Planococcus lenghuensis (CGMCC 1.15921, JCM 32719, Y42)

Name: Planococcus lenghuensis (CGMCC 1.15921, JCM 32719, Y42)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 164341

Type strain

Strain Designation Y42

Culture col. no. CGMCC 1.15921 JCM 32719 Y42

NCBI tax ID(s) 2213202

Special Collections JCM Literature strains

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

Links

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

Gram-positive colony-forming aerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 133773

JCM 32719

@ref 20215

Last LPSN update 2026-02-09 11:39:49

Domain Bacteria

Phylum Bacillota

Class Bacilli

Order Caryophanales

Family Caryophanaceae

Genus Planococcus

Species Planococcus lenghuensis

Full scientific name Planococcus lenghuensis Yang et al. 2024

Morphology

Cell morphology

@ref	Gram stain	Cell length	Motility	Confidence
68343	positive	1 µm
125439				90.2

Colony morphology

@ref	Colony size	Colony color	Colony shape	Incubation period	Medium used
68343	0.7-1 mm	orange	circular	4 days	LB (Luria-Bertani) agar

Culture and growth conditions

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
67770	positive	growth	25	mesophilic
68343	positive	growth	10-35
68343	positive	optimum	25	mesophilic

Culture pH

@ref	Ability	Type	PH	PH range
68343	positive	optimum	7.5
68343	positive	growth	7-9	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
68343	aerobe
125439	aerobe	92.1

Spore formation

@ref	Spore formation	Confidence
125439		94.9

Halophily

@ref	Salt	Growth	Tested relation	Concentration
68343	NaCl	positive	growth	0-8 %(w/v)
68343	NaCl	positive	optimum	1-3 %(w/v)

Observation

@ref	Observation
67770	quinones: MK-7
68343	degrade petroleum

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68343	17521 ChEBI	(-)-quinic acid	-	assimilation
68343	16810 ChEBI	2-oxoglutarate	-	assimilation
68343	73918 ChEBI	3-O-methyl-D-glucose	-	assimilation
68343	16411 ChEBI	acetic acid	+	assimilation
68343	13705 ChEBI	acetoacetate	+	assimilation
68343	36219 ChEBI	alpha-lactose	-	assimilation
68343	17057 ChEBI	cellobiose	-	assimilation
68343	62968 ChEBI	cellulose	-	hydrolysis
68343	16947 ChEBI	citrate	-	assimilation
68343	17108 ChEBI	D-arabinose	-	assimilation
68343	18333 ChEBI	D-arabitol	-	assimilation
68343	29990 ChEBI	D-aspartate	+	assimilation
68343	15824 ChEBI	D-fructose	+	assimilation
68343	78697 ChEBI	D-fructose 6-phosphate	+	assimilation
68343	28847 ChEBI	D-fucose	-	assimilation
68343	15895 ChEBI	D-galactonic acid lactone	-	assimilation
68343	12936 ChEBI	D-galactose	-	assimilation
68343	18024 ChEBI	D-galacturonic acid	+	assimilation
68343	8391 ChEBI	D-gluconate	+	assimilation
68343	17634 ChEBI	D-glucose	+	assimilation
68343	14314 ChEBI	D-glucose 6-phosphate	-	assimilation
68343	15748 ChEBI	D-glucuronate	+	assimilation
68343	15588 ChEBI	D-malate	-	assimilation
68343	16899 ChEBI	D-mannitol	+	assimilation
68343	16024 ChEBI	D-mannose	-	assimilation
68343	33801 ChEBI	D-saccharate	-	assimilation
68343	17814 ChEBI	D-salicin	-	assimilation
68343	16523 ChEBI	D-serine	-	assimilation
68343	17924 ChEBI	D-sorbitol	-	assimilation
68343	23652 ChEBI	dextrin	+	assimilation
68343	15740 ChEBI	formate	-	assimilation
68343	35390 ChEBI	galactarate	-	assimilation
68343	5291 ChEBI	gelatin	+	hydrolysis
68343	28066 ChEBI	gentiobiose	-	assimilation
68343	17234 ChEBI	glucose	+	fermentation
68343	32323 ChEBI	glucuronamide	+	assimilation
68343	17754 ChEBI	glycerol	-	assimilation
68343	17596 ChEBI	inosine	-	assimilation
68343	16977 ChEBI	L-alanine	-	assimilation
68343	16467 ChEBI	L-arginine	-	assimilation
68343	29991 ChEBI	L-aspartate	-	assimilation
68343	18287 ChEBI	L-fucose	-	assimilation
68343	29985 ChEBI	L-glutamate	-	assimilation
68343	15971 ChEBI	L-histidine	-	assimilation
68343		L-lactate	-	assimilation
68343	15589 ChEBI	L-malate	+	assimilation
68343	18183 ChEBI	L-pyroglutamic acid	-	assimilation
68343	62345 ChEBI	L-rhamnose	-	assimilation
68343	17115 ChEBI	L-serine	-	assimilation
68343	17306 ChEBI	maltose	-	assimilation
68343	28053 ChEBI	melibiose	-	assimilation
68343	17268 ChEBI	myo-inositol	-	assimilation
68343	59640 ChEBI	N-acetylglucosamine	-	assimilation
68343	17632 ChEBI	nitrate	+	reduction
68343	17309 ChEBI	pectin	-	assimilation
68343	16634 ChEBI	raffinose	-	assimilation
68343	132106 ChEBI	sodium propionate	-	assimilation
68343	17164 ChEBI	stachyose	-	assimilation
68343	28017 ChEBI	starch	-	hydrolysis
68343	17992 ChEBI	sucrose	+	assimilation
68343	27082 ChEBI	trehalose	-	assimilation
68343	32528 ChEBI	turanose	-	assimilation
68343	53423 ChEBI	tween 40	+	hydrolysis
68343	53426 ChEBI	tween 80	-	hydrolysis

