Cypionkella psychrotolerans (PAMC 27389, JCM 30764, KCTC 42640)

Name: Cypionkella psychrotolerans (PAMC 27389, JCM 30764, KCTC 42640)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 141126

Type strain

Culture col. no. PAMC 27389 JCM 30764 KCTC 42640

NCBI tax ID(s) 1678131

Special Collections JCM KCTC Literature strains

Links

Cypionkella psychrotolerans PAMC 27389 is a facultative aerobe, Gram-negative, ovoid-shaped prokaryote that was isolated from terrestrial soil sample.

Gram-negative ovoid-shaped facultative aerobe genome sequence 16S sequence

Name and taxonomic classification

SI-ID 27892

KCTC 42640,JCM 30764

@ref 20215

Last LPSN update 2025-12-16 10:03:46

Domain Pseudomonadati

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Rhodobacterales

Family Paracoccaceae

Genus Cypionkella

Species Cypionkella psychrotolerans

Full scientific name Cypionkella psychrotolerans (Lee et al. 2016) Hördt et al. 2020

Synonyms (1)

Pseudorhodobacter psychrotolerans

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
44035	negative	1.0-2.0 µm	0.5-1.0 µm	ovoid-shaped
125439	negative				93.6
125438	negative				99

Colony morphology

@ref	Colony size	Colony color	Incubation period	Medium used
44035	1.0-2.0 mm	cream	7 days	modified TYS agar

Culture and growth conditions

Culture medium

@ref	Name	Growth
44035	modified TYS
44035	modified TYS agar
44035	Reasoner's 2A agar (R2A)

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
44035	positive	growth	0-37
44035	positive	optimum	15-20	psychrophilic
67770	positive	growth	15	psychrophilic
67771	positive	growth	15	psychrophilic

Culture pH

@ref	Ability	Type	PH	PH range
44035	positive	optimum	6.5-7.0
44035	positive	growth	5.5-9.0	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
44035	facultative aerobe
67771	aerobe
125439	obligate aerobe	99.4

Halophily

@ref	Salt	Growth	Tested relation	Concentration
44035	Marine salts	positive	growth	0.5-3.0 %(w/v)
44035	Marine salts	positive	optimum	0.5 %(w/v)

