Strain identifier

BacDive ID: 6198

Type strain: Yes

Species: Pelagibacterium halotolerans

Strain Designation: B2

Strain history: X.-W. Xu B2.

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General

@ref: 16304

BacDive-ID: 6198

DSM-Number: 22347

keywords: genome sequence, 16S sequence, Bacteria, mesophilic

description: Pelagibacterium halotolerans B2 is a mesophilic bacterium that was isolated from Sea water.

NCBI tax id

NCBI tax idMatching level
531813species
1082931strain

strain history

@refhistory
16304<- X.-W. Xu, Zhejiang Univ., Zijingang Campus, P.R. China; B2
67770X.-W. Xu B2.

doi: 10.13145/bacdive6198.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Hyphomicrobiales
  • family: 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

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

@refgrowthtypetemperaturerange
16304positivegrowth28mesophilic
67770positivegrowth30mesophilic

Physiology and metabolism

observation

  • @ref: 67770
  • observation: quinones: Q-10, Q-9

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitude
16304Sea waterEast China Sea (30° 58' 16'' N 125° 59' 24'' E)ChinaCHNAsia30.9711125.99
67770Seawater 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: ena
  • NCBI tax ID: 1082931

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pelagibacterium halotolerans B2GCA_000230555completencbi1082931
66792Pelagibacterium halotolerans B21082931.4completepatric1082931
66792Pelagibacterium halotolerans B21082931.15plasmidpatric1082931
66792Pelagibacterium halotolerans B22511231054completeimg1082931

GC content

  • @ref: 16304
  • GC-content: 59.3
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes83.295no
flagellatedno52.714no
gram-positiveno96.602no
anaerobicno98.851no
aerobicyes91.66no
halophileno78.922no
spore-formingno96.43no
glucose-utilyes86.892no
thermophileno97.946yes
glucose-fermentno92.316no

External links

@ref: 16304

culture collection no.: DSM 22347, CGMCC 1.7692, JCM 15775

straininfo link

  • @ref: 75678
  • straininfo: 400210

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny20817840Pelagibacterium 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 MInt J Syst Evol Microbiol10.1099/ijs.0.023325-02010China, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Hyphomicrobiaceae/*classification/genetics/*isolation & purification/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiologyMetabolism
Phylogeny28840801Pelagibacterium 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 WInt J Syst Evol Microbiol10.1099/ijsem.0.0020542017Bacterial 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/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
16304Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22347)https://www.dsmz.de/collection/catalogue/details/culture/DSM-22347
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
69479João 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
75678Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID400210.1StrainInfo: A central database for resolving microbial strain identifiers