Strain identifier

BacDive ID: 7305

Type strain: Yes

Species: Cryobacterium arcticum

Strain Designation: SK1

Strain history: DSM 22823 <-- L. Ganzert SK1 <-- F. Bruns and A. Lipski.

NCBI tax ID(s): 670052 (species)

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General

@ref: 16535

BacDive-ID: 7305

DSM-Number: 22823

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

description: Cryobacterium arcticum SK1 is a psychrophilic bacterium that was isolated from soil covered by a sparse plant layer.

NCBI tax id

  • NCBI tax id: 670052
  • Matching level: species

strain history

@refhistory
16535<- L. Ganzert, Alfred Wegener Inst. Polar and Marine Res. in the Helmholtz Association, Res. Unit Potsdam, Germany; SK1 <- F. Bruns and A. Lipski
67770DSM 22823 <-- L. Ganzert SK1 <-- F. Bruns and A. Lipski.

doi: 10.13145/bacdive7305.20230509.8.1

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 arcticum
  • full scientific name: Cryobacterium arcticum Bajerski et al. 2011

@ref: 16535

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Cryobacterium

species: Cryobacterium arcticum

full scientific name: Cryobacterium arcticum Bajerski et al. 2011

strain designation: SK1

type strain: yes

Morphology

colony morphology

@refcolony colormedium used
69226Ivory (1014)suter with tyrosine
69226Lemon yellow (1012), ivory (1014)ISP 2
69226Light ivory (1015)ISP 3
69226Zinc yellow (1018)ISP 4
69226Zinc yellow (1018)ISP 5
69226Zinc yellow (1018)ISP 6
69226Zinc yellow (1018)ISP 7
69226Zinc yellow (1018)suter without tyrosine

multicellular morphology

@refforms multicellular complexcomplex namemedium name
69226noAerial myceliumISP 2
69226noAerial myceliumISP 3
69226noAerial myceliumISP 4
69226noAerial myceliumISP 5
69226noAerial myceliumISP 6
69226noAerial myceliumISP 7
69226noAerial myceliumsuter with tyrosine
69226noAerial myceliumsuter without tyrosine

pigmentation

@refproductionname
69226yesMelanin
69226nosoluble pigment

multimedia

@refmultimedia contentcaptionintellectual property rights
69226DSM_22823_image3.jpegPlates (GYM, ISP2, ISP3, ISP4, ISP5, ISP7)Helmholtz-Zentrum für Infektionsforschung GmbH
69226DSM_22823_image4.jpegPlates (GYM, ISP2, ISP3, ISP4, ISP5, ISP7)Helmholtz-Zentrum für Infektionsforschung GmbH

Culture and growth conditions

culture medium

  • @ref: 16535
  • name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/92
  • composition: Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
16535positivegrowth20psychrophilic
67770positivegrowth20psychrophilic

Physiology and metabolism

halophily

  • @ref: 69226
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-5 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6922622599arabinose+growth
6922662968cellulose-growth
6922628757fructose+growth
6922617234glucose+growth
6922617268inositol-growth
6922637684mannose+growth
6922616634raffinose+growth
6922626546rhamnose+growth
6922617992sucrose+growth
6922618222xylose+growth
6837917632nitrate-reduction
683794853esculin+hydrolysis
683795291gelatin-hydrolysis
6837917634D-glucose+fermentation
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837917306maltose+fermentation
6837917716lactose-fermentation
6837917992sucrose+fermentation
6837928087glycogen-fermentation

enzymes

@refvalueactivityec
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
68382acid phosphatase-3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382alkaline phosphatase-3.1.3.1
68379gelatinase-
68379beta-glucosidase+3.2.1.21
68379N-acetyl-beta-glucosaminidase-3.2.1.52
68379alpha-glucosidase+3.2.1.20
68379beta-galactosidase+3.2.1.23
68379beta-glucuronidase-3.2.1.31
68379alkaline phosphatase-3.1.3.1
68379pyrrolidonyl arylamidase-3.4.19.3
68379pyrazinamidase-3.5.1.B15

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
69226-----++-++/--+--+/-+-+-

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
69226-+/-+/--++/-+/-+/---+/-++-++-+-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitude
16535soil covered by a sparse plant layerStore Koldewey (76° 25' N 18° 44' W)GreenlandGRLNorth America76.4167-18.7333
67770Soil from Store KoldeweyGreenlandGRLNorth America

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Host#Plants

taxonmaps

  • @ref: 69479
  • File name: preview.99_4303.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_133;97_2614;98_3238;99_4303&stattab=map
  • Last taxonomy: Cryobacterium
  • 16S sequence: GQ406814
  • Sequence Identity:
  • Total samples: 6140
  • soil counts: 2872
  • aquatic counts: 1251
  • animal counts: 1381
  • plant counts: 636

Safety information

risk assessment

  • @ref: 16535
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 16535
  • description: Cryobacterium arcticum strain SK1 16S ribosomal RNA gene, partial sequence
  • accession: GQ406814
  • length: 1365
  • database: ena
  • NCBI tax ID: 670052

Genome sequences

  • @ref: 67770
  • description: Cryobacterium arcticum SK-1
  • accession: GCA_003185895
  • assembly level: contig
  • database: ncbi
  • NCBI tax ID: 670052

GC content

  • @ref: 16535
  • GC-content: 67.8
  • method: high performance liquid chromatography (HPLC)

External links

@ref: 16535

culture collection no.: DSM 22823, JCM 19546, NCCB 100316

straininfo link

  • @ref: 76755
  • straininfo: 402773

literature

  • topic: Phylogeny
  • Pubmed-ID: 20817836
  • title: Cryobacterium arcticum sp. nov., a psychrotolerant bacterium from an Arctic soil.
  • authors: Bajerski F, Ganzert L, Mangelsdorf K, Lipski A, Wagner D
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.027128-0
  • year: 2010
  • mesh: Actinomycetales/*classification/genetics/*isolation & purification/metabolism, Arctic Regions, Cold Temperature, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil Microbiology
  • topic2: Metabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
16535Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22823)https://www.dsmz.de/collection/catalogue/details/culture/DSM-22823
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
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/
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
69226Wink, J.https://cdn.dsmz.de/wink/DSM%2022823.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
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
76755Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID402773.1StrainInfo: A central database for resolving microbial strain identifiers