Archive BacDiveID:10.13145/bacdive11238.20230509.8.1

Strain identifier

BacDive ID: 11238

Type strain:

Species: Nocardiopsis sinuspersici

Strain Designation: HM6

Strain history: <- J. Hamedi, Univ. Tehran, Iran; HM6 <- F. Mohammadipanah

NCBI tax ID(s): 501010 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.

General

@ref: 16116

BacDive-ID: 11238

DSM-Number: 45277

keywords: genome sequence, 16S sequence, Bacteria, aerobe, spore-forming, mesophilic, Gram-positive, rod-shaped

description: Nocardiopsis sinuspersici HM6 is an aerobe, spore-forming, mesophilic bacterium that was isolated from sandy rhizospheric soil at a depth of 10 cm.

NCBI tax id

NCBI tax id: 501010
Matching level: species

strain history

@ref: 16116
history: <- J. Hamedi, Univ. Tehran, Iran; HM6 <- F. Mohammadipanah

doi: 10.13145/bacdive11238.20230509.8.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/actinomycetota
domain: Bacteria
phylum: Actinomycetota
class: Actinomycetes
order: Streptosporangiales
family: Nocardiopsidaceae
genus: Nocardiopsis
species: Nocardiopsis sinuspersici
full scientific name: Nocardiopsis sinuspersici Hamedi et al. 2010
synonyms
- @ref: 20215
- synonym: Nocardiopsis arvandica

@ref: 16116

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardiopsaceae

genus: Nocardiopsis

species: Nocardiopsis sinuspersici

full scientific name: Nocardiopsis sinuspersici Hamedi et al. 2010

strain designation: HM6

type strain: yes

Morphology

cell morphology

@ref	gram stain	cell shape	motility	confidence
29670	positive	rod-shaped
69480			no	91.601
69480	positive			100

colony morphology

@ref	colony color	incubation period	medium used
21425	Ivory (1014)	10-14 days	ISP 2
21425	Ivory (1014)	10-14 days	ISP 3
21425	Ivory (1014)/ Maize yellow (1006)	10-14 days	ISP 4
21425	Ivory (1014)	10-14 days	ISP 5
21425	Ivory (1014)	10-14 days	ISP 6
21425	Ivory (1014)/ Grey beige (1019)	10-14 days	ISP 7
21425	Pale brown (8025)	10-14 days	Suter with tyrosine
21425	Ivory (1014)	10-14 days	Suter without tyrosine
61395		4-5 days

