Strain identifier

BacDive ID: 2090

Type strain: Yes

Species: Caldisphaera lagunensis

Strain Designation: IC-154

Strain history: T. Itoh and P. C. Sanchez IC-154.

NCBI tax ID(s): 1056495 (strain), 200415 (species)

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General

@ref: 6178

BacDive-ID: 2090

DSM-Number: 15908

keywords: genome sequence, 16S sequence, Archaea, anaerobe, chemoorganotroph, spore-forming, thermophilic, coccus-shaped

description: Caldisphaera lagunensis IC-154 is an anaerobe, chemoorganotroph, spore-forming archaeon that was isolated from an acidic hot spring.

NCBI tax id

NCBI tax idMatching level
1056495strain
200415species

strain history

@refhistory
6178<- T. Itoh, JCM; IC-154 <- T. Itoh and P. C. Sanchez {1996}
67770T. Itoh and P. C. Sanchez IC-154.

doi: 10.13145/bacdive2090.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/archaea
  • keyword: phylum/thermoproteota
  • domain: Archaea
  • phylum: Thermoproteota
  • class: Thermoprotei
  • order: Acidilobales
  • family: Caldisphaeraceae
  • genus: Caldisphaera
  • species: Caldisphaera lagunensis
  • full scientific name: Caldisphaera lagunensis Itoh et al. 2003

@ref: 6178

domain: Archaea

phylum: Crenarchaeota

class: Thermoprotei

order: Acidilobales

family: Caldisphaeraceae

genus: Caldisphaera

species: Caldisphaera lagunensis

full scientific name: Caldisphaera lagunensis Itoh et al. 2003

strain designation: IC-154

type strain: yes

Morphology

cell morphology

@refcell lengthcell shapemotilitygram stainconfidence
231680.8-1.1 µmcoccus-shapedno
69480negative99.932

multimedia

  • @ref: 66793
  • multimedia content: EM_DSM_15908_1.jpg
  • caption: electron microscopic image
  • intellectual property rights: © HZI/Manfred Rohde

Culture and growth conditions

culture medium

  • @ref: 6178
  • name: CALDISPHAERA MEDIUM (DSMZ Medium 991)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/991
  • composition: Name: CALDISPHAERA MEDIUM (DSMZ Medium 991) Composition: Sulfur 9.8912 g/l Trisodium citrate x 2 H2O 2.90801 g/l (NH4)2SO4 1.28586 g/l Na2S x 9 H2O 0.49456 g/l Yeast extract 0.49456 g/l KH2PO4 0.276954 g/l MgSO4 x 7 H2O 0.24728 g/l CaCl2 x 2 H2O 0.0692384 g/l FeCl3 x 6 H2O 0.0197824 g/l Na2B4O7 x 10 H2O 0.00445104 g/l MnCl2 x 4 H2O 0.00178042 g/l Sodium resazurin 0.00049456 g/l ZnSO4 x 7 H2O 0.000217606 g/l Pyridoxine hydrochloride 9.8912e-05 g/l (DL)-alpha-Lipoic acid 4.9456e-05 g/l CuCl2 x 2 H2O 4.9456e-05 g/l Thiamine HCl 4.9456e-05 g/l Calcium D-(+)-pantothenate 4.9456e-05 g/l p-Aminobenzoic acid 4.9456e-05 g/l Nicotinic acid 4.9456e-05 g/l Riboflavin 4.9456e-05 g/l Na2MoO4 x 2 H2O 2.96736e-05 g/l VOSO4 x 2 H2O 2.96736e-05 g/l Folic acid 1.97824e-05 g/l Biotin 1.97824e-05 g/l CoSO4 x 7 H2O 9.8912e-06 g/l Vitamin B12 9.8912e-07 g/l Distilled water

culture temp

@refgrowthtypetemperaturerangeconfidence
6178positivegrowth75thermophilic
23168nogrowth40thermophilic
23168nogrowth82hyperthermophilic
23168positivemaximum80hyperthermophilic
23168positiveminimum45thermophilic
23168positiveoptimum70-78thermophilic
67770positivegrowth75thermophilic
69480thermophilic99.999

culture pH

@refabilitytypepHPH range
23168positivegrowth2.3-5.4acidophile
23168positiveoptimum3.5-4.0

