Name: Promicromonospora kroppenstedtii RS16
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 12604

Type strain:

Species: Promicromonospora kroppenstedtii

Strain Designation: RS16

Culture col. no.: DSM 19349, LMG 24382, JCM 16033

Strain history: LMG 24382 <-- M. E. Trujillo RS16 <-- R. I. Santamaría.

NCBI tax ID(s): 926564 (strain), 440482 (species)

SI-ID 323094

LMG 24382, DSM 19349, JCM 16033

Special Collections

Section

When using BacDive for research please cite our paper

Promicromonospora kroppenstedtii RS16 is an aerobe, spore-forming, mesophilic bacterium that was isolated from garden 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	09-12-2024 (DD-MM-YYYY)
	Domain	*Bacteria*
	Phylum	*Actinomycetota*
	Class	*Actinomycetes*
	Order	*Micrococcales*
	Family	*Promicromonosporaceae*
	Genus	*Promicromonospora*
	Species	**Promicromonospora kroppenstedtii**
	Full Scientific Name (LPSN)	Promicromonospora kroppenstedtii Alonso-Vega et al. 2008

Information on morphological and physiological properties Morphology

[Ref.: #32414]	Gram stain	positive
[Ref.: #125438]	Gram stain	positive Confidence in %90.729
[Ref.: #125439]	Gram stain	positive Confidence in %98.6

[Ref.: #32414]	Motility	no
[Ref.: #125438]	Motility	no Confidence in %94

[Ref.: #19782]	Colony color	Zinc yellow (1018)
[Ref.: #19782]	Incubation period	10-14 days
[Ref.: #19782]	Cultivation medium used	ISP 2

[Ref.: #19782]	Colony color	Zinc yellow (1018)
[Ref.: #19782]	Incubation period	10-14 days
[Ref.: #19782]	Cultivation medium used	ISP 3

[Ref.: #19782]	Colony color	Zinc yellow (1018)
[Ref.: #19782]	Incubation period	10-14 days
[Ref.: #19782]	Cultivation medium used	ISP 4

[Ref.: #19782]	Colony color	Zinc yellow (1018)
[Ref.: #19782]	Incubation period	10-14 days
[Ref.: #19782]	Cultivation medium used	ISP 5

[Ref.: #19782]	Colony color	Zinc yellow (1018)
[Ref.: #19782]	Incubation period	10-14 days
[Ref.: #19782]	Cultivation medium used	ISP 6

[Ref.: #19782]	Colony color	Zinc yellow (1018)
[Ref.: #19782]	Incubation period	10-14 days
[Ref.: #19782]	Cultivation medium used	ISP 7

[Ref.: #32414]

Pigment production

[Ref.: #19782]	Multicellular complex forming ability	no
[Ref.: #19782]	Medium Name (multicellularity)	ISP 2

[Ref.: #19782]	Multicellular complex forming ability	no
[Ref.: #19782]	Medium Name (multicellularity)	ISP 3

[Ref.: #19782]	Multicellular complex forming ability	no
[Ref.: #19782]	Medium Name (multicellularity)	ISP 4

[Ref.: #19782]	Multicellular complex forming ability	no
[Ref.: #19782]	Medium Name (multicellularity)	ISP 5

[Ref.: #19782]	Multicellular complex forming ability	no
[Ref.: #19782]	Medium Name (multicellularity)	ISP 6

[Ref.: #19782]	Multicellular complex forming ability	no
[Ref.: #19782]	Medium Name (multicellularity)	ISP 7

Information on culture and growth conditions Culture and growth conditions

[Ref.: #8064]

Culture medium

GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)

[Ref.: #8064]

Culture medium growth

[Ref.: #8064]

Culture medium link

Medium recipe at MediaDive

[Ref.: #8064]

Culture medium composition

expand / minimize

[Ref.: #19782]

Culture medium

ISP 2

[Ref.: #19782]

Culture medium growth

[Ref.: #19782]

Culture medium composition

expand / minimize

[Ref.: #19782]

