identifier
BacDive ID: 6117
Type strain: 
Species: Sulfurovum lithotrophicum
Strain Designation: 42BKT
Strain history: F. Inagaki 42BKT.
NCBI tax ID(s): 206403 (species)
version 8.1 (current version)
General
@ref: 16777
BacDive-ID: 6117
DSM-Number: 23290
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-negative, ovoid-shaped
description: Sulfurovum lithotrophicum 42BKT is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from marine sediment.
NCBI tax id
- NCBI tax id: 206403
- Matching level: species
strain history
| @ref | history |
|---|---|
| 16777 | <- T. Itoh, JCM/RIKEN <- F. Inagaki, Subground Animalcule Retrieval (SUGAR) Program, Japan Agency for Marine-Earth Science and Technology (JAMSTEC); 42BKT |
| 67770 | F. Inagaki 42BKT. |
doi: 10.13145/bacdive6117.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Epsilonproteobacteria
- order: Campylobacterales
- family: Helicobacteraceae
- genus: Sulfurovum
- species: Sulfurovum lithotrophicum
- full scientific name: Sulfurovum lithotrophicum Inagaki et al. 2004
@ref: 16777
domain: Bacteria
phylum: Proteobacteria
class: Epsilonproteobacteria
order: Campylobacterales
family: Helicobacteraceae
genus: Sulfurovum
species: Sulfurovum lithotrophicum
full scientific name: Sulfurovum lithotrophicum Inagaki et al. 2004
strain designation: 42BKT
type strain: yes
Morphology
cell morphology
- @ref: 30186
- gram stain: negative
- cell length: 0.5-1.2 µm
- cell width: 0.4-0.8 µm
- cell shape: ovoid-shaped
- motility: no
Culture and growth conditions
culture medium
- @ref: 16777
- name: SULFURIMONAS MJ MEDIUM (DSMZ Medium 1011)
- growth: yes
- link: https://mediadive.dsmz.de/medium/1011
- composition: Name: SULFURIMONAS MJ MEDIUM (DSMZ Medium 1011; with strain-specific modifications) Composition: MgCl2 x 6 H2O 4.13452 g/l NaNO3 1.97824 g/l NaHCO3 1.48368 g/l Na2S2O3 x 5 H2O 1.48368 g/l KCl 0.326409 g/l NH4Cl 0.24728 g/l K2HPO4 0.138477 g/l MgSO4 x 7 H2O 0.0296736 g/l Nitrilotriacetic acid 0.0148368 g/l Fe(NH4)2(SO4)2 x 6 H2O 0.0098912 g/l NaCl 0.0098912 g/l MnSO4 x H2O 0.0049456 g/l CoSO4 x 7 H2O 0.00178042 g/l ZnSO4 x 7 H2O 0.00178042 g/l CaCl2 x 2 H2O 0.00098912 g/l FeSO4 x 7 H2O 0.00098912 g/l NiCl2 x 6 H2O 0.000296736 g/l AlK(SO4)2 x 12 H2O 0.000197824 g/l CuSO4 x 5 H2O 9.8912e-05 g/l Pyridoxine hydrochloride 9.8912e-05 g/l Na2MoO4 x 2 H2O 9.8912e-05 g/l H3BO3 9.8912e-05 g/l p-Aminobenzoic acid 4.9456e-05 g/l (DL)-alpha-Lipoic acid 4.9456e-05 g/l Calcium D-(+)-pantothenate 4.9456e-05 g/l Nicotinic acid 4.9456e-05 g/l Riboflavin 4.9456e-05 g/l Thiamine HCl 4.9456e-05 g/l Folic acid 1.97824e-05 g/l Biotin 1.97824e-05 g/l Na2WO4 x 2 H2O 3.95648e-06 g/l Na2SeO3 x 5 H2O 2.96736e-06 g/l Vitamin B12 9.8912e-07 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 16777 | positive | growth | 28 | mesophilic |
| 30186 | positive | growth | 10-40 | |
| 30186 | positive | optimum | 29 | mesophilic |
| 67770 | positive | growth | 28 | mesophilic |
culture pH
| @ref | ability | type | pH | PH range |
|---|---|---|---|---|
| 30186 | positive | growth | 4.5-9.0 | alkaliphile |
| 30186 | positive | optimum | 6.75 |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance |
|---|---|
| 16777 | anaerobe |
| 30186 | anaerobe |
spore formation
- @ref: 30186
- spore formation: no
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent | latitude | longitude |
|---|---|---|---|---|---|---|---|
| 16777 | marine sediment | Mid-Okinawa Trough, Iheya North hydrothermal system | Japan | JPN | Asia | 27.7833 | 126.9 |
| 67770 | Gas-bubbling sediment at the Iheya hydrothermal system in the mid-Okinawa Trough | Japan | JPN | Asia |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Marine |
