Name: Cypionkella psychrotolerans PAMC 27389
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 141126

Type strain:

Species: Cypionkella psychrotolerans

Culture col. no.: PAMC 27389, JCM 30764, KCTC 42640

Strain history: <- Yung Mi Lee, KOPRI

NCBI tax ID(s): 1678131 (species)

Section

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

Gram-negative
ovoid-shaped
facultative 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	*Pseudomonadota*
	Class	*Alphaproteobacteria*
	Order	*Rhodobacterales*
	Family	*Paracoccaceae*
	Genus	*Cypionkella*
	Species	**Cypionkella psychrotolerans**
	Full Scientific Name (LPSN)	Cypionkella psychrotolerans (Lee et al. 2016) Hördt et al. 2020

Synonym

Pseudorhodobacter psychrotolerans

Information on morphological and physiological properties Morphology

[Ref.: #44035]	Gram stain	negative

[Ref.: #44035]	Cell length	1.0-2.0 µm

[Ref.: #44035]	Cell width	0.5-1.0 µm

[Ref.: #44035]	Cell shape	ovoid-shaped

[Ref.: #44035]	Motility	no

[Ref.: #44035]	Colony size	1.0-2.0 mm
[Ref.: #44035]	Colony color	cream
[Ref.: #44035]	Incubation period	7 days
[Ref.: #44035]	Cultivation medium used	modified TYS agar

Information on culture and growth conditions Culture and growth conditions

[Ref.: #44035]

Culture medium

modified TYS

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Culture medium growth

[Ref.: #44035]

Culture medium

modified TYS agar

[Ref.: #44035]

Culture medium growth

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Culture medium

Reasoner's 2A agar (R2A)

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Culture medium growth

		Temperature
[Ref.: #44035]	growth	0-37 °C
[Ref.: #44035]	optimum	15-20 °C
[Ref.: #67770]	growth	15 °C
[Ref.: #67771]	growth	15 °C

[Ref.: #44035]	Temperature range	psychrophilic
[Ref.: #67770]	Temperature range	psychrophilic
[Ref.: #67771]	Temperature range	psychrophilic

	pH	Kind of pH		pH
[Ref.: #44035]			optimum	6.5-7.0
[Ref.: #44035]			growth	5.5-9.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #44035]	Oxygen tolerance	facultative aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #44035]		Marine salts		growth	0.5-3.0	%(w/v)
[Ref.: #44035]		Marine salts		optimum	0.5	%(w/v)

[Ref.: #67770]

