Name: Planococcus rifietoensis M8
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 11962

Type strain:

Species: Planococcus rifietoensis

Strain Designation: M8

Culture col. no.: DSM 15069, ATCC BAA-790, CIP 108240

Strain history: CIP <- 2004, A. Gambacorta, ICB Istituto di Chimica Biomolecolare, Naples, Italy: strain M8

NCBI tax ID(s): 200991 (species)

SI-ID 128005

ATCC BAA-790, DSM 15069, CIP 108240

Special Collections

DSMZ
CIP

Section

Planococcus rifietoensis M8 is an obligate aerobe, Gram-positive bacterium that was isolated from sulfurous mineral water spring, algal mat.

Gram-positive
obligate aerobe
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	*Bacillota*
	Class	*Bacilli*
	Order	*Caryophanales*
	Family	*Caryophanaceae*
	Genus	*Planococcus*
	Species	**Planococcus rifietoensis**
	Full Scientific Name (LPSN)	Planococcus rifietoensis corrig. Romano et al. 2003

Synonym

Planococcus rifietensis

Information on morphological and physiological properties Morphology

[Ref.: #122237]	Gram stain	positive

[Ref.: #122237]	Cell shape	ovoid-shaped

[Ref.: #122237]	Motility	no

Information on culture and growth conditions Culture and growth conditions

[Ref.: #5693]

Culture medium

NUTRIENT AGAR (DSMZ Medium 1)

[Ref.: #5693]

Culture medium growth

[Ref.: #5693]

Culture medium link

Medium recipe at MediaDive

[Ref.: #5693]

Culture medium composition

expand / minimize

[Ref.: #33923]

Culture medium

MEDIUM 3 - Columbia agar

[Ref.: #33923]

Culture medium growth

[Ref.: #33923]

Culture medium composition

expand / minimize

[Ref.: #122237]

Culture medium

CIP Medium 72

[Ref.: #122237]

Culture medium growth

[Ref.: #122237]

Culture medium link

Medium recipe provided by DSMZ

[Ref.: #122237]

Culture medium

CIP Medium 3

[Ref.: #122237]

Culture medium growth

[Ref.: #122237]

Culture medium link

Medium recipe provided by DSMZ

	Kind of temperature		Temperature
[Ref.: #5693]		growth	28 °C
[Ref.: #33923]		growth	37 °C
[Ref.: #122237]		growth	10-37 °C
[Ref.: #122237]	no	growth	41 °C
[Ref.: #122237]	no	growth	45 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #122237]

Oxygen tolerance

obligate aerobe

	Salt	Tested relation		Salt conc.
[Ref.: #122237]	NaCl	no	growth	0	%
[Ref.: #122237]	NaCl	no	growth	2	%
[Ref.: #122237]	NaCl	no	growth	4	%
[Ref.: #122237]	NaCl	no	growth	6	%
[Ref.: #122237]	NaCl	no	growth	8	%
[Ref.: #122237]	NaCl	no	growth	10	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #122237]	hippurate ChEBI	+	hydrolysis
[Ref.: #122237]	nitrate ChEBI	-	reduction
[Ref.: #122237]	nitrite ChEBI	-	reduction

	Antibiotica	Metabolite	Antibiotic sensitivity	Antibiotic resistance
[Ref.: #122237]		0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)	yes	no

	Metabolite production	Metabolite	Production
[Ref.: #122237]		indole ChEBI	no

	Physiological tests	Metabolite	Voges-Proskauer-test
[Ref.: #122237]		acetoin ChEBI	-

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	-	3.1.3.2	* from API zym
[Ref.: #122237]	alcohol dehydrogenase	-	1.1.1.1
[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.: #122237]	amylase	-
[Ref.: #122237]	beta-galactosidase	+	3.2.1.23
[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.: #122237]	caseinase	-	3.4.21.50
[Ref.: #122237]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	+	3.4.11.3	* from API zym
[Ref.: #122237]	DNase	+
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #122237]	gamma-glutamyltransferase	+	2.3.2.2
[Ref.: #122237]	gelatinase	-
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #122237]	lysine decarboxylase	-	4.1.1.18
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #122237]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #122237]	oxidase	-
[Ref.: #122237]	phenylalanine ammonia-lyase	-	4.3.1.24
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #122237]	tryptophan deaminase	-
[Ref.: #122237]	tween esterase	-
[Ref.: #122237]	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.: #122237]	11016	-	+	+	+	-	+	-	+	-	-	-	+	-	+	-	+	-	-	-	-

