Strain identifier
BacDive ID: 13869
Type strain: 
Species: Parvibaculum hydrocarboniclasticum
Strain history: C. Vetriani EPR 92.
NCBI tax ID(s): 884688 (species)
version 8.1 (current version)
General
@ref: 16750
BacDive-ID: 13869
DSM-Number: 23209
keywords: 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, motile, rod-shaped
description: Parvibaculum hydrocarboniclasticum DSM 23209 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from hydrothermal fluids.
NCBI tax id
- NCBI tax id: 884688
- Matching level: species
strain history
| @ref | history |
|---|---|
| 16750 | <- C. Vetriani, Rutgers, State Univ. New Jersey, New Brunswick, USA; EPR92 <- R. Rosario-Passapera <- C. Vetriani <- R. Wong |
| 67770 | C. Vetriani EPR 92. |
doi: 10.13145/bacdive13869.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Hyphomicrobiales
- family: Parvibaculaceae
- genus: Parvibaculum
- species: Parvibaculum hydrocarboniclasticum
- full scientific name: Parvibaculum hydrocarboniclasticum Rosario-Passapera et al. 2012
@ref: 16750
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhizobiales
family: Parvibaculaceae
genus: Parvibaculum
species: Parvibaculum hydrocarboniclasticum
full scientific name: Parvibaculum hydrocarboniclasticum Rosario-Passapera et al. 2012
type strain: yes
Morphology
cell morphology
- @ref: 30598
- gram stain: negative
- cell length: 1.4 µm
- cell width: 0.4 µm
- cell shape: rod-shaped
- motility: yes
Culture and growth conditions
culture medium
- @ref: 16750
- name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)
- growth: yes
- link: https://mediadive.dsmz.de/medium/514
- composition: Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 16750 | positive | growth | 30 | mesophilic |
| 30598 | positive | growth | 20-40 | |
| 30598 | positive | optimum | 35 | mesophilic |
| 67770 | positive | growth | 35 | mesophilic |
culture pH
| @ref | ability | type | pH | PH range |
|---|---|---|---|---|
| 30598 | positive | growth | 4-8.5 | alkaliphile |
| 30598 | positive | optimum | 7.5 |
Physiology and metabolism
oxygen tolerance
- @ref: 30598
- oxygen tolerance: aerobe
halophily
| @ref | salt | growth | tested relation | concentration |
|---|---|---|---|---|
| 30598 | NaCl | positive | growth | 01-05 % |
| 30598 | NaCl | positive | optimum | 2.5 % |
observation
- @ref: 67770
- observation: quinones: Q-10
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 30598 | catalase | + | 1.11.1.6 |
| 30598 | cytochrome oxidase | + | 1.9.3.1 |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | latitude | longitude |
|---|---|---|---|---|
| 16750 | hydrothermal fluids | East Pacific Rise, Tica vent (9° 50' N 104° 17' W) at a depth of 2513 m | 9.8333 | -104.283 |
| 67770 | Hydrothermal vent fluids collected from the East Pacific Rise |
isolation source categories
| Cat1 | Cat2 |
|---|---|
| #Environmental | #Aquatic |
| #Condition | #Thermophilic (>45°C) |
taxonmaps
- @ref: 69479
- File name: preview.99_15790.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_631;96_8053;97_9690;98_11909;99_15790&stattab=map
- Last taxonomy: Parvibaculum
- 16S sequence: GU574708
- Sequence Identity:
- Total samples: 1318
- soil counts: 448
- aquatic counts: 796
- animal counts: 39
- plant counts: 35
Safety information
risk assessment
- @ref: 16750
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 16750
- description: Parvibaculum hydrocarboniclasticum strain EPR92 16S ribosomal RNA gene, partial sequence
- accession: GU574708
- length: 1304
- database: ena
- NCBI tax ID: 884688
GC content
| @ref | GC-content | method |
|---|---|---|
| 16750 | 60.7 | high performance liquid chromatography (HPLC) |
| 30598 | 60.7 |
External links
@ref: 16750
culture collection no.: DSM 23209, JCM 16666, EPR 92
straininfo link
- @ref: 83045
- straininfo: 407864
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 22268074 | Parvibaculum hydrocarboniclasticum sp. nov., a mesophilic, alkane-oxidizing alphaproteobacterium isolated from a deep-sea hydrothermal vent on the East Pacific Rise. | Rosario-Passapera R, Keddis R, Wong R, Lutz RA, Starovoytov V, Vetriani C | Int J Syst Evol Microbiol | 10.1099/ijs.0.039594-0 | 2012 | Alkanes/metabolism, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Hydrothermal Vents/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Pacific Ocean, Phyllobacteriaceae/*classification/genetics/isolation & purification/metabolism, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA | Metabolism |
| Phylogeny | 26476620 | Pyruvatibacter mobilis gen. nov., sp. nov., a marine bacterium from the culture broth of Picochlorum sp. 122. | Wang G, Tang M, Wu H, Dai S, Li T, Chen C, He H, Fan J, Xiang W, Li X | Int J Syst Evol Microbiol | 10.1099/ijsem.0.000692 | 2015 | Alphaproteobacteria/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Chlorophyta/*microbiology, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Ubiquinone/analogs & derivatives/chemistry | Genetics |
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
|---|---|---|---|---|---|---|
| 16750 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23209) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-23209 | |||
| 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 | |||
| 30598 | 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 | 26929 | 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 | |||
| 83045 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID407864.1 | StrainInfo: A central database for resolving microbial strain identifiers |