Strain identifier

BacDive ID: 16896

Type strain: Yes

Species: Caldimicrobium rimae

Strain Designation: DS

Strain history: <- M. Miroshnichenko; DS

NCBI tax ID(s): 444091 (species)

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General

@ref: 8087

BacDive-ID: 16896

DSM-Number: 19393

keywords: 16S sequence, Bacteria, anaerobe, thermophilic, Gram-negative, motile, rod-shaped

description: Caldimicrobium rimae DS is an anaerobe, thermophilic, Gram-negative bacterium that was isolated from terrestrial neutral hot spring.

NCBI tax id

  • NCBI tax id: 444091
  • Matching level: species

strain history

  • @ref: 8087
  • history: <- M. Miroshnichenko; DS

doi: 10.13145/bacdive16896.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/thermodesulfobacteriota
  • domain: Bacteria
  • phylum: Thermodesulfobacteriota
  • class: Thermodesulfobacteria
  • order: Thermodesulfobacteriales
  • family: Thermodesulfobacteriaceae
  • genus: Caldimicrobium
  • species: Caldimicrobium rimae
  • full scientific name: Caldimicrobium rimae Miroshnichenko et al. 2009

@ref: 8087

domain: Bacteria

phylum: Thermodesulfobacteria

class: Thermodesulfobacteria

order: Thermodesulfobacteriales

family: Thermodesulfobacteriaceae

genus: Caldimicrobium

species: Caldimicrobium rimae

full scientific name: Caldimicrobium rimae Miroshnichenko et al. 2009

strain designation: DS

type strain: yes

Morphology

cell morphology

  • @ref: 29094
  • gram stain: negative
  • cell length: 1.1 µm
  • cell width: 0.5 µm
  • cell shape: rod-shaped
  • motility: yes

pigmentation

  • @ref: 29094
  • production: no

Culture and growth conditions

culture medium

  • @ref: 8087
  • name: CALDIMICROBIUM MEDIUM (DSMZ Medium 778b)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/778b
  • composition: Name: CALDIMICROBIUM MEDIUM (DSMZ Medium 778b) Composition: NaHCO3 2.49252 g/l Na2S2O3 x 5 H2O 1.99402 g/l Na2-fumarate 1.59521 g/l Yeast extract 0.997009 g/l Na2S x 9 H2O 0.498504 g/l CaCl2 x 2 H2O 0.329013 g/l MgCl2 x 6 H2O 0.329013 g/l KCl 0.329013 g/l NH4Cl 0.329013 g/l KH2PO4 0.329013 g/l HCl 0.00249252 g/l FeCl2 x 4 H2O 0.00149551 g/l Sodium resazurin 0.000498504 g/l NaOH 0.000498504 g/l NiCl2 x 6 H2O 0.000199402 g/l CoCl2 x 6 H2O 0.000189432 g/l Pyridoxine hydrochloride 9.97009e-05 g/l MnCl2 x 4 H2O 9.97009e-05 g/l ZnCl2 6.97906e-05 g/l Nicotinic acid 4.98504e-05 g/l (DL)-alpha-Lipoic acid 4.98504e-05 g/l p-Aminobenzoic acid 4.98504e-05 g/l Riboflavin 4.98504e-05 g/l Thiamine HCl 4.98504e-05 g/l Calcium D-(+)-pantothenate 4.98504e-05 g/l Na2MoO4 x 2 H2O 3.58923e-05 g/l Biotin 1.99402e-05 g/l Folic acid 1.99402e-05 g/l H3BO3 5.98205e-06 g/l Na2WO4 x 2 H2O 3.98804e-06 g/l Na2SeO3 x 5 H2O 2.99103e-06 g/l CuCl2 x 2 H2O 1.99402e-06 g/l Vitamin B12 9.97009e-07 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
8087positivegrowth70thermophilic
29094positivegrowth52-82hyperthermophilic
29094positiveoptimum75thermophilic

culture pH

@refabilitytypepH
29094positivegrowth6.8-7.4
29094positiveoptimum7.1

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
8087anaerobe
29094anaerobe

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2909416236ethanol+carbon source
2909425115malate+carbon source
2909430031succinate+carbon source

metabolite production

  • @ref: 29094
  • Chebi-ID: 16136
  • metabolite: hydrogen sulfide
  • production: yes

Isolation, sampling and environmental information

isolation

  • @ref: 8087
  • sample type: terrestrial neutral hot spring
  • geographic location: Kamchatka, eastern solfataric field of Uzon Caldera, Treshchinnyi ('Crack') Spring
  • country: Russia
  • origin.country: RUS
  • continent: Asia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_38323.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_515;96_3604;97_4427;98_28122;99_38323&stattab=map
  • Last taxonomy: Caldimicrobium rimae subclade
  • 16S sequence: EF554596
  • Sequence Identity:
  • Total samples: 158
  • soil counts: 5
  • aquatic counts: 142
  • animal counts: 4
  • plant counts: 7

Safety information

risk assessment

  • @ref: 8087
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 8087
  • description: Caldimicrobium rimae strain DS 16S ribosomal RNA gene, partial sequence
  • accession: EF554596
  • length: 1464
  • database: ena
  • NCBI tax ID: 444091

GC content

@refGC-contentmethod
808735.2thermal denaturation, midpoint method (Tm)
2909435.2

External links

@ref: 8087

culture collection no.: DSM 19393, VKM B-2460

straininfo link

  • @ref: 85902
  • straininfo: 403676

literature

  • topic: Phylogeny
  • Pubmed-ID: 19406789
  • title: Caldimicrobium rimae gen. nov., sp. nov., an extremely thermophilic, facultatively lithoautotrophic, anaerobic bacterium from the Uzon Caldera, Kamchatka.
  • authors: Miroshnichenko ML, Lebedinsky AV, Chernyh NA, Tourova TP, Kolganova TV, Spring S, Bonch-Osmolovskaya EA
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.006072-0
  • year: 2009
  • mesh: *Autotrophic Processes, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis/genetics, Genes, rRNA, Gram-Negative Facultatively Anaerobic Rods/*classification/genetics/isolation & purification/physiology, Hot Springs/*microbiology, *Hot Temperature, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Russia, Sequence Analysis, DNA, Species Specificity
  • topic2: Stress

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
8087Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19393)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19393
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
29094Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2552328776041
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
85902Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID403676.1StrainInfo: A central database for resolving microbial strain identifiers