pigmentation

@ref: 29670
production: yes

Culture and growth conditions

culture medium

@ref	name	growth	link	composition
16116	GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)	yes	https://mediadive.dsmz.de/medium/65	Name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) Composition: Agar 18.0 g/l Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l CaCO3 2.0 g/l Distilled water
16116	TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)	yes	https://mediadive.dsmz.de/medium/535	Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
21425	ISP 2	yes		Name: ISP 2 / Yeast Malt Agar (5265); 5265 Composition Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.0 Usage: Maintenance and Taxonomy Organisms: All Actinomycetes
21425	ISP 3	yes		Name: ISP 3; 5315 Composition Dog oat flakes 20.0 g/l Trace element solution (5314) 2.5 ml/l Agar 18.0 g/l Preparation: Oat flakes are cooked for 20 minutes, trace element solution and agar are added (in the case of non rolled oat flakes the suspension has to bee filtrated). Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.8 Usage: Maintenance and taxonomy (e.g. SEM As liquid medium for metabolite production) Organisms: All Actinomycetes Trace element solution 5314 Name: Trace element solution 5314; 5314 Composition CaCl2 x H2O 3.0 g/l Fe-III-citrate 1.0 g/l MnSO4 0.2 g/l ZnCl2 0.1 g/l CuSO4 x 5 H2O 0.025 g/l Sodium tetra borate 0.2 g/l CoCl2 x 6 H2O 0.004 g/l Sodium molybdate 0.01 g/l Preparation: Use double destillated water. Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Trace element solution for different media Organisms:
21425	ISP 4	yes		Name: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml
21425	ISP 5	yes		Name: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes
21425	ISP 6	yes		Name: ISP 6 (5318) Composition Peptone 15.0 g/l Proteose peptose 5.0 g/l Ferric ammonium citrate 0.5 g/l Sodium glycerophosphate 1.0 g/l Sodium thiosulfate 0.08 g/l Yeast extract 1.0 g/l Agar 15.0 g/l Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigments Organisms: All Actinomycetes
21425	ISP 7	yes		Name: ISP 7 (5322) Composition Glycerol 15.0 g/l L-Tyrosine 0.5 g/l L-Asparagine 1.0 g/l K2HPO4 0.5 g/l NaCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Trace element solution 5343 1.0 ml/l Agar 20.0 Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.3 Usage: Production of melanoid pigments Organisms: All Actinomycetes
21425	Suter with tyrosine	yes		Name: Synthetically suter medium (5337) with and without tyrosine - see Kutzner,H.J., R. M. Kroppensted and F. Korn-Wendisch. (1986) Composition: Glycerol 15.0 g/l Tyrosine 1.0 (optional, see preparation comment) L-arginine 5.0 g/l L-glutamic acid 5.0 g/l L-methionine 0.3 g/l L-isoleucine 0.3 g/l K2HPO4 0.5 g/l MgSO4 x 7 H2O 0.2 g/l Agar 20.0 g/l Trace element solution (5341) 1.0 ml Composition of Trace element solution (5341): CuSO4 x 5 H2O 10.0 g/l CaCl2 x 2 H2O 10.0 g/l FeSO4 x 7 H2O 10.0 g/l ZnSO4 x 7 H2O 10.0 g/l MnSO4 x 7 H2O 40.0 g/l Preparation: Control medium is prepared without tyrosine Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigment Organisms: All Actinomycetes
21425	Suter without tyrosine	yes		Name: Synthetically suter medium (5337) with and without tyrosine - see Kutzner,H.J., R. M. Kroppensted and F. Korn-Wendisch. (1986) Composition: Glycerol 15.0 g/l Tyrosine 1.0 (optional, see preparation comment) L-arginine 5.0 g/l L-glutamic acid 5.0 g/l L-methionine 0.3 g/l L-isoleucine 0.3 g/l K2HPO4 0.5 g/l MgSO4 x 7 H2O 0.2 g/l Agar 20.0 g/l Trace element solution (5341) 1.0 ml Composition of Trace element solution (5341): CuSO4 x 5 H2O 10.0 g/l CaCl2 x 2 H2O 10.0 g/l FeSO4 x 7 H2O 10.0 g/l ZnSO4 x 7 H2O 10.0 g/l MnSO4 x 7 H2O 40.0 g/l Preparation: Control medium is prepared without tyrosine Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigment Organisms: All Actinomycetes
16116	GPHF-MEDIUM (DSMZ Medium 553)	yes	https://mediadive.dsmz.de/medium/553	Name: GPHF-MEDIUM (DSMZ Medium 553) Composition: Agar 20.0 g/l Glucose 10.0 g/l Beef extract 5.0 g/l Yeast extract 5.0 g/l Casein peptone 5.0 g/l CaCl2 x 2 H2O 0.74 g/l Distilled water
16116	STARCH - MINERAL SALT - AGAR (STMS) (DSMZ Medium 252)	yes	https://mediadive.dsmz.de/medium/252	Name: STARCH - MINERAL SALT - AGAR (STMS) (DSMZ Medium 252) Composition: Agar 14.985 g/l Starch 9.99001 g/l (NH4)2SO4 1.998 g/l CaCO3 1.998 g/l K2HPO4 0.999001 g/l MgSO4 x 7 H2O 0.999001 g/l NaCl 0.999001 g/l FeSO4 x 7 H2O 0.000999001 g/l MnCl2 x 4 H2O 0.000999001 g/l ZnSO4 x 7 H2O 0.000999001 g/l Distilled water

culture temp

@ref	growth	type	temperature	range
16116	positive	growth	28	mesophilic
29670	positive	growth	15-37
29670	positive	optimum	28	mesophilic
61395	positive	growth	37	mesophilic

culture pH

@ref	ability	type	pH	PH range
29670	positive	growth	05-12	alkaliphile
29670	positive	optimum	7

