Strain identifier
BacDive ID: 11927
Type strain: 
Species: Hydrogenovibrio crunogenus
Strain Designation: TH-55
Strain history: <- J. Kuever, Max-Planck-Inst. Marine Microbiology, Bremen, Germany; TH-55 <- C. O. Wirsen, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
NCBI tax ID(s): 39765 (species)
version 9 (current version)
General
@ref: 4712
BacDive-ID: 11927
DSM-Number: 12353
keywords: 16S sequence, Bacteria, Gram-negative, motile
description: Hydrogenovibrio crunogenus TH-55 is a Gram-negative, motile bacterium that was isolated from scrapings from outer tube of tubeworm from hydrothermal vent aerea, 2550 m depth.
NCBI tax id
- NCBI tax id: 39765
- Matching level: species
strain history
- @ref: 4712
- history: <- J. Kuever, Max-Planck-Inst. Marine Microbiology, Bremen, Germany; TH-55 <- C. O. Wirsen, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
doi: 10.13145/bacdive11927.20240510.9
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Beggiatoales
- family: Piscirickettsiaceae
- genus: Hydrogenovibrio
- species: Hydrogenovibrio crunogenus
- full scientific name: Hydrogenovibrio crunogenus (Jannasch et al. 1985) Boden et al. 2017
synonyms
- @ref: 20215
- synonym: Thiomicrospira crunogena
@ref: 4712
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Thiotrichales
family: Piscirickettsiaceae
genus: Hydrogenovibrio
species: Hydrogenovibrio crunogenus
full scientific name: Hydrogenovibrio crunogenus (Jannasch et al. 1985) Boden et al. 2017
strain designation: TH-55
type strain: yes
Morphology
cell morphology
- @ref: 43182
- gram stain: negative
- motility: yes
Culture and growth conditions
culture medium
- @ref: 4712
- name: THIOMICROSPIRA PELOPHILA MEDIUM (DSMZ Medium 142)
- growth: yes
- link: https://mediadive.dsmz.de/medium/142
- composition: Name: THIOMICROSPIRA PELOPHILA MEDIUM (DSMZ Medium 142) Composition: NaCl 24.8756 g/l Na2S2O3 x 5 H2O 4.97512 g/l MgSO4 x 7 H2O 1.49254 g/l (NH4)2SO4 0.995025 g/l K2HPO4 0.497512 g/l Na2-EDTA 0.00995025 g/l ZnSO4 x 7 H2O 0.00437811 g/l Bromothymol blue 0.0039801 g/l CaCl2 x 2 H2O 0.00110249 g/l MnCl2 x 4 H2O 0.00100697 g/l FeSO4 x 7 H2O 0.000995025 g/l CoCl2 x 6 H2O 0.000320398 g/l CuSO4 x 5 H2O 0.000312438 g/l Pyridoxine hydrochloride 0.000298507 g/l (NH4)6Mo7O24 x 4 H2O 0.000218905 g/l Nicotinic acid 0.000199005 g/l Thiamine-HCl x 2 H2O 0.000199005 g/l Vitamin B12 9.95025e-05 g/l Calcium pantothenate 9.95025e-05 g/l p-Aminobenzoic acid 7.9602e-05 g/l D-(+)-biotin 1.99005e-05 g/l Distilled water
culture temp
- @ref: 4712
- growth: positive
- type: growth
- temperature: 25
Physiology and metabolism
spore formation
| @ref | type of spore | spore formation |
|---|---|---|
| 43182 | endospore | no |
| 43182 | exospore (microbial cyst) | no |
observation
- @ref: 43182
- observation: produce carboxysomes
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 43182 | 16094 | thiosulfate | + | electron donor |
| 43182 | 15138 | sulfide | + | electron donor |
| 43182 | 18022 | thiocyanate | - | electron donor |
| 43182 | 17359 | sulfite | - | electron donor |
| 43182 | 18248 | iron | - | electron donor |
| 43182 | 18291 | manganese | - | electron donor |
| 43182 | 28938 | ammonium | + | nitrogen source |
| 43182 | 17632 | nitrate | - | nitrogen source |
| 43182 | 16301 | nitrite | - | nitrogen source |
| 43182 | 17632 | nitrate | - | reduction |
metabolite production
- @ref: 43182
- Chebi-ID: 30411
- metabolite: cobalamin
- production: yes
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 43182 | cytochrome oxidase | + | 1.9.3.1 |
| 43182 | NiFe-hydrogenase | + |
