Strain identifier

BacDive ID: 158506

Type strain: Yes

Species: Deinococcus fonticola

Strain Designation: FeSDHB5-19

Strain history: <- J. Makk, Eötvös Loránd Univ. Budapest, Hungary; FeSDHB5-19

NCBI tax ID(s): 2528713 (species)

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General

@ref: 65182

BacDive-ID: 158506

DSM-Number: 106917

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, coccus-shaped, colony-forming

description: Deinococcus fonticola FeSDHB5-19 is an aerobe, mesophilic, Gram-negative bacterium that forms circular colonies and was isolated from biofilm sample of thermal spring.

NCBI tax id

  • NCBI tax id: 2528713
  • Matching level: species

strain history

  • @ref: 65182
  • history: <- J. Makk, Eötvös Loránd Univ. Budapest, Hungary; FeSDHB5-19

doi: 10.13145/bacdive158506.20230509.8.1

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 fonticola
  • full scientific name: Deinococcus fonticola Makk et al. 2019

@ref: 65182

domain: Bacteria

phylum: Deinococcus-Thermus

class: Deinococci

order: Deinococcales

family: Deinococcaceae

genus: Deinococcus

species: Deinococcus fonticola

full scientific name: Deinococcus fonticola Makk et al. 2019

strain designation: FeSDHB5-19

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell shapemotilityconfidence
67935negative1.0-2.0 µmcoccus-shapedno
69480negative95.263

colony morphology

  • @ref: 67935
  • colony size: 4.0-5.0 mm
  • colony color: pale pink
  • colony shape: circular
  • incubation period: 3 days
  • medium used: TGY agar

Culture and growth conditions

culture medium

  • @ref: 65182
  • name: GLYCEROL-YEAST EXTRACT-PEPTONE MEDIUM (DSMZ Medium 1484)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/1484
  • composition: Name: Glycerol-Yeast extract-Peptone Medium (DSMZ Medium 1484) Composition: Agar 15.0 g/l Yeast extract 5.0 g/l Bacto peptone 3.0 g/l Betaine 1.25 g/l Sodium pyruvate 1.25 g/l MgSO4 x 7 H2O 0.03 g/l Nitrilotriacetic acid 0.015 g/l NaCl 0.01 g/l MnSO4 x H2O 0.005 g/l ZnSO4 x 7 H2O 0.0018 g/l CoSO4 x 7 H2O 0.0018 g/l FeSO4 x 7 H2O 0.001 g/l CaCl2 x 2 H2O 0.001 g/l NiCl2 x 6 H2O 0.0003 g/l AlK(SO4)2 x 12 H2O 0.0002 g/l Pyridoxine hydrochloride 0.0001 g/l Na2MoO4 x 2 H2O 0.0001 g/l H3BO3 0.0001 g/l CuSO4 x 5 H2O 0.0001 g/l (DL)-alpha-Lipoic acid 5e-05 g/l p-Aminobenzoic acid 5e-05 g/l Calcium D-(+)-pantothenate 5e-05 g/l Nicotinic acid 5e-05 g/l Riboflavin 5e-05 g/l Thiamine HCl 5e-05 g/l Folic acid 2e-05 g/l Biotin 2e-05 g/l Na2WO4 x 2 H2O 4e-06 g/l Na2SeO3 x 5 H2O 3e-06 g/l Vitamin B12 1e-06 g/l Glycerol Distilled water

culture temp

@refgrowthtypetemperaturerange
65182positivegrowth28mesophilic
67935positivegrowth10-32
67935positiveoptimum28mesophilic

culture pH

@refabilitytypepHPH range
67935positivegrowth5.0-10.0alkaliphile
67935positiveoptimum6.5-7.5