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	cellulose degradation	100	5 of 5
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	valine metabolism	100	9 of 9
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	vitamin K metabolism	100	5 of 5
[Ref.: #66794]	ribulose monophosphate pathway	100	2 of 2
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	pentose phosphate pathway	100	11 of 11
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	acetate fermentation	100	4 of 4
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	palmitate biosynthesis	95.45	21 of 22
[Ref.: #66794]	NAD metabolism	94.44	17 of 18
[Ref.: #66794]	tetrahydrofolate metabolism	92.86	13 of 14
[Ref.: #66794]	threonine metabolism	90	9 of 10
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	isoleucine metabolism	87.5	7 of 8
[Ref.: #66794]	C4 and CAM-carbon fixation	87.5	7 of 8
[Ref.: #66794]	peptidoglycan biosynthesis	86.67	13 of 15
[Ref.: #66794]	propanol degradation	85.71	6 of 7
[Ref.: #66794]	vitamin B1 metabolism	84.62	11 of 13
[Ref.: #66794]	leucine metabolism	84.62	11 of 13
[Ref.: #66794]	glutamate and glutamine metabolism	82.14	23 of 28
[Ref.: #66794]	propionate fermentation	80	8 of 10
[Ref.: #66794]	lipoate biosynthesis	80	4 of 5
[Ref.: #66794]	flavin biosynthesis	80	12 of 15
[Ref.: #66794]	gallate degradation	80	4 of 5
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	serine metabolism	77.78	7 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	77.78	7 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	77.78	7 of 9
[Ref.: #66794]	purine metabolism	77.66	73 of 94
[Ref.: #66794]	ketogluconate metabolism	75	6 of 8
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	pyrimidine metabolism	73.33	33 of 45
[Ref.: #66794]	alanine metabolism	72.41	21 of 29
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	Entner Doudoroff pathway	70	7 of 10
[Ref.: #66794]	phenylalanine metabolism	69.23	9 of 13
[Ref.: #66794]	lysine metabolism	69.05	29 of 42
[Ref.: #66794]	non-pathway related	68.42	26 of 38
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	glycolate and glyoxylate degradation	66.67	4 of 6
[Ref.: #66794]	methionine metabolism	65.38	17 of 26
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	64.71	11 of 17
[Ref.: #66794]	citric acid cycle	64.29	9 of 14
[Ref.: #66794]	glutathione metabolism	64.29	9 of 14
[Ref.: #66794]	heme metabolism	64.29	9 of 14
[Ref.: #66794]	proline metabolism	63.64	7 of 11
[Ref.: #66794]	vitamin B6 metabolism	63.64	7 of 11
[Ref.: #66794]	tryptophan metabolism	63.16	24 of 38
[Ref.: #66794]	oxidative phosphorylation	61.54	56 of 91
[Ref.: #66794]	urea cycle	61.54	8 of 13
[Ref.: #66794]	cysteine metabolism	61.11	11 of 18
[Ref.: #66794]	metabolism of amino sugars and derivatives	60	3 of 5
[Ref.: #66794]	glycine betaine biosynthesis	60	3 of 5
[Ref.: #66794]	factor 420 biosynthesis	60	3 of 5
[Ref.: #66794]	starch degradation	60	6 of 10
[Ref.: #66794]	3-chlorocatechol degradation	60	3 of 5
[Ref.: #66794]	histidine metabolism	58.62	17 of 29
[Ref.: #66794]	lipid metabolism	58.06	18 of 31
[Ref.: #66794]	isoprenoid biosynthesis	57.69	15 of 26
[Ref.: #66794]	ubiquinone biosynthesis	57.14	4 of 7
[Ref.: #66794]	d-mannose degradation	55.56	5 of 9
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	myo-inositol biosynthesis	50	5 of 10
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	CMP-KDO biosynthesis	50	2 of 4
[Ref.: #66794]	alginate biosynthesis	50	2 of 4
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	biotin biosynthesis	50	2 of 4
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	cis-vaccenate biosynthesis	50	1 of 2
[Ref.: #66794]	degradation of sugar alcohols	50	8 of 16
[Ref.: #66794]	arginine metabolism	45.83	11 of 24
[Ref.: #66794]	lipid A biosynthesis	44.44	4 of 9
[Ref.: #66794]	degradation of pentoses	42.86	12 of 28
[Ref.: #66794]	reductive acetyl coenzyme A pathway	42.86	3 of 7
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
[Ref.: #66794]	vitamin B12 metabolism	41.18	14 of 34
[Ref.: #66794]	ascorbate metabolism	40.91	9 of 22
[Ref.: #66794]	phenylacetate degradation (aerobic)	40	2 of 5
[Ref.: #66794]	3-phenylpropionate degradation	40	6 of 15
[Ref.: #66794]	coenzyme M biosynthesis	40	4 of 10
[Ref.: #66794]	sulfate reduction	38.46	5 of 13
[Ref.: #66794]	phenylpropanoid biosynthesis	38.46	5 of 13
[Ref.: #66794]	dTDPLrhamnose biosynthesis	37.5	3 of 8
[Ref.: #66794]	androgen and estrogen metabolism	37.5	6 of 16
[Ref.: #66794]	cholesterol biosynthesis	36.36	4 of 11
[Ref.: #66794]	metabolism of disaccharids	36.36	4 of 11
[Ref.: #66794]	degradation of sugar acids	36	9 of 25
[Ref.: #66794]	tyrosine metabolism	35.71	5 of 14
[Ref.: #66794]	phenol degradation	35	7 of 20
[Ref.: #66794]	polyamine pathway	34.78	8 of 23
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	octane oxidation	33.33	1 of 3
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	degradation of hexoses	33.33	6 of 18
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	carotenoid biosynthesis	31.82	7 of 22
[Ref.: #66794]	arachidonic acid metabolism	27.78	5 of 18
[Ref.: #66794]	d-xylose degradation	27.27	3 of 11
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	carnitine metabolism	25	2 of 8
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	23.08	3 of 13
[Ref.: #66794]	nitrate assimilation	22.22	2 of 9
[Ref.: #66794]	allantoin degradation	22.22	2 of 9
[Ref.: #66794]	4-hydroxymandelate degradation	22.22	2 of 9
		Only first 10 entries are displayed. Click here to see all.