Isolation, sampling and environmental information
isolation
- @ref: 4712
- sample type: scrapings from outer tube of tubeworm from hydrothermal vent aerea, 2550 m depth
- geographic location: East Pacific Rise
- country: Mexico
- origin.country: MEX
- continent: North America
- latitude: 21
- longitude: -109
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Hydrothermal vent |
| #Host | #Invertebrates (Other) | #Annelida |
| #Condition | #Thermophilic (>45°C) |
taxonmaps
- @ref: 69479
- File name: preview.99_1999.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_118;96_1109;97_1299;98_1564;99_1999&stattab=map
- Last taxonomy: Hydrogenovibrio crunogenus subclade
- 16S sequence: KJ573629
- Sequence Identity:
- Total samples: 900
- soil counts: 104
- aquatic counts: 727
- animal counts: 48
- plant counts: 21
Safety information
risk assessment
- @ref: 4712
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | Thiomicrospira crunogena strain TH-55 16S ribosomal RNA gene, partial sequence | KJ573629 | 1478 | nuccore | 39765 |
| 4712 | Thiomicrospira crunogena 16S ribosomal RNA (16S rRNA) gene, partial sequence | L40810 | 1457 | nuccore | 39765 |
GC content
- @ref: 4712
- GC-content: 41.8-42.6
- method: thermal denaturation, midpoint method (Tm)
External links
@ref: 4712
culture collection no.: DSM 12353, ATCC 35932, LMD 84.20
straininfo link
- @ref: 81141
- straininfo: 41378
literature
| Pubmed-ID | title | authors | journal | DOI | year | topic | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| 9758841 | Comparison of a new thiomicrospira strain from the mid-atlantic ridge with known hydrothermal vent isolates | Wirsen CO, Brinkhoff T, Kuever J, Muyzer G, Molyneaux S, Jannasch HW | Appl Environ Microbiol | 10.1128/AEM.64.10.4057-4059.1998 | 1998 | |||
| 15545479 | Thiomicrospira thermophila sp. nov., a novel microaerobic, thermotolerant, sulfur-oxidizing chemolithomixotroph isolated from a deep-sea hydrothermal fumarole in the TOTO caldera, Mariana Arc, Western Pacific. | Takai K, Hirayama H, Nakagawa T, Suzuki Y, Nealson KH, Horikoshi K | Int J Syst Evol Microbiol | 10.1099/ijs.0.63284-0 | 2004 | Phylogeny | Bacterial Typing Techniques, Base Composition, Carbon Dioxide/metabolism, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Flagella/ultrastructure, Genes, rRNA, Molecular Sequence Data, Movement, Nucleic Acid Hybridization, Oxidation-Reduction, Oxygen/metabolism, Pacific Ocean, Phylogeny, Piscirickettsiaceae/*classification/cytology/*isolation & purification/physiology, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Sulfur Compounds/*metabolism, Temperature, Water Microbiology | Metabolism |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 4712 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 12353) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-12353 | |||
| 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 | |||
| 20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
| 43182 | Rich Boden, Kathleen M. Scott, John Williams, Sydney Russel, Kirsten Antonen, Alex W. Rae and Lee P. Hutt | 10.1099/ijsem.0.001855 | An evaluation of Thiomicrospira, Hydrogenovibrio and Thioalkalimicrobium: reclassification of four species of Thiomicrospira to each Thiomicrorhabdus gen. nov. and Hydrogenovibrio, and reclassification of all four species of Thioalkalimicrobium to Thiomicrospira | IJSEM 67: 1140-1151 2017 | 28581925 | |
| 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 | |||
| 81141 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID41378.1 | StrainInfo: A central database for resolving microbial strain identifiers |