Strain identifier

BacDive ID: 3869

Type strain: Yes

Species: Deinococcus marmoris

Strain Designation: AA-63

Strain history: CIP <- 2005, DSMZ <- P. Hirsch, C. Albrechts Univ., Kiel, Germany: strain AA-63

NCBI tax ID(s): 1121381 (strain), 249408 (species)

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General

@ref: 4819

BacDive-ID: 3869

DSM-Number: 12784

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

description: Deinococcus marmoris AA-63 is an aerobe, psychrophilic, Gram-positive bacterium that was isolated from marble rock.

NCBI tax id

NCBI tax idMatching level
249408species
1121381strain

strain history

@refhistory
4819<- P. Hirsch; AA-63
120841CIP <- 2005, DSMZ <- P. Hirsch, C. Albrechts Univ., Kiel, Germany: strain AA-63

doi: 10.13145/bacdive3869.20230509.8.1

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 marmoris
  • full scientific name: Deinococcus marmoris Hirsch et al. 2006

@ref: 4819

domain: Bacteria

phylum: Deinococcus-Thermus

class: Deinococci

order: Deinococcales

family: Deinococcaceae

genus: Deinococcus

species: Deinococcus marmoris

full scientific name: Deinococcus marmoris Hirsch et al. 2006

strain designation: AA-63

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell shapemotilityconfidence
43357positive1.0-4.5 µmcoccus-shapedno
69480positive99.231
69480no92.177
120841positivecoccus-shapedno

colony morphology

  • @ref: 43357
  • colony color: pink to red
  • medium used: PYGV medium

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4819PYGV AGAR (DSMZ Medium 621)yeshttps://mediadive.dsmz.de/medium/621Name: 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
43357PYGV mediumyes
120841CIP Medium 331yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=331

culture temp

@refgrowthtypetemperaturerange
4819positivegrowth15psychrophilic
43357positiveoptimum9-16psychrophilic
43357positivegrowth4-25

culture pH

  • @ref: 43357
  • ability: positive
  • type: growth
  • pH: 4-9
  • PH range: alkaliphile

Physiology and metabolism

oxygen tolerance

  • @ref: 43357
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no99
69480no99.382

halophily

@refsaltgrowthtested relationconcentration
43357NaClpositivegrowth0-2 %
43357NaClpositiveoptimum1 %

observation

  • @ref: 43357
  • observation: Vitamin requirements are: Biotin, PABS and riboflavin

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4335730089acetate+carbon source
4335715963ribitol+assimilation
4335722605arabinitol+assimilation
43357casein+hydrolysis
4335762968cellulose-hydrolysis
4335717634D-glucose+growth
4335717634D-glucose+carbon source
4335716024D-mannose-growth
4335716551D-trehalose+carbon source
4335725115malate+assimilation
4335716991dna+hydrolysis
433574853esculin-hydrolysis
433574853esculin-growth
433575291gelatin+hydrolysis
433575291gelatin+/-hydrolysis
4335724265gluconate+carbon source
4335717234glucose-builds acid from
4335729985L-glutamate+carbon source
4335717716lactose+builds acid from
4335717632nitrate-reduction
4335715361pyruvate+carbon source
4335728017starch+/-hydrolysis
4335730031succinate+carbon source

antibiotic resistance

@refChEBImetaboliteis antibioticis resistantresistance conc.
4335748923erythromycinyesyes10 µg/mL
4335717698chloramphenicolyesyes1 µg/mL
4335718208penicillin gyesno50 µg/mL
4335740009d-cycloserineyesno10 µg/mL
4335717076streptomycinyesno10 µg/mL
4335727902tetracyclineyesno10 µg/mL

enzymes

@refvalueactivityec
43357cytochrome oxidase+1.9.3.1
43357lipase-
43357amylase-
43357beta-galactosidase+3.2.1.23
43357urease-3.5.1.5
43357neuramindase-3.2.1.18

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcontinentcountryorigin.country
4819marble rockMcMurdo Dry ValleysAustralia and Oceania
43357Antarctic marbleAntarcticaAustralia and OceaniaAntarcticaATA
120841Marble rockMcMurdo dry valleysAntarcticaAntarcticaATA