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

[Ref.: #5693]	Sample type/isolated from	sulfurous mineral water spring, algal mat
[Ref.: #5693]	Geographic location (country and/or sea, region)	Savignano Irpino, Campina
[Ref.: #5693]	Country	Italy
[Ref.: #5693]	Country ISO 3 Code	ITA
[Ref.: #5693]	Continent	Europe

[Ref.: #122237]	Sample type/isolated from	Algal mat, sulphurous mineral water spring
[Ref.: #122237]	Country	Italy
[Ref.: #122237]	Country ISO 3 Code	ITA
[Ref.: #122237]	Continent	Europe
[Ref.: #122237]	Isolation date	2002
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Spring
#Host	#Algae	-
#Condition	#Sulfuric	-

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AJ493659 (>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.: #5693]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #122237]	Biosafety level	1	Risk group (French 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.: #5693]	Planococcus rifitiensis 16S rRNA gene, strain M8	AJ493659	1531	GenBank ENA	200991 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Planococcus rifietoensis M8	GCA_001465795	complete	GenBank ENA	200991 tax ID	*
[Ref.: #66792]	Planococcus rifietoensis M8	2687453186	complete	JGI IMG/M	200991 tax ID	*

[Ref.: #5693]

GC-content

47.9 mol%

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 rifietoensis M8 NCBI: GCA_001465795.2
[Ref.: #69481]	spore-forming	spore-formingⓘ	yes	72	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Planococcus rifietoensis M8 NCBI: GCA_001465795.2
[Ref.: #69480]	gram-positive	gram-positiveⓘ	yes	78.713	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	96.194	yes
[Ref.: #69480]	aerobic	aerobicⓘ	yes	82.774	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	yes	55.69	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	95.395	no
[Ref.: #69480]	flagellated	motile2+ⓘ	yes	56.317	no

Availability in culture collections External links

[Ref.: #5693]

Culture collection no.

DSM 15069, ATCC BAA-790, CIP 108240

[Ref.: #81174]

SI-ID 128005

Literature:

Topic	Title	Authors	Journal	DOI	Year
Genetics	Complete genome of Planococcus rifietoensis M8(T), a halotolerant and potentially plant growth promoting bacterium.	See-Too WS, Convey P, Pearce DA, Lim YL, Ee R, Yin WF, Chan KG	J Biotechnol	10.1016/j.jbiotec.2016.01.026	2016	*

References

#5693

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 15069

#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 )

#33923 ; 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) .

#66794

Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )

#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 )

#81174

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-ID128005.1 )

#122237 Collection of Institut Pasteur ; Curators of the CIP; CIP 108240
* These data were automatically processed and therefore are not curated

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