Planococcus halocryophilus (DSM 24743, JCM 17719, Or1)

Name: Planococcus halocryophilus (DSM 24743, JCM 17719, Or1)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 11967

Type strain

Strain Designation Or1

Culture col. no. DSM 24743 JCM 17719 Or1

NCBI tax ID(s) 1215089

Special Collections DSMZ JCM Literature strains

History <- N. Mykytczuk, McGill Univ., Quebec, Canada; Or1 <- R.C. Wilhelm N. C. S. Mykytczuk Or1 <-- R. C. Wilhelm.

Links

Planococcus halocryophilus Or1 is an aerobe, psychrophilic, Gram-positive prokaryote that was isolated from permafrost active-layer soil.

Gram-positive motile coccus-shaped aerobe psychrophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 406361

JCM 17719,DSM 24743

@ref 20215

Last LPSN update 2026-02-09 11:20:43

Domain Bacteria

Phylum Bacillota

Class Bacilli

Order Caryophanales

Family Caryophanaceae

Genus Planococcus

Species Planococcus halocryophilus

Full scientific name Planococcus halocryophilus Mykytczuk et al. 2012

Morphology

Cell morphology

@ref	Gram stain	Cell width	Cell shape	Motility
30425	positive	1 µm	coccus-shaped

Colony morphology

17749

Incubation period2-3 days

Pigmentation

30425

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
17749	TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)		Medium recipe at MediaDive	Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
17749	positive	growth	20	psychrophilic
26761	positive	growth	-10-37	psychrophilic
30425	positive	optimum	25	mesophilic
67770	positive	growth	25	mesophilic

Culture pH

@ref	Ability	Type	PH	PH range
30425	positive	optimum	7.5
30425	positive	growth	06-11	alkaliphile

Physiology and metabolism

Oxygen tolerance

30425

Oxygen toleranceaerobe

Spore formation

30425

Spore formationno

Halophily

@ref	Salt	Growth	Tested relation	Concentration
30425	NaCl	positive	growth	0-19 %

Murein

@ref	Murein short key	Type
17749	A11.33	A4alpha L-Lys-D-Glu

Observation

67770

Observationquinones: MK-7, MK-8, MK-6

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
30425	30089 ChEBI	acetate	+	carbon source
30425	16449 ChEBI	alanine	+	carbon source
30425	29016 ChEBI	arginine	+	carbon source
30425	17057 ChEBI	cellobiose	+	carbon source
30425	23652 ChEBI	dextrin	+	carbon source
30425	28757 ChEBI	fructose	+	carbon source
30425	28260 ChEBI	galactose	+	carbon source
30425	5291 ChEBI	gelatin	+	carbon source
30425	24265 ChEBI	gluconate	+	carbon source
30425	5417 ChEBI	glucosamine	+	carbon source
30425	17234 ChEBI	glucose	+	carbon source
30425	29987 ChEBI	glutamate	+	carbon source
30425	17754 ChEBI	glycerol	+	carbon source
30425	24996 ChEBI	lactate	+	carbon source
30425	17716 ChEBI	lactose	+	carbon source
30425	17306 ChEBI	maltose	+	carbon source
30425	29864 ChEBI	mannitol	+	carbon source
30425	37684 ChEBI	mannose	+	carbon source
30425	26546 ChEBI	rhamnose	+	carbon source
30425	33942 ChEBI	ribose	+	carbon source
30425	17822 ChEBI	serine	+	carbon source
30425	17992 ChEBI	sucrose	+	carbon source
30425	27082 ChEBI	trehalose	+	carbon source

Metabolite production

@ref	Chebi-ID	Metabolite	Production
30425	16136 ChEBI	hydrogen sulfide
30425	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
30425	35581 ChEBI	indole	+

Enzymes

@ref	Value	Activity
30425	gelatinase	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Permafrost
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
17749	permafrost active-layer soil	Ellesmere Island, Eureka	Canada	CAN	North America
67770	Permafrost active-layer soil at Eureka	Ellesmere Island, in the Canadian high Arctic	Canada	CAN	North America

Taxonmaps

69479

Global distribution of 16S sequence JF742665 (>99% sequence identity) for Planococcus from Microbeatlas

Aquatic Samples	353
Soil Samples	566
Animal Samples	550
Plant Samples	97
Total Samples	1566