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Geologic
#Condition#Psychrophilic (<10°C)
#Climate#Cold#Polar

taxonmaps

  • @ref: 69479
  • File name: preview.99_4109.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_90;96_2085;97_2512;98_3106;99_4109&stattab=map
  • Last taxonomy: Deinococcus marmoris subclade
  • 16S sequence: AJ585986
  • Sequence Identity:
  • Total samples: 301
  • soil counts: 108
  • aquatic counts: 47
  • animal counts: 123
  • plant counts: 23

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
48191Risk group (German classification)
1208411Risk group (French classification)

Sequence information

16S sequences

  • @ref: 4819
  • description: Deinococcus sp. AA63 16S rRNA gene, strain AA63
  • accession: AJ585986
  • length: 1490
  • database: ena
  • NCBI tax ID: 249408

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Deinococcus marmoris DSM 12784GCA_000701405scaffoldncbi1121381
66792Deinococcus marmoris DSM 127841121381.3wgspatric1121381
66792Deinococcus marmoris DSM 127842561511138draftimg1121381

GC content

@refGC-contentmethod
481962.8
4335762.8thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno99no
motileno90.124yes
flagellatedno94.569yes
gram-positiveyes85.534yes
anaerobicno98.441no
halophileno93.441yes
spore-formingno88.39no
glucose-utilyes86.482yes
aerobicyes90.622yes
glucose-fermentno90.92no
thermophileno87.73yes

External links

@ref: 4819

culture collection no.: DSM 12784, CIP 109039, NRRL B-41042

straininfo link

  • @ref: 73379
  • straininfo: 215463

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15612620Deinococcus frigens sp. nov., Deinococcus saxicola sp. nov., and Deinococcus marmoris sp. nov., low temperature and draught-tolerating, UV-resistant bacteria from continental Antarctica.Hirsch P, Gallikowski CA, Siebert J, Peissl K, Kroppenstedt R, Schumann P, Stackebrandt E, Anderson RSyst Appl Microbiol10.1078/07232020423700082004Anaerobiosis, 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 RaysEnzymology
Phylogeny19667390Deinococcus aerolatus sp. nov. and Deinococcus aerophilus sp. nov., isolated from air samples.Yoo SH, Weon HY, Kim SJ, Kim YS, Kim BY, Kwon SWInt J Syst Evol Microbiol10.1099/ijs.0.016030-02009*Air Microbiology, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Deinococcus/*classification/genetics/*isolation & purification/physiology, Fatty Acids/analysis, Genes, rRNA, Genotype, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Species SpecificityGenetics
Phylogeny22228662Deinococcus humi sp. nov., isolated from soil.Srinivasan S, Lee JJ, Lim S, Joe M, Kim MKInt J Syst Evol Microbiol10.1099/ijs.0.037234-02012Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Deinococcus/*classification/genetics/isolation & purification, Fatty Acids/analysis, Gamma Rays, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/analysisGenetics
Phylogeny27974735Deinococcus rubrus sp. nov., a Bacterium Isolated from Antarctic Coastal Sea Water.Srinivasan S, Lim S, Lim JH, Jung HY, Kim MKJ Microbiol Biotechnol10.4014/jmb.1609.090022017Antarctic Regions, Bacteria/*classification/genetics/isolation & purification/metabolism, DNA Barcoding, Taxonomic, Deinococcus/*classification/genetics/isolation & purification/metabolism, Fatty Acids/metabolism, Genes, Bacterial, Genome, Bacterial, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, *Water MicrobiologyMetabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
4819Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 12784)https://www.dsmz.de/collection/catalogue/details/culture/DSM-12784
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
43357Peter Hirsch, Claudia A. Gallikowski, Jörg Siebert, Klaus Peissl, Reiner Kroppenstedt, Peter Schumann, Erko Stackebrandt, Robert Anderson10.1078/0723202042370008Deinococcus frigens sp. nov., Deinococcus saxicola sp. nov., and Deinococcus marmoris sp. nov., Low Temperature and Draught-tolerating, UV-resistant Bacteria from Continental AntarcticaSyst Appl Microbiol. 27: 636-645 200415612620
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
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
73379Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID215463.1StrainInfo: A central database for resolving microbial strain identifiers
120841Curators of the CIPCollection of Institut Pasteur (CIP 109039)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109039