Strain identifier

BacDive ID: 24745

Type strain: Yes

Species: Thermogemmatispora carboxidivorans

Strain Designation: PM5

Strain history: <- G. King, Louisiana State Univ., USA; PM5 <- C. King, Louisiana State Univ., USA

NCBI tax ID(s): 1382306 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 21218

BacDive-ID: 24745

DSM-Number: 45816

keywords: genome sequence, 16S sequence, Bacteria, microaerophile, spore-forming, thermophilic, Gram-positive, filament-shaped

description: Thermogemmatispora carboxidivorans PM5 is a microaerophile, spore-forming, thermophilic bacterium that was isolated from geothermally heated microbial mat on a decayed dead tree stump acting as steam vent.

NCBI tax id

  • NCBI tax id: 1382306
  • Matching level: species

strain history

  • @ref: 21218
  • history: <- G. King, Louisiana State Univ., USA; PM5 <- C. King, Louisiana State Univ., USA

doi: 10.13145/bacdive24745.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/chloroflexota
  • domain: Bacteria
  • phylum: Chloroflexota
  • class: Ktedonobacteria
  • order: Thermogemmatisporales
  • family: Thermogemmatisporaceae
  • genus: Thermogemmatispora
  • species: Thermogemmatispora carboxidivorans
  • full scientific name: Thermogemmatispora carboxidivorans King and King 2014

@ref: 21218

domain: Bacteria

phylum: Chloroflexi

class: Ktedonobacteria

order: Thermogemmatisporales

family: Thermogemmatisporaceae

genus: Thermogemmatispora

species: Thermogemmatispora carboxidivorans

full scientific name: Thermogemmatispora carboxidivorans King and King 2014 emend. Nouioui et al. 2018

strain designation: PM5

type strain: yes

Morphology

cell morphology

  • @ref: 43391
  • gram stain: positive
  • cell shape: filament-shaped
  • motility: no

colony morphology

  • @ref: 43391
  • colony color: orange
  • incubation period: 4 days
  • medium used: Thermomicrobium medium

multimedia

  • @ref: 21218
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_45816.jpg
  • caption: Medium 592 55°C pH6.5
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
43391Thermomicrobium mediumyes
21218THERMOMICROBIUM ROSEUM MEDIUM (DSMZ Medium 592)yeshttps://mediadive.dsmz.de/medium/592Name: THERMOMICROBIUM ROSEUM MEDIUM (DSMZ Medium 592) Composition: Agar 20.0 g/l (NH4)2SO4 1.3 g/l Yeast extract 1.0 g/l Tryptone 1.0 g/l KH2PO4 0.28 g/l MgSO4 x 7 H2O 0.247 g/l CaCl2 x 2 H2O 0.074 g/l Na2B4O7 x 10 H2O 0.044 g/l FeCl3 x 6 H2O 0.019 g/l MnCl2 x 4 H2O 0.018 g/l ZnSO4 x 7 H2O 0.0022 g/l CuCl2 x H2O 0.0005 g/l VOSO4 x 2 H2O 0.0003 g/l Na2MoO4 x 2 H2O 0.0003 g/l Distilled water
21218R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
21218positivegrowth55thermophilic
43391positiveoptimum55thermophilic
43391positivegrowth40-65thermophilic

culture pH

@refabilitytypepH
43391positivegrowth4.1-8
43391positiveoptimum6

Physiology and metabolism

oxygen tolerance

  • @ref: 43391
  • oxygen tolerance: microaerophile

spore formation

  • @ref: 43391
  • type of spore: exospore (microbial cyst)
  • spore formation: yes

