Strain identifier

BacDive ID: 5929

Type strain: Yes

Species: Halococcus dombrowskii

Strain Designation: H4

Strain history: CIP <- 2004, NCIMB <- H. Stan Lotter, Salzburg Univ., Salzburg, Austria: strain H4

NCBI tax ID(s): 179637 (species)

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General

@ref: 5282

BacDive-ID: 5929

DSM-Number: 14522

keywords: genome sequence, 16S sequence, Archaea, mesophilic, Gram-positive, coccus-shaped

description: Halococcus dombrowskii H4 is a mesophilic, Gram-positive, coccus-shaped archaeon that was isolated from dry rock salt from salt mine.

NCBI tax id

  • NCBI tax id: 179637
  • Matching level: species

strain history

@refhistory
5282<- H. Stan-Lotter; H4
67770DSM 14522 <-- H. Stan-Lotter H4.
118961CIP <- 2004, NCIMB <- H. Stan Lotter, Salzburg Univ., Salzburg, Austria: strain H4

doi: 10.13145/bacdive5929.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/archaea
  • keyword: phylum/methanobacteriota
  • domain: Archaea
  • phylum: Methanobacteriota
  • class: Halobacteria
  • order: Halobacteriales
  • family: Halococcaceae
  • genus: Halococcus
  • species: Halococcus dombrowskii
  • full scientific name: Halococcus dombrowskii Stan-Lotter et al. 2002

@ref: 5282

domain: Archaea

phylum: Euryarchaeota

class: Halobacteria

order: Halobacteriales

family: Halococcaceae

genus: Halococcus

species: Halococcus dombrowskii

full scientific name: Halococcus dombrowskii Stan-Lotter et al. 2002

strain designation: H4

type strain: yes

Morphology

cell morphology

  • @ref: 118961
  • gram stain: positive
  • cell shape: coccus-shaped
  • motility: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5282MEDIUM FOR H. DOMBROWSKII (DSMZ Medium 954)yeshttps://mediadive.dsmz.de/medium/954Name: MEDIUM FOR H. DOMBROWSKII (DSMZ Medium 954) Composition: NaCl 200.0 g/l MgCl2 x 6 H2O 20.0 g/l Agar 20.0 g/l Tris 12.1 g/l Yeast extract 5.0 g/l Casamino acids 5.0 g/l KCl 2.0 g/l CaCl2 x 2 H2O 0.2 g/l Distilled water
33060MEDIUM 598 - for Halococcus dombrowskiiyesDistilled water make up to (1000.000 ml);Sodium chloride (200.000 g);Potassium chloride (2.000 g);Magnesium chloride hexahydrate (20.000 g);Calcium chloride dihydrate (0.200 g);Agar (20.000 g);Yeast extract (5.000 g);Casamino acids (5.000 g);Trizma base (
118961CIP Medium 598yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=598

culture temp

@refgrowthtypetemperaturerange
5282positivegrowth37mesophilic
33060positivegrowth37mesophilic
67770positivegrowth37mesophilic
118961positivegrowth25-37mesophilic
118961nogrowth5psychrophilic
118961nogrowth15psychrophilic
118961nogrowth41thermophilic
118961nogrowth45thermophilic

Physiology and metabolism

halophily

@refsaltgrowthtested relationconcentration
118961NaClnogrowth0 %
118961NaClnogrowth2 %
118961NaClnogrowth4 %
118961NaClnogrowth6 %
118961NaClnogrowth8 %
118961NaClnogrowth10 %

observation

  • @ref: 67770
  • observation: quinones: MK-8, MK-8(H2)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
11896116947citrate-carbon source
1189614853esculin-hydrolysis
118961606565hippurate+hydrolysis
11896117632nitrate-builds gas from
11896117632nitrate-reduction
11896116301nitrite-builds gas from
11896116301nitrite-reduction
11896115792malonate-assimilation

metabolite production

  • @ref: 118961
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11896115688acetoin-
11896117234glucose-

enzymes

@refvalueactivityec
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
118961oxidase+
118961beta-galactosidase+3.2.1.23
118961alcohol dehydrogenase-1.1.1.1
118961gelatinase-
118961catalase+1.11.1.6
118961lysine decarboxylase-4.1.1.18
118961ornithine decarboxylase-4.1.1.17
118961phenylalanine ammonia-lyase-4.3.1.24
118961tryptophan deaminase-
118961urease-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
118961--++-+-----+--------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
5282dry rock salt from salt mineBad IschlAustriaAUTEurope
67770Dry Permina rock salt from the salt mine in Bad IschlAustriaAUTEurope
118961Dry rock saltBad IschlAustriaAUTEurope1997

isolation source categories

Cat1Cat2Cat3
#Engineered#Other#Mine
#Environmental#Terrestrial
#Condition#Saline

taxonmaps

  • @ref: 69479
  • File name: preview.99_187216.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_17821;96_68869;97_89516;98_121797;99_187216&stattab=map
  • Last taxonomy: Halococcus
  • 16S sequence: AJ420376
  • Sequence Identity:
  • Total samples: 276
  • soil counts: 14
  • aquatic counts: 97
  • animal counts: 164
  • plant counts: 1

