Name: Planococcus lenghuensis Y42
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 164341

Type strain:

Species: Planococcus lenghuensis

Strain Designation: Y42

Culture col. no.: JCM 32719, CGMCC 1.15921

Strain history: B. Zhang; Northwest Inst. of Eco-Eviron. & Resour., CAS, China; Y42.

NCBI tax ID(s): 2213202 (species)

Section

Planococcus lenghuensis Y42 is an aerobe, mesophilic, Gram-positive bacterium that forms circular colonies and was isolated from Oil-contaminated soil in the Lenghu oil field.

colony-forming
Gram-positive
aerobe
mesophilic
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 lenghuensis"
	Full Scientific Name (LPSN)	Planococcus lenghuensis Yang et al. 2020

Information on morphological and physiological properties Morphology

[Ref.: #68343]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %100

[Ref.: #68343]	Cell length	1 µm

[Ref.: #69480]	Motility	yes Confidence in %92.448

[Ref.: #68343]	Colony size	0.7-1 mm
[Ref.: #68343]	Colony color	orange
[Ref.: #68343]	Colony shape	circular
[Ref.: #68343]	Incubation period	4 days
[Ref.: #68343]	Cultivation medium used	LB (Luria-Bertani) agar

Information on culture and growth conditions Culture and growth conditions

		Temperature
[Ref.: #67770]	growth	25 °C
[Ref.: #68343]	growth	10-35 °C
[Ref.: #68343]	optimum	25 °C

[Ref.: #67770]	Temperature range	mesophilic
[Ref.: #68343]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #68343]			optimum	7.5
[Ref.: #68343]			growth	7-9

Information on physiology and metabolism Physiology and metabolism

[Ref.: #68343]

Oxygen tolerance

aerobe

[Ref.: #69480]	Ability of spore formation	no Confidence in %94.91
[Ref.: #69481]	Ability of spore formation	yes Confidence in %100

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #68343]		NaCl		growth	0-8	%(w/v)
[Ref.: #68343]		NaCl		optimum	1-3	%(w/v)

[Ref.: #67770]	Observation	quinones: MK-7
[Ref.: #68343]	Observation	degrade petroleum