halophily

@refsaltgrowthtested relationconcentration
43391NaClpositivegrowth1 %
43391NaClnogrowth2 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4339130089acetate-growth
4339115347acetone+growth
4339116449alanine+growth
4339122599arabinose-growth
4339135391aspartate+growth
4339117750betaine-growth
43391casein+hydrolysis
4339162968cellulose+hydrolysis
4339117029chitin+hydrolysis
4339116947citrate-growth
4339117170dimethylamine-growth
4339124996lactate-growth
4339125115malate-growth
433914853esculin+hydrolysis
4339116236ethanol+growth
4339128757fructose-growth
4339129806fumarate-growth
4339128260galactose-growth
4339124175galacturonate-growth
433915291gelatin+hydrolysis
4339124265gluconate+growth
4339117234glucose+growth
4339124297glucuronate-growth
4339117754glycerol+growth
4339115428glycine-growth
4339129805glycolate-growth
4339117268myo-inositol-growth
4339129985L-glutamate+growth
4339117716lactose+growth
4339115792malonate-growth
4339129864mannitol-growth
4339137684mannose+growth
4339117790methanol+growth
4339116830methylamine-growth
4339117632nitrate+reduction
4339126271proline-growth
4339128831propanol-growth
4339117272propionate-growth
4339115361pyruvate+growth
4339126546rhamnose-growth
4339133942ribose-growth
4339117822serine-growth
4339128017starch+hydrolysis
4339130031succinate-growth
4339117992sucrose+growth
4339130929tartrate-growth
4339118139trimethylamine-growth
4339127266valine-growth
4339137166xylan+hydrolysis
4339118222xylose-growth

metabolite production

  • @ref: 43391
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
43391catalase+1.11.1.6
43391gelatinase+
43391beta-galactosidase+3.2.1.23
43391arginine dihydrolase-3.5.3.6
43391urease-3.5.1.5

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitude
21218geothermally heated microbial mat on a decayed dead tree stump acting as steam ventHawai National Volcanoes Park, Puhimau geothermal area (19° 23' 22.2'' N 155° 14' 56.6'' W)USAUSANorth America19.3895-155.249
43391East rif zone of Kilauea Volcano, HawaiiUSAUSANorth America19-155

isolation source categories

Cat1Cat2Cat3
#Environmental#Microbial community#Microbial mat
#Host#Plants#Decomposing plant
#Host#Plants#Tree
#Host Body-Site#Plant
#Environmental#Terrestrial#Volcanic

taxonmaps

  • @ref: 69479
  • File name: preview.99_5270.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_510;96_2559;97_3128;98_3929;99_5270&stattab=map
  • Last taxonomy: Thermogemmatispora carboxidivorans subclade
  • 16S sequence: KF193526
  • Sequence Identity:
  • Total samples: 1171
  • soil counts: 843
  • aquatic counts: 177
  • animal counts: 100
  • plant counts: 51

Safety information

risk assessment

  • @ref: 21218
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 21218
  • description: Thermogemmatispora carboxidivorans strain PM5 from USA 16S ribosomal RNA gene, partial sequence
  • accession: KF193526
  • length: 1296
  • database: ena
  • NCBI tax ID: 1382306

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Thermogemmatispora carboxidivorans PM5GCA_000702505contigncbi1382306
66792Thermogemmatispora carboxidivorans PM52561511072draftimg1382306

GC content

@refGC-contentmethod
4339159high performance liquid chromatography (HPLC)
2121859.0high performance liquid chromatography (HPLC)

External links

@ref: 21218

culture collection no.: DSM 45816, ATCC BAA 2534

straininfo link

  • @ref: 88573
  • straininfo: 408195

literature

  • topic: Phylogeny
  • Pubmed-ID: 24425739
  • title: Description of Thermogemmatispora carboxidivorans sp. nov., a carbon-monoxide-oxidizing member of the class Ktedonobacteria isolated from a geothermally heated biofilm, and analysis of carbon monoxide oxidation by members of the class Ktedonobacteria.
  • authors: King CE, King GM
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.059675-0
  • year: 2014
  • mesh: Base Composition, *Biofilms, Carbon Monoxide/*metabolism, Chloroflexi/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, Hawaii, Hot Temperature, Molecular Sequence Data, Nucleic Acid Hybridization, Oxidation-Reduction, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics
  • topic2: Stress

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
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
21218Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-45816Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45816)
43391C. E. King, G. M. KingDescription of Thermogemmatispora carboxidivorans sp. nov., a carbon-monoxide-oxidizing member of the class Ktedonobacteria isolated from a geothermally heated biofilm, and analysis of carbon monoxide oxidation by members of the class Ktedonobacteria10.1099/ijs.0.059675-0IJSEM 64: 1244-1251 201424425739
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
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/
88573Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID408195.1