Name: Planococcus citreus 628
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 11955

Type strain:

Species: Planococcus citreus

Strain Designation: 628

Culture col. no.: DSM 20549, ATCC 14404, CCM 316, NCMB 1493, JCM 2532, CECT 951, CGMCC 1.2714, CIP 81.74, IAM 12456, IAM 12541, IAM 13052, IFO 15849, LMG 17319, NBRC 15849, NCIMB 1493, VKM B-1307

Strain history: CIP <- 1981, CCM <- C.E. ZoBell: strain 628, Micrococcus aquivivus

NCBI tax ID(s): 1373 (species)

SI-ID 13977

LMG 17319, ATCC 14404, CCM 316, IAM 12541, IFO 15849, JCM 2532, NCIMB 1493, NCMB 1493, IAM 12456, IAM 13052, NCMB567, VKM B-1307, CECT 951, NCIMB 567, NBRC 15849, CGMCC 1.2714, DSM 20549, CIP 81.74

Special Collections

Other strains from Planococcus citreus

Section

Planococcus citreus 628 is an obligate aerobe, mesophilic, motile bacterium that was isolated from seawater.

motile
oval-shaped
mesophilic
obligate aerobe
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	*Bacillota*
	Class	*Bacilli*
	Order	*Caryophanales*
	Family	*Caryophanaceae*
	Genus	*Planococcus*
	Species	**Planococcus citreus**
	Full Scientific Name (LPSN)	Planococcus citreus Migula 1894 (Approved Lists 1980)

Information on morphological and physiological properties Morphology

[Ref.: #118304]	Cell shape	oval-shaped

[Ref.: #118304]	Motility	yes

Information on culture and growth conditions Culture and growth conditions

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Culture medium

NUTRIENT AGAR WITH NaCl (DSMZ Medium 101)

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Culture medium growth

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Culture medium link

Medium recipe at MediaDive

[Ref.: #8777]

Culture medium composition

expand / minimize

[Ref.: #37979]

Culture medium

MEDIUM 3 - Columbia agar

[Ref.: #37979]

Culture medium growth

[Ref.: #37979]

Culture medium composition

expand / minimize

[Ref.: #118304]

Culture medium

CIP Medium 72

[Ref.: #118304]

Culture medium growth

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Culture medium link

Medium recipe provided by DSMZ

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Culture medium

CIP Medium 3

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Culture medium growth

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Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #8777]	growth	26 °C
[Ref.: #37979]	growth	30 °C
[Ref.: #67770]	growth	30 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #118304]

Oxygen tolerance

obligate aerobe

[Ref.: #8777]	Murein short key	A11.33
[Ref.: #8777]	Murein types	A4alpha L-Lys-D-Glu

[Ref.: #67770]

Observation

quinones: MK-8 (MK-7)

	Metabolite utilization	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #118304]		nitrate ChEBI	-	reduction
[Ref.: #118304]		nitrite ChEBI	-	reduction

	Metabolite production	Metabolite	Production
[Ref.: #118304]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[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.: #118304]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	+	3.4.11.3	* from API zym
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[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.: #118304]	oxidase	-
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #118304]	urease	-	3.5.1.5
[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.: #118304]	13500	-	+	+	+	-	+	-	+	-	-	-	-	-	-	-	+	-	-	-	-

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

[Ref.: #8777]	Sample type/isolated from	seawater

[Ref.: #67770]	Sample type/isolated from	Seawater

[Ref.: #118304]	Sample type/isolated from	Environment, Seawater
* marker position based on {}

Isolation sources categories

#Environmental

#Aquatic

#Marine

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence LC379145 (>99% sequence identity) for Planococcus from Microbeatlas

Aquatic Samples	2240
Soil Samples	6586
Animal Samples	2949
Plant Samples	1109
Total Samples	12884

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

[Ref.: #8777]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #118304]	Biosafety level	1	Risk group (French classification)

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

16S Sequence information:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Planococcus citreus 5S ribosomal RNA	X13005	116	GenBank ENA	1373 tax ID
[Ref.: #67770]	Planococcus citreus gene for 16S rRNA, partial sequence, strain: JCM 2532	LC379145	1473	GenBank ENA	1373 tax ID
[Ref.: #124043]	Planococcus citreus strain DSM 20549 16S ribosomal RNA gene, partial sequence.	OQ626007	1320	GenBank ENA	1373 tax ID	*
[Ref.: #20218]	Planococcus citreus strain DSM 20549 16S-23S rRNA intergenic spacer region	AF145717	185	GenBank ENA	1373 tax ID	*
[Ref.: #20218]	Planococcus citreus gene for 16S rRNA, partial sequence, strain: NBRC 15849	AB680985	1476	GenBank ENA	1373 tax ID	*
[Ref.: #20218]	P.citreus 16S rRNA	X62172	1432	GenBank ENA	1373 tax ID	*
[Ref.: #124043]	Planococcus citreus strain DSM 20549 16S ribosomal RNA gene, partial sequence.	OQ618963	1352	GenBank ENA	1373 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Planococcus citreus DSM 20549	GCA_004761885	contig	GenBank ENA	1373 tax ID
[Ref.: #67770]	Planococcus citreus DSM 20549	GCA_003664125	scaffold	GenBank ENA	1373 tax ID
[Ref.: #66792]	Planococcus citreus strain DSM 20549	1373.6	wgs	PATRIC	1373 tax ID	*
[Ref.: #66792]	Planococcus citreus strain DSM 20549	1373.5	wgs	PATRIC	1373 tax ID	*
[Ref.: #66792]	Planococcus citreus DSM 20549	2770939644	draft	JGI IMG/M	1373 tax ID	*

[Ref.: #8777]	GC-content	51.2 mol%
[Ref.: #67770]	GC-content	47.5 mol%	fluorimetric
[Ref.: #67770]	GC-content	51.2 mol%	thermal denaturation, midpoint method (Tm)

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

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Planococcus citreus DSM 20549 NCBI: GCA_003664125.1
[Ref.: #69481]	spore-forming	spore-formingⓘ	yes	67	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Planococcus citreus strain DSM 20549 PATRIC: 1373.6
[Ref.: #69480]	gram-positive	gram-positiveⓘ	yes	78.237	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	96.474	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	yes	58.223	no
[Ref.: #69480]	aerobic	aerobicⓘ	yes	80.401	yes
[Ref.: #69480]	thermophilic	thermophileⓘ	no	94.339	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	yes	54.404	no

Availability in culture collections External links

[Ref.: #8777]

Culture collection no.

DSM 20549, ATCC 14404, CCM 316, NCMB 1493, JCM 2532, CECT 951, CGMCC 1.2714, CIP 81.74, IAM 12456, IAM 12541, IAM 13052, IFO 15849, LMG 17319, NBRC 15849, NCIMB 1493, VKM B-1307

[Ref.: #81168]

SI-ID 13977

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Planococcus maritimus sp. nov., isolated from sea water of a tidal flat in Korea.	Yoon JH, Weiss N, Kang KH, Oh TK, Park YH	Int J Syst Evol Microbiol	10.1099/ijs.0.02557-0	2003	*

References

#8777

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 20549

#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 )

#20218

Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )

#37979 ; Curators of the CIP;

#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 .

#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 )

#81168

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-ID13977.1 )

#118304 Collection of Institut Pasteur ; Curators of the CIP; CIP 81.74

#124043

Dr. Isabel Schober, Dr. Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .

* These data were automatically processed and therefore are not curated

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Planococcus citreus DSM 20549

Planococcus citreus strain DSM 20549

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