Strain identifier

BacDive ID: 133550

Type strain: Yes

Species: Natronorubrum daqingense

Strain Designation: JX313

Strain history: CGMCC 1.8909 <-- S. Wang et al. JX313.

NCBI tax ID(s): 588898 (species)

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General

@ref: 29481

BacDive-ID: 133550

keywords: genome sequence, 16S sequence, Archaea, aerobe, Gram-variable, coccus-shaped

description: Natronorubrum daqingense JX313 is an aerobe, Gram-variable, coccus-shaped archaeon that was isolated from saline-alkaline soil.

NCBI tax id

  • NCBI tax id: 588898
  • Matching level: species

strain history

  • @ref: 67770
  • history: CGMCC 1.8909 <-- S. Wang et al. JX313.

doi: 10.13145/bacdive133550.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/archaea
  • keyword: phylum/methanobacteriota
  • domain: Archaea
  • phylum: Methanobacteriota
  • class: Halobacteria
  • order: Natrialbales
  • family: Natrialbaceae
  • genus: Natronorubrum
  • species: Natronorubrum daqingense
  • full scientific name: Natronorubrum daqingense (Wang et al. 2010) de la Haba et al. 2022

  • synonyms

    • @ref: 20215
    • synonym: Haloterrigena daqingensis

@ref: 29481

domain: Archaea

phylum: Euryarchaeota

class: Halobacteria

order: Natrialbales

family: Natrialbaceae

genus: Haloterrigena

species: Haloterrigena daqingensis

strain designation: JX313

type strain: yes

Morphology

cell morphology

@refgram staincell widthcell shapemotilityconfidence
29481variable0.8-1.3 µmcoccus-shapedno
69480no92.408
69480negative99.922

pigmentation

  • @ref: 29481
  • production: yes

Culture and growth conditions

culture temp

@refgrowthtypetemperaturerange
29481positivegrowth20-50
29481positiveoptimum35mesophilic
67770positivegrowth37mesophilic

culture pH

@refabilitytypepHPH range
29481positivegrowth8-10.5alkaliphile
29481positiveoptimum10

Physiology and metabolism

oxygen tolerance

  • @ref: 29481
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.971

halophily

@refsaltgrowthtested relationconcentration
29481NaClpositivegrowth1.7-5.5 %
29481NaClpositiveoptimum2-2.5 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2948130089acetate+carbon source
2948135391aspartate+carbon source
2948129987glutamate+carbon source
2948115361pyruvate+carbon source
2948130031succinate+carbon source

enzymes

  • @ref: 29481
  • value: catalase
  • activity: +
  • ec: 1.11.1.6

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
29481saline-alkaline soil
67770Saline-alkaline soil from DaqingHeilongjiang ProvinceChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Condition#Alkaline
#Condition#Saline

taxonmaps

  • @ref: 69479
  • File name: preview.99_187305.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_17652;96_68920;97_89572;98_121863;99_187305&stattab=map
  • Last taxonomy: Natrialbaceae
  • 16S sequence: FJ545273
  • Sequence Identity:
  • Total samples: 770
  • soil counts: 99
  • aquatic counts: 204
  • animal counts: 446
  • plant counts: 21

Sequence information

16S sequences

  • @ref: 29481
  • description: Haloterrigena daqingensis strain JX313 16S ribosomal RNA gene, partial sequence
  • accession: FJ545273
  • length: 1475
  • database: nuccore
  • NCBI tax ID: 588898

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Natronorubrum daqingense JX313GCA_001971705completencbi588898
66792Natronorubrum daqingense CGMCC 1.8909GCA_900156445contigncbi588898
66792Haloterrigena daqingensis JX3132740891999completeimg588898
66792Haloterrigena daqingensis CGMCC 1.89092681812915draftimg588898
66792Haloterrigena daqingensis strain CGMCC 1.8909588898.4wgspatric588898

GC content

@refGC-contentmethod
2948159.3
6777059.3thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno96.049yes
gram-positiveno97.589yes
anaerobicno96.885yes
aerobicyes84.963no
halophileyes87.665no
spore-formingno92.72no
glucose-utilyes87.426no
thermophileno86.877yes
motileno77.917no
glucose-fermentno87.34no

External links

@ref: 29481

culture collection no.: CGMCC 1.8909, NBRC 105739, JCM 18238

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19915113Haloterrigena daqingensis sp. nov., an extremely haloalkaliphilic archaeon isolated from a saline-alkaline soil.Wang S, Yang Q, Liu ZH, Sun L, Wei D, Zhang JZ, Song JZ, Yuan HFInt J Syst Evol Microbiol10.1099/ijs.0.013995-02009Base Composition, Carbohydrate Metabolism, China, Cluster Analysis, DNA, Archaeal/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Genes, rRNA, Halobacteriaceae/*classification/genetics/*isolation & purification/physiology, Hydrogen-Ion Concentration, Locomotion, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, Pigments, Biological/biosynthesis, RNA, Archaeal/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Sodium Chloride/metabolism, *Soil Microbiology, TemperatureMetabolism
Genetics34245190Complete genome sequencing and comparative genome analysis of the extremely halophilic archaea, Haloterrigena daqingensis.Wang S, Narsing Rao MP, Wei D, Sun L, Fang BZ, Li WQ, Yu LH, Li WJBiotechnol Appl Biochem10.1002/bab.22202021

Reference

@idauthorstitledoi/urlID_cross_referencepubmedjournal
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
29481Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172588128776041
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
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa102533211880Nucleic Acids Res. 49: D498-D508 2020
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.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