Strain identifier

BacDive ID: 5965

Type strain: Yes

Species: Natronococcus occultus

Strain Designation: SP4

Strain history: CIP <- 1995, NCIMB <- W.D. Grant: strain SP4

NCBI tax ID(s): 694430 (strain), 29288 (species)

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General

@ref: 1377

BacDive-ID: 5965

DSM-Number: 3396

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

description: Natronococcus occultus SP4 is a mesophilic, Gram-positive, coccus-shaped archaeon of the family Natrialbaceae.

NCBI tax id

NCBI tax idMatching level
29288species
694430strain

strain history

@refhistory
1377<- B.J. Tindall <- Ross, SP4
67770NCIMB 2192 <-- W. G. Grant SP4.
121380CIP <- 1995, NCIMB <- W.D. Grant: strain SP4

doi: 10.13145/bacdive5965.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/archaea
  • keyword: phylum/methanobacteriota
  • domain: Archaea
  • phylum: Methanobacteriota
  • class: Halobacteria
  • order: Natrialbales
  • family: Natrialbaceae
  • genus: Natronococcus
  • species: Natronococcus occultus
  • full scientific name: Natronococcus occultus Tindall et al. 1984

@ref: 1377

domain: Archaea

phylum: Euryarchaeota

class: Halobacteria

order: Halobacteriales

family: Natrialbaceae

genus: Natronococcus

species: Natronococcus occultus

full scientific name: Natronococcus occultus Tindall et al. 1984

strain designation: SP4

type strain: yes

Morphology

cell morphology

  • @ref: 121380
  • gram stain: positive
  • cell shape: coccus-shaped
  • motility: no

multimedia

  • @ref: 66793
  • multimedia content: EM_DSM_3396_1.jpg
  • caption: electron microscopic image
  • intellectual property rights: © HZI/Manfred Rohde

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
1377NATRONOBACTERIA MEDIUM (DSMZ Medium 371)yeshttps://mediadive.dsmz.de/medium/371Name: NATRONOBACTERIA MEDIUM (DSMZ Medium 371) Composition: NaCl 200.0 g/l Agar 20.0 g/l Casamino acids 5.0 g/l Yeast extract 5.0 g/l Na2CO3 5.0 g/l Na2-glutamate 1.0 g/l KH2PO4 1.0 g/l KCl 1.0 g/l NH4Cl 1.0 g/l MgSO4 x 7 H2O 0.24 g/l CaSO4 x 2 H2O 0.17 g/l HCl 0.0025 g/l FeCl2 x 4 H2O 0.0015 g/l CoCl2 x 6 H2O 0.00019 g/l MnCl2 x 4 H2O 0.0001 g/l ZnCl2 7e-05 g/l Na2MoO4 x 2 H2O 3.6e-05 g/l NiCl2 x 6 H2O 2.4e-05 g/l H3BO3 6e-06 g/l CuCl2 x 2 H2O 2e-06 g/l Distilled water
39037MEDIUM 136 - for Natronococcus occultus, Natrialba magadii and Halorubrum vacuolatumyesSolution 2 - M0437 (600.000 ml);Solution 1 - M0437 (400.000 ml)
121380CIP Medium 136yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=136

culture temp

@refgrowthtypetemperaturerange
1377positivegrowth37mesophilic
39037positivegrowth37mesophilic
67770positivegrowth37mesophilic
121380positivegrowth30-45
121380nogrowth10psychrophilic

Physiology and metabolism

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1213804853esculin-hydrolysis
12138017632nitrate+reduction
12138016301nitrite-reduction

metabolite production

  • @ref: 121380
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

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
121380oxidase+
121380beta-galactosidase+3.2.1.23
121380alcohol dehydrogenase-1.1.1.1
121380gelatinase-
121380catalase+1.11.1.6
121380lysine decarboxylase-4.1.1.18
121380ornithine decarboxylase-4.1.1.17
121380urease-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
121380--++-----+------+---

Isolation, sampling and environmental information

isolation

@refgeographic locationcountryorigin.countrycontinentsample type
1377Magadi LakeKenyaKENAfrica
67770KenyaKENAfricaSalt pan liquor from the Lake Magadi
121380KenyaKENAfricaEnvironment, Soda lake, Magadi lake

taxonmaps

  • @ref: 69479
  • File name: preview.99_187218.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_17652;96_68871;97_89518;98_121799;99_187218&stattab=map
  • Last taxonomy: Natronococcus occultus subclade
  • 16S sequence: AB477981
  • Sequence Identity:
  • Total samples: 2
  • soil counts: 1
  • aquatic counts: 1

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
13771Risk group (German classification)
1213801Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Natronococcus occultus gene for 16S ribosomal RNA, partial sequence, strain: JCM 8859AB4779811432ena694430
20218Natronococcus occultus gene for 16S rRNA, complete sequence, strain: JCM 8859AB6634701472ena694430
20218N.occultus 16S ribosomal RNAZ283781464ena694430

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Natronococcus occultus SP4GCA_000328685completencbi694430
66792Natronococcus occultus SP4, DSM 33962506520044completeimg694430
66792Natronococcus occultus SP4694430.9plasmidpatric694430
66792Natronococcus occultus SP4694430.10plasmidpatric694430
66792Natronococcus occultus SP4694430.4completepatric694430

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno86.529no
flagellatedno97.263no
gram-positiveno97.076no
anaerobicno96.82no
aerobicyes85.352no
halophileyes90.386no
spore-formingno92.333no
thermophileno84.72yes
glucose-utilyes91.162no
glucose-fermentno86.665no

External links

@ref: 1377

culture collection no.: DSM 3396, ATCC 43101, CCM 3871, NCMB 2192, JCM 8859, CIP 104548, IAM 13184, NBRC 102186, NCIMB 2192, VKM B-1752

straininfo link

  • @ref: 75454
  • straininfo: 45105

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny7547296Natronococcus amylolyticus sp. nov., a haloalkaliphilic archaeon.Kanal H, Kobayashi T, Aono R, Kudo TInt J Syst Bacteriol10.1099/00207713-45-4-7621995Archaea/*classification/genetics, Base Sequence, DNA, Bacterial/chemistry, DNA, Ribosomal/chemistry, Molecular Sequence Data, RNA, Ribosomal, 16S/geneticsGenetics
Genetics9395342The cell wall polymer of the extremely halophilic archaeon Natronococcus occultus.Niemetz R, Karcher U, Kandler O, Tindall BJ, Konig HEur J Biochem10.1111/j.1432-1033.1997.00905.x1997Amino Acid Sequence, Carbohydrate Conformation, Carbohydrate Sequence, Cell Wall/*chemistry, Chromatography, High Pressure Liquid, Chromatography, Ion Exchange, Glycoconjugates/analysis/*chemistry, Hydrolysis, Molecular Sequence Data, Monosaccharides/analysis, Natronococcus/*chemistry, Oligosaccharides/analysis/*chemistry, Peptides/*analysis/*chemistry, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
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

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
1377Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 3396)https://www.dsmz.de/collection/catalogue/details/culture/DSM-3396
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
39037Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16469
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)
66793Mukherjee et al.10.1038/nbt.3886GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life 35: 676-683 201728604660
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
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
75454Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID45105.1StrainInfo: A central database for resolving microbial strain identifiers
121380Curators of the CIPCollection of Institut Pasteur (CIP 104548)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104548