Strain identifier

BacDive ID: 17843

Type strain: Yes

Species: Chthonomonas calidirosea

Strain Designation: T49

Strain history: <- M. Stott, Wairakei Res. Centre, Taupo, New Zealand; T49 <- M. Crowe

NCBI tax ID(s): 454171 (species)

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General

@ref: 17467

BacDive-ID: 17843

DSM-Number: 23976

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

description: Chthonomonas calidirosea T49 is an aerobe, thermophilic, Gram-negative bacterium that was isolated from geothermally heated soil.

NCBI tax id

  • NCBI tax id: 454171
  • Matching level: species

strain history

  • @ref: 17467
  • history: <- M. Stott, Wairakei Res. Centre, Taupo, New Zealand; T49 <- M. Crowe

doi: 10.13145/bacdive17843.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/armatimonadota
  • domain: Bacteria
  • phylum: Armatimonadota
  • class: Chthonomonadia
  • order: Chthonomonadales
  • family: Chthonomonadaceae
  • genus: Chthonomonas
  • species: Chthonomonas calidirosea
  • full scientific name: Chthonomonas calidirosea Lee et al. 2011

@ref: 17467

domain: Bacteria

phylum: Armatimonadetes

class: Chthonomonadetes

order: Chthonomonadales

family: Chthonomonadaceae

genus: Chthonomonas

species: Chthonomonas calidirosea

full scientific name: Chthonomonas calidirosea Lee et al. 2011

strain designation: T49

type strain: yes

Morphology

cell morphology

  • @ref: 43389
  • gram stain: negative
  • cell length: 2.5-3 µm
  • cell width: 0.5-0.7 µm
  • cell shape: rod-shaped
  • motility: yes

colony morphology

@refincubation periodcolony sizecolony colorcolony shapemedium used
174673-7 days
433897 days2-4 mmlight pink to dark pink/orangecircularAOM1 solid medium

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
17467CHTHONOMONAS MEDIUM (DSMZ Medium 1291)yeshttps://mediadive.dsmz.de/medium/1291Name: CHTHONOMONAS MEDIUM (DSMZ Medium 1291) Composition: (NH4)2SO4 4.0 g/l MgCl2 x 6 H2O 1.0 g/l Gellan Gum 0.5 g/l K2HPO4 0.45 g/l Yeast extract 0.01 g/l Na2-EDTA x 2 H2O 0.0052 g/l FeCl2 x 4 H2O 0.0015 g/l Pyridoxine hydrochloride 0.0003 g/l Nicotinic acid 0.0002 g/l Thiamine-HCl x 2 H2O 0.0002 g/l CoCl2 x 6 H2O 0.00019 g/l Calcium pantothenate 0.0001 g/l MnCl2 x 4 H2O 0.0001 g/l Vitamin B12 0.0001 g/l p-Aminobenzoic acid 8e-05 g/l ZnCl2 7e-05 g/l Na2MoO4 x 2 H2O 3.6e-05 g/l NiCl2 x 6 H2O 2.4e-05 g/l D-(+)-biotin 2e-05 g/l H3BO3 6e-06 g/l CuCl2 x 2 H2O 2e-06 g/l CaCl2 x 2 H2O Distilled water
43389AOM1 solid mediumyescontained 100 mg B vitamins, 100 mg yeast extract per litre

culture temp

@refgrowthtypetemperaturerange
17467positivegrowth65thermophilic
43389positiveoptimum68thermophilic
43389nogrowth76thermophilic
43389nogrowth37mesophilic
43389positivegrowth50-73thermophilic

culture pH

@refabilitytypepH
43389positivegrowth4.7-5.8
43389positiveoptimum5.3
43389nogrowth4.5
43389nogrowth6.2

Physiology and metabolism

oxygen tolerance

  • @ref: 43389
  • oxygen tolerance: aerobe

spore formation

  • @ref: 43389
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
43389NaClpositiveoptimum0 %
43389NaClpositivegrowth2 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
433892511agarose-growth
4338931206ammonium chloride+nitrogen source
4338985146carboxymethylcellulose+growth
43389casamino acids-aerobic growth
43389casamino acids-nitrogen source
4338917057cellobiose+growth
4338917029chitin+growth
4338917108D-arabinose+growth
4338915824D-fructose+growth
4338912936D-galactose+growth
4338918024D-galacturonic acid-growth
4338917634D-glucose+growth
4338916024D-mannose+growth
4338963150D-rhamnose+growth
4338916988D-ribose+growth
4338965327D-xylose+growth
4338923652dextrin+growth
4338917997dinitrogen-nitrogen source
43389115156disodium fumarate-aerobic growth
4338927680galactomannan+growth
4338985248gellan gum+growth
4338928087glycogen+growth
4338930849L-arabinose+growth
4338917716lactose+growth
4338925115malate+aerobic growth
4338917306maltose+growth
43389506227N-acetylglucosamine+growth
4338917632nitrate-nitrogen source
4338917309pectin+growth
4338927941pullulan+growth
4338916634raffinose+growth
4338932954sodium acetate-aerobic growth
4338953311sodium alginate-growth
4338953258sodium citrate-aerobic growth
4338975228sodium lactate-aerobic growth
4338950144sodium pyruvate+aerobic growth
4338928017starch+growth
4338917992sucrose+growth
4338927082trehalose+growth
4338910057xanthan+growth
4338937166xylan+growth
43389yeast extract-aerobic growth
43389yeast extract+nitrogen source