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
17749	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	Planococcus halocryophilus strain DSM 24743	complete		1215089.4		1215089	99.6
66792	Planococcus halocryophilus Or1	complete			2700988612	1005941	99.16
66792	ASM168758v2 assembly for Planococcus halocryophilus DSM 24743	complete	GCA_001687585	1215089.14	2773857975	1215089	91.18
67770	PlanoHalo1.0 assembly for Planococcus halocryophilus Or1	contig	GCA_000342445	1005941.3	2537562134	1005941	52.72

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
17749	Planococcus halocryophilus Or1 16S ribosomal RNA gene, complete sequence	JF742665	1555		1005941

GC content

@ref	GC-content (mol%)	Method
17749	40.5	sequence analysis
30425	40.5
67770	40.5	thermal denaturation, midpoint method (Tm)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Planococcus halocryophilus strain DSM 24743
PATRIC: 1215089.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	86.00	no
125439	gram_stain	BacteriaNetⓘ	variable	79.10	no
125439	motility	BacteriaNetⓘ	yes	82.50	no
125439	spore_formation	BacteriaNetⓘ	yes	86.90	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Planococcus halocryophilus DSM 24743
NCBI: GCA_001687585.2

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	76.89	no
125438	anaerobic	anaerobicⓘ	no	97.73	yes
125438	aerobic	aerobicⓘ	yes	84.74	yes
125438	spore-forming	spore-formingⓘ	yes	55.59	yes
125438	thermophilic	thermophileⓘ	no	92.64	yes
125438	flagellated	motile2+ⓘ	yes	53.79	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Machine Learning Algorithms Applied to Identify Microbial Species by Their Motility.	Riekeles M, Schirmack J, Schulze-Makuch D.	Life (Basel)	10.3390/life11010044	2021
	Bacterial Diversity of Marine Biofilm Communities in Terra Nova Bay (Antarctica) by Culture-Dependent and -Independent Approaches.	Bisaccia M, Binda E, Caruso G, Azzaro M, Dell' Acqua O, Di Cesare A, Eckert EM, Marinelli F.	Environ Microbiol	10.1111/1462-2920.70045	2025
	Cold adaptation of tRNA nucleotidyltransferases: A tradeoff in activity, stability and fidelity.	Ernst FGM, Erber L, Sammler J, Juhling F, Betat H, Morl M.	RNA Biol	10.1080/15476286.2017.1391445	2018
	Bacterial growth at -15 °C; molecular insights from the permafrost bacterium Planococcus halocryophilus Or1.	Mykytczuk NC, Foote SJ, Omelon CR, Southam G, Greer CW, Whyte LG.	ISME J	10.1038/ismej.2013.8	2013
	Biological Contamination Prevention for Outer Solar System Moons of Astrobiological Interest: What Do We Need to Know?	Rettberg P, Antunes A, Brucato J, Cabezas P, Collins G, Haddaji A, Kminek G, Leuko S, McKenna-Lawlor S, Moissl-Eichinger C, Fellous JL, Olsson-Francis K, Pearce D, Rabbow E, Royle S, Saunders M, Sephton M, Spry A, Walter N, Wimmer Schweingruber R, Treuet JC.	Astrobiology	10.1089/ast.2018.1996	2019
Phylogeny	Planococcus ruber sp. nov., isolated from a polluted farmland soil sample.	Wang X, Wang Z, Zhao X, Huang X, Zhou Y, Li WJ	Int J Syst Evol Microbiol	10.1099/ijsem.0.001960	2017
Phylogeny	Planococcus faecalis sp. nov., a carotenoid-producing species isolated from stools of Antarctic penguins.	Kim JH, Kang HJ, Yu BJ, Kim SC, Lee PC	Int J Syst Evol Microbiol	10.1099/ijsem.0.000423	2015
Phylogeny	Planococcus halocryophilus sp. nov., an extreme sub-zero species from high Arctic permafrost.	Mykytczuk NCS, Wilhelm RC, Whyte LG	Int J Syst Evol Microbiol	10.1099/ijs.0.035782-0	2011

References

#17749	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 24743
#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 )
#26761	IJSEM 1937 2012 ( DOI 10.1099/ijs.0.035782-0 , PubMed 22003043 )
#30425	Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #26761
#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;
#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 halocryophilus (DSM 24743, JCM 17719, Or1)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Murein

Observation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_001687585

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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