Name: Nocardiopsis sediminis 1SS5-02
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 133129

Type strain:

Species: Nocardiopsis sediminis

Strain Designation: 1SS5-02

Culture col. no.: BCC 75410, NBRC 110934, DSM 108655

Strain history: <- NBRC; NBRC 110934 <- C Suriyachadkun, BIOTEC; 1SS5-02 <- P. Suksaard; 1SS5-02

NCBI tax ID(s): 1778267 (species)

SI-ID 397785

DSM 108655

Special Collections

Section

When using BacDive for research please cite our paper

Nocardiopsis sediminis 1SS5-02 is an aerobe, spore-forming, mesophilic bacterium that forms irregular colonies and was isolated from mangrove sediment.

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

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	*Streptosporangiales*
	Family	*Nocardiopsidaceae*
	Genus	*Nocardiopsis*
	Species	**Nocardiopsis sediminis**
	Full Scientific Name (LPSN)	Nocardiopsis sediminis Muangham et al. 2016

Information on morphological and physiological properties Morphology

[Ref.: #24890]	Gram stain	positive

[Ref.: #24890]	Motility	no

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Colony shape

irregular

Information on culture and growth conditions Culture and growth conditions

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Culture medium

ISP2 agar

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Culture medium growth

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Culture medium

GYE agar (Glucose Yeast Extract)

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Culture medium growth

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Culture medium

R2A MEDIUM (DSMZ Medium 830)

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Culture medium growth

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Culture medium link

Medium recipe at MediaDive

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Culture medium composition

expand / minimize

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Culture medium

GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)

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Culture medium growth

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Culture medium link

Medium recipe at MediaDive

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Culture medium composition

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Culture medium

ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84)

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Culture medium growth

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Culture medium link

Medium recipe at MediaDive

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Culture medium composition

expand / minimize

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Culture medium

STARCH - MINERAL SALT - AGAR (STMS) (DSMZ Medium 252)

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Culture medium growth

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Culture medium link

Medium recipe at MediaDive

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Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #24890]			optimum	25.0-28.0 °C
[Ref.: #64827]			growth	28 °C

	pH	Kind of pH		pH
[Ref.: #24890]			growth	6.0-11.0

Information on physiology and metabolism Physiology and metabolism

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Oxygen tolerance

aerobe

[Ref.: #24890]	Spore description	rod-shaped (0.4 µm x 0.7 µm in size),smooth-surfaced and non-motile
[Ref.: #24890]	Type of spore	spore
[Ref.: #24890]	Ability of spore formation	yes

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #24890]		NaCl		growth	0.0-4.0	%(w/v)
[Ref.: #24890]		NaCl	no	growth	10	%(w/v)

[Ref.: #24890]	Murein short key	A31
[Ref.: #24890]	Murein types	A1gamma m-Dpm-direct

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #24890]	adenine ChEBI	-	hydrolysis
[Ref.: #24890]	arbutin ChEBI	-	hydrolysis
[Ref.: #24890]	casein	+	hydrolysis
[Ref.: #24890]	cellobiose ChEBI	+	carbon source
[Ref.: #24890]	cellulose ChEBI	-	hydrolysis
[Ref.: #24890]	D-fructose ChEBI	+	carbon source
[Ref.: #24890]	D-galactose ChEBI	+	carbon source
[Ref.: #24890]	D-mannitol ChEBI	+	carbon source
[Ref.: #24890]	D-mannose ChEBI	+	carbon source
[Ref.: #24890]	D-ribose ChEBI	+	carbon source
[Ref.: #24890]	D-sorbitol ChEBI	-	carbon source
[Ref.: #24890]	dextran ChEBI	-	carbon source
[Ref.: #24890]	esculin ChEBI	-	hydrolysis
[Ref.: #24890]	gelatin ChEBI	+	hydrolysis
[Ref.: #24890]	hypoxanthine ChEBI	-	hydrolysis
[Ref.: #24890]	L-arabinose ChEBI	+	carbon source
[Ref.: #24890]	L-asparagine ChEBI	+	nitrogen source
[Ref.: #24890]	L-histidine ChEBI	+	nitrogen source
[Ref.: #24890]	L-rhamnose ChEBI	+	carbon source
[Ref.: #24890]	L-tyrosine ChEBI	-	hydrolysis
[Ref.: #24890]	lactose ChEBI	-	carbon source
[Ref.: #24890]	maltose ChEBI	+	carbon source
[Ref.: #24890]	melibiose ChEBI	-	carbon source
[Ref.: #24890]	myo-inositol ChEBI	+	carbon source
[Ref.: #24890]	nitrate ChEBI	-	reduction
[Ref.: #24890]	potassium nitrate ChEBI	+	nitrogen source
[Ref.: #24890]	propionate ChEBI	-	carbon source
[Ref.: #24890]	raffinose ChEBI	-	carbon source
[Ref.: #24890]	ribitol ChEBI	+	carbon source
[Ref.: #24890]	sodium citrate ChEBI	-	carbon source
[Ref.: #24890]	starch ChEBI	+	hydrolysis
[Ref.: #24890]	trehalose ChEBI	+	carbon source
[Ref.: #24890]	tween 80 ChEBI	+	hydrolysis
[Ref.: #24890]	urea ChEBI	+	hydrolysis
[Ref.: #24890]	xanthine ChEBI	-	hydrolysis
[Ref.: #24890]	xylan ChEBI	-	hydrolysis
[Ref.: #24890]	xylitol ChEBI	-	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #24890]		hydrogen sulfide ChEBI	yes

