Strain identifier

BacDive ID: 5883

Type strain: Yes

Species: Haloterrigena turkmenica

Strain Designation: VKM B-1734, 4

Strain history: CIP <- 2000, NCIMB <- BKM <- Zvyagintseva and Tarasov: strain 4

NCBI tax ID(s): 543526 (strain), 62320 (species)

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General

@ref: 2088

BacDive-ID: 5883

DSM-Number: 5511

keywords: genome sequence, 16S sequence, Archaea, mesophilic, Gram-negative

description: Haloterrigena turkmenica VKM B-1734 is a mesophilic, Gram-negative archaeon of the family Natrialbaceae.

NCBI tax id

NCBI tax idMatching level
62320species
543526strain

strain history

@refhistory
2088<- VKM
67770VKM B-1734 <-- I. S. Zvyagintseva 4k.
123698CIP <- 2000, NCIMB <- BKM <- Zvyagintseva and Tarasov: strain 4

doi: 10.13145/bacdive5883.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/archaea
  • keyword: phylum/methanobacteriota
  • domain: Archaea
  • phylum: Methanobacteriota
  • class: Halobacteria
  • order: Natrialbales
  • family: Natrialbaceae
  • genus: Haloterrigena
  • species: Haloterrigena turkmenica
  • full scientific name: Haloterrigena turkmenica (Zvyagintseva and Tarasov 1989) Ventosa et al. 1999

  • synonyms

    • @ref: 20215
    • synonym: Halococcus turkmenicus

@ref: 2088

domain: Archaea

phylum: Euryarchaeota

class: Halobacteria

order: Halobacteriales

family: Natrialbaceae

genus: Haloterrigena

species: Haloterrigena turkmenica

full scientific name: Haloterrigena turkmenica (Zvyagintseva and Tarasov 1989) Ventosa et al. 1999

strain designation: VKM B-1734, 4

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480negative99.848
123698negativeoval-shapedno

multimedia

  • @ref: 66793
  • multimedia content: EM_DSM_5511_1.jpg
  • caption: electron microscopic image
  • intellectual property rights: © HZI/Manfred Rohde

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
2088HALOBACTERIA MEDIUM (DSMZ Medium 372)yeshttps://mediadive.dsmz.de/medium/372Name: HALOBACTERIA MEDIUM (DSMZ Medium 372) Composition: NaCl 200.0 g/l MgSO4 x 7 H2O 20.0 g/l Agar 20.0 g/l Yeast extract 5.0 g/l Casamino acids 5.0 g/l Na3-citrate 3.0 g/l KCl 2.0 g/l Na glutamate 1.0 g/l FeCl2 x 4 H2O 0.036 g/l MnCl2 x 4 H2O 0.00036 g/l Distilled water
38625MEDIUM 305 - for Halorubrum trapanicumyesDistilled water make up to (1000.000 ml);Sodium chloride (250.000 g);Potassium chloride (2.000 g);ManganeseII chloride tetrahydrate (0.360 mg);Magnesium sulphate heptahydrate (20.000 g);Agar (20.000 g);Yeast extract (10.000 g);Ferrous chloride tetrahydrat
123698CIP Medium 204yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=204

culture temp

@refgrowthtypetemperaturerange
2088positivegrowth37mesophilic
38625positivegrowth37mesophilic
67770positivegrowth37mesophilic
123698positivegrowth37-45
123698nogrowth5psychrophilic
123698nogrowth15psychrophilic
123698nogrowth25mesophilic
123698nogrowth30mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no99
69480no99.952

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12369816947citrate-carbon source
1236984853esculin-hydrolysis
123698606565hippurate-hydrolysis
12369817632nitrate+builds gas from
12369817632nitrate+reduction
12369816301nitrite+builds gas from
12369816301nitrite-reduction
12369815792malonate-assimilation

metabolite production

  • @ref: 123698
  • 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
123698oxidase+
123698beta-galactosidase-3.2.1.23
123698alcohol dehydrogenase-1.1.1.1
123698gelatinase-
123698catalase+1.11.1.6
123698gamma-glutamyltransferase-2.3.2.2
123698lysine decarboxylase-4.1.1.18
123698ornithine decarboxylase-4.1.1.17
123698phenylalanine ammonia-lyase-4.3.1.24
123698tryptophan deaminase-
123698urease-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
123698--++-------+--------