Observation

67770

Observationquinones: Q-10

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
44035	16808 ChEBI	2-dehydro-D-gluconate	-	builds acid from
44035	355715 ChEBI	4-nitrophenyl beta-D-galactopyranoside	+	assimilation
44035	58143 ChEBI	5-dehydro-D-gluconate	-	builds acid from
44035	17128 ChEBI	adipate	-	assimilation
44035	27613 ChEBI	amygdalin	-	builds acid from
44035	18305 ChEBI	arbutin	-	builds acid from
44035	17057 ChEBI	cellobiose	-	builds acid from
44035	16947 ChEBI	citrate	-	assimilation
44035	17108 ChEBI	D-arabinose	+/-	builds acid from
44035	18333 ChEBI	D-arabitol	-	builds acid from
44035	15824 ChEBI	D-fructose	+/-	builds acid from
44035	28847 ChEBI	D-fucose	+	builds acid from
44035	12936 ChEBI	D-galactose	-	builds acid from
44035	17634 ChEBI	D-glucose	-	assimilation
44035	17634 ChEBI	D-glucose	-	builds acid from
44035	16899 ChEBI	D-mannitol	-	builds acid from
44035	16899 ChEBI	D-mannitol	+	assimilation
44035	16024 ChEBI	D-mannose	-	builds acid from
44035	16024 ChEBI	D-mannose	+	assimilation
44035	16988 ChEBI	D-ribose	+	builds acid from
44035	17924 ChEBI	D-sorbitol	-	builds acid from
44035	17317 ChEBI	D-sorbose	-	builds acid from
44035	16443 ChEBI	D-tagatose	-	builds acid from
44035	65327 ChEBI	D-xylose	+/-	builds acid from
44035	27689 ChEBI	decanoate	-	assimilation
44035	17113 ChEBI	erythritol	+/-	builds acid from
44035	4853 ChEBI	esculin	+	builds acid from
44035	4853 ChEBI	esculin	+	hydrolysis
44035	31605 ChEBI	ferric citrate	+	builds acid from
44035	16813 ChEBI	galactitol	-	builds acid from
44035	5291 ChEBI	gelatin	+	hydrolysis
44035	28066 ChEBI	gentiobiose	-	builds acid from
44035	17234 ChEBI	glucose	+	fermentation
44035	17754 ChEBI	glycerol	-	builds acid from
44035	28087 ChEBI	glycogen	-	builds acid from
44035	17368 ChEBI	hypoxanthine	+	hydrolysis
44035	15443 ChEBI	inulin	-	builds acid from
44035	30849 ChEBI	L-arabinose	+	assimilation
44035	30849 ChEBI	L-arabinose	+/-	builds acid from
44035	18403 ChEBI	L-arabitol	-	builds acid from
44035	16467 ChEBI	L-arginine	-	assimilation
44035	18287 ChEBI	L-fucose	+	builds acid from
44035	62345 ChEBI	L-rhamnose	+	builds acid from
44035	65328 ChEBI	L-xylose	-	builds acid from
44035	17716 ChEBI	lactose	-	builds acid from
44035	25115 ChEBI	malate	-	assimilation
44035	17306 ChEBI	maltose	-	builds acid from
44035	17306 ChEBI	maltose	+	assimilation
44035	6731 ChEBI	melezitose	-	builds acid from
44035	28053 ChEBI	melibiose	-	builds acid from
44035	320061 ChEBI	methyl alpha-D-glucopyranoside	-	builds acid from
44035	43943 ChEBI	methyl alpha-D-mannoside	-	builds acid from
44035	74863 ChEBI	methyl beta-D-xylopyranoside	-	builds acid from
44035	17268 ChEBI	myo-inositol	-	builds acid from
44035	506227 ChEBI	N-acetylglucosamine	-	builds acid from
44035	506227 ChEBI	N-acetylglucosamine	+	assimilation
44035	17632 ChEBI	nitrate	-	reduction
44035	18401 ChEBI	phenylacetate	-	assimilation
44035	32032 ChEBI	potassium gluconate	-	assimilation
44035	32032 ChEBI	potassium gluconate	-	builds acid from
44035	16634 ChEBI	raffinose	-	builds acid from
44035	15963 ChEBI	ribitol	-	builds acid from
44035	17814 ChEBI	salicin	+	builds acid from
44035		skimmed milk	-	hydrolysis
44035	28017 ChEBI	starch	-	builds acid from
44035	28017 ChEBI	starch	-	hydrolysis
44035	17992 ChEBI	sucrose	-	builds acid from
44035	27082 ChEBI	trehalose	-	builds acid from
44035	32528 ChEBI	turanose	-	builds acid from
44035	53424 ChEBI	tween 20	+	hydrolysis
44035	53423 ChEBI	tween 40	-	hydrolysis
44035	53425 ChEBI	tween 60	+/-	hydrolysis
44035	53426 ChEBI	tween 80	-	hydrolysis
44035	16199 ChEBI	urea	-	assimilation
44035	15318 ChEBI	xanthine	-	hydrolysis
44035	17151 ChEBI	xylitol	+/-	builds acid from

Metabolite production

@ref	Chebi-ID	Metabolite	Production
44035	30033 ChEBI	bacteriochlorophyll alpha
44035	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
44035	acid phosphatase	+	3.1.3.2
44035	alkaline phosphatase	+	3.1.3.1
44035	alpha-chymotrypsin	+	3.4.21.1
44035	alpha-fucosidase	-	3.2.1.51
44035	alpha-galactosidase	-	3.2.1.22
44035	alpha-glucosidase	+	3.2.1.20
44035	alpha-mannosidase	-	3.2.1.24
44035	beta-galactosidase	+	3.2.1.23
44035	beta-glucosidase	-	3.2.1.21
44035	beta-glucuronidase	+	3.2.1.31
44035	catalase	+	1.11.1.6
44035	cystine arylamidase	+	3.4.11.3
44035	cytochrome oxidase	+	1.9.3.1
44035	esterase (C 4)	+
44035	esterase Lipase (C 8)	+
44035	leucine arylamidase	+	3.4.11.1
44035	lipase (C 14)	-
44035	N-acetyl-beta-glucosaminidase	-	3.2.1.52
44035	trypsin	+	3.4.21.4
44035	valine arylamidase	+