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68343]	(-)-quinic acid ChEBI	-	assimilation
[Ref.: #68343]	2-oxoglutarate ChEBI	-	assimilation
[Ref.: #68343]	3-O-methyl-D-glucose ChEBI	-	assimilation
[Ref.: #68343]	acetic acid ChEBI	+	assimilation
[Ref.: #68343]	acetoacetate ChEBI	+	assimilation
[Ref.: #68343]	alpha-lactose ChEBI	-	assimilation
[Ref.: #68343]	cellobiose ChEBI	-	assimilation
[Ref.: #68343]	cellulose ChEBI	-	hydrolysis
[Ref.: #68343]	citrate ChEBI	-	assimilation
[Ref.: #68343]	D-arabinose ChEBI	-	assimilation
[Ref.: #68343]	D-arabitol ChEBI	-	assimilation
[Ref.: #68343]	D-aspartate ChEBI	+	assimilation
[Ref.: #68343]	D-fructose ChEBI	+	assimilation
[Ref.: #68343]	D-fructose 6-phosphate ChEBI	+	assimilation
[Ref.: #68343]	D-fucose ChEBI	-	assimilation
[Ref.: #68343]	D-galactonic acid lactone ChEBI	-	assimilation
[Ref.: #68343]	D-galactose ChEBI	-	assimilation
[Ref.: #68343]	D-galacturonic acid ChEBI	+	assimilation
[Ref.: #68343]	D-gluconate ChEBI	+	assimilation
[Ref.: #68343]	D-glucose ChEBI	+	assimilation
[Ref.: #68343]	D-glucose 6-phosphate ChEBI	-	assimilation
[Ref.: #68343]	D-glucuronate ChEBI	+	assimilation
[Ref.: #68343]	D-malate ChEBI	-	assimilation
[Ref.: #68343]	D-mannitol ChEBI	+	assimilation
[Ref.: #68343]	D-mannose ChEBI	-	assimilation
[Ref.: #68343]	D-saccharate ChEBI	-	assimilation
[Ref.: #68343]	D-salicin ChEBI	-	assimilation
[Ref.: #68343]	D-serine ChEBI	-	assimilation
[Ref.: #68343]	D-sorbitol ChEBI	-	assimilation
[Ref.: #68343]	dextrin ChEBI	+	assimilation
[Ref.: #68343]	formate ChEBI	-	assimilation
[Ref.: #68343]	galactarate ChEBI	-	assimilation
[Ref.: #68343]	gelatin ChEBI	+	hydrolysis
[Ref.: #68343]	gentiobiose ChEBI	-	assimilation
[Ref.: #68343]	glucose ChEBI	+	fermentation
[Ref.: #68343]	glucuronamide ChEBI	+	assimilation
[Ref.: #68343]	glycerol ChEBI	-	assimilation
[Ref.: #68343]	inosine ChEBI	-	assimilation
[Ref.: #68343]	L-alanine ChEBI	-	assimilation
[Ref.: #68343]	L-arginine ChEBI	-	assimilation
[Ref.: #68343]	L-aspartate ChEBI	-	assimilation
[Ref.: #68343]	L-fucose ChEBI	-	assimilation
[Ref.: #68343]	L-glutamate ChEBI	-	assimilation
[Ref.: #68343]	L-histidine ChEBI	-	assimilation
[Ref.: #68343]	L-lactate	-	assimilation
[Ref.: #68343]	L-malate ChEBI	+	assimilation
[Ref.: #68343]	L-pyroglutamic acid ChEBI	-	assimilation
[Ref.: #68343]	L-rhamnose ChEBI	-	assimilation
[Ref.: #68343]	L-serine ChEBI	-	assimilation
[Ref.: #68343]	maltose ChEBI	-	assimilation
[Ref.: #68343]	melibiose ChEBI	-	assimilation
[Ref.: #68343]	myo-inositol ChEBI	-	assimilation
[Ref.: #68343]	N-acetylglucosamine ChEBI	-	assimilation
[Ref.: #68343]	nitrate ChEBI	+	reduction
[Ref.: #68343]	pectin ChEBI	-	assimilation
[Ref.: #68343]	raffinose ChEBI	-	assimilation
[Ref.: #68343]	sodium propionate ChEBI	-	assimilation
[Ref.: #68343]	stachyose ChEBI	-	assimilation
[Ref.: #68343]	starch ChEBI	-	hydrolysis
[Ref.: #68343]	sucrose ChEBI	+	assimilation
[Ref.: #68343]	trehalose ChEBI	-	assimilation
[Ref.: #68343]	turanose ChEBI	-	assimilation
[Ref.: #68343]	tween 40 ChEBI	+	hydrolysis
[Ref.: #68343]	tween 80 ChEBI	-	hydrolysis
	Only first 10 entries are displayed. Click here to see all.

	Antibiotica	Metabolite	Antibiotic resistance
[Ref.: #68343]		lithium chloride ChEBI	yes
[Ref.: #68343]		tetrazolium violet ChEBI	yes

	Metabolite	Production
[Ref.: #68343]	acetoin ChEBI	no
[Ref.: #68343]	hydrogen sulfide ChEBI	yes
[Ref.: #68343]	indole ChEBI	no

	Physiological tests	Metabolite	Voges-Proskauer-test	Methylred-test
[Ref.: #68343]		acetoin ChEBI	-
[Ref.: #68343]		glucose ChEBI		+

	Enzyme	Enzyme activity	EC number
[Ref.: #68343]	alkaline phosphatase	+	3.1.3.1
[Ref.: #68343]	alpha-chymotrypsin	+	3.4.21.1
[Ref.: #68343]	catalase	+	1.11.1.6
[Ref.: #68343]	cystine arylamidase	+	3.4.11.3
[Ref.: #68343]	cytochrome oxidase	-	1.9.3.1
[Ref.: #68343]	esterase (C 4)	+
[Ref.: #68343]	esterase Lipase (C 8)	+
[Ref.: #68343]	leucine arylamidase	+	3.4.11.1
[Ref.: #68343]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #68343]	valine arylamidase	+

