Strain identifier
BacDive ID: 141129
Type strain:
Species: Cuniculiplasma divulgatum
Strain Designation: S5
Strain history: O. Golyshina; Bangor Univ., UK; S5.
NCBI tax ID(s): 1673428 (species)
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
@ref | cell shape | gram stain | confidence |
---|---|---|---|
44041 | pleomorphic-shaped | ||
69480 | negative | 99.968 |
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
@ref | growth | type | temperature | range |
---|---|---|---|---|
44041 | positive | growth | 10-48 | |
44041 | positive | optimum | 37-40 | |
67770 | positive | growth | 37 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
44041 | positive | growth | 0.5-4.0 | acidophile |
44041 | positive | optimum | 1.0-1.2 |
Physiology and metabolism
oxygen tolerance
- @ref: 44041
- oxygen tolerance: facultative anaerobe
nutrition type
- @ref: 44041
- type: organoheterotroph
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | yes | 100 |
69480 | no | 99.995 |
observation
@ref | observation |
---|---|
44041 | cell wall |
67770 | quinones: Menaquinones and thermoplasmaquinones |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent | enrichment culture | enrichment culture composition | enrichment culture duration | enrichment culture temperature |
---|---|---|---|---|---|---|---|---|---|
44041 | acidic streamer formed on the surfaces of copper-ore-containing suldic deposits | Cantareras Mine | Spain | ESP | Europe | modified 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 days | 37 |
67770 | Acidic water from the surface of a copper mine site in Mynydd Parys | Anglesey | United Kingdom | GBR | Europe |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#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
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
44041 | Cuniculiplasma divulgatum strain S5 16S ribosomal RNA gene, partial sequence | KT005321 | 1469 | nuccore | 1673428 |
67770 | Cuniculiplasma divulgatum strain PM4 16S ribosomal RNA gene, partial sequence | KT005320 | 1469 | ena | 1673428 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Cuniculiplasma divulgatum S5(T) (=JCM 30642; =VKM B-2941) | GCA_900083515 | complete | ncbi | 1673428 |
66792 | Cuniculiplasma divulgatum S5 | 2773858060 | complete | img | 1673428 |
GC content
- @ref: 67770
- GC-content: 37.3
- method: genome sequence analysis
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | yes | 100 | no |
motile | no | 86.612 | no |
flagellated | no | 98.029 | no |
gram-positive | no | 90.308 | no |
anaerobic | no | 55.507 | no |
aerobic | no | 91.531 | yes |
halophile | no | 87.066 | no |
spore-forming | no | 94.033 | no |
glucose-ferment | no | 64.513 | no |
thermophile | yes | 95.57 | no |
glucose-util | yes | 82.919 | no |
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
@id | authors | title | doi/url | journal | pubmed |
---|---|---|---|---|---|
20215 | Parte, 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 DSMZ | 10.1099/ijsem.0.004332 | ||
44041 | Olga V. Golyshina, Heinrich Lünsdorf, Ilya V. Kublanov, Nadine I. Goldenstein, Kai-Uwe Hinrichs and Peter N. Golyshin | 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 | 10.1099/ijsem.0.000725 | IJSEM 66: 332-340 2016 | 26518885 |
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | ||
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | |||
69479 | João 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 beta | https://microbeatlas.org/ | ||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Predictions 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 | ||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | Predictions based on the model GenomeNet Sporulation v. 1 | 10.21203/rs.3.rs-2527258/v1 |