Chthonomonas calidirosea (DSM 23976, ICMP 18418, T49)

Name: Chthonomonas calidirosea (DSM 23976, ICMP 18418, T49)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 17843

Type strain

Strain Designation T49

Culture col. no. DSM 23976 ICMP 18418 T49

NCBI tax ID(s) 454171

Special Collections DSMZ Literature strains

Links

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

Gram-negative motile rod-shaped aerobe thermophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 404327

ICMP 18418,DSM 23976

@ref 20215

Last LPSN update 2025-12-16 09:51:12

Domain Bacillati

Phylum Armatimonadota

Class Chthonomonadia

Order Chthonomonadales

Family Chthonomonadaceae

Genus Chthonomonas

Species Chthonomonas calidirosea

Full scientific name Chthonomonas calidirosea Lee et al. 2011

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility
43389	negative	2.5-3 µm	0.5-0.7 µm	rod-shaped

Colony morphology

@ref	Colony size	Colony color	Colony shape	Incubation period	Medium used
17467				3-7 days
43389	2-4 mm	light pink to dark pink/orange	circular	7 days	AOM1 solid medium

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
17467	CHTHONOMONAS MEDIUM (DSMZ Medium 1291)		Medium recipe at MediaDive	Name: 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
43389	AOM1 solid medium			contained 100 mg B vitamins, 100 mg yeast extract per litre

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
17467	positive	growth	65	thermophilic
43389	positive	optimum	68	thermophilic
43389	negative	growth	76
43389	negative	growth	37
43389	positive	growth	50-73	thermophilic

Culture pH

@ref	Ability	Type	PH
43389	positive	optimum	5.3
43389	positive	growth	4.7-5.8
43389		growth	4.5
43389		growth	6.2

Physiology and metabolism

Oxygen tolerance

43389

Oxygen toleranceaerobe

Spore formation

43389

Spore formationno

Halophily

@ref	Salt	Growth	Tested relation	Concentration
43389	NaCl	positive	optimum	0 %
43389	NaCl	positive	growth	2 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
43389	2511 ChEBI	agarose	-	growth
43389	31206 ChEBI	ammonium chloride	+	nitrogen source
43389	85146 ChEBI	carboxymethylcellulose	+	growth
43389		casamino acids	-	aerobic growth
43389		casamino acids	-	nitrogen source
43389	17057 ChEBI	cellobiose	+	growth
43389	17029 ChEBI	chitin	+	growth
43389	17108 ChEBI	D-arabinose	+	growth
43389	15824 ChEBI	D-fructose	+	growth
43389	12936 ChEBI	D-galactose	+	growth
43389	18024 ChEBI	D-galacturonic acid	-	growth
43389	17634 ChEBI	D-glucose	+	growth
43389	16024 ChEBI	D-mannose	+	growth
43389	63150 ChEBI	D-rhamnose	+	growth
43389	16988 ChEBI	D-ribose	+	growth
43389	65327 ChEBI	D-xylose	+	growth
43389	23652 ChEBI	dextrin	+	growth
43389	17997 ChEBI	dinitrogen	-	nitrogen source
43389	115156 ChEBI	disodium fumarate	-	aerobic growth
43389	27680 ChEBI	galactomannan	+	growth
43389	85248 ChEBI	gellan gum	+	growth
43389	28087 ChEBI	glycogen	+	growth
43389	30849 ChEBI	L-arabinose	+	growth
43389	17716 ChEBI	lactose	+	growth
43389	25115 ChEBI	malate	+	aerobic growth
43389	17306 ChEBI	maltose	+	growth
43389	506227 ChEBI	N-acetylglucosamine	+	growth
43389	17632 ChEBI	nitrate	-	nitrogen source
43389	17309 ChEBI	pectin	+	growth
43389	27941 ChEBI	pullulan	+	growth
43389	16634 ChEBI	raffinose	+	growth
43389	32954 ChEBI	sodium acetate	-	aerobic growth
43389	53311 ChEBI	sodium alginate	-	growth
43389	53258 ChEBI	sodium citrate	-	aerobic growth
43389	75228 ChEBI	sodium lactate	-	aerobic growth
43389	50144 ChEBI	sodium pyruvate	+	aerobic growth
43389	28017 ChEBI	starch	+	growth
43389	17992 ChEBI	sucrose	+	growth
43389	27082 ChEBI	trehalose	+	growth
43389	10057 ChEBI	xanthan	+	growth
43389	37166 ChEBI	xylan	+	growth
43389		yeast extract	-	aerobic growth
43389		yeast extract	+	nitrogen source

