Strain identifier

BacDive ID: 133374

Type strain: Yes

Species: Polymorphobacter glacialis

Strain Designation: B555-2

NCBI tax ID(s): 1614636 (species)

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General

@ref: 25242

BacDive-ID: 133374

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

description: Polymorphobacter glacialis B555-2 is an aerobe, psychrophilic, Gram-negative bacterium that was isolated from ice core in Muztagh Glacier.

NCBI tax id

  • NCBI tax id: 1614636
  • Matching level: species

doi: 10.13145/bacdive133374.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Sphingomonadales
  • family: Sphingosinicellaceae
  • genus: Polymorphobacter
  • species: Polymorphobacter glacialis
  • full scientific name: Polymorphobacter glacialis Xing et al. 2017

@ref: 25242

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Sphingomonadales

family: Sphingomonadaceae

genus: Polymorphobacter

species: Polymorphobacter glacialis

strain designation: B555-2

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapeconfidence
25242negative1.0-1.3 µm0.6-0.7 µmrod-shaped
69480negative99.979

colony morphology

  • @ref: 25242
  • colony color: orange
  • incubation period: 7 days
  • medium used: R2A

Culture and growth conditions

culture medium

  • @ref: 25242
  • name: Reasoner's 2A agar (R2A)
  • growth: yes

culture temp

@refgrowthtypetemperaturerange
25242positivegrowth0-20psychrophilic
25242positiveoptimum15psychrophilic

culture pH

@refabilitytypepHPH range
25242positivegrowth7-9alkaliphile
25242positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 25242
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
25242no
69481no100
69480no99.989

halophily

  • @ref: 25242
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0.6 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2524217128adipate-carbon source
2524217634D-glucose-carbon source
2524216899D-mannitol-carbon source
2524216024D-mannose-carbon source
2524227689decanoate-carbon source
252425291gelatin-hydrolysis
2524230849L-arabinose-carbon source
2524225115malate-carbon source
2524217306maltose-carbon source
25242506227N-acetylglucosamine-carbon source
2524217632nitrate-reduction
2524218401phenylacetate-carbon source
2524216947citrate+carbon source
252424853esculin+hydrolysis
252424853esculin+carbon source
2524253258sodium citrate+carbon source

metabolite production

@refChebi-IDmetaboliteproduction
2524216136hydrogen sulfideno
2524235581indoleno

enzymes

@refvalueactivityec
25242acid phosphatase+/-3.1.3.2
25242alkaline phosphatase+3.1.3.1
25242alpha-chymotrypsin+/-3.4.21.1
25242alpha-fucosidase-3.2.1.51
25242alpha-galactosidase-3.2.1.22
25242alpha-glucosidase-3.2.1.20
25242alpha-mannosidase-3.2.1.24
25242beta-galactosidase-3.2.1.23
25242beta-glucosidase-3.2.1.21
25242beta-glucuronidase-3.2.1.31
25242catalase+1.11.1.6
25242cystine arylamidase-3.4.11.3
25242cytochrome oxidase-1.9.3.1
25242esterase (C 4)+
25242esterase Lipase (C 8)+
25242leucine arylamidase+3.4.11.1
25242lipase (C 14)-
25242N-acetyl-beta-glucosaminidase-3.2.1.52
25242naphthol-AS-BI-phosphohydrolase+/-
25242trypsin-3.4.21.4
25242valine arylamidase+/-

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    25242C12:0 2OH3.4
    25242C14:0 2OH10.1
    25242C16:08.2
    25242C16:1ω7c / C16:1ω6c42.8
    25242C17:1ω6c4.2
    25242C18:1ω7c / C18:1ω6c28.8
    25242C16:0 iso 3OH1.2
  • type of FA analysis: whole cell analysis
  • incubation medium: R2A
  • agar/liquid: agar
  • incubation temperature: 15
  • incubation time: 7
  • software version: Sherlock 6.0
  • system: MIS MIDI
  • cutoff value:

Isolation, sampling and environmental information

isolation

  • @ref: 25242
  • sample type: ice core in Muztagh Glacier
  • geographic location: Muztagh Glacier, Tibet, China
  • country: China
  • origin.country: CHN
  • continent: Asia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Glacier
#Environmental#Aquatic#Ice
#Environmental#Terrestrial#Core sample

taxonmaps

  • @ref: 69479
  • File name: preview.99_22388.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_20;96_1995;97_2398;98_16878;99_22388&stattab=map
  • Last taxonomy: Polymorphobacter
  • 16S sequence: KP013180
  • Sequence Identity:
  • Total samples: 16848
  • soil counts: 2630
  • aquatic counts: 12147
  • animal counts: 1756
  • plant counts: 315

Sequence information

16S sequences

  • @ref: 25242
  • description: 16S rRNA gene sequences
  • accession: KP013180
  • length: 1388
  • database: ena
  • NCBI tax ID: 1614636

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Polymorphobacter glacialis CGMCC 1.15519GCA_014643455contigncbi1614636
66792Polymorphobacter glacialis strain CGMCC 1.155191614636.3wgspatric1614636

GC content

  • @ref: 25242
  • GC-content: 62.1
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno52.274no
gram-positiveno97.49no
anaerobicno99.454no
aerobicyes95.238yes
halophileno89.793yes
spore-formingno96.023yes
thermophileno97.978yes
glucose-utilyes75.017yes
flagellatedno92.58no
glucose-fermentno93.767no

External links

@ref: 25242

culture collection no.: CGMCC 1.15519, KCTC 52396

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny27902289Polymorphobacter glacialis sp. nov., isolated from ice core.Xing T, Liu Y, Wang N, Xu B, Shen L, Liu K, Gu Z, Guo B, Zhou Y, Liu HInt J Syst Evol Microbiol10.1099/ijsem.0.0016722017Bacterial Typing Techniques, Base Composition, Carotenoids/chemistry, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Ice Cover/*microbiology, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sphingomonadaceae/*classification/genetics/isolation & purification, Ubiquinone/chemistryTranscriptome
Phylogeny31851602Polymorphobacter arshaanensis sp. nov., containing the photosynthetic gene pufML, isolated from a volcanic lake.Phurbu D, Liu ZX, Liu HC, Lhamo Y, Yangzom P, Li AH, Zhou YGInt J Syst Evol Microbiol10.1099/ijsem.0.0038802020Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Lakes/*microbiology, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sphingomonadaceae/*classification/isolation & purification, Ubiquinone/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorstitledoi/urljournalpubmed
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
25242T. L. Xing, Yongqin,Wang, Ninglian,Xu, Baiqing,Shen, Liang,Liu, Keshao,Gu, Zhengquan,Guo, Bixi,Zhou, Yuguang,Liu, HongcanPolymorphobacter glacialis sp. nov., isolated from ice core10.1099/ijsem.0.001672IJSEM 67: 617-620 201727902289
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
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/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1