enzymes

@refvalueactivityec
43389catalase+1.11.1.6
43389cytochrome oxidase-1.9.3.1
43389acid phosphatase+3.1.3.2
43389esterase+
43389esterase Lipase (C 8)+
43389naphthol-AS-BI-phosphohydrolase+
43389alpha-galactosidase+3.2.1.22
433896-phospho-beta-galactosidase+3.2.1.85
43389alpha-glucosidase+3.2.1.20
43389beta-glucosidase+3.2.1.21
43389N-acetyl-beta-glucosaminidase+3.2.1.52
43389alpha-mannosidase+3.2.1.24
43389alpha-fucosidase+3.2.1.51

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitude
17467geothermally heated soilRotorua, Hell's Gate, TikitereNew ZealandNZLAustralia and Oceania
43389geothermally heated soilsHell's Gate, TikitereNew ZealandNZLAustralia and Oceania-38176

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_387.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15884;96_265;97_292;98_325;99_387&stattab=map
  • Last taxonomy: Chthonomonas calidirosea subclade
  • 16S sequence: AM749780
  • Sequence Identity:
  • Total samples: 1022
  • soil counts: 472
  • aquatic counts: 336
  • animal counts: 161
  • plant counts: 53

Safety information

risk assessment

  • @ref: 17467
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 17467
  • description: Chthonomonas calidirosea partial 16S rRNA gene, strain T49
  • accession: AM749780
  • length: 1411
  • database: ena
  • NCBI tax ID: 1303518

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Chthonomonas calidirosea T49GCA_000427095chromosomencbi1303518
66792Chthonomonas calidirosea T491303518.3completepatric1303518
66792Chthonomonas calidirosea T49, DSM 239762524614646completeimg1303518

GC content

  • @ref: 17467
  • GC-content: 54.6
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes84.199yes
gram-positiveno93.709no
anaerobicno94.354yes
halophileno96.274no
spore-formingno89.862yes
thermophileyes96.224no
glucose-utilyes87.628yes
flagellatedno82.921no
aerobicyes79.105yes
glucose-fermentno83.51no

External links

@ref: 17467

culture collection no.: DSM 23976, ICMP 18418

straininfo link

  • @ref: 86834
  • straininfo: 404327

literature

  • topic: Phylogeny
  • Pubmed-ID: 21097641
  • title: Chthonomonas calidirosea gen. nov., sp. nov., an aerobic, pigmented, thermophilic micro-organism of a novel bacterial class, Chthonomonadetes classis nov., of the newly described phylum Armatimonadetes originally designated candidate division OP10.
  • authors: Lee KC, Dunfield PF, Morgan XC, Crowe MA, Houghton KM, Vyssotski M, Ryan JLJ, Lagutin K, McDonald IR, Stott MB
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.027235-0
  • year: 2010
  • mesh: Aerobiosis, Bacteria/*classification/genetics/*isolation & purification, Bacterial Physiological Phenomena, Base Composition, Carbohydrate Metabolism, Catalase/metabolism, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Gossypium, Hydrogen-Ion Concentration, Locomotion, Molecular Sequence Data, New Zealand, Oxidoreductases/metabolism, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/metabolism, Temperature
  • topic2: Metabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
17467Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23976)https://www.dsmz.de/collection/catalogue/details/culture/DSM-23976
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
43389Kevin C.-Y. Lee, Peter F. Dunfield, Xochitl C. Morgan, Michelle A. Crowe, Karen M. Houghton, Mikhail Vyssotski, Jason L. J. Ryan, Kirill Lagutin, Ian R. McDonald, Matthew B. Stott10.1099/ijs.0.027235-0Chthonomonas calidirosea gen. nov., sp. nov., an aerobic, pigmented, thermophilic microorganism of a novel bacterial class, Chthonomonadetes classis nov., of the newly described phylum Armatimonadetes originally designated candidate division OP10IJSEM 61: 2482-2490 201121097641
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)
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
86834Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID404327.1StrainInfo: A central database for resolving microbial strain identifiers