Strain identifier
BacDive ID: 11929
Type strain: 
Species: Hydrogenovibrio crunogenus
Strain Designation: XCL-2
Strain history: <- K.M. Scott, University of South Florida, Tampa, USA; XCL-2 <- D. Nelson, University of California, Davis
NCBI tax ID(s): 39765 (species)
version 9 (current version)
General
@ref: 17939
BacDive-ID: 11929
DSM-Number: 25203
keywords: genome sequence, Bacteria
description: Hydrogenovibrio crunogenus XCL-2 is a bacterium that was isolated from hydrothermal vents.
NCBI tax id
- NCBI tax id: 39765
- Matching level: species
strain history
- @ref: 17939
- history: <- K.M. Scott, University of South Florida, Tampa, USA; XCL-2 <- D. Nelson, University of California, Davis
doi: 10.13145/bacdive11929.20240510.9
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: 17939
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: XCL-2
type strain: no
Morphology
colony morphology
- @ref: 17939
- incubation period: 3-7 days
Culture and growth conditions
culture medium
- @ref: 17939
- 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: 17939
- growth: positive
- type: growth
- temperature: 20
Isolation, sampling and environmental information
isolation
- @ref: 17939
- sample type: hydrothermal vents
- geographic location: Pacific Ocean, Galapagos Rift
- country: Ecuador
- origin.country: ECU
- continent: Middle and South America
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Hydrothermal vent |
| #Condition | #Thermophilic (>45°C) |
Safety information
risk assessment
- @ref: 17939
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
Genome sequences
- @ref: 66792
- description: Hydrogenovibrio crunogenus XCL-2
- accession: 637000325
- assembly level: complete
- database: img
- NCBI tax ID: 317025
GC content
- @ref: 17939
- GC-content: 43
- method: sequence analysis
External links
@ref: 17939
culture collection no.: DSM 25203
straininfo link
- @ref: 81143
- straininfo: 405057
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Genetics | 17105352 | The genome of deep-sea vent chemolithoautotroph Thiomicrospira crunogena XCL-2. | Scott KM, Sievert SM, Abril FN, Ball LA, Barrett CJ, Blake RA, Boller AJ, Chain PS, Clark JA, Davis CR, Detter C, Do KF, Dobrinski KP, Faza BI, Fitzpatrick KA, Freyermuth SK, Harmer TL, Hauser LJ, Hugler M, Kerfeld CA, Klotz MG, Kong WW, Land M, Lapidus A, Larimer FW, Longo DL, Lucas S, Malfatti SA, Massey SE, Martin DD, McCuddin Z, Meyer F, Moore JL, Ocampo LH Jr, Paul JH, Paulsen IT, Reep DK, Ren Q, Ross RL, Sato PY, Thomas P, Tinkham LE, Zeruth GT | PLoS Biol | 10.1371/journal.pbio.0040383 | 2006 | Bacterial Adhesion/genetics, Carbon Dioxide/metabolism, Chemotaxis/genetics, *Genome, Bacterial, Molecular Sequence Data, Phosphates/metabolism, Piscirickettsiaceae/*genetics/metabolism, Prophages/genetics, Sequence Alignment, Signal Transduction | Metabolism |
| Phylogeny | 20975831 | Metagenomic comparison of two Thiomicrospira lineages inhabiting contrasting deep-sea hydrothermal environments. | Brazelton WJ, Baross JA | PLoS One | 10.1371/journal.pone.0013530 | 2010 | Genes, Bacterial, *Genomics, *Marine Biology, Phylogeny, Piscirickettsiaceae/classification/*genetics | Genetics |
| Enzymology | 22949195 | Preliminary X-ray crystallographic analysis of alpha-carbonic anhydrase from Thiomicrospira crunogena XCL-2. | Diaz Torres N, Gonzalez G, Biswas S, Scott KM, McKenna R | Acta Crystallogr Sect F Struct Biol Cryst Commun | 10.1107/S1744309112031053 | 2012 | Carbonic Anhydrases/*chemistry, Crystallography, X-Ray, Piscirickettsiaceae/*enzymology | |