Physiology and metabolism

oxygen tolerance

@ref	oxygen tolerance
29670	aerobe
61395	aerobe

spore formation

@ref	spore formation	confidence
29670	yes
69481	yes	100
69480	yes	100

halophily

@ref	salt	growth	tested relation	concentration
21425	NaCl	positive	maximum	10 %
29670	NaCl	positive	growth	0-15 %
29670	NaCl	positive	optimum	2.5 %

observation

@ref: 29670
observation: aggregates in chains

metabolite utilization

@ref	Chebi-ID	metabolite	utilization activity	kind of utilization tested
21425	17234	glucose	+
21425	22599	arabinose	+
21425	17992	sucrose	+
21425	18222	xylose	+
21425	17268	myo-inositol	-
21425	37684	mannose	+
21425	28757	fructose	+
21425	26546	rhamnose	+
21425	16634	raffinose	+
21425	62968	cellulose	-
29670	16947	citrate	+	carbon source
29670	28260	galactose	+	carbon source
29670	17754	glycerol	+	carbon source
29670	17716	lactose	+	carbon source
29670	15792	malonate	+	carbon source
29670	17306	maltose	+	carbon source
29670	29864	mannitol	+	carbon source
29670	37684	mannose	+	carbon source
29670	28053	melibiose	+	carbon source
29670	17272	propionate	+	carbon source
29670	15361	pyruvate	+	carbon source
29670	26546	rhamnose	+	carbon source
29670	17992	sucrose	+	carbon source
29670	18222	xylose	+	carbon source
29670	17632	nitrate	+	reduction
68379	17632	nitrate	-	reduction
68379	4853	esculin	-	hydrolysis
68379	17634	D-glucose	-	fermentation
68379	16988	D-ribose	-	fermentation
68379	65327	D-xylose	-	fermentation
68379	16899	D-mannitol	-	fermentation
68379	17306	maltose	-	fermentation
68379	17716	lactose	-	fermentation
68379	17992	sucrose	+	fermentation
68379	28087	glycogen	-	fermentation

enzymes

@ref	value	activity	ec
68379	beta-glucosidase	-	3.2.1.21
68379	N-acetyl-beta-glucosaminidase	+	3.2.1.52
68379	alpha-glucosidase	+	3.2.1.20
68379	beta-galactosidase	-	3.2.1.23
68379	beta-glucuronidase	-	3.2.1.31
68379	alkaline phosphatase	+	3.1.3.1
68379	pyrrolidonyl arylamidase	-	3.4.19.3
68379	pyrazinamidase	-	3.5.1.B15
68382	alkaline phosphatase	+	3.1.3.1
68382	esterase (C 4)	+
68382	esterase lipase (C 8)	+
68382	leucine arylamidase	+	3.4.11.1
68382	trypsin	-	3.4.21.4
68382	alpha-chymotrypsin	+	3.4.21.1
68382	acid phosphatase	+	3.1.3.2
68382	naphthol-AS-BI-phosphohydrolase	+
68382	alpha-galactosidase	-	3.2.1.22
68382	beta-galactosidase	-	3.2.1.23
68382	beta-glucuronidase	-	3.2.1.31
68382	alpha-glucosidase	+	3.2.1.20
68382	beta-glucosidase	+	3.2.1.21
68382	N-acetyl-beta-glucosaminidase	+	3.2.1.52
68382	alpha-mannosidase	-	3.2.1.24
68382	alpha-fucosidase	-	3.2.1.51

API coryne

@ref	NIT	PYZ	PYRA	PAL	beta GUR	beta GAL	alpha GLU	beta NAG	ESC	URE	GEL	GLU	RIB	XYL	MAN	MAL	LAC	SAC	GLYG
21425	-	-	-	+	-	-	+	+	-	+/-	+/-	-	-	-	-	-	-	+	-

API zym

@ref	Alkaline phosphatase	Esterase	Esterase Lipase	Lipase	Leucine arylamidase	Valine arylamidase	Cystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
21425	+	+	+	+/-	+	+/-	+/-	-	+	+	+	-	-	-	+	+	+	-	-

Isolation, sampling and environmental information

isolation

@ref	sample type	geographic location	country	origin.country	continent
16116	sandy rhizospheric soil at a depth of 10 cm	Khuzestan Province, Sarbandar, seashore of Persian Gulf	Iran	IRN	Asia
61395	Soil,rhizospherical	Persian Gulf,Sarbandar region	Iran	IRN	Asia

isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Sandy
#Environmental	#Terrestrial	#Soil
#Host Body-Site	#Plant	#Rhizosphere

taxonmaps

@ref: 69479
File name: preview.99_4414.png
url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_152;96_659;97_762;98_3317;99_4414&stattab=map
Last taxonomy: Nocardiopsis
16S sequence: EU410476
Sequence Identity:
Total samples: 22
soil counts: 7
animal counts: 14
plant counts: 1

Safety information

risk assessment

@ref	biosafety level	biosafety level comment
16116	1	Risk group (German classification)
21425	L1	German classification

