Strain identifier

BacDive ID: 24035

Type strain: Yes

Species: Chryseobacterium frigidisoli

Strain Designation: PB4

Strain history: <- D. Wagner, Alfred Wegener Inst. Polar and Marine Res. (AWI) in the Helmholtz Association, Res. Unit Potsdam, Germany; PB4 <- L. Padur, AWI Potsdam, Germany

NCBI tax ID(s): 1125876 (species)

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General

@ref: 20930

BacDive-ID: 24035

DSM-Number: 26000

keywords: genome sequence, 16S sequence, Bacteria, aerobe, psychrophilic, Gram-negative, rod-shaped

description: Chryseobacterium frigidisoli PB4 is an aerobe, psychrophilic, Gram-negative bacterium that was isolated from sandy dry permafrost from a glacier forefield.

NCBI tax id

  • NCBI tax id: 1125876
  • Matching level: species

strain history

  • @ref: 20930
  • history: <- D. Wagner, Alfred Wegener Inst. Polar and Marine Res. (AWI) in the Helmholtz Association, Res. Unit Potsdam, Germany; PB4 <- L. Padur, AWI Potsdam, Germany

doi: 10.13145/bacdive24035.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Flavobacteriia
  • order: Flavobacteriales
  • family: Weeksellaceae
  • genus: Chryseobacterium
  • species: Chryseobacterium frigidisoli
  • full scientific name: Chryseobacterium frigidisoli Bajerski et al. 2013

  • synonyms

    • @ref: 20215
    • synonym: Halpernia frigidisoli

@ref: 20930

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Weeksellaceae

genus: Chryseobacterium

species: Chryseobacterium frigidisoli

full scientific name: Chryseobacterium frigidisoli Bajerski et al. 2013

strain designation: PB4

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
30891negative2.75 µm0.45 µmrod-shapedno
125438no91.5
125438negative98.5
125439negative99.7

pigmentation

  • @ref: 30891
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 20930
  • name: NUTRIENT AGAR (DSMZ Medium 1)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/1
  • composition: Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water

culture temp

@refgrowthtypetemperature
20930positivegrowth20
30891positivegrowth0-25
30891positiveoptimum20

culture pH

@refabilitytypepHPH range
30891positivegrowth5.5-8.5alkaliphile
30891positiveoptimum6.5

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
30891aerobe
125439obligate aerobe98.8

spore formation

@refspore formationconfidence
30891no
125439no94.4

halophily

@refsaltgrowthtested relationconcentration
30891NaClpositivegrowth0-5 %
30891NaClpositiveoptimum0.5 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3089115963ribitol+carbon source
3089118403L-arabitol+carbon source
3089117057cellobiose+carbon source
3089128757fructose+carbon source
3089128260galactose+carbon source
3089117234glucose+carbon source
3089117754glycerol+carbon source
3089128087glycogen+carbon source
3089117716lactose+carbon source
3089117306maltose+carbon source
3089129864mannitol+carbon source
3089137684mannose+carbon source
3089128053melibiose+carbon source
30891506227N-acetylglucosamine+carbon source
3089116634raffinose+carbon source
3089126546rhamnose+carbon source
3089133942ribose+carbon source
3089117814salicin+carbon source
3089130911sorbitol+carbon source
3089117992sucrose+carbon source
3089127082trehalose+carbon source
3089117151xylitol+carbon source
3089118222xylose+carbon source

metabolite production

  • @ref: 30891
  • Chebi-ID: 35581
  • metabolite: indole
  • production: yes

metabolite tests

  • @ref: 30891
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: +

enzymes

@refvalueactivityec
30891catalase+1.11.1.6
30891gelatinase+
30891cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

  • @ref: 20930
  • sample type: sandy dry permafrost from a glacier forefield
  • geographic location: Larsemann Hills (S 69°24', E 76°20')
  • continent: Australia and Oceania
  • latitude: -69.4
  • longitude: 76.3333

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Glacier
#Environmental#Terrestrial#Permafrost
#Environmental#Terrestrial#Sandy

taxonmaps

  • @ref: 69479
  • File name: preview.99_68125.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_76;96_19049;97_23613;98_47976;99_68125&stattab=map
  • Last taxonomy: Chryseobacterium frigidisoli subclade
  • 16S sequence: JN390676
  • Sequence Identity:
  • Total samples: 444
  • soil counts: 68
  • aquatic counts: 153
  • animal counts: 200
  • plant counts: 23

Safety information

risk assessment

  • @ref: 20930
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 20930
  • description: Chryseobacterium frigidisoli strain PB4 16S ribosomal RNA gene, partial sequence
  • accession: JN390676
  • length: 1301
  • database: nuccore
  • NCBI tax ID: 1125876

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Halpernia frigidisoli DSM 26000GCA_900113805contigncbi1125876
66792Chryseobacterium frigidisoli strain DSM 260001125876.4wgspatric1125876
66792Chryseobacterium frigidisoli DSM 260002684622856draftimg1125876

GC content

@refGC-contentmethod
2093033.7high performance liquid chromatography (HPLC)
3089133.7

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno98.5yes
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no91.896yes
125438spore-formingspore-formingAbility to form endo- or exosporesno88.528no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes87.383yes
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno96.577yes
125438motile2+flagellatedAbility to perform flagellated movementno91.5no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno94.4
125439BacteriaNetmotilityAbility to perform movementno74.5
125439BacteriaNetgram_stainReaction to gram-stainingnegative99.7
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe98.8

External links

@ref: 20930

culture collection no.: DSM 26000, LMG 27025

straininfo link

  • @ref: 88008
  • straininfo: 380503

literature

  • topic: Phylogeny
  • Pubmed-ID: 23291884
  • title: Chryseobacterium frigidisoli sp. nov., a psychrotolerant species of the family Flavobacteriaceae isolated from sandy permafrost from a glacier forefield.
  • authors: Bajerski F, Ganzert L, Mangelsdorf K, Padur L, Lipski A, Wagner D
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.046904-0
  • year: 2013
  • mesh: Antarctic Regions, Bacterial Typing Techniques, Chryseobacterium/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/analysis, Ice Cover/*microbiology, Molecular Sequence Data, *Phylogeny, Polyamines/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/analysis
  • topic2: Genetics

Reference

@idauthorstitledoi/urlcatalogueID_cross_referencepubmedjournal
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
20930Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-26000Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 26000)
30891Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172722128776041
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa102533211880Nucleic Acids Res. 49: D498-D508 2020
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
88008Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID380503.1
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg OvermannPredicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets10.1101/2024.08.12.607695
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardydeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1https://github.com/GenomeNet/deepG