Physiology and metabolism

oxygen tolerance

  • @ref: 67935
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
67935no
69480no99.585
69481no96

halophily

@refsaltgrowthtested relationconcentration
67935NaClpositivegrowth0.0-1.5 %
67935NaClpositiveoptimum0.0-0.5 %

observation

@refobservation
67935The polar lipid profile is dominated by several unidentified glycolipids and phosphoglycolipids
67935The predominant respiratory quinone is MK-8
67935The cell-wall peptidoglycan contains l-ornithine as the diagnostic diamino acid and corresponds to type A3ß l-Orn-Gly1-2
67935The whole-cell sugars are glucose and low amounts of galactose
67935Cells occur singly or form pairs or tetrads
67935Cells show strong gamma and UV radiation resistance (D10<8?kGy and (D10~800 Jm-2)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6793517632nitrate-reduction
6793516301nitrite-reduction
67935casein-hydrolysis
679355291gelatin-hydrolysis
6793517634D-glucose-fermentation
6793517634D-glucose-oxidation
6793528017starch-hydrolysis
6793553426tween 80-hydrolysis
679354853esculin-hydrolysis
679355291gelatin+hydrolysis
6793516947citrate-assimilation
6793516199urea-hydrolysis
6793517634D-glucose-assimilation
6793516899D-mannitol-assimilation
6793517268myo-inositol-assimilation
6793517924D-sorbitol-assimilation
6793562345L-rhamnose-assimilation
6793517992sucrose-assimilation
6793528053melibiose-assimilation
6793527613amygdalin-assimilation
6793530849L-arabinose-assimilation
67935esculin ferric citrate-builds acid from
6793565327D-xylose-builds acid from
6793516988D-ribose-builds acid from
67935potassium 5-dehydro-D-gluconate-builds acid from
6793530849L-arabinose-builds acid from
6793516443D-tagatose-builds acid from
6793517634D-glucose-builds acid from
6793517306maltose-builds acid from
67935potassium 2-dehydro-D-gluconate-builds acid from
6793527082trehalose-builds acid from
6793532528turanose-builds acid from
6793512936D-galactose-builds acid from
6793515824D-fructose-builds acid from
6793517992sucrose-builds acid from
6793517057cellobiose-builds acid from
6793528053melibiose-builds acid from
6793518305arbutin+builds acid from
6793516024D-mannose-builds acid from
6793517814salicin-builds acid from
6793517716lactose-builds acid from
6793516899D-mannitol-builds acid from
6793528087glycogen-builds acid from
6793528017starch-builds acid from
6793517108D-arabinose-builds acid from
679356731melezitose-builds acid from
6793518287L-fucose-builds acid from
6793562345L-rhamnose-builds acid from
6793528066gentiobiose-builds acid from
6793517924D-sorbitol-builds acid from
6793518333D-arabitol-builds acid from
6793562318D-lyxose-builds acid from
6793528847D-fucose-builds acid from
6793517754glycerol-builds acid from
6793559640N-acetylglucosamine-builds acid from
67935320061methyl alpha-D-glucopyranoside-builds acid from
6793517268myo-inositol-builds acid from
6793532032potassium gluconate-builds acid from
6793574863methyl beta-D-xylopyranoside-builds acid from
6793516634raffinose-builds acid from
6793527613amygdalin-builds acid from
6793543943methyl alpha-D-mannoside-builds acid from
6793517113erythritol-builds acid from
6793565328L-xylose-builds acid from
6793515963ribitol-builds acid from
6793517266L-sorbose-builds acid from
6793516813galactitol-builds acid from
6793515443inulin-builds acid from
6793517151xylitol-builds acid from
6793518403L-arabitol-builds acid from

metabolite production

@refChebi-IDmetaboliteproduction
6793516136hydrogen sulfideyes
6793535581indoleno
6793515688acetoinno

metabolite tests

@refChebi-IDmetabolitemethylred-testvoges-proskauer-test
6793517234glucose-
6793515688acetoin-

