Strain identifier

BacDive ID: 7302

Type strain: Yes

Species: Cryobacterium psychrotolerans

Strain Designation: 0549, 549

Strain history: CIP <- 2007, JCM <- 2006, D. Zhang and P. Zhou, China Academy Sciences, Beijing, China: strain 0549

NCBI tax ID(s): 386301 (species)

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General

@ref: 15817

BacDive-ID: 7302

DSM-Number: 21575

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

description: Cryobacterium psychrotolerans 0549 is an aerobe, psychrophilic, Gram-positive bacterium that was isolated from Frozen soil collected from the China No. 1 glacier.

NCBI tax id

  • NCBI tax id: 386301
  • Matching level: species

strain history

@refhistory
15817<- JCM <- D. Zhang and P. Zhou; 0549
67770D.-C. Zhang and P.-J. Zhou 0549.
122033CIP <- 2007, JCM <- 2006, D. Zhang and P. Zhou, China Academy Sciences, Beijing, China: strain 0549

doi: 10.13145/bacdive7302.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Microbacteriaceae
  • genus: Cryobacterium
  • species: Cryobacterium psychrotolerans
  • full scientific name: Cryobacterium psychrotolerans Zhang et al. 2007

@ref: 15817

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Cryobacterium

species: Cryobacterium psychrotolerans

full scientific name: Cryobacterium psychrotolerans Zhang et al. 2007 emend. Nouioui et al. 2018

strain designation: 0549, 549

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31980positive1.8-3.6 µm0.5-0.8 µmrod-shapedyes
69480positive100
122033negativerod-shapedyes

pigmentation

  • @ref: 31980
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
15817RICH MEDIUM (DSMZ Medium 736)yeshttps://mediadive.dsmz.de/medium/736Name: RICH MEDIUM (DSMZ Medium 736) Composition: Agar 20.0 g/l Bacto peptone 10.0 g/l Yeast extract 5.0 g/l Malt extract 5.0 g/l Casamino acids 5.0 g/l Glycerol 2.0 g/l Meat extract 2.0 g/l MgSO4 x 7 H2O 1.0 g/l Tween 80 0.05 g/l Distilled water
33309MEDIUM691 - for Flavobacterium glacieiyes
122033CIP Medium 691yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=691

culture temp

@refgrowthtypetemperaturerange
15817positivegrowth22psychrophilic
31980positivegrowth04-27
31980positiveoptimum20-22psychrophilic
33309positivegrowth20psychrophilic
67770positivegrowth20psychrophilic

culture pH

@refabilitytypepHPH range
31980positivegrowth05-10alkaliphile
31980positiveoptimum06-07

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31980aerobe
122033obligate aerobe

spore formation

@refspore formationconfidence
69481no98
69480no99.972

halophily

@refsaltgrowthtested relationconcentration
31980NaClpositivegrowth0-4 %
31980NaClpositiveoptimum2 %

observation

  • @ref: 67770
  • observation: quinones: MK-12, MK-11, MK-10

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3198030089acetate+carbon source
3198022599arabinose+carbon source
3198017057cellobiose+carbon source
3198028757fructose+carbon source
3198028260galactose+carbon source
3198017234glucose+carbon source
3198017754glycerol+carbon source
3198024996lactate+carbon source
3198017716lactose+carbon source
3198017306maltose+carbon source
3198037684mannose+carbon source
3198033942ribose+carbon source
3198017814salicin+carbon source
3198030031succinate+carbon source
3198017992sucrose+carbon source
3198018222xylose+carbon source
319804853esculin+hydrolysis
3198017632nitrate+reduction
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose-builds acid from
6837128066gentiobiose-builds acid from
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
6837128017starch-builds acid from
6837116634raffinose-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose-builds acid from
6837117992sucrose-builds acid from
6837128053melibiose-builds acid from
6837117716lactose-builds acid from
6837117306maltose-builds acid from
6837117057cellobiose-builds acid from
6837117814salicin-builds acid from
6837118305arbutin-builds acid from
6837127613amygdalin-builds acid from
6837159640N-acetylglucosamine-builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose-builds acid from
6837115824D-fructose-builds acid from
6837117634D-glucose-builds acid from
6837112936D-galactose-builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose-builds acid from
6837116988D-ribose-builds acid from
6837130849L-arabinose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from
12203317632nitrate+reduction
12203316301nitrite-reduction

metabolite production

  • @ref: 122033
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
31980catalase+1.11.1.6
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase+3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase+3.4.11.3
68382valine arylamidase+
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)+
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
122033oxidase-
122033catalase+1.11.1.6
122033urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
122033-+++++++--++---++---