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
52821Risk group (German classification)
1189611Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Halococcus dombrowskii strain DSM 14522 16S-23S ribosomal RNA intergenic spacer, partial sequenceEU984226257ena179637
5282Halococcus dombrowskii partial 16S rRNA gene sequence, strain H4AJ4203761472ena179637

Genome sequences

  • @ref: 66792
  • description: Halococcus dombrowskii H4
  • accession: GCA_022870485
  • assembly level: complete
  • database: ncbi
  • NCBI tax ID: 179637

GC content

@refGC-contentmethod
528261.3
6777061.3high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedno97.495no
gram-positiveno95.766no
anaerobicno95.249no
aerobicyes82.649no
halophileyes90.92no
spore-formingno93.847no
motileno81.642no
glucose-fermentno85.16no
thermophileno87.469yes
glucose-utilyes87.104no

External links

@ref: 5282

culture collection no.: DSM 14522, ATCC BAA 364, NCIMB 13803, JCM 12289, CIP 108355

straininfo link

  • @ref: 75410
  • straininfo: 100672

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny12361290Halococcus dombrowskii sp. nov., an archaeal isolate from a Permian alpine salt deposit.Stan-Lotter H, Pfaffenhuemer M, Legat A, Busse HJ, Radax C, Gruber CInt J Syst Evol Microbiol10.1099/00207713-52-5-18072002Archaeal Proteins/isolation & purification, Austria, Base Composition, DNA, Archaeal/chemistry/genetics, DNA, Ribosomal/genetics, Genes, Archaeal, Geologic Sediments/microbiology, Halococcus/*classification/genetics/*isolation & purification/metabolism, Lipids/analysis, Mining, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Archaeal/genetics, RNA, Ribosomal, 16S/genetics, SaltsEnzymology
Phylogeny17329792Halococcus qingdaonensis sp. nov., a halophilic archaeon isolated from a crude sea-salt sample.Wang QF, Li W, Yang H, Liu YL, Cao HH, Dornmayr-Pfaffenhuemer M, Stan-Lotter H, Guo GQInt J Syst Evol Microbiol10.1099/ijs.0.64673-02007Base Composition, China, DNA, Archaeal/genetics, DNA, Ribosomal/genetics, Halococcus/*classification/genetics/isolation & purification/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, *Sodium ChlorideGenetics
Phylogeny17911282Halococcus thailandensis sp. nov., from fish sauce in Thailand.Namwong S, Tanasupawat S, Visessanguan W, Kudo T, Itoh TInt J Syst Evol Microbiol10.1099/ijs.0.65218-02007Aerobiosis, Base Composition, DNA, Archaeal/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fish Products/*microbiology, Food Microbiology, Genes, rRNA, Glycolipids/analysis, Halococcus/chemistry/*classification/genetics/*isolation & purification, Hydrogen-Ion Concentration, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, RNA, Archaeal/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Sodium Chloride/metabolism, Temperature, Thailand, Vitamin K 2/analysisBiotechnology
Cultivation19215203Investigating the effects of simulated martian ultraviolet radiation on Halococcus dombrowskii and other extremely halophilic archaebacteria.Fendrihan S, Berces A, Lammer H, Musso M, Ronto G, Polacsek TK, Holzinger A, Kolb C, Stan-Lotter HAstrobiology10.1089/ast.2007.02342009Archaea/cytology/*radiation effects/ultrastructure, Crystallization, Culture Media, Dose-Response Relationship, Radiation, *Extraterrestrial Environment, Geologic Sediments/microbiology, Halococcus/cytology/*radiation effects/ultrastructure, *Mars, Microbial Viability/radiation effects, Salts/chemistry, *Space Simulation, *Ultraviolet Rays
Metabolism20437233Identification of polyhydroxyalkanoates in Halococcus and other haloarchaeal species.Legat A, Gruber C, Zangger K, Wanner G, Stan-Lotter HAppl Microbiol Biotechnol10.1007/s00253-010-2611-62010Australia, Geologic Sediments/microbiology, Halobacteriaceae/*chemistry/isolation & purification/metabolism/ultrastructure, Halococcus/*chemistry/isolation & purification/metabolism/ultrastructure, Hydroxybutyrates/*chemistry/metabolism, Magnetic Resonance Spectroscopy, Microscopy, Electron, Transmission, Polyesters/*chemistry/metabolismEnzymology
Phylogeny24132728Halococcus sediminicola sp. nov., an extremely halophilic archaeon isolated from a marine sediment.Yim KJ, Cha IT, Whon TW, Lee HW, Song HS, Kim KN, Nam YD, Lee SJ, Bae JW, Rhee SK, Choi JS, Seo MJ, Roh SW, Kim DAntonie Van Leeuwenhoek10.1007/s10482-013-0054-72013Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry/metabolism, Geologic Sediments/*microbiology, Halococcus/*classification/genetics/*isolation & purification/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sodium Chloride/metabolismMetabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
5282Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 14522)https://www.dsmz.de/collection/catalogue/details/culture/DSM-14522
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
33060Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5968
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
75410Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID100672.1StrainInfo: A central database for resolving microbial strain identifiers
118961Curators of the CIPCollection of Institut Pasteur (CIP 108355)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108355