Fatty acid profile

Metadata FA analysis

@ref

44035

Fatty acid	Percentage
C18:1ω7c / C18:1ω6c	84.7
11-methyl C18:1ω7c	5.3
C18:0 3OH	3.1
C18:0	1.8
C17:1 anteiso ω9c	1.7
C19:010-methyl	1.2
C16:0	0.8

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Climate	#Cold	#Polar
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Sampling date	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude	Enrichment culture	Enrichment culture duration	Enrichment culture temperature	Isolation procedure
44035	terrestrial soil sample	2011-02-12	King George Island	Antarctica	ATA	Australia and Oceania	-62.2062	-58.79 -62.2062/-58.79	R2A agar (BD Difco)	11 days	15	serially diluted (100µl) in 0.85 %(w/v) NaCl
67770	Terrestrial soil collected on King George Island			Antarctica	ATA	Antarctica
67771	From terrestrial soil			Republic of Korea	KOR	Asia

Taxonmaps

69479

Global distribution of 16S sequence KT163920 (>99% sequence identity) for Cypionkella from Microbeatlas

Aquatic Samples	2894
Soil Samples	192
Animal Samples	115
Plant Samples	132
Total Samples	3333

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	IMG accession	NCBI tax ID	Score
67770	ASM129453v1 assembly for Cypionkella psychrotolerans PAMC 27389	contig	GCA_001294535	2788500356	1678131	60.12

16S sequences

@ref	Description	Accession	Database
44035	Cypionkella psychrotolerans strain PAMC 27389 16S ribosomal RNA gene, partial sequence	KT163920

GC content

@ref	GC-content (mol%)	Method
44035	60.1	genome sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Cypionkella psychrotolerans PAMC 27389
NCBI: GCA_001294535

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	87.60	no
125439	motility	BacteriaNetⓘ	no	80.80	no
125439	gram_stain	BacteriaNetⓘ	negative	93.60	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.40	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Cypionkella psychrotolerans PAMC 27389
NCBI: GCA_001294535.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	99.00	no
125438	anaerobic	anaerobicⓘ	no	93.53	yes
125438	aerobic	aerobicⓘ	yes	83.20	no
125438	spore-forming	spore-formingⓘ	no	89.22	no
125438	thermophilic	thermophileⓘ	no	98.48	yes
125438	flagellated	motile2+ⓘ	no	71.20	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
	Phosphate (Bio)mineralization Remediation of ⁹⁰Sr-Contaminated Groundwaters.	Robinson C, Shaw S, Lloyd JR, Graham J, Morris K.	ACS ES T Water	10.1021/acsestwater.3c00159	2023
Genetics	Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria.	Hordt A, Lopez MG, Meier-Kolthoff JP, Schleuning M, Weinhold LM, Tindall BJ, Gronow S, Kyrpides NC, Woyke T, Goker M.	Front Microbiol	10.3389/fmicb.2020.00468	2020
Phylogeny	Fertoeibacter niger gen. nov., sp. nov. a novel alkaliphilic bacterium of the family Rhodobacteraceae.	Szuroczki S, Abbaszade G, Buni D, Boka K, Schumann P, Neumann-Schaal M, Vajna B, Toth E	Int J Syst Evol Microbiol	10.1099/ijsem.0.004762	2021

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 )
#44035	Y. M. Lee, J. Y. Yang, K. Baek, S. J. Han, S. C. Shin, C. Y. Hwang, S. G. Hong and H. K. Lee: Pseudorhodobacter psychrotolerans sp. nov., a psychrotolerant bacterium isolated from terrestrial soil, and emended description of the genus Pseudorhodobacter. IJSEM 66: 1068 - 1073 2016 ( DOI 10.1099/ijsem.0.000841 , PubMed 26653106 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#67771	Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;
#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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Cypionkella psychrotolerans (PAMC 27389, JCM 30764, KCTC 42640)

Name and taxonomic classification