Strain identifier
BacDive ID: 6092
Type strain: 
Species: Guyparkeria hydrothermalis
Strain Designation: R3
Strain history: <- P. Durand, Station Biologique, CNRS, Roscoff, France; R3 <- P. Durand {1989}
NCBI tax ID(s): 923 (species)
version 8.1 (current version)
General
@ref: 3012
BacDive-ID: 6092
DSM-Number: 7121
keywords: genome sequence, 16S sequence, Bacteria, halophilic, chemoautolithotroph, mesophilic, Gram-negative, motile, rod-shaped, colony-forming
description: Guyparkeria hydrothermalis R3 is a halophilic, chemoautolithotroph, mesophilic bacterium that forms circular colonies and was isolated from deep-sea hydrothermal vent.
NCBI tax id
- NCBI tax id: 923
- Matching level: species
strain history
- @ref: 3012
- history: <- P. Durand, Station Biologique, CNRS, Roscoff, France; R3 <- P. Durand {1989}
doi: 10.13145/bacdive6092.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Chromatiales
- family: Thioalkalibacteraceae
- genus: Guyparkeria
- species: Guyparkeria hydrothermalis
- full scientific name: Guyparkeria hydrothermalis (Durand et al. 1997) Boden 2017
synonyms
@ref synonym 20215 Halothiobacillus hydrothermalis 20215 Thiobacillus hydrothermalis
@ref: 3012
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Chromatiales
family: Thioalkalibacteraceae
genus: Guyparkeria
species: Guyparkeria hydrothermalis
full scientific name: Guyparkeria hydrothermalis (Durand et al. 1997) Boden 2017
strain designation: R3
type strain: yes
Morphology
cell morphology
- @ref: 43579
- gram stain: negative
- cell length: 1 µm
- cell width: 0.5 µm
- cell shape: rod-shaped
- motility: yes
- flagellum arrangement: polar
colony morphology
- @ref: 43579
- colony size: 1-3 mm
- colony color: off-white
- colony shape: circular
- medium used: Basal salts agar
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 3012 | GUYPARKERIA HYDROTHERMALIS MEDIUM (DSMZ Medium 574) | yes | https://mediadive.dsmz.de/medium/574 | Name: GUYPARKERIA HYDROTHERMALIS MEDIUM (DSMZ Medium 574) Composition: NaCl 25.0 g/l Na2S2O3 x 5 H2O 2.5 g/l MgSO4 x 7 H2O 1.5 g/l (NH4)2SO4 1.0 g/l KH2PO4 0.4 g/l NaHCO3 0.2 g/l Na2-EDTA 0.05 g/l Phenol red 0.01 g/l CaCl2 x 2 H2O 0.0055 g/l MnCl2 x 4 H2O 0.0051 g/l FeSO4 x 7 H2O 0.005 g/l ZnSO4 x 7 H2O 0.0022 g/l CoCl2 x 6 H2O 0.0016 g/l CuSO4 x 5 H2O 0.0016 g/l (NH4)6Mo7O24 x 4 H2O 0.0011 g/l Tris-HCl buffer Distilled water |
| 43579 | Basal salts agar | yes | supplemented with thiosulfate |
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 3012 | positive | growth | 35 | mesophilic |
| 43579 | positive | growth | 11-45 | |
| 43579 | positive | optimum | 35-40 |
culture pH
| @ref | ability | type | pH | PH range |
|---|---|---|---|---|
| 43579 | positive | growth | 6.0-9.0 | alkaliphile |
| 43579 | positive | optimum | 7.5-8.0 |
Physiology and metabolism
nutrition type
- @ref: 43579
- type: chemoautolithotroph
halophily
| @ref | halophily level | salt | growth | tested relation | concentration |
|---|---|---|---|---|---|
| 43579 | halophilic | NaCl | positive | optimum | 0.43 M |
| 43579 | NaCl | positive | optimum | 2.5 %(w/v) | |
| 43579 | NaCl | positive | maximum | 2 M | |
| 43579 | NaCl | positive | maximum | 11.6 %(w/v) |
observation
- @ref: 43579
- observation: quinone UQ-8
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 43579 | 18022 | thiocyanate | - | electron donor |
| 43579 | 33403 | elemental sulfur | + | electron donor |
| 43579 | 15138 | sulfide | + | electron donor |
| 43579 | 15226 | tetrathionate | + | electron donor |
| 43579 | 16094 | thiosulfate | + | electron donor |
| 43579 | 28938 | ammonium | + | nitrogen source |
| 43579 | 17632 | nitrate | + | reduction |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 3012 | deep-sea hydrothermal vent | Basin | Fiji | FJI | Australia and Oceania |
| 43579 | fragments of chimney of deep-water hydrothermal vent, North Fiji Basin, Pacific Ocean | North Fiji Basin | Fiji | FJI | Australia and Oceania |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Condition | #Thermophilic (>45°C) | |
| #Environmental | #Aquatic | #Hydrothermal vent |
| #Environmental | #Aquatic | #Marine |
taxonmaps
- @ref: 69479
- File name: preview.99_77669.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_122;96_3167;97_3882;98_4932;99_77669&stattab=map
- Last taxonomy: Guyparkeria
- 16S sequence: M90662
- Sequence Identity:
- Total samples: 117
- soil counts: 28
- aquatic counts: 89
Safety information
risk assessment
- @ref: 3012
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 3012
- description: Thiobacillus hydrothermalis 16S ribosomal RNA
- accession: M90662
- length: 1504
- database: ena
- NCBI tax ID: 923
Genome sequences
- @ref: 66792
- description: Guyparkeria hydrothermalis R3
- accession: GCA_023555375
- assembly level: contig
- database: ncbi
- NCBI tax ID: 923
GC content
| @ref | GC-content | method |
|---|---|---|
| 3012 | 67.1 | |
| 3012 | 67.4 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| flagellated | yes | 76.297 | no |
| gram-positive | no | 98.587 | yes |
| anaerobic | no | 95.941 | no |
| aerobic | no | 68.283 | no |
| halophile | yes | 65.442 | yes |
| spore-forming | no | 97.275 | no |
| motile | yes | 89.689 | yes |
| glucose-ferment | no | 86.914 | no |
| thermophile | no | 74.043 | no |
| glucose-util | yes | 55.06 | no |
External links
@ref: 3012
culture collection no.: DSM 7121, ATCC 51453
straininfo link
- @ref: 75580
- straininfo: 42993
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 3012 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 7121) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-7121 | |||
| 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 | |||
| 43579 | Rich Boden | 10.1099/ijsem.0.002222 | Reclassification of Halothiobacillus hydrothermalis and Halothiobacillus halophilus to Guyparkeria gen. nov. in the Thioalkalibacteraceae fam. nov., with emended descriptions of the genus Halothiobacillus and family Halothiobacillaceae | IJSEM 67: 3919-3928 2017 | 28884673 | |
| 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) | |||
| 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 | |||
| 75580 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID42993.1 | StrainInfo: A central database for resolving microbial strain identifiers |