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
122033------------------------+/-------------------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
15817Frozen soil collected from the China No. 1 glacierXinjiang Uygur Autonomous RegionChinaCHNAsia
67770Frozen soil from the China No. 1 glacierXinjiang Uygur Autonomous RegionChinaCHNAsia
122033China N°1 glacierXinjiang UygurChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Glacier
#Environmental#Terrestrial#Soil

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
158171Risk group (German classification)
1220331Risk group (French classification)

Sequence information

16S sequences

  • @ref: 15817
  • description: Cryobacterium psychrotolerans strain 0549 16S ribosomal RNA gene, partial sequence
  • accession: DQ515963
  • length: 1399
  • database: ena
  • NCBI tax ID: 386301

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Cryobacterium psychrotolerans strain CGMCC 1.5382386301.9wgspatric386301
66792Cryobacterium psychrotolerans strain CGMCC 1.5382386301.10wgspatric386301
66792Cryobacterium psychrotolerans CGMCC 1.53822667527402draftimg386301
67770Cryobacterium psychrotolerans CGMCC 1.5382GCA_900101115scaffoldncbi386301
67770Cryobacterium psychrotolerans CGMCC 1.5382GCA_004564325contigncbi386301

GC content

@refGC-contentmethod
1581767thermal denaturation, midpoint method (Tm)
3198067
6777068.3genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno98no
gram-positiveyes90.863yes
anaerobicno99.402no
halophileno90.865no
spore-formingno89.963no
glucose-utilyes82.734yes
aerobicyes86.835no
motileyes79.869yes
flagellatedno87.683no
thermophileno95.567yes
glucose-fermentno89.705no

External links

@ref: 15817

culture collection no.: DSM 21575, CGMCC 1.5382, JCM 13925, CIP 109566

straininfo link

  • @ref: 76752
  • straininfo: 302752

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17392221Cryobacterium psychrotolerans sp. nov., a novel psychrotolerant bacterium isolated from the China No. 1 glacier.Zhang DC, Wang HX, Cui HL, Yang Y, Liu HC, Dong XZ, Zhou PJInt J Syst Evol Microbiol10.1099/ijs.0.64750-02007Actinomycetales/*classification/genetics/isolation & purification/physiology, China, *Cold Temperature, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Ice Cover/*microbiology, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/geneticsGenetics
Phylogeny18450721Cryobacterium mesophilum sp. nov., a novel mesophilic bacterium.Dastager SG, Lee JC, Ju YJ, Park DJ, Kim CJInt J Syst Evol Microbiol10.1099/ijs.0.65650-02008Actinomycetales/*classification/genetics/isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Genotype, Korea, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Species SpecificityGenetics
Phylogeny19661491Cryobacterium roopkundense sp. nov., a psychrophilic bacterium isolated from glacial soil.Reddy GSN, Pradhan S, Manorama R, Shivaji SInt J Syst Evol Microbiol10.1099/ijs.0.011775-02009Actinomycetales/*classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, *Cold Temperature, DNA, Ribosomal/analysis/genetics, Fatty Acids/analysis, Genes, rRNA, Genotype, Ice Cover/*microbiology, India, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Species SpecificityGenetics
Phylogeny23315411Cryobacterium levicorallinum sp. nov., a psychrophilic bacterium isolated from glacier ice.Liu Q, Liu H, Zhang J, Zhou Y, Xin YInt J Syst Evol Microbiol10.1099/ijs.0.046896-02013Actinomycetales/*classification/genetics/metabolism, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/analysis, Ice, Ice Cover/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics
Phylogeny31222464Cryobacterium tepidiphilum sp. nov., isolated from rhizosphere soil of lettuce (var. ramosa Hort.).Wang Y, Cao P, Sun P, Zhao J, Sun X, Zhang J, Li C, Xiang W, Wang XAntonie Van Leeuwenhoek10.1007/s10482-019-01287-32019Actinobacteria/chemistry/*classification/genetics/*isolation & purification, Bacterial Typing Techniques, Base Composition, Genome, Bacterial, Lettuce/*microbiology, Multilocus Sequence Typing, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhizosphere, *Soil MicrobiologyGenetics
Phylogeny31671046Cryobacterium soli sp. nov., isolated from forest soil.Gong C, Lai Q, Cai H, Jiang Y, Liao H, Liu Y, Xue DInt J Syst Evol Microbiol10.1099/ijsem.0.0038202020Actinobacteria/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Forests, Glycolipids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
15817Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21575)https://www.dsmz.de/collection/catalogue/details/culture/DSM-21575
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
31980Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2823428776041
33309Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7323
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 updates33211880Nucleic Acids Res. 49: D498-D508 2020
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
76752Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID302752.1StrainInfo: A central database for resolving microbial strain identifiers
122033Curators of the CIPCollection of Institut Pasteur (CIP 109566)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109566