Culture medium

ISP 3

[Ref.: #19782]

Culture medium growth

[Ref.: #19782]

Culture medium composition

expand / minimize

[Ref.: #19782]

Culture medium

ISP 4

[Ref.: #19782]

Culture medium growth

[Ref.: #19782]

Culture medium composition

expand / minimize

[Ref.: #19782]

Culture medium

ISP 5

[Ref.: #19782]

Culture medium growth

[Ref.: #19782]

Culture medium composition

expand / minimize

[Ref.: #19782]

Culture medium

ISP 6

[Ref.: #19782]

Culture medium growth

[Ref.: #19782]

Culture medium composition

expand / minimize

[Ref.: #19782]

Culture medium

ISP 7

[Ref.: #19782]

Culture medium growth

[Ref.: #19782]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #8064]	growth	28 °C
[Ref.: #19782]	optimum	28 °C
[Ref.: #32414]	growth	12-37 °C
[Ref.: #32414]	optimum	28 °C
[Ref.: #67770]	growth	28 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #32414]	Oxygen tolerance	aerobe
[Ref.: #125438]	Oxygen tolerance	aerobe Confidence in %90.341
[Ref.: #125439]	Oxygen tolerance	obligate aerobe Confidence in %96.7

[Ref.: #32414]

Ability of spore formation

yes

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #32414]		NaCl		growth	<8	%

[Ref.: #67770]

Observation

quinones: MK-9(H₄), MK-9(H₆), MK-8(H₄)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #32414]	2-dehydro-D-gluconate ChEBI	+	carbon source
[Ref.: #32414]	5-dehydro-D-gluconate ChEBI	+	carbon source
[Ref.: #32414]	arabinose ChEBI	+	carbon source
[Ref.: #32414]	cellobiose ChEBI	+	carbon source
[Ref.: #32414]	fucose ChEBI	+	carbon source
[Ref.: #32414]	glucose ChEBI	+	carbon source
[Ref.: #32414]	glycerol ChEBI	+	carbon source
[Ref.: #32414]	lactose ChEBI	+	carbon source
[Ref.: #32414]	mannitol ChEBI	+	carbon source
[Ref.: #32414]	nitrate ChEBI	+	reduction
[Ref.: #32414]	raffinose ChEBI	+	carbon source
[Ref.: #32414]	ribose ChEBI	+	carbon source
[Ref.: #32414]	sorbitol ChEBI	+	carbon source
[Ref.: #32414]	sucrose ChEBI	+	carbon source
[Ref.: #32414]	trehalose ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Enzyme	Enzyme activity	EC number
[Ref.: #32414]	acid phosphatase	+	3.1.3.2
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #68382]	alkaline phosphatase	+	3.1.3.1	* from API zym
[Ref.: #68382]	alpha-chymotrypsin	+	3.4.21.1	* from API zym
[Ref.: #68382]	alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #68382]	alpha-galactosidase	+	3.2.1.22	* from API zym
[Ref.: #68382]	alpha-glucosidase	+	3.2.1.20	* from API zym
[Ref.: #68382]	alpha-mannosidase	+	3.2.1.24	* from API zym
[Ref.: #68382]	beta-galactosidase	+	3.2.1.23	* from API zym
[Ref.: #68382]	beta-glucosidase	+	3.2.1.21	* from API zym
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #32414]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #32414]	cytochrome oxidase	+	1.9.3.1
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #32414]	gelatinase	+
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	+	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #68382]	trypsin	+	3.4.21.4	* from API zym
[Ref.: #68382]	valine arylamidase	+		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® zym:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #19782]	606	not determinedn.d.	+	+	+	-	+	+	-	+	+	+	+	+	+	-	+	+	+	+	-

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

[Ref.: #8064]	Sample type/isolated from	garden soil
[Ref.: #8064]	Geographic location (country and/or sea, region)	Zamora
[Ref.: #8064]	Country	Spain
[Ref.: #8064]	Country ISO 3 Code	ESP
[Ref.: #8064]	Continent	Europe