Sequence information

16S sequences

@ref: 16116
description: Nocardiopsis sinuspersici strain HM6 16S ribosomal RNA gene, partial sequence
accession: EU410476
length: 1520
database: ena
NCBI tax ID: 501010

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Nocardiopsis sinuspersici strain DSM 45277	501010.4	wgs	patric	501010
66792	Nocardiopsis sinuspersici UTMC 00102	GCA_001998325	scaffold	ncbi	501010

GC content

@ref	GC-content	method
16116	71.6	high performance liquid chromatography (HPLC)
29670	71.6

Genome-based predictions

predictions

trait	prediction	confidence	training_data
spore-forming	yes	100	no
gram-positive	yes	92.449	no
anaerobic	no	98.892	yes
halophile	yes	70.66	no
spore-forming	yes	92.793	no
glucose-util	yes	89.33	yes
thermophile	no	95.801	yes
motile	no	91.584	no
aerobic	yes	95.121	no
flagellated	no	98.14	no
glucose-ferment	no	91.123	yes

External links

@ref: 16116

culture collection no.: DSM 45277, CCUG 57624, UTMC 00102

straininfo link

@ref: 80473
straininfo: 402148

literature

topic	Pubmed-ID	title	authors	journal	DOI	year	mesh	topic2
Phylogeny	19933587	Nocardiopsis sinuspersici sp. nov., isolated from sandy rhizospheric soil.	Hamedi J, Mohammadipanah F, von Jan M, Potter G, Schumann P, Sproer C, Klenk HP, Kroppenstedt RM	Int J Syst Evol Microbiol	10.1099/ijs.0.018366-0	2009	Actinomycetales/chemistry/classification/genetics/isolation & purification, Bacterial Typing Techniques, Cell Wall/chemistry, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Glucose/analysis, Iran, Microscopy, Electron, Scanning, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Rhizosphere, Ribose/analysis, Sequence Analysis, DNA, Soil Microbiology	Genetics
Phylogeny	20562242	Nocardiopsis arvandica sp. nov., isolated from sandy soil.	Hamedi J, Mohammadipanah F, Potter G, Sproer C, Schumann P, Goker M, Klenk HP	Int J Syst Evol Microbiol	10.1099/ijs.0.022756-0	2010	Actinomycetales/classification/genetics/isolation & purification/metabolism, DNA, Bacterial/genetics, Fatty Acids/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil Microbiology	Metabolism
Genetics	28522715	Complete Draft Genome Sequence of the Actinobacterium Nocardiopsis sinuspersici UTMC102 (DSM 45277(T)), Which Produces Serine Protease.	Tokovenko B, Ruckert C, Kalinowski J, Mohammadipanah F, Wink J, Rosenkranzer B, Myronovskyi M, Luzhetskyy A	Genome Announc	10.1128/genomeA.00362-17	2017

Reference

@id	authors	catalogue	doi/url	title	ID_cross_reference	pubmed
16116	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45277)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-45277
20215	Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.		10.1099/ijsem.0.004332	List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
21425	Wink, J.		http://www.dsmz.de/microorganisms/wink_pdf/DSM45277.pdf	Compendium of Actinobacteria . HZI-Helmholtz-Centre for Infection Research, Braunschweig
29670	Barberan A, Caceres Velazquez H, Jones S, Fierer N.		10.1128/mSphere.00237-17	Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information	26056	28776041
61395	Curators of the CCUG	Culture Collection University of Gothenburg (CCUG) (CCUG 57624)	https://www.ccug.se/strain?id=57624
66792	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann		https://diaspora-project.de/progress.html#genomes	Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
68379				Automatically annotated from API Coryne
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.		https://microbeatlas.org/	MicrobeAtlas 1.0 beta
69480	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann		https://diaspora-project.de/progress.html#genomes	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		10.21203/rs.3.rs-2527258/v1	Predictions based on the model GenomeNet Sporulation v. 1
80473	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID402148.1	StrainInfo: A central database for resolving microbial strain identifiers

General

NCBI tax id

strain history

Name and taxonomic classification

LPSN

synonyms

Morphology

cell morphology

colony morphology

pigmentation

Culture and growth conditions

culture medium

culture temp

culture pH

Physiology and metabolism

oxygen tolerance

spore formation

halophily

observation

metabolite utilization

enzymes

API coryne

API zym

Isolation, sampling and environmental information

isolation

isolation source categories

taxonmaps

Safety information

risk assessment

Sequence information

16S sequences

Genome sequences

GC content

Genome-based predictions

predictions

External links

straininfo link

literature

Reference