Strain identifier

BacDive ID: 5969

Type strain: Yes

Species: Halostagnicola larsenii

Strain Designation: XH-48

Strain history: A. Ventosa XH-48.

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General

@ref: 7132

BacDive-ID: 5969

DSM-Number: 17691

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

description: Halostagnicola larsenii XH-48 is an aerobe, mesophilic, Gram-negative archaeon that was isolated from sediment of saline Lake Xilinhot .

NCBI tax id

NCBI tax idMatching level
353800species
797299strain

strain history

@refhistory
7132<- A. Ventosa, Univ. Seville, Dept. Microbiol. Parasitol., Spain; XH-48 <- A. M. Castillo et al.
67770A. Ventosa XH-48.

doi: 10.13145/bacdive5969.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/archaea
  • keyword: phylum/methanobacteriota
  • domain: Archaea
  • phylum: Methanobacteriota
  • class: Halobacteria
  • order: Natrialbales
  • family: Natrialbaceae
  • genus: Halostagnicola
  • species: Halostagnicola larsenii
  • full scientific name: Halostagnicola larsenii Castillo et al. 2006

@ref: 7132

domain: Archaea

phylum: Euryarchaeota

class: Halobacteria

order: Halobacteriales

family: Natrialbaceae

genus: Halostagnicola

species: Halostagnicola larsenii

full scientific name: Halostagnicola larsenii Castillo et al. 2006

strain designation: XH-48

type strain: yes

Morphology

cell morphology

  • @ref: 31790
  • gram stain: negative
  • cell length: 01-03 µm
  • cell width: 0.5-1 µm
  • cell shape: rod-shaped
  • motility: no

pigmentation

  • @ref: 31790
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 7132
  • name: HALOPIGER MEDIUM (DSMZ Medium 1138)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/1138
  • composition: Name: HALOPIGER MEDIUM (DSMZ Medium 1138) Composition: NaCl 195.0 g/l MgSO4 x 7 H2O 50.8 g/l MgCl2 x 6 H2O 32.5 g/l Yeast extract 5.0 g/l KCl 5.0 g/l CaCl2 x 2 H2O 0.8 g/l NaBr 0.6 g/l NaHCO3 0.16 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
7132positivegrowth37mesophilic
31790positivegrowth25-50
31790positiveoptimum37mesophilic
67770positivegrowth37mesophilic

culture pH

@refabilitytypepHPH range
31790positivegrowth06-09alkaliphile
31790positiveoptimum07-08

Physiology and metabolism

oxygen tolerance

  • @ref: 31790
  • oxygen tolerance: aerobe

spore formation

  • @ref: 31790
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
31790NaClpositivegrowth15-30 %
31790NaClpositiveoptimum20 %

observation

  • @ref: 31790
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3179030089acetate+carbon source
3179022599arabinose+carbon source
3179028757fructose+carbon source
3179028260galactose+carbon source
3179017234glucose+carbon source
3179029987glutamate+carbon source
3179017754glycerol+carbon source
3179017716lactose+carbon source
3179017306maltose+carbon source
3179029864mannitol+carbon source
3179017272propionate+carbon source
3179033942ribose+carbon source
3179027082trehalose+carbon source
3179018222xylose+carbon source
3179017632nitrate+reduction

enzymes

@refvalueactivityec
31790catalase+1.11.1.6
31790cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitude
7132sediment of saline Lake Xilinhot (43° 55' N 115° 37' E)Inner MongoliaChinaCHNAsia43.9167115.617
67770Sediment of a saline lake (Lake Xilinhot) in Inner MongoliaChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Lake (large)
#Environmental#Aquatic#Sediment
#Condition#Saline

taxonmaps

  • @ref: 69479
  • File name: preview.99_187283.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_17652;96_68906;97_89556;98_121847;99_187283&stattab=map
  • Last taxonomy: Halostagnicola larsenii
  • 16S sequence: AB663441
  • Sequence Identity:
  • Total samples: 6
  • soil counts: 1
  • aquatic counts: 5