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
6178anaerobe
23168anaerobe
69480anaerobe96.56

nutrition type

  • @ref: 23168
  • type: chemoorganotroph

spore formation

@refspore formationconfidence
69481yes100
69480no99.991

halophily

  • @ref: 23168
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: <1.5 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2316830089acetate-carbon source
2316817968butyrate-carbon source
2316816947citrate-carbon source
2316817108D-arabinose-carbon source
2316815824D-fructose-carbon source
2316812936D-galactose-carbon source
2316817634D-glucose-carbon source
2316816988D-ribose-carbon source
2316865327D-xylose-carbon source
2316816397formamide-carbon source
2316815740formate-carbon source
2316829806fumarate-carbon source
2316815589L-malate-carbon source
2316824996lactate-carbon source
2316817716lactose-carbon source
2316817306maltose-carbon source
2316837684mannose-carbon source
2316817790methanol-carbon source
2316816830methylamine-carbon source
2316817272propionate-carbon source
2316815361pyruvate-carbon source
2316830031succinate-carbon source
2316817992sucrose-carbon source
2316818139trimethylamine-carbon source
2316830089acetate-energy source
2316817968butyrate-energy source
2316816947citrate-energy source
2316817108D-arabinose-energy source
2316815824D-fructose-energy source
2316812936D-galactose-energy source
2316817634D-glucose-energy source
2316816988D-ribose-energy source
2316865327D-xylose-energy source
2316816397formamide-energy source
2316815740formate-energy source
2316829806fumarate-energy source
2316815589L-malate-energy source
2316824996lactate-energy source
2316817716lactose-energy source
2316817306maltose-energy source
2316837684mannose-energy source
2316817790methanol-energy source
2316816830methylamine-energy source
2316817272propionate-energy source
2316815361pyruvate-energy source
2316830031succinate-energy source
2316817992sucrose-energy source
2316818139trimethylamine-energy source
23168casamino acids+carbon source
231685291gelatin+carbon source
2316828087glycogen+carbon source
23168peptone+carbon source
2316828017starch+carbon source
23168yeast extract+carbon source
23168casamino acids+energy source
231685291gelatin+energy source
2316828087glycogen+energy source
23168peptone+energy source
2316828017starch+energy source
23168yeast extract+energy source

antibiotic resistance

@refChEBImetaboliteis antibioticis resistantis sensitive
2316817698chloramphenicolyesyes
231686104kanamycinyesyes
2316817076streptomycinyesyes
2316828001vancomycinyesyes
2316848923erythromycinyesyes
2316828368novobiocinyesyes
2316828077rifampicinyesyes

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
6178an acidic hot springMt. MaquilingPhilippinesPHLAsia
23168a hot spring on Mt MaquilingLaguna
67770Acidic hot spring at Mt. MaquilingPhilippinesPHLAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Thermal spring
#Condition#Acidic
#Condition#Thermophilic (>45°C)

taxonmaps

  • @ref: 69479
  • File name: preview.99_187093.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_18209;96_68781;97_89423;98_121692;99_187093&stattab=map
  • Last taxonomy: Caldisphaera lagunensis subclade
  • 16S sequence: AB087499
  • Sequence Identity:
  • Total samples: 257
  • soil counts: 9
  • aquatic counts: 248

Safety information

risk assessment

  • @ref: 6178
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 6178
  • description: Caldisphaera lagunensis gene for 16S rRNA, partial sequence
  • accession: AB087499
  • length: 1466
  • database: ena
  • NCBI tax ID: 1056495

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Caldisphaera lagunensis DSM 15908GCA_000317795completencbi1056495
66792Caldisphaera lagunensis DSM 159082510065009completeimg1056495
66792Caldisphaera lagunensis DSM 159081056495.6completepatric1056495

GC content

@refGC-contentmethod
617831
2316830.7high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileno82.538yes
flagellatedno97.168yes
gram-positiveno96.556no
anaerobicyes95.026yes
aerobicno90.29no
halophileno84.565no
spore-formingno96.103no
thermophileyes100yes
glucose-utilyes83.926no
glucose-fermentno66.293no

External links

@ref: 6178

culture collection no.: DSM 15908, ANMR 0165, JCM 11604, MCC-UPLB 1331

straininfo link

  • @ref: 71737
  • straininfo: 111750

literature

  • topic: Phylogeny
  • Pubmed-ID: 12892143
  • title: Caldisphaera lagunensis gen. nov., sp. nov., a novel thermoacidophilic crenarchaeote isolated from a hot spring at Mt Maquiling, Philippines.
  • authors: Itoh T, Suzuki K, Sanchez PC, Nakase T
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.02580-0
  • year: 2003
  • mesh: Base Composition, Crenarchaeota/*classification/genetics/*isolation & purification/metabolism, DNA, Archaeal/chemistry/genetics, DNA, Ribosomal/genetics, Fresh Water/microbiology, Hot Temperature, Microscopy, Electron, Molecular Sequence Data, Phenotype, Philippines, Phylogeny, RNA, Archaeal/genetics, RNA, Ribosomal, 16S/genetics, Terminology as Topic
  • topic2: Stress

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
6178Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15908)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15908
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
23168T. Itoh, K. Suzuki, P. C. Sanchez, T. Nakase10.1099/ijs.0.02580-0Caldisphaera lagunensis gen. nov., sp. nov., a novel thermoacidophilic crenarchaeote isolated from a hot spring at Mt Maquiling, PhilippinesIJSEM 53: 1149-1154 200312892143
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/
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
71737Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID111750.1StrainInfo: A central database for resolving microbial strain identifiers