Archive BacDiveID:10.13145/bacdive3866.20230509.8.1

Strain identifier

BacDive ID: 3866

Type strain:

Species: Deinococcus frigens

Strain Designation: AA-692

Strain history: CIP <- 2006, DSMZ <- P. Hirsch, C.A. Gallikowski, Christian-Albrechts Univ., Kiel, Germany: strain AA-692

NCBI tax ID(s): 1121380 (strain), 249403 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.

General

@ref: 4831

BacDive-ID: 3866

DSM-Number: 12807

keywords: genome sequence, 16S sequence, Bacteria, psychrophilic, Gram-positive

description: Deinococcus frigens AA-692 is a psychrophilic, Gram-positive bacterium that was isolated from soil .

NCBI tax id

NCBI tax id	Matching level
249403	species
1121380	strain

strain history

@ref	history
4831	<- P. Hirsch <- P. Hirsch and C. A. Gallikowski; AA-692
119460	CIP <- 2006, DSMZ <- P. Hirsch, C.A. Gallikowski, Christian-Albrechts Univ., Kiel, Germany: strain AA-692

doi: 10.13145/bacdive3866.20230509.8.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/deinococcota
domain: Bacteria
phylum: Deinococcota
class: Deinococci
order: Deinococcales
family: Deinococcaceae
genus: Deinococcus
species: Deinococcus frigens
full scientific name: Deinococcus frigens Hirsch et al. 2006

@ref: 4831

domain: Bacteria

phylum: Deinococcus-Thermus

class: Deinococci

order: Deinococcales

family: Deinococcaceae

genus: Deinococcus

species: Deinococcus frigens

full scientific name: Deinococcus frigens Hirsch et al. 2006

strain designation: AA-692

type strain: yes

Morphology

cell morphology

@ref	gram stain	confidence	motility	cell shape
69480	positive	100
69480		94.137	no
119460	positive		no	coccus-shaped

Culture and growth conditions

culture medium

@ref	name	growth	link	composition
4831	PYGV AGAR (DSMZ Medium 621)	yes	https://mediadive.dsmz.de/medium/621	Name: PYGV AGAR (DSMZ Medium 621) Composition: Agar 15.0 g/l MgSO4 x 7 H2O 0.625264 g/l Glucose 0.25 g/l Peptone 0.25 g/l Yeast extract 0.25 g/l Nitrilotriacetic acid 0.210526 g/l CaCl2 x 2 H2O 0.0703158 g/l FeSO4 x 7 H2O 0.00208422 g/l Na2MoO4 x 2 H2O 0.000266736 g/l Pyridoxine hydrochloride 0.0001 g/l p-Aminobenzoic acid 5e-05 g/l D-Calcium pantothenate 5e-05 g/l Nicotinamide 5e-05 g/l Thiamine-HCl x 2 H2O 5e-05 g/l Riboflavine 5e-05 g/l Folic acid 2e-05 g/l Biotin 2e-05 g/l Vitamin B12 1e-06 g/l Metall salt sol. 44 Distilled water
119460	CIP Medium 566	yes	https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=566
119460	CIP Medium 331	yes	https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=331

culture temp

@ref: 4831
growth: positive
type: growth
temperature: 15
range: psychrophilic

Physiology and metabolism

spore formation

@ref	spore formation	confidence
69481	no	98
69480	no	99.437

Isolation, sampling and environmental information

isolation

@ref	sample type	geographic location	continent	country	origin.country
4831	soil (0-4 cm, pH 6.3)	McMurdo Dry Valleys	Australia and Oceania
119460	Environment, Soil (0-4 cm, pH 6.3)	McMurdo dry valleys	Antarctica	Antarctica	ATA

isolation source categories

Cat1: #Environmental
Cat2: #Terrestrial
Cat3: #Soil

taxonmaps

@ref: 69479
File name: preview.99_5606.png
url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_90;96_2085;97_3319;98_4182;99_5606&stattab=map
Last taxonomy: Deinococcus frigens subclade
16S sequence: AJ585981
Sequence Identity:
Total samples: 97
soil counts: 30
aquatic counts: 20
animal counts: 46
plant counts: 1

Safety information

risk assessment

@ref	biosafety level	biosafety level comment
4831	1	Risk group (German classification)
119460	1	Risk group (French classification)

Sequence information

16S sequences

@ref: 4831
description: Deinococcus sp. AA692 16S rRNA gene, strain AA692
accession: AJ585981
length: 1490
database: ena
NCBI tax ID: 249403

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Deinococcus frigens DSM 12807	GCA_000701425	scaffold	ncbi	1121380
66792	Deinococcus frigens DSM 12807	1121380.3	wgs	patric	1121380
66792	Deinococcus frigens DSM 12807	2561511139	draft	img	1121380

GC content

@ref: 4831
GC-content: 63.8-65.5

Genome-based predictions

predictions

trait	prediction	confidence	training_data
spore-forming	no	98	no
motile	no	91.327	no
flagellated	no	96.208	no
gram-positive	yes	85.305	no
anaerobic	no	98.234	no
halophile	no	92.516	no
spore-forming	no	92.726	no
glucose-util	yes	88.846	no
aerobic	yes	89.237	no
thermophile	no	84.478	no
glucose-ferment	no	90.281	no

External links

@ref: 4831

culture collection no.: DSM 12807, CIP 109230, NRRL B-41046

straininfo link

@ref: 73376
straininfo: 215462

literature

topic: Phylogeny
Pubmed-ID: 15612620
title: Deinococcus frigens sp. nov., Deinococcus saxicola sp. nov., and Deinococcus marmoris sp. nov., low temperature and draught-tolerating, UV-resistant bacteria from continental Antarctica.
authors: Hirsch P, Gallikowski CA, Siebert J, Peissl K, Kroppenstedt R, Schumann P, Stackebrandt E, Anderson R
journal: Syst Appl Microbiol
DOI: 10.1078/0723202042370008
year: 2004
mesh: Anaerobiosis, Antarctic Regions, Cell Wall/chemistry, Culture Media/chemistry, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Deinococcus/*classification/*isolation & purification/physiology/radiation effects, Genes, rRNA, Gentian Violet, Hydrogen-Ion Concentration, Lipids/analysis/isolation & purification, Molecular Sequence Data, Movement, Osmotic Pressure, Phenazines, Phylogeny, Pigments, Biological, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Temperature, Ultraviolet Rays
topic2: Enzymology

Reference

@id	authors	catalogue	doi/url	title
4831	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 12807)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-12807
20215	Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.		10.1099/ijsem.0.004332	List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
66792	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann		https://diaspora-project.de/progress.html#genomes	Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69479	João 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
69480	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann		https://diaspora-project.de/progress.html#genomes	Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481	Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch		10.21203/rs.3.rs-2527258/v1	Predictions based on the model GenomeNet Sporulation v. 1
73376	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID215462.1	StrainInfo: A central database for resolving microbial strain identifiers
119460	Curators of the CIP	Collection of Institut Pasteur (CIP 109230)	https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109230