| #Environmental | #Aquatic | #Sediment |
taxonmaps
- @ref: 69479
- File name: preview.99_638.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_132;96_398;97_450;98_517;99_638&stattab=map
- Last taxonomy: Sulfurovum lithotrophicum
- 16S sequence: AB091292
- Sequence Identity:
- Total samples: 73
- soil counts: 8
- aquatic counts: 65
Safety information
risk assessment
- @ref: 16777
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 16777
- description: Sulfurovum lithotrophicum gene for 16S ribosomal RNA, partial sequence
- accession: AB091292
- length: 1406
- database: ena
- NCBI tax ID: 206403
Genome sequences
- @ref: 67770
- description: Sulfurovum lithotrophicum ATCC BAA-797
- accession: GCA_000987835
- assembly level: complete
- database: ncbi
- NCBI tax ID: 206403
GC content
| @ref | GC-content | method |
|---|---|---|
| 16777 | 48.0 | high performance liquid chromatography (HPLC) |
| 30186 | 48 | |
| 67770 | 48 | high performance liquid chromatography (HPLC) |
External links
@ref: 16777
culture collection no.: DSM 23290, ATCC BAA 797, JCM 12117
straininfo link
- @ref: 75604
- straininfo: 134309
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 15388698 | Sulfurovum lithotrophicum gen. nov., sp. nov., a novel sulfur-oxidizing chemolithoautotroph within the epsilon-Proteobacteria isolated from Okinawa Trough hydrothermal sediments. | Inagaki F, Takai K, Nealson KH, Horikoshi K | Int J Syst Evol Microbiol | 10.1099/ijs.0.03042-0 | 2004 | Base Composition, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Epsilonproteobacteria/*classification/*isolation & purification/physiology/ultrastructure, Genes, rRNA/genetics, Geologic Sediments/*microbiology, Gram-Negative Bacteria/classification/isolation & purification/physiology/ultrastructure, Hydrogen-Ion Concentration, Japan, Molecular Sequence Data, Nitrates/metabolism, Oxidation-Reduction, Oxygen/metabolism, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sulfur/*metabolism, Temperature, Thiosulfates/metabolism, Water Microbiology | Enzymology |
| Phylogeny | 27116914 | Sulfurovum riftiae sp. nov., a mesophilic, thiosulfate-oxidizing, nitrate-reducing chemolithoautotrophic epsilonproteobacterium isolated from the tube of the deep-sea hydrothermal vent polychaete Riftia pachyptila. | Giovannelli D, Chung M, Staley J, Starovoytov V, Le Bris N, Vetriani C | Int J Syst Evol Microbiol | 10.1099/ijsem.0.001106 | 2016 | Animals, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Epsilonproteobacteria/*classification/genetics/isolation & purification, Fatty Acids/chemistry, Hydrothermal Vents/*microbiology, Nitrates/metabolism, Oxidation-Reduction, Phospholipids/chemistry, *Phylogeny, Polychaeta/*microbiology, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Thiosulfates/metabolism, Vitamin K 2/analogs & derivatives/chemistry | Metabolism |
| Genetics | 28904743 | Complete genome sequence of the sulfur-oxidizing chemolithoautotrophic Sulfurovum lithotrophicum 42BKT(T). | Jeon W, Priscilla L, Park G, Lee H, Lee N, Lee D, Kwon H, Ahn I, Lee C, Lee H, Ahn J | Stand Genomic Sci | 10.1186/s40793-017-0265-z | 2017 |
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
|---|---|---|---|---|---|---|
| 16777 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23290) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-23290 | |||
| 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 | |||
| 30186 | 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 | 26534 | 28776041 | |
| 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 | |||
| 75604 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID134309.1 | StrainInfo: A central database for resolving microbial strain identifiers |