Safety information

risk assessment

  • @ref: 7132
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Halostagnicola larsenii gene for 16S rRNA, partial sequenceAB3014891433ena797299
20218Halostagnicola larsenii gene for 16S rRNA, complete sequence, strain: JCM 13463AB6634411473ena797299
7132Halostagnicola larsenii partial 16S rRNA gene, type strain XH-48TAM1175711372ena797299

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Halostagnicola larsenii XH-48GCA_000517625completencbi797299
66792Halostagnicola larsenii XH-48, DSM 176912510065051completeimg797299
67770Halostagnicola larsenii XH-48, complete genomeCP007055ncbi797299
66792Halostagnicola larsenii XH-48797299.3completepatric797299
66792Halostagnicola larsenii XH-48797299.7plasmidpatric797299
66792Halostagnicola larsenii XH-48797299.8plasmidpatric797299
66792Halostagnicola larsenii XH-48797299.9plasmidpatric797299
66792Halostagnicola larsenii XH-48797299.6plasmidpatric797299

GC content

@refGC-contentmethod
713261.0thermal denaturation, midpoint method (Tm)
3179061
6777061thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno82.818yes
flagellatedno96.106yes
gram-positiveno95.812yes
anaerobicno97.818no
halophileyes89.495yes
spore-formingno93.431yes
thermophileno81.386yes
glucose-utilyes93.869no
aerobicyes93.514no
glucose-fermentno80.471no

External links

@ref: 7132

culture collection no.: DSM 17691, CECT 7116, CGMCC 1.5338, JCM 13463

straininfo link

  • @ref: 75458
  • straininfo: 297210

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16825623Halostagnicola larsenii gen. nov., sp. nov., an extremely halophilic archaeon from a saline lake in Inner Mongolia, China.Castillo AM, Gutierrez MC, Kamekura M, Xue Y, Ma Y, Cowan DA, Jones BE, Grant WD, Ventosa AInt J Syst Evol Microbiol10.1099/ijs.0.64286-02006Aerobiosis, Anaerobiosis, Base Composition, China, DNA, Archaeal/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Enzymes/analysis, Genes, rRNA, Geologic Sediments/*microbiology, Halobacteriaceae/*classification/cytology/genetics/*isolation & purification/physiology, Lipids/chemistry/isolation & purification, Magnesium Chloride/metabolism, Microscopy, Phase-Contrast, Molecular Sequence Data, Mongolia, Phylogeny, RNA, Archaeal/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Sodium Chloride/metabolism, *Water MicrobiologyEnzymology
Phylogeny20081018Halostagnicola kamekurae sp. nov., an extremely halophilic archaeon from solar salt.Nagaoka S, Minegishi H, Echigo A, Usami RInt J Syst Evol Microbiol10.1099/ijs.0.014449-02010Base Composition, DNA, Archaeal/genetics, Halobacteriaceae/*classification/genetics/isolation & purification, Lipids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Philippines, *Phylogeny, RNA, Ribosomal, 16S/genetics, Salts, Sequence Analysis, DNAGenetics
Phylogeny20543148Halostagnicola alkaliphila sp. nov., an alkaliphilic haloarchaeon from commercial rock salt.Nagaoka S, Minegishi H, Echigo A, Shimane Y, Kamekura M, Usami RInt J Syst Evol Microbiol10.1099/ijs.0.023119-02010Alkalies/*metabolism, China, DNA, Archaeal/genetics, Fatty Acids/metabolism, Halobacteriaceae/*classification/genetics/*isolation & purification/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Sodium Chloride/*metabolismMetabolism
Phylogeny25479949Halostagnicola bangensis sp. nov., an alkaliphilic haloarchaeon from a soda lake.Corral P, Corcelli A, Ventosa AInt J Syst Evol Microbiol10.1099/ijs.0.0000062014Base Composition, DNA, Archaeal/genetics, Halobacteriaceae/*classification/genetics/isolation & purification, Lakes, Lipids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Tibet, *Water MicrobiologyGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
7132Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17691)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17691
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
31790Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604128061
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
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
75458Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID297210.1StrainInfo: A central database for resolving microbial strain identifiers