Strain identifier
BacDive ID: 6198
Type strain: 
Species: Pelagibacterium halotolerans
Strain Designation: B2
Strain history: X.-W. Xu B2.
NCBI tax ID(s): 1082931 (strain), 531813 (species)
version 9.1 (current version)
General
@ref: 16304
BacDive-ID: 6198
DSM-Number: 22347
keywords: genome sequence, 16S sequence, Bacteria, Gram-negative
description: Pelagibacterium halotolerans B2 is a Gram-negative bacterium that was isolated from Sea water.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 1082931 | strain |
| 531813 | species |
strain history
| @ref | history |
|---|---|
| 16304 | <- X.-W. Xu, Zhejiang Univ., Zijingang Campus, P.R. China; B2 |
| 67770 | X.-W. Xu B2. |
doi: 10.13145/bacdive6198.20240916.9.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Hyphomicrobiales
- family: Devosiaceae
- genus: Pelagibacterium
- species: Pelagibacterium halotolerans
- full scientific name: Pelagibacterium halotolerans Xu et al. 2011
@ref: 16304
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhizobiales
family: Devosiaceae
genus: Pelagibacterium
species: Pelagibacterium halotolerans
full scientific name: Pelagibacterium halotolerans Xu et al. 2011
strain designation: B2
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 96.6
Culture and growth conditions
culture medium
- @ref: 16304
- 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 |
|---|---|---|---|
| 16304 | positive | growth | 28 |
| 67770 | positive | growth | 30 |
Physiology and metabolism
spore formation
- @ref: 69480
- spore formation: no
- confidence: 94.369
observation
- @ref: 67770
- observation: quinones: Q-10, Q-9
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent | latitude | longitude |
|---|---|---|---|---|---|---|---|
| 16304 | Sea water | East China Sea (30° 58' 16'' N 125° 59' 24'' E) | China | CHN | Asia | 30.9711 | 125.99 |
| 67770 | Seawater sample collected from the East China Sea |
isolation source categories
- Cat1: #Environmental
- Cat2: #Aquatic
- Cat3: #Marine
taxonmaps
- @ref: 69479
- File name: preview.99_2682.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_5;96_1428;97_1704;98_2079;99_2682&stattab=map
- Last taxonomy: Pelagibacterium halotolerans
- 16S sequence: EU709017
- Sequence Identity:
- Total samples: 77
- soil counts: 17
- aquatic counts: 38
- animal counts: 19
- plant counts: 3
Safety information
risk assessment
- @ref: 16304
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 16304
- description: Pelagibacterium halotolerans B2 16S ribosomal RNA gene, partial sequence
- accession: EU709017
- length: 1408
- database: nuccore
- NCBI tax ID: 1082931
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Pelagibacterium halotolerans B2 | GCA_000230555 | complete | ncbi | 1082931 |
| 66792 | Pelagibacterium halotolerans B2 | 1082931.4 | complete | patric | 1082931 |
| 66792 | Pelagibacterium halotolerans B2 | 1082931.15 | plasmid | patric | 1082931 |
| 66792 | Pelagibacterium halotolerans B2 | 2511231054 | complete | img | 1082931 |
GC content
- @ref: 16304
- GC-content: 59.3
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
| @ref | trait | model | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 69480 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 96.6 | no |
| 69480 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 94.472 | no |
| 69480 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 84.758 | no |
| 69480 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 94.369 | no |
| 69480 | thermophilic | thermophile | Ability to grow at temperatures above or equal to 45°C | no | 95.963 | yes |
| 69480 | flagellated | motile2+ | Ability to perform flagellated movement | yes | 66.586 | no |
External links
@ref: 16304
culture collection no.: DSM 22347, CGMCC 1.7692, JCM 15775
straininfo link
- @ref: 75678
- straininfo: 400210
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 20817840 | Pelagibacterium halotolerans gen. nov., sp. nov. and Pelagibacterium luteolum sp. nov., novel members of the family Hyphomicrobiaceae. | Xu XW, Huo YY, Wang CS, Oren A, Cui HL, Vedler E, Wu M | Int J Syst Evol Microbiol | 10.1099/ijs.0.023325-0 | 2010 | China, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Hyphomicrobiaceae/*classification/genetics/*isolation & purification/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology | Metabolism |
| Phylogeny | 28840801 | Pelagibacterium lentulum sp. nov., a marine bacterium from the culture broth of Picochlorum sp. 122. | Wang G, Yu K, Wang Y, Su H, Wu H, Li T, Liang J, Huang W, Xiang W | Int J Syst Evol Microbiol | 10.1099/ijsem.0.002054 | 2017 | Bacterial Typing Techniques, Base Composition, Chlorophyta/*microbiology, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, Hyphomicrobiaceae/*classification/genetics/metabolism, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Ubiquinone/chemistry | Transcriptome |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 16304 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22347) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-22347 | |||
| 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) | |||
| 66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
| 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 | |||
| 69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
| 75678 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID400210.1 | StrainInfo: A central database for resolving microbial strain identifiers |