[Ref.: #67770]	Sample type/isolated from	Sandy soil
[Ref.: #67770]	Geographic location (country and/or sea, region)	Zamora
[Ref.: #67770]	Country	Spain
[Ref.: #67770]	Country ISO 3 Code	ESP
[Ref.: #67770]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Environmental	#Terrestrial	#Soil
#Engineered	#Agriculture	#Garden

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AM709608 (>99% sequence identity) for Promicromonospora from Microbeatlas

Aquatic Samples	29
Soil Samples	788
Animal Samples	66
Plant Samples	501
Total Samples	1384

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

[Ref.: #8064]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #19782]	Biosafety level	1	Risk group (German classification)

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.: #8064]	Promicromonospora kroppenstedtii partial 16S rRNA gene, type strain RS16T	AM709608	1450	GenBank ENA	926564 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Promicromonospora kroppenstedtii DSM 19349	GCA_000515355	scaffold	GenBank ENA	926564 tax ID
[Ref.: #66792]	Promicromonospora kroppenstedtii DSM 19349	926564.3	wgs	PATRIC	926564 tax ID	*
[Ref.: #66792]	Promicromonospora kroppenstedtii RS16, DSM 19349	2507525000	draft	JGI IMG/M	926564 tax ID	*

[Ref.: #8064]	GC-content	70.8 mol%
[Ref.: #67770]	GC-content	70.8 mol%	thermal denaturation, midpoint method (Tm)

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

	Model	Trait	Prediction	Confidence in %	In training data
	Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Promicromonospora kroppenstedtii DSM 19349 PATRIC: 926564.3
[Ref.: #125438]	gram-positive	gram-positiveⓘ	yes	90.729	yes
[Ref.: #125438]	anaerobic	anaerobicⓘ	no	95.798	yes
[Ref.: #125438]	aerobic	aerobicⓘ	yes	90.341	yes
[Ref.: #125438]	spore-forming	spore-formingⓘ	yes	68.596	yes
[Ref.: #125438]	thermophile	thermophilicⓘ	no	98.967	no
[Ref.: #125438]	motile2+	flagellatedⓘ	no	94	no

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Promicromonospora kroppenstedtii DSM 19349 NCBI: GCA_000515355
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	no	56.1
[Ref.: #125439]	BacteriaNet	motilityⓘ	no	74.6
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	positive	98.6
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	obligate aerobe	96.7

Availability in culture collections External links

[Ref.: #8064]

Culture collection no.

DSM 19349, LMG 24382, JCM 16033

[Ref.: #81818]

SI-ID 323094

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Promicromonospora callitridis sp. nov., an endophytic actinobacterium isolated from the surface-sterilized root of an Australian native pine tree.	Kaewkla O, Franco CMM	Int J Syst Evol Microbiol	10.1099/ijsem.0.002165	2017	*
Phylogeny	Promicromonospora kroppenstedtii sp. nov., isolated from sandy soil.	Alonso-Vega P, Santamaria RI, Martinez-Molina E, Trujillo ME	Int J Syst Evol Microbiol	10.1099/ijs.0.65458-0	2008	*

References

#8064

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 19349

#19782

Wink, J.: Compendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig .

#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 )

#32414

Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #28637 (see below)

#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) .

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#68382

Automatically annotated from API zym .

#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 .

#81818

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-ID323094.1 )

#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 .

#28637

IJSEM 1476 2008 ( DOI 10.1099/ijs.0.65458-0 , PubMed 18523198 )

* These data were automatically processed and therefore are not curated

Change proposal

You found an error in BacDive? Please tell us about it!

Note that changes will be reviewed and judged. If your changes are legitimate, changes will occur within the next BacDive update. Only proposed changes supported by the according reference will be reviewed. The BacDive team reserves the right to reject proposed changes.

Search for species Promicromonospora kroppenstedtii in external resources:
SILVA
BRENDA
PANGAEA
GBIF

Promicromonospora kroppenstedtii DSM 19349

Promicromonospora kroppenstedtii DSM 19349

Change proposal

Change proposal