Isolation, sampling and environmental information

isolation

@refgeographic locationsample typecountryorigin.countrycontinent
38625Turkmenia
67770AshgabatSalt soil crustTurkmenistanTKMAsia
123698Environment, Saline soilTurkmenistanTKMAsia

taxonmaps

  • @ref: 69479
  • File name: preview.99_187194.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_17652;96_68845;97_89497;98_121777;99_187194&stattab=map
  • Last taxonomy: Haloterrigena turkmenica
  • 16S sequence: AB004878
  • Sequence Identity:
  • Total samples: 1
  • aquatic counts: 1

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
20881Risk group (German classification)
1236981Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Halococcus turkmenicus DNA for 16S rRNAAB0048781473ena543526
20218Halococcus turkmenicus 16S rRNA gene, partialAJ002954181ena543526

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Haloterrigena turkmenica DSM 5511GCA_000025325completencbi543526
66792Haloterrigena turkmenica VKM B-1734, DSM 5511646311934draftimg543526
66792Haloterrigena turkmenica DSM 5511543526.27plasmidpatric543526
66792Haloterrigena turkmenica DSM 5511543526.29plasmidpatric543526
66792Haloterrigena turkmenica DSM 5511543526.26plasmidpatric543526
66792Haloterrigena turkmenica DSM 5511543526.13completepatric543526
66792Haloterrigena turkmenica DSM 5511543526.28plasmidpatric543526
66792Haloterrigena turkmenica DSM 5511543526.30plasmidpatric543526
66792Haloterrigena turkmenica DSM 5511543526.25plasmidpatric543526

GC content

@refGC-contentmethod
6777064.26genome sequence analysis
6777059.8thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno99no
motileno80.847no
flagellatedno95.434no
gram-positiveno95.091no
anaerobicno97.991no
aerobicyes90.733no
halophileyes92.698no
spore-formingno91.075no
thermophileno91.545yes
glucose-utilyes91.269no
glucose-fermentno80.559no

External links

@ref: 2088

culture collection no.: DSM 5511, VKM B-1734, JCM 9101, ATCC 51198, CIP 106419, NCIMB 13204

straininfo link

  • @ref: 75362
  • straininfo: 42854

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16280523Haloterrigena saccharevitans sp. nov., an extremely halophilic archaeon from Xin-Jiang, China.Xu XW, Liu SJ, Tohty D, Oren A, Wu M, Zhou PJInt J Syst Evol Microbiol10.1099/ijs.0.63761-02005Base Composition, China, DNA, Archaeal/analysis/chemistry/genetics, DNA, Ribosomal/analysis/chemistry/genetics, Halobacteriales/*classification/genetics/growth & development/metabolism, Lipids/analysis, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride, *Water MicrobiologyGenetics
Phylogeny19060076Haloterrigena salina sp. nov., an extremely halophilic archaeon isolated from a salt lake.Gutierrez MC, Castillo AM, Kamekura M, Ventosa AInt J Syst Evol Microbiol10.1099/ijs.0.2008/001602-02008Fatty Acids/analysis, Halobacteriaceae/chemistry/*classification/genetics/*physiology, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Salts, Species Specificity, *Water MicrobiologyGenetics
Phylogeny31006074Haloterrigena salifodinae sp. nov., an extremely halophilic archaeon isolated from a subterranean rock salt.Chen S, Xu Y, Sun S, Chen FAntonie Van Leeuwenhoek10.1007/s10482-019-01264-w2019Base Composition, China, Cluster Analysis, Cytosol/chemistry, DNA, Archaeal/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Halobacteriaceae/*classification/genetics/*isolation & purification/physiology, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil MicrobiologyTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
2088Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 5511)https://www.dsmz.de/collection/catalogue/details/culture/DSM-5511
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
38625Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18548
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
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
75362Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID42854.1StrainInfo: A central database for resolving microbial strain identifiers
123698Curators of the CIPCollection of Institut Pasteur (CIP 106419)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106419