Enzymes

@ref	Value	Activity	Ec
43389	6-phospho-beta-galactosidase	+	3.2.1.85
43389	acid phosphatase	+	3.1.3.2
43389	alpha-fucosidase	+	3.2.1.51
43389	alpha-galactosidase	+	3.2.1.22
43389	alpha-glucosidase	+	3.2.1.20
43389	alpha-mannosidase	+	3.2.1.24
43389	beta-glucosidase	+	3.2.1.21
43389	catalase	+	1.11.1.6
43389	cytochrome oxidase	-	1.9.3.1
43389	esterase	+
43389	esterase Lipase (C 8)	+
43389	N-acetyl-beta-glucosaminidase	+	3.2.1.52
43389	naphthol-AS-BI-phosphohydrolase	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil
#Condition	#Thermophilic (>45°C)	-
#Environmental	#Aquatic	-

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude
17467	geothermally heated soil	Rotorua, Hell's Gate, Tikitere	New Zealand	NZL	Australia and Oceania
43389	geothermally heated soils	Hell's Gate, Tikitere	New Zealand	NZL	Australia and Oceania	-38	176 -38/176

Taxonmaps

69479

Global distribution of 16S sequence AM749780 (>99% sequence identity) for Chthonomonas calidirosea subclade from Microbeatlas

Aquatic Samples	336
Soil Samples	472
Animal Samples	161
Plant Samples	53
Total Samples	1022

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
17467	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	T49 assembly for Chthonomonas calidirosea T49	chromosome	GCA_000427095	1303518.3	2524614646	1303518	85.49

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
17467	Chthonomonas calidirosea partial 16S rRNA gene, strain T49	AM749780	1411		1303518

GC content

@ref	GC-content (mol%)	Method
17467	54.6	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Chthonomonas calidirosea T49, DSM 23976
IMG: 2524614646

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	69.70	no
125439	motility	BacteriaNetⓘ	yes	56.90	no
125439	gram_stain	BacteriaNetⓘ	negative	85.70	no
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	82.20	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Chthonomonas calidirosea T49
PATRIC: 1303518.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	86.90	yes
125438	anaerobic	anaerobicⓘ	no	76.66	yes
125438	spore-forming	spore-formingⓘ	no	65.19	no
125438	aerobic	aerobicⓘ	yes	68.09	yes
125438	thermophilic	thermophileⓘ	no	75.57	no
125438	flagellated	motile2+ⓘ	no	55.48	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Enrichment of Root Endophytic Bacteria from Populus deltoides and Single-Cell-Genomics Analysis.	Utturkar SM, Cude WN, Robeson MS, Yang ZK, Klingeman DM, Land ML, Allman SL, Lu TY, Brown SD, Schadt CW, Podar M, Doktycz MJ, Pelletier DA.	Appl Environ Microbiol	10.1128/aem.01285-16	2016
Phylogeny	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.	Lee KC, Dunfield PF, Morgan XC, Crowe MA, Houghton KM, Vyssotski M, Ryan JLJ, Lagutin K, McDonald IR, Stott MB	Int J Syst Evol Microbiol	10.1099/ijs.0.027235-0	2010

References

#17467	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 23976
#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. IJSEM ( DOI 10.1099/ijsem.0.004332 )
#43389	Kevin 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. Stott: Chthonomonas 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 OP10. IJSEM 61: 2482 - 2490 2011 ( DOI 10.1099/ijs.0.027235-0 , PubMed 21097641 )
#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) .
#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 .
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Chthonomonas calidirosea (DSM 23976, ICMP 18418, T49)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000427095

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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