Strain identifier

BacDive ID: 14098

Type strain: Yes

Species: Pedobacter cryoconitis

Strain Designation: A37

Strain history: CIP <- 2004, R. Margesin, Innsbruck Univ., Innsbruck, Austria: strain A37

NCBI tax ID(s): 188932 (species)

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General

@ref: 5562

BacDive-ID: 14098

DSM-Number: 14825

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

description: Pedobacter cryoconitis A37 is an obligate aerobe, psychrophilic, Gram-negative bacterium that was isolated from glacier cryoconite.

NCBI tax id

  • NCBI tax id: 188932
  • Matching level: species

strain history

@refhistory
5562<- R. Margesin; A37
329122004, R. Margesin, Innsbruck Univ., Innsbruck, Austria: strain A37
118797CIP <- 2004, R. Margesin, Innsbruck Univ., Innsbruck, Austria: strain A37

doi: 10.13145/bacdive14098.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Sphingobacteriia
  • order: Sphingobacteriales
  • family: Sphingobacteriaceae
  • genus: Pedobacter
  • species: Pedobacter cryoconitis
  • full scientific name: Pedobacter cryoconitis Margesin et al. 2003

@ref: 5562

domain: Bacteria

phylum: Bacteroidetes

class: Sphingobacteriia

order: Sphingobacteriales

family: Sphingobacteriaceae

genus: Pedobacter

species: Pedobacter cryoconitis

full scientific name: Pedobacter cryoconitis Margesin et al. 2003

strain designation: A37

type strain: yes

Morphology

cell morphology

  • @ref: 118797
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5562R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
32912MEDIUM 372 - for AquabacteriumyesDistilled water make up to (1000.000 ml);Magnesium sulphate heptahydrate (0.050 g);Agar (15.000 g);Glucose (0.500 g);Yeast extract (0.500 g);Pyruvic acid (0.300g);Tween 80 (1.000 ml);Casamino acids (0.500 g);Proteose Peptone N°3 (0.500 g);Di Potassium mon
118797CIP Medium 372yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=372

culture temp

@refgrowthtypetemperaturerange
5562positivegrowth20psychrophilic
32912positivegrowth22psychrophilic
118797positivegrowth5-25psychrophilic
118797nogrowth30mesophilic
118797nogrowth37mesophilic
118797nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 118797
  • oxygen tolerance: obligate aerobe

compound production

  • @ref: 5562
  • compound: protease

halophily

@refsaltgrowthtested relationconcentration
118797NaClpositivegrowth0-2 %
118797NaClnogrowth4 %
118797NaClnogrowth6 %
118797NaClnogrowth8 %
118797NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
11879716947citrate-carbon source
1187974853esculin+hydrolysis
11879717632nitrate-reduction
11879716301nitrite-reduction

antibiotic resistance

  • @ref: 118797
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

  • @ref: 118797
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
118797oxidase+
118797beta-galactosidase+3.2.1.23
118797alcohol dehydrogenase-1.1.1.1
118797gelatinase+
118797amylase+
118797DNase+
118797caseinase+3.4.21.50
118797catalase+1.11.1.6
118797tween esterase-
118797lecithinase+
118797lipase-
118797lysine decarboxylase-4.1.1.18
118797ornithine decarboxylase-4.1.1.17
118797protease+
118797tryptophan deaminase-
118797urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382cystine arylamidase-3.4.11.3
68382trypsin+3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase+3.2.1.22
68382beta-galactosidase+3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase+3.2.1.21
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382alpha-mannosidase+3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
118797-+++-++-+-++++-++++-

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
118797+++++-+++++++++++++-+-+-----------++-----+------------++---+--------------------------+------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
5562glacier cryoconiteStubai Alps (Tyrol)AustriaAUTEurope
118797Cryoconite glacierAustriaAUTEurope

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Glacier
#Environmental#Terrestrial#Geologic
#Condition#Psychrophilic (<10°C)

taxonmaps

  • @ref: 69479
  • File name: preview.99_3561.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_115;96_319;97_355;98_401;99_3561&stattab=map
  • Last taxonomy: Pedobacter
  • 16S sequence: AJ438170
  • Sequence Identity:
  • Total samples: 1824
  • soil counts: 462
  • aquatic counts: 295
  • animal counts: 556
  • plant counts: 511

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
55621Risk group (German classification)
1187971Risk group (French classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: Pedobacter cryoconitis partial 16S rRNA gene, strain DSM 14825T
  • accession: AJ438170
  • length: 1495
  • database: ena
  • NCBI tax ID: 188932

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pedobacter cryoconitis DSM 14825GCA_003259615scaffoldncbi188932
66792Pedobacter cryoconitis strain DSM 14825188932.11wgspatric188932
66792Pedobacter cryoconitis DSM 148252593339302draftimg188932

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno85.695no
flagellatedno96.54no
gram-positiveno97.576no
anaerobicno99.072no
aerobicyes84.877no
halophileno94.432no
spore-formingno91.854no
glucose-utilyes88.246no
thermophileno99.645yes
glucose-fermentno85.481no

External links

@ref: 5562

culture collection no.: DSM 14825, CIP 108372, LMG 21415

straininfo link

  • @ref: 83266
  • straininfo: 86365

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny13130009Pedobacter cryoconitis sp. nov., a facultative psychrophile from alpine glacier cryoconite.Margesin R, Sproer C, Schumann P, Schinner FInt J Syst Evol Microbiol10.1099/ijs.0.02436-02003Bacteroidetes/classification/genetics/*isolation & purification/metabolism, Base Composition, Cold Climate, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/genetics, Ice, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Water MicrobiologyGenetics
Phylogeny17082391Pedobacter ginsengisoli sp. nov., a DNase-producing bacterium isolated from soil of a ginseng field in South Korea.Ten LN, Liu QM, Im WT, Lee M, Yang DC, Lee STInt J Syst Evol Microbiol10.1099/ijs.0.64414-02006Bacteroidetes/*classification/cytology/*isolation & purification/physiology, Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Deoxyribonucleases/*biosynthesis, Fatty Acids/analysis/chemistry, Genes, rRNA, Korea, Molecular Sequence Data, Movement, Nucleic Acid Hybridization, *Panax, Phylogeny, Quinones/analysis/chemistry, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, *Soil MicrobiologyGenetics
Phylogeny28109203Pedobacter lusitanus sp. nov., isolated from sludge of a deactivated uranium mine.Covas C, Caetano T, Cruz A, Santos T, Dias L, Klein G, Abdulmawjood A, Rodriguez-Alcala LM, Pimentel LL, Gomes A, Freitas AC, Garcia-Serrano A, Fontecha J, Mendo SInt J Syst Evol Microbiol10.1099/ijsem.0.0018142017Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, DNA, Ribosomal Spacer/genetics, Fatty Acids/chemistry, Genes, Bacterial, *Mining, Nucleic Acid Hybridization, Pedobacter/*classification/genetics/isolation & purification, Phospholipids/chemistry, *Phylogeny, Portugal, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/*microbiology, Sphingolipids, *Uranium, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
5562Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 14825)https://www.dsmz.de/collection/catalogue/details/culture/DSM-14825
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
32912Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5987
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
68382Automatically annotated from API zym
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
83266Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID86365.1StrainInfo: A central database for resolving microbial strain identifiers
118797Curators of the CIPCollection of Institut Pasteur (CIP 108372)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108372