Fatty acid profile

Metadata FA analysis

Reference

[Ref.: #68343]

Fatty acid	Percentage
C15:0 anteiso	39
C17:1 iso I and/or C17:1 anteiso/iso B	8.8
C15:0 iso	8.2
C16:1 w7c alcohol	7.7
C17:0 anteiso	7.3
C17:0 iso	5.1
C16:0 iso	4.5
C16:1 w11c	3.3
C14:0 iso	2.3
C16:0	1.4
C18:0 iso	0.6
C18:0	0.5

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

[Ref.: #67770]	Sample type/isolated from	Oil-contaminated soil in the Lenghu oil field
[Ref.: #67770]	Country	China
[Ref.: #67770]	Country ISO 3 Code	CHN
[Ref.: #67770]	Continent	Asia

[Ref.: #68343]	Sample type/isolated from	oil-contaminated soil
[Ref.: #68343]	Geographic location (country and/or sea, region)	Qinghai-Tibet Plateau, Qaidam Basin, Lenghu oil ?eld
[Ref.: #68343]	Enrichment culture	216L agar
[Ref.: #68343]	Enrichment culture duration	1 week
[Ref.: #68343]	Enrichment culture temperature	20 ̊C
* marker position based on {}

[Ref.: #69479]

Global distribution of 16S sequence KX024697 (>99% sequence identity) for Planococcus from Microbeatlas

Aquatic Samples	131
Soil Samples	241
Animal Samples	144
Plant Samples	38
Total Samples	554

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.: #68343]	Planococcus sp. Y42 16S ribosomal RNA gene, partial sequence	KX024697.2	1557	ENA	2213202 tax ID
[Ref.: #67770]	Planococcus sp. Y42 16S ribosomal RNA gene, partial sequence	KX024697	1557	ENA	2213202 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #68343]	Planococcus lenghuensis Y42	GCA_001999905	complete	GenBank	2213202 tax ID

[Ref.: #67770]

GC-content

48.3 mol%

genome sequence analysis

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Planococcus lenghuensis Y42 NCBI: GCA_001999905.1
[Ref.: #69481]	spore-forming	yes	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Planococcus lenghuensis Y42 NCBI: GCA_001999905.1
[Ref.: #69480]	flagellated	no	53.113	no
[Ref.: #69480]	gram-positive	yes	92.627	yes
[Ref.: #69480]	anaerobic	no	99.174	yes
[Ref.: #69480]	aerobic	yes	93.419	yes
[Ref.: #69480]	halophile	yes	57.709	no
[Ref.: #69480]	spore-forming	yes	56.308	no
[Ref.: #69480]	glucose-util	yes	86.424	yes
[Ref.: #69480]	thermophile	no	98.166	no
[Ref.: #69480]	motile	yes	82.141	no
[Ref.: #69480]	glucose-ferment	no	81.743	yes

Availability in culture collections External links

[Ref.: #67770]

Culture collection no.

JCM 32719, CGMCC 1.15921

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Planococcus lenghuensis sp. nov., an oil-degrading bacterium isolated from petroleum-contaminated soil.	Yang R, Zhang B, Wang J, Tai X, Sun H, Zhang G, Zhang W, Chen T, Liu G	Antonie Van Leeuwenhoek	10.1007/s10482-020-01394-6	2020	*

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 )

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

#68343

Ruiqi Yang, Binglin Zhang, Jincheng Wang, Xisheng Tai, Haili Sun, Gaosen Zhang, Wei Zhang, Tuo Chen & Guangxiu Liu: Planococcus lenghuensis sp. nov., an oil-degrading bacterium isolated from petroleum-contaminated soil. Antonie Van Leeuwenhoek 113: 839 - 850 2020 ( DOI 10.1007/s10482-020-01394-6 )

#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 )

* These data were automatically processed and therefore are not curated

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