Strain identifier

BacDive ID: 141129

Type strain: Yes

Species: Cuniculiplasma divulgatum

Strain Designation: S5

Strain history: O. Golyshina; Bangor Univ., UK; S5.

NCBI tax ID(s): 1673428 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 44041

BacDive-ID: 141129

keywords: genome sequence, 16S sequence, Archaea, facultative anaerobe, organoheterotroph, spore-forming, pleomorphic-shaped

description: Cuniculiplasma divulgatum S5 is a facultative anaerobe, organoheterotroph, spore-forming archaeon that was isolated from acidic streamer formed on the surfaces of copper-ore-containing suldic deposits.

NCBI tax id

  • NCBI tax id: 1673428
  • Matching level: species

strain history

  • @ref: 67770
  • history: O. Golyshina; Bangor Univ., UK; S5.

doi: 10.13145/bacdive141129.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/archaea
  • keyword: phylum/methanobacteriota
  • domain: Archaea
  • phylum: Methanobacteriota
  • class: Thermoplasmata
  • order: Thermoplasmatales
  • family: Cuniculiplasmataceae
  • genus: Cuniculiplasma
  • species: Cuniculiplasma divulgatum
  • full scientific name: Cuniculiplasma divulgatum Golyshina et al. 2016

@ref: 44041

domain: Archaea

phylum: Euryarchaeota

class: Thermoplasmata

order: Thermoplasmatales

family: Cuniculiplasmataceae

genus: Cuniculiplasma

species: Cuniculiplasma divulgatum

strain designation: S5

type strain: yes

Morphology

cell morphology

@refcell shapegram stainconfidence
44041pleomorphic-shaped
69480negative99.968

Culture and growth conditions

culture medium

  • @ref: 44041
  • name: modified medium 88 (DSMZ)
  • growth: yes
  • composition: All g/l (NH 4)2SO4, 1.3; KH2PO4, 0.28; MgSO4 . 0.7 H2O, 0.25; CaCl2 . 2 H2O, 0.07; FeCl3 . 6 H2O, 0.02. Other salts in medium 88 were replaced with the trace element solution SL-10 from DSMZ medium 320 at a concentration of 1 : 1000. Beef extract (3 g/l), 0.06 % betaine and Kao and Michayluk’s vitamin solution (Sigma-Aldrich) at 1 : 100 (v/v) were added to the medium. The medium was adjusted to pH 1.0–1.2 with concentrated H2SO4.

culture temp

@refgrowthtypetemperaturerange
44041positivegrowth10-48
44041positiveoptimum37-40
67770positivegrowth37mesophilic

culture pH

@refabilitytypepHPH range
44041positivegrowth0.5-4.0acidophile
44041positiveoptimum1.0-1.2

Physiology and metabolism

oxygen tolerance

  • @ref: 44041
  • oxygen tolerance: facultative anaerobe

nutrition type

  • @ref: 44041
  • type: organoheterotroph

spore formation

@refspore formationconfidence
69481yes100
69480no99.995

observation

@refobservation
44041cell wall
67770quinones: Menaquinones and thermoplasmaquinones

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentenrichment cultureenrichment culture compositionenrichment culture durationenrichment culture temperature
44041acidic streamer formed on the surfaces of copper-ore-containing suldic depositsCantareras MineSpainESPEuropemodified medium 88 (DSMZ)All g/l (NH 4)2SO4, 1.3; KH2PO4, 0.28; MgSO4 . 0.7 H2O, 0.25; CaCl2 . 2 H2O, 0.07; FeCl3 . 6 H2O, 0.02. Other salts in medium 88 were replaced with the trace element solution SL-10 from DSMZ medium 320 at a concentration of 1 : 1000. Beef extract (3 g/l), 0.06 % betaine and Kao and Michayluk’s vitamin solution (Sigma-Aldrich) at 1 : 100 (v/v) were added to the medium. The medium was adjusted to pH 1.0–1.2 with concentrated H2SO4.5 days37
67770Acidic water from the surface of a copper mine site in Mynydd ParysAngleseyUnited KingdomGBREurope

isolation source categories

Cat1Cat2Cat3
#Condition#Acidic
#Engineered#Other#Mine
#Environmental#Microbial community
#Environmental#Terrestrial#Geologic

taxonmaps

  • @ref: 69479
  • File name: preview.99_187314.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_18093;96_68924;97_89578;98_121870;99_187314&stattab=map
  • Last taxonomy: Cuniculiplasma divulgatum subclade
  • 16S sequence: KT005320
  • Sequence Identity:
  • Total samples: 142
  • soil counts: 5
  • aquatic counts: 135
  • animal counts: 2

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
44041Cuniculiplasma divulgatum strain S5 16S ribosomal RNA gene, partial sequenceKT0053211469nuccore1673428
67770Cuniculiplasma divulgatum strain PM4 16S ribosomal RNA gene, partial sequenceKT0053201469ena1673428

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Cuniculiplasma divulgatum S5(T) (=JCM 30642; =VKM B-2941)GCA_900083515completencbi1673428
66792Cuniculiplasma divulgatum S52773858060completeimg1673428

GC content

  • @ref: 67770
  • GC-content: 37.3
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileno86.612no
flagellatedno98.029no
gram-positiveno90.308no
anaerobicno55.507no
aerobicno91.531yes
halophileno87.066no
spore-formingno94.033no
glucose-fermentno64.513no
thermophileyes95.57no
glucose-utilyes82.919no

External links

@ref: 44041

culture collection no.: JCM 30642, VKM B-2941

literature

  • topic: Phylogeny
  • Pubmed-ID: 26518885
  • title: The novel extremely acidophilic, cell-wall-deficient archaeon Cuniculiplasma divulgatum gen. nov., sp. nov. represents a new family, Cuniculiplasmataceae fam. nov., of the order Thermoplasmatales.
  • authors: Golyshina OV, Lunsdorf H, Kublanov IV, Goldenstein NI, Hinrichs KU, Golyshin PN
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.000725
  • year: 2015
  • mesh: Base Composition, Cell Wall/chemistry, DNA, Archaeal/genetics, Lipids/chemistry, Mining, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Spain, Thermoplasmales/*classification/genetics/isolation & purification, United Kingdom, Vitamin K 2/chemistry, *Water Microbiology
  • topic2: Genetics

Reference

@idauthorstitledoi/urljournalpubmed
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
44041Olga V. Golyshina, Heinrich Lünsdorf, Ilya V. Kublanov, Nadine I. Goldenstein, Kai-Uwe Hinrichs and Peter N. GolyshinThe novel extremely acidophilic, cell-wall-deficient archaeon Cuniculiplasma divulgatum gen. nov., sp. nov. represents a new family, Cuniculiplasmataceae fam. nov., of the order Thermoplasmatales10.1099/ijsem.0.000725IJSEM 66: 332-340 201626518885
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
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