Strain identifier

BacDive ID: 6173

Type strain: Yes

Species: Devosia psychrophila

Strain Designation: Cr7-05

Strain history: CIP <- 2010, R. Margesin, Innsbruck Univ., Innsbruck, Austria: strain Cr7-05

NCBI tax ID(s): 728005 (species)

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General

@ref: 16628

BacDive-ID: 6173

DSM-Number: 22950

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

description: Devosia psychrophila Cr7-05 is an aerobe, psychrophilic, Gram-negative bacterium that was isolated from glacier cryoconite.

NCBI tax id

  • NCBI tax id: 728005
  • Matching level: species

strain history

@refhistory
16628<- R. Margesin, Inst. Microbiology, Univ. Innsbruck, Austria; Cr7-05
122020CIP <- 2010, R. Margesin, Innsbruck Univ., Innsbruck, Austria: strain Cr7-05

doi: 10.13145/bacdive6173.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Hyphomicrobiales
  • family: Devosiaceae
  • genus: Devosia
  • species: Devosia psychrophila
  • full scientific name: Devosia psychrophila Zhang et al. 2012

@ref: 16628

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Devosiaceae

genus: Devosia

species: Devosia psychrophila

full scientific name: Devosia psychrophila Zhang et al. 2012

strain designation: Cr7-05

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
29880negative04-05 µm0.4-0.6 µmrod-shapedyes
69480yes97.007
69480negative99.982
122020negativerod-shapedno

pigmentation

  • @ref: 29880
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
16628R2A 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
37921MEDIUM 566- Reasoner's 2A agar for Flavobacterium micromatiyesDistilled water make up to (1000.000 ml);R2A agar (18.200 g)
122020CIP Medium 566yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=566

culture temp

@refgrowthtypetemperaturerange
16628positivegrowth10psychrophilic
29880positivegrowth1-20psychrophilic
37921positivegrowth15psychrophilic

culture pH

  • @ref: 29880
  • ability: positive
  • type: growth
  • pH: 07-08

Physiology and metabolism

oxygen tolerance

  • @ref: 29880
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.997

halophily

  • @ref: 29880
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-1 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2988022599arabinose+carbon source
2988017234glucose+carbon source
2988017306maltose+carbon source
2988029864mannitol+carbon source
2988037684mannose+carbon source
29880506227N-acetylglucosamine+carbon source
12202017632nitrate-reduction
12202016301nitrite-reduction

metabolite production

  • @ref: 122020
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
29880acid phosphatase+3.1.3.2
29880alkaline phosphatase+3.1.3.1
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
122020oxidase-
122020catalase-1.11.1.6
122020urease-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
122020-----------+--------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitude
16628glacier cryoconiteTyrol, Oetztaler Alps, Pitztaler Jöchl glacier (46° 56' 31.22'' N 10° 55' 20.15'' E)AustriaAUTEurope46.94210.9223
122020Alpine glacier cryoconiteTyrolAustriaAUTEurope

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_1884.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_5;96_1058;97_1236;98_1484;99_1884&stattab=map
  • Last taxonomy: Devosia psychrophila
  • 16S sequence: GU441678
  • Sequence Identity:
  • Total samples: 215
  • soil counts: 64
  • aquatic counts: 45
  • animal counts: 99
  • plant counts: 7

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
166281Risk group (German classification)
1220201Risk group (French classification)

Sequence information

16S sequences

  • @ref: 16628
  • description: Devosia psychrophila strain Cr7-05 16S ribosomal RNA gene, partial sequence
  • accession: GU441678
  • length: 1474
  • database: ena
  • NCBI tax ID: 728005

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Devosia psychrophila CGMCC 1.10210GCA_900112505scaffoldncbi728005
66792Devosia psychrophila Cr7-05GCA_000971275contigncbi728005
66792Devosia psychrophila strain CGMCC 1.10210728005.4wgspatric728005
66792Devosia psychrophila CGMCC 1.102102617270931draftimg728005
66792Devosia psychrophila Cr7-052627853832draftimg728005

GC content

@refGC-contentmethod
1662861.4thermal denaturation, midpoint method (Tm)
2988061.4

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes87.438yes
flagellatedno71.545no
gram-positiveno96.83no
anaerobicno98.254no
aerobicyes92.104yes
halophileno96.471yes
spore-formingno95.163no
glucose-fermentno89.911no
thermophileno98.756yes
glucose-utilyes92.614yes

External links

@ref: 16628

culture collection no.: DSM 22950, CGMCC 1.10210, CIP 110130

straininfo link

  • @ref: 75656
  • straininfo: 379343

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny21551324Devosia psychrophila sp. nov. and Devosia glacialis sp. nov., from alpine glacier cryoconite, and an emended description of the genus Devosia.Zhang DC, Redzic M, Liu HC, Zhou YG, Schinner F, Margesin RInt J Syst Evol Microbiol10.1099/ijs.0.023937-02011Bacterial Typing Techniques, Base Composition, Cluster Analysis, Cold Temperature, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Hyphomicrobiaceae/*classification/genetics/*isolation & purification/physiology, Ice Cover/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Ubiquinone/analysisGenetics
Phylogeny23416574Devosia submarina sp. nov., isolated from deep-sea surface sediments.Romanenko LA, Tanaka N, Svetashev VIInt J Syst Evol Microbiol10.1099/ijs.0.046607-02013DNA, Bacterial/genetics, Fatty Acids/analysis, Geologic Sediments/*microbiology, Hyphomicrobiaceae/*classification/genetics/isolation & purification, Japan, Lipids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/microbiology, Sequence Analysis, DNA, Ubiquinone/analogs & derivatives/analysis, Water MicrobiologyGenetics
Phylogeny26475689Methyloterrigena soli gen. nov., sp. nov., a methanol-utilizing bacterium isolated from chloroethylene-contaminated soil.Kim HS, Srinivasan S, Lee SSInt J Syst Evol Microbiol10.1099/ijsem.0.0006802015Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Hyphomicrobiaceae/*classification/genetics/isolation & purification, Methanol/*metabolism, Molecular Sequence Data, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Soil Pollutants, Ubiquinone/analogs & derivatives/chemistry, Vinyl ChlorideGenetics
Phylogeny34435948Devosia beringensis sp. nov., isolated from surface sediment of the Bering Sea.Zhang YX, Yu Y, Luo W, Zeng YX, Du ZJ, Li HRInt J Syst Evol Microbiol10.1099/ijsem.0.0049952021Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Hyphomicrobiaceae/*classification/isolation & purification, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
16628Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22950)https://www.dsmz.de/collection/catalogue/details/culture/DSM-22950
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
29880Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2625328776041
37921Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7954
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)
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
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
75656Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID379343.1StrainInfo: A central database for resolving microbial strain identifiers
122020Curators of the CIPCollection of Institut Pasteur (CIP 110130)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110130