| Metabolism | 25998503 | Activity and anion inhibition studies of the alpha-carbonic anhydrase from Thiomicrospira crunogena XCL-2 Gammaproteobacterium. | Mahon BP, Diaz-Torres NA, Pinard MA, Tu C, Silverman DN, Scott KM, McKenna R | Bioorg Med Chem Lett | 10.1016/j.bmcl.2015.05.001 | 2015 | Carbonic Anhydrase Inhibitors/chemical synthesis/chemistry/*pharmacology, Carbonic Anhydrases/*metabolism, Dose-Response Relationship, Drug, Gammaproteobacteria/*enzymology, Molecular Structure, Structure-Activity Relationship | Enzymology |
| Enzymology | 26249355 | Structural and biophysical characterization of the alpha-carbonic anhydrase from the gammaproteobacterium Thiomicrospira crunogena XCL-2: insights into engineering thermostable enzymes for CO2 sequestration. | Diaz-Torres NA, Mahon BP, Boone CD, Pinard MA, Tu C, Ng R, Agbandje-McKenna M, Silverman D, Scott K, McKenna R | Acta Crystallogr D Biol Crystallogr | 10.1107/S1399004715012183 | 2015 | Biocatalysis, Carbon Dioxide/*metabolism, Carbonic Anhydrases/*chemistry/genetics/*metabolism, Catalytic Domain, Crystallography, X-Ray, Enzyme Stability, Gammaproteobacteria/*chemistry/*enzymology/genetics, Humans, Models, Molecular, Protein Conformation, Protein Engineering, Protein Multimerization, Temperature | Metabolism |
| Metabolism | 26581415 | Dissolved inorganic carbon uptake in Thiomicrospira crunogena XCL-2 is Deltap- and ATP-sensitive and enhances RubisCO-mediated carbon fixation. | Menning KJ, Menon BB, Fox G, Scott KM | Arch Microbiol | 10.1007/s00203-015-1172-6 | 2015 | Adenosine Triphosphate/metabolism, Carbon/*metabolism, Carbon Cycle/*physiology, Gene Expression Regulation, Bacterial, Piscirickettsiaceae/enzymology/genetics/*metabolism, Ribulose-Bisphosphate Carboxylase/*metabolism | Enzymology |
| Metabolism | 26691758 | Sulfonamide inhibition studies of the alpha-carbonic anhydrase from the gammaproteobacterium Thiomicrospira crunogena XCL-2, TcruCA. | Vullo D, Bhatt A, Mahon BP, McKenna R, Supuran CT | Bioorg Med Chem Lett | 10.1016/j.bmcl.2015.11.104 | 2015 | Anti-Bacterial Agents/chemistry/*pharmacology, Carbon Dioxide/metabolism, Carbonic Anhydrase Inhibitors/chemistry/*pharmacology, Carbonic Anhydrases/*metabolism, Gammaproteobacteria/*drug effects/*enzymology, Molecular Docking Simulation, Sulfonamides/chemistry/*pharmacology | Enzymology |
| Metabolism | 31060509 | Horizontal acquisition of hydrogen conversion ability and other habitat adaptations in the Hydrogenovibrio strains SP-41 and XCL-2. | Gonnella G, Adam N, Perner M | BMC Genomics | 10.1186/s12864-019-5710-5 | 2019 | *Acclimatization, Bacterial Proteins/genetics/metabolism, *Ecosystem, Genome, Bacterial, Hydrogen/*metabolism, Hydrogenase/genetics/metabolism, Molecular Sequence Annotation, Piscirickettsiaceae/classification/*genetics | Genetics |
Reference
| @id | authors | catalogue | doi/url | title |
|---|---|---|---|---|
| 17939 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 25203) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-25203 | |
| 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 | |
| 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) | |
| 81143 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID405057.1 | StrainInfo: A central database for resolving microbial strain identifiers |