Geodermatophilus amargosae G12, G96 | Type strain | DSM 46136, ATCC 25081, CBS 236.69, CCUG 62971, IFO 13316, IMET 9240, JCM 3153, KCC A-0153, MTCC 11559, NBRC 13316, KCTC 9360, NRRL B-3578, NRRL WC-3937, KCC A-0152 | BacDiveID:5818

Strain identifier

BacDive ID: 5818

Type strain:

Species: Geodermatophilus amargosae

Strain Designation: G12, G96

Culture col. no.: DSM 46136, ATCC 25081, CBS 236.69, CCUG 62971, IFO 13316, IMET 9240, JCM 3153, KCC A-0153, MTCC 11559, NBRC 13316, KCTC 9360, NRRL B-3578, NRRL WC-3937, KCC A-0152

Strain history: <- IFO <- KCC <- G.M. Luedemann G-12

NCBI tax ID(s): 1296565 (species)

SI-ID 125967

ATCC 25081, DSM 46136, IFO 13316, IMET 9240, JCM 3153, NRRL B-3578, CBS 236.69, KCTC 9360, NBRC 13316, CCUG 62971

Section

Geodermatophilus amargosae G12 is an aerobe, spore-forming, mesophilic bacterium that was isolated from desert soil.

Gram-positive
spore-forming
aerobe
mesophilic
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Actinomycetota*
	Class	*Actinomycetes*
	Order	*Geodermatophilales*
	Family	*Geodermatophilaceae*
	Genus	*Geodermatophilus*
	Species	**Geodermatophilus amargosae**
	Full Scientific Name (LPSN)	Geodermatophilus amargosae Montero-Calasanz et al. 2014

Synonym

"Geodermatophilus obscurus subsp. amargosae"

Information on morphological and physiological properties Morphology

[Ref.: #67771]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %100

Incubation period

6-10 days

Multimedia content

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Information on culture and growth conditions Culture and growth conditions

Culture medium

GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)

Culture medium growth

Culture medium link

Medium recipe provided by DSMZ

	Temperatures	Kind of temperature		Temperature
[Ref.: #12459]			growth	28 °C
[Ref.: #62920]			growth	30 °C
[Ref.: #67770]			growth	28 °C
[Ref.: #67771]			growth	28 °C

[Ref.: #12459]	Temperature range	mesophilic
[Ref.: #62920]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic
[Ref.: #67771]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #62920]	Oxygen tolerance	aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe

Ability of spore formation

yes Confidence in %95

Name of produced compound

Actinorhodin

Observation

quinones: MK-9(H₄)

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #12459]	Sample type/isolated from	desert soil
[Ref.: #12459]	Geographic location (country and/or sea, region)	Nevada, Amargosa Desert
[Ref.: #12459]	Country	USA
[Ref.: #12459]	Country ISO 3 Code	USA
[Ref.: #12459]	Continent	North America

[Ref.: #62920]	Sample type/isolated from	Soil,desert
[Ref.: #62920]	Sampling date	1976
[Ref.: #62920]	Country	USA
[Ref.: #62920]	Country ISO 3 Code	USA
[Ref.: #62920]	Continent	North America

[Ref.: #67770]	Sample type/isolated from	Soil, Amargosa Desert
[Ref.: #67770]	Geographic location (country and/or sea, region)	NV
[Ref.: #67770]	Country	USA
[Ref.: #67770]	Country ISO 3 Code	USA
[Ref.: #67770]	Continent	North America

[Ref.: #67771]	Sample type/isolated from	From soil
[Ref.: #67771]	Geographic location (country and/or sea, region)	Amargosa desert
[Ref.: #67771]	Country	USA
[Ref.: #67771]	Country ISO 3 Code	USA
[Ref.: #67771]	Continent	North America
* marker position based on {}

Isolation sources categories

#Environmental	#Terrestrial	#Desert
#Environmental	#Terrestrial	#Soil
#Condition	#Xerophilic	-

What are isolation sources categories?

Global distribution of 16S sequence HF679056 (>99% sequence identity) for Geodermatophilus from Microbeatlas

Aquatic Samples	408
Soil Samples	4562
Animal Samples	721
Plant Samples	1119
Total Samples	6810

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

Biosafety level

1

Risk group (German classification)
According to TRBA 466

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #12459]	Geodermatophilus amargosae partial 16S rRNA gene, strain DSM 46136, isolate G96	HF679056	1513	ENA	1296565 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Geodermatophilus amargosae DSM 46136	GCA_900116515	scaffold	GenBank	1296565 tax ID
[Ref.: #66792]	Geodermatophilus amargosae strain DSM 46136	1296565.3	wgs	PATRIC	1296565 tax ID	*
[Ref.: #66792]	Geodermatophilus amargosae DSM 46136	2599185195	draft	JGI IMG/M	1296565 tax ID	*

[Ref.: #12459]	GC-content	73.0 mol%	high performance liquid chromatography (HPLC)
[Ref.: #67770]	GC-content	73 mol%	high performance liquid chromatography (HPLC)

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Geodermatophilus amargosae DSM 46136 NCBI: GCA_900116515.1
[Ref.: #69481]	spore-forming	yes	95	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Geodermatophilus amargosae strain DSM 46136 PATRIC: 1296565.3
[Ref.: #69480]	motile	yes	76.848	no
[Ref.: #69480]	gram-positive	yes	92.99	yes
[Ref.: #69480]	anaerobic	no	98.893	yes
[Ref.: #69480]	aerobic	yes	91.324	yes
[Ref.: #69480]	halophile	no	87.035	no
[Ref.: #69480]	spore-forming	no	67.072	no
[Ref.: #69480]	thermophile	no	98.297	yes
[Ref.: #69480]	glucose-util	yes	90.315	no
[Ref.: #69480]	flagellated	no	92.024	no
[Ref.: #69480]	glucose-ferment	no	88.746	no

Availability in culture collections External links

Culture collection no.

DSM 46136, ATCC 25081, CBS 236.69, CCUG 62971, IFO 13316, IMET 9240, JCM 3153, KCC A-0153, MTCC 11559, NBRC 13316, KCTC 9360, NRRL B-3578, NRRL WC-3937, KCC A-0152

SI-ID 125967

*

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Description of Geodermatophilus amargosae sp. nov., to accommodate the not validly named Geodermatophilus obscurus subsp. amargosae (Luedemann, 1968).	Montero-Calasanz Mdel C, Goker M, Rohde M, Sproer C, Schumann P, Mayilraj S, Goodfellow M, Klenk HP	Curr Microbiol	10.1007/s00284-013-0479-2	2013	*

References

#12459

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 46136

#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 )

#20216

Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie e. V. Hans-Knöll-Institut (HKI) Curators of the HKI: Collection Description Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie e. V. Hans-Knöll-Institut (HKI) .

#62920 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 62971

#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) .

#66793

Mukherjee et al.: GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life. 35: 676 - 683 2017 ( DOI 10.1038/nbt.3886 , PubMed 28604660 )

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#67771 Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;

#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 .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#75300

Reimer, 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 identifiers . ( DOI 10.60712/SI-ID125967.1 )

* These data were automatically processed and therefore are not curated

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