Antibiotic resistance

@ref	ChEBI	Metabolite	Is resistant
68343	48607	lithium chloride
68343	75193	tetrazolium violet

Metabolite production

@ref	Chebi-ID	Metabolite
68343	15688 ChEBI	acetoin
68343	16136 ChEBI	hydrogen sulfide
68343	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Methylred-test
68343	15688 ChEBI	acetoin	-
68343	17234 ChEBI	glucose		+

Enzymes

@ref	Value	Activity	Ec
68343	alkaline phosphatase	+	3.1.3.1
68343	alpha-chymotrypsin	+	3.4.21.1
68343	catalase	+	1.11.1.6
68343	cystine arylamidase	+	3.4.11.3
68343	cytochrome oxidase	-	1.9.3.1
68343	esterase (C 4)	+
68343	esterase Lipase (C 8)	+
68343	leucine arylamidase	+	3.4.11.1
68343	naphthol-AS-BI-phosphohydrolase	+
68343	valine arylamidase	+

Fatty acid profile

Metadata FA analysis

@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

Isolation, sampling and environmental information

Isolation

@ref	Sample type	Geographic location	Enrichment culture	Enrichment culture duration	Enrichment culture temperature	Country	Country ISO 3 Code	Continent
67770	Oil-contaminated soil in the Lenghu oil field					China	CHN	Asia
68343	oil-contaminated soil	Qinghai-Tibet Plateau, Qaidam Basin, Lenghu oil ?eld	216L agar	1 week	20

Taxonmaps

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

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	IMG accession	NCBI tax ID	Score
68343	ASM199990v1 assembly for Planococcus lenghuensis Y42	complete	GCA_001999905	2724679746	2213202	76.61

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
67770	Planococcus lenghuensis 16S ribosomal RNA gene, partial sequence	KX024697	1557		2213202
68343	Planococcus lenghuensis 16S ribosomal RNA gene, partial sequence	KX024697.2	1557		2213202

GC content

@ref	GC-content (mol%)	Method
67770	48.3	genome sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Planococcus lenghuensis Y42
NCBI: GCA_001999905

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	94.90	no
125439	motility	BacteriaNetⓘ	yes	90.20	no
125439	gram_stain	BacteriaNetⓘ	variable	86.60	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	92.10	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Planococcus lenghuensis Y42
NCBI: GCA_001999905.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	75.42	yes
125438	anaerobic	anaerobicⓘ	no	94.96	no
125438	aerobic	aerobicⓘ	yes	82.85	yes
125438	spore-forming	spore-formingⓘ	yes	56.59	no
125438	thermophilic	thermophileⓘ	no	87.44	no
125438	flagellated	motile2+ⓘ	yes	54.80	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Validation List no. 216. Valid publication of new names and new combinations effectively published outside the IJSEM.	Oren A, Goker M.	Int J Syst Evol Microbiol	10.1099/ijsem.0.006229	2024
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 .
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Planococcus lenghuensis (CGMCC 1.15921, JCM 32719, Y42)

Name and taxonomic classification