	Enzyme	Enzyme activity	EC number
[Ref.: #24890]	acid phosphatase	-	3.1.3.2
[Ref.: #24890]	alkaline phosphatase	+	3.1.3.1
[Ref.: #24890]	alpha-chymotrypsin	-	3.4.21.1
[Ref.: #24890]	alpha-fucosidase	-	3.2.1.51
[Ref.: #24890]	alpha-galactosidase	-	3.2.1.22
[Ref.: #24890]	alpha-glucosidase	+	3.2.1.20
[Ref.: #24890]	alpha-mannosidase	+	3.2.1.24
[Ref.: #24890]	beta-galactosidase	-	3.2.1.23
[Ref.: #24890]	beta-glucosidase	+	3.2.1.21
[Ref.: #24890]	beta-glucuronidase	-	3.2.1.31
[Ref.: #24890]	catalase	+	1.11.1.6
[Ref.: #24890]	cystine arylamidase	-	3.4.11.3
[Ref.: #24890]	cytochrome oxidase	+	1.9.3.1
[Ref.: #24890]	esterase (C 4)	+
[Ref.: #24890]	esterase lipase (C 8)	+
[Ref.: #24890]	leucine arylamidase	+	3.4.11.1
[Ref.: #24890]	lipase (C 14)	-
[Ref.: #24890]	N-acetyl-beta-glucosaminidase	-	3.2.1.52
[Ref.: #24890]	naphthol-AS-BI-phosphohydrolase	-
[Ref.: #24890]	trypsin	-	3.4.21.4
[Ref.: #24890]	valine arylamidase	+
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Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #24890]	Sample type/isolated from	mangrove sediment
[Ref.: #24890]	Geographic location (country and/or sea, region)	Laem Son National Park,Ranong province
[Ref.: #24890]	Country	Thailand
[Ref.: #24890]	Country ISO 3 Code	THA
[Ref.: #24890]	Continent	Asia
[Ref.: #24890]	Geographic location	9.0000°/98.0000°
[Ref.: #24890]	Enrichment culture	SC (starch casein)
[Ref.: #24890]	Enrichment culture composition	half-strength synthetic seawater (Marinium Reef Sea Salt, Mariscience International), supplemented with nystatin (50 µg ml-1 ) and nalidixic acid (25 µg ml-1)
[Ref.: #24890]	Enrichment culture duration	14 days
[Ref.: #24890]	Enrichment culture temperature	28 ̊C

[Ref.: #64827]	Sample type/isolated from	Mangrove sediment
[Ref.: #64827]	Geographic location (country and/or sea, region)	Laem Son National Park, Ranong Province (9° 22' 14.9'', N 98° 24' 38.2'' E)
[Ref.: #64827]	Country	Thailand
[Ref.: #64827]	Country ISO 3 Code	THA
[Ref.: #64827]	Continent	Asia
[Ref.: #64827]	Geographic location	9.3708°/98.4106°
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Mangrove
#Environmental	#Aquatic	#Sediment
#Host	#Plants	#Tree

What are isolation sources categories?

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Global distribution of 16S sequence LC110387 (>99% sequence identity) for Nocardiopsis from Microbeatlas

Aquatic Samples
Soil Samples	60
Animal Samples	6
Plant Samples	2
Total Samples	68

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

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Biosafety level

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.: #64827]	Nocardiopsis sediminis gene for 16S ribosomal RNA, partial sequence	LC110387	1501	GenBank ENA	1778267 tax ID

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GC-content

73.5 mol%

high performance liquid chromatography (HPLC)

Availability in culture collections External links

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Culture collection no.

BCC 75410, NBRC 110934, DSM 108655

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SI-ID 397785

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Nocardiopsissediminis sp. nov., isolated from mangrove sediment.	Muangham S, Suksaard P, Mingma R, Matsumoto A, Takahashi Y, Duangmal K	Int J Syst Evol Microbiol	10.1099/ijsem.0.001273	2016	*

References

#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 )

#24890

S. S. Muangham, Paweena,Mingma, Ratchanee,Matsumoto, Atsuko,Takahashi, Yoko,Duangmal, Kannika: Nocardiopsis sediminis sp. nov., isolated from mangrove sediment. IJSEM 66: 3835 - 3840 2016 ( DOI 10.1099/ijsem.0.001273 , PubMed 27381319 )

#64827

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 108655

#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 .

#91374

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-ID397785.1 )

* These data were automatically processed and therefore are not curated

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