enzymes

@refvalueactivityec
67935cytochrome oxidase+1.9.3.1
67935catalase+1.11.1.6
67935arginine dihydrolase-3.5.3.6
67935lysine decarboxylase-4.1.1.18
67935ornithine decarboxylase-4.1.1.17
67935tryptophan deaminase-4.1.99.1
67935esterase (C 4)+
67935esterase Lipase (C 8)+
67935leucine arylamidase+3.4.11.1
67935acid phosphatase+3.1.3.2
67935alkaline phosphatase+3.1.3.1
67935naphthol-AS-BI-phosphohydrolase+
67935trypsin+/-3.4.21.4
67935alpha-glucosidase+/-3.2.1.20
67935lipase (C 14)-
67935valine arylamidase-
67935cystine arylamidase-3.4.11.3
67935alpha-chymotrypsin-3.4.21.1
67935alpha-galactosidase-3.2.1.22
67935beta-galactosidase-3.2.1.23
67935beta-glucuronidase-3.2.1.31
67935beta-glucosidase-3.2.1.21
67935N-acetyl-beta-glucosaminidase-3.2.1.52
67935alpha-mannosidase-3.2.1.24
67935alpha-fucosidase-3.2.1.51

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudesampling date
65182biofilm sample of thermal springDiana-Hygieia Thermal Spring (47.489056 N, 19.047713 E)HungaryHUNEurope47.489119.0477
67935gamma-irradiated biofilm sample of a radioactive hydrothermal spring caveGellért Hill, BudapestHungaryHUNEurope47.489119.04772015-10

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Thermal spring
#Environmental#Biofilm

taxonmaps

  • @ref: 69479
  • File name: preview.99_17459.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_90;96_8955;97_10765;98_13206;99_17459&stattab=map
  • Last taxonomy: Deinococcus fonticola subclade
  • 16S sequence: LT853728
  • Sequence Identity:
  • Total samples: 4048
  • soil counts: 326
  • aquatic counts: 942
  • animal counts: 2667
  • plant counts: 113

Sequence information

16S sequences

  • @ref: 65182
  • description: Deinococcus sp. partial 16S rRNA gene, strain FeSDHB5-19
  • accession: LT853728
  • length: 1405
  • database: ena
  • NCBI tax ID: 47478

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Deinococcus sp. FeSDHB5-192528713.3wgspatric2528713
67935Deinococcus fonticola FeSDHB5-19GCA_004634215contigncbi2528713

GC content

@refGC-contentmethod
6793563.5genome sequence analysis
6793560.9high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno96no
motileno86.748yes
gram-positiveyes67.083yes
anaerobicno97.438yes
aerobicyes88.752yes
halophileno94.003yes
spore-formingno91.945yes
glucose-utilyes86.457no
flagellatedno93.549yes
thermophileno88.864yes
glucose-fermentno88.934yes

External links

@ref: 65182

culture collection no.: DSM 106917, NCAIM B.02639

straininfo link

  • @ref: 111301
  • straininfo: 405447

literature

  • topic: Phylogeny
  • Pubmed-ID: 31038452
  • title: Deinococcus fonticola sp. nov., isolated from a radioactive thermal spring in Hungary.
  • authors: Makk J, Enyedi NT, Toth E, Anda D, Szabo A, Felfoldi T, Schumann P, Madl-Szonyi J, Borsodi AK
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.003383
  • year: 2019
  • mesh: Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Deinococcus/*classification/isolation & purification, Fatty Acids/chemistry, *Gamma Rays, Glycolipids/chemistry, Hot Springs/*microbiology, Hungary, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry
  • topic2: Transcriptome

Reference

@idauthorstitledoi/urlcataloguejournal
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
65182Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-106917Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 106917)
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
67935Judit Makk, Nóra Tünde Enyedi, Erika Tóth, Dóra Anda, Attila Szabó, Tamás Felföldi, Peter Schumann, Judit Mádl-Szonyi, Andrea K. BorsodiDeinococcus fonticola sp. nov., isolated from a radioactive thermal spring in Hungary10.1099/ijsem.0.003383IJSEM 69: 1724-1730 2019
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
111301Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID405447.1