Observation

quinones: Q-10

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #44035]	2-dehydro-D-gluconate ChEBI	-	builds acid from
[Ref.: #44035]	4-nitrophenyl beta-D-galactopyranoside ChEBI	+	assimilation
[Ref.: #44035]	5-dehydro-D-gluconate ChEBI	-	builds acid from
[Ref.: #44035]	adipate ChEBI	-	assimilation
[Ref.: #44035]	amygdalin ChEBI	-	builds acid from
[Ref.: #44035]	arbutin ChEBI	-	builds acid from
[Ref.: #44035]	cellobiose ChEBI	-	builds acid from
[Ref.: #44035]	citrate ChEBI	-	assimilation
[Ref.: #44035]	D-arabinose ChEBI	+/-	builds acid from
[Ref.: #44035]	D-arabitol ChEBI	-	builds acid from
[Ref.: #44035]	D-fructose ChEBI	+/-	builds acid from
[Ref.: #44035]	D-fucose ChEBI	+	builds acid from
[Ref.: #44035]	D-galactose ChEBI	-	builds acid from
[Ref.: #44035]	D-glucose ChEBI	-	assimilation
[Ref.: #44035]	D-glucose ChEBI	-	builds acid from
[Ref.: #44035]	D-mannitol ChEBI	-	builds acid from
[Ref.: #44035]	D-mannitol ChEBI	+	assimilation
[Ref.: #44035]	D-mannose ChEBI	-	builds acid from
[Ref.: #44035]	D-mannose ChEBI	+	assimilation
[Ref.: #44035]	D-ribose ChEBI	+	builds acid from
[Ref.: #44035]	D-sorbitol ChEBI	-	builds acid from
[Ref.: #44035]	D-sorbose ChEBI	-	builds acid from
[Ref.: #44035]	D-tagatose ChEBI	-	builds acid from
[Ref.: #44035]	D-xylose ChEBI	+/-	builds acid from
[Ref.: #44035]	decanoate ChEBI	-	assimilation
[Ref.: #44035]	erythritol ChEBI	+/-	builds acid from
[Ref.: #44035]	esculin ChEBI	+	builds acid from
[Ref.: #44035]	esculin ChEBI	+	hydrolysis
[Ref.: #44035]	ferric citrate ChEBI	+	builds acid from
[Ref.: #44035]	galactitol ChEBI	-	builds acid from
[Ref.: #44035]	gelatin ChEBI	+	hydrolysis
[Ref.: #44035]	gentiobiose ChEBI	-	builds acid from
[Ref.: #44035]	glucose ChEBI	+	fermentation
[Ref.: #44035]	glycerol ChEBI	-	builds acid from
[Ref.: #44035]	glycogen ChEBI	-	builds acid from
[Ref.: #44035]	hypoxanthine ChEBI	+	hydrolysis
[Ref.: #44035]	inulin ChEBI	-	builds acid from
[Ref.: #44035]	L-arabinose ChEBI	+	assimilation
[Ref.: #44035]	L-arabinose ChEBI	+/-	builds acid from
[Ref.: #44035]	L-arabitol ChEBI	-	builds acid from
[Ref.: #44035]	L-arginine ChEBI	-	assimilation
[Ref.: #44035]	L-fucose ChEBI	+	builds acid from
[Ref.: #44035]	L-rhamnose ChEBI	+	builds acid from
[Ref.: #44035]	L-xylose ChEBI	-	builds acid from
[Ref.: #44035]	lactose ChEBI	-	builds acid from
[Ref.: #44035]	malate ChEBI	-	assimilation
[Ref.: #44035]	maltose ChEBI	-	builds acid from
[Ref.: #44035]	maltose ChEBI	+	assimilation
[Ref.: #44035]	melezitose ChEBI	-	builds acid from
[Ref.: #44035]	melibiose ChEBI	-	builds acid from
[Ref.: #44035]	methyl alpha-D-glucopyranoside ChEBI	-	builds acid from
[Ref.: #44035]	methyl alpha-D-mannoside ChEBI	-	builds acid from
[Ref.: #44035]	methyl beta-D-xylopyranoside ChEBI	-	builds acid from
[Ref.: #44035]	myo-inositol ChEBI	-	builds acid from
[Ref.: #44035]	N-acetylglucosamine ChEBI	-	builds acid from
[Ref.: #44035]	N-acetylglucosamine ChEBI	+	assimilation
[Ref.: #44035]	nitrate ChEBI	-	reduction
[Ref.: #44035]	phenylacetate ChEBI	-	assimilation
[Ref.: #44035]	potassium gluconate ChEBI	-	assimilation
[Ref.: #44035]	potassium gluconate ChEBI	-	builds acid from
[Ref.: #44035]	raffinose ChEBI	-	builds acid from
[Ref.: #44035]	ribitol ChEBI	-	builds acid from
[Ref.: #44035]	salicin ChEBI	+	builds acid from
[Ref.: #44035]	skimmed milk	-	hydrolysis
[Ref.: #44035]	starch ChEBI	-	builds acid from
[Ref.: #44035]	starch ChEBI	-	hydrolysis
[Ref.: #44035]	sucrose ChEBI	-	builds acid from
[Ref.: #44035]	trehalose ChEBI	-	builds acid from
[Ref.: #44035]	turanose ChEBI	-	builds acid from
[Ref.: #44035]	tween 20 ChEBI	+	hydrolysis
[Ref.: #44035]	tween 40 ChEBI	-	hydrolysis
[Ref.: #44035]	tween 60 ChEBI	+/-	hydrolysis
[Ref.: #44035]	tween 80 ChEBI	-	hydrolysis
[Ref.: #44035]	urea ChEBI	-	assimilation
[Ref.: #44035]	xanthine ChEBI	-	hydrolysis
[Ref.: #44035]	xylitol ChEBI	+/-	builds acid from
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #44035]		bacteriochlorophyll alpha ChEBI	no
[Ref.: #44035]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #44035]	acid phosphatase	+	3.1.3.2
[Ref.: #44035]	alkaline phosphatase	+	3.1.3.1
[Ref.: #44035]	alpha-chymotrypsin	+	3.4.21.1
[Ref.: #44035]	alpha-fucosidase	-	3.2.1.51
[Ref.: #44035]	alpha-galactosidase	-	3.2.1.22
[Ref.: #44035]	alpha-glucosidase	+	3.2.1.20
[Ref.: #44035]	alpha-mannosidase	-	3.2.1.24
[Ref.: #44035]	beta-galactosidase	+	3.2.1.23
[Ref.: #44035]	beta-glucosidase	-	3.2.1.21
[Ref.: #44035]	beta-glucuronidase	+	3.2.1.31
[Ref.: #44035]	catalase	+	1.11.1.6
[Ref.: #44035]	cystine arylamidase	+	3.4.11.3
[Ref.: #44035]	cytochrome oxidase	+	1.9.3.1
[Ref.: #44035]	esterase (C 4)	+
[Ref.: #44035]	esterase Lipase (C 8)	+
[Ref.: #44035]	leucine arylamidase	+	3.4.11.1
[Ref.: #44035]	lipase (C 14)	-
[Ref.: #44035]	N-acetyl-beta-glucosaminidase	-	3.2.1.52
[Ref.: #44035]	trypsin	+	3.4.21.4
[Ref.: #44035]	valine arylamidase	+
	Only first 10 entries are displayed. Click here to see all.

Fatty acid profile

Metadata FA analysis

Reference

[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

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

[Ref.: #44035]	Sample type/isolated from	terrestrial soil sample
[Ref.: #44035]	Sampling date	2011-02-12
[Ref.: #44035]	Geographic location (country and/or sea, region)	King George Island
[Ref.: #44035]	Country	Antarctica
[Ref.: #44035]	Country ISO 3 Code	ATA
[Ref.: #44035]	Continent	Australia and Oceania
[Ref.: #44035]	Geographic location	-62.2062°/-58.7900°
[Ref.: #44035]	Enrichment culture	R2A agar (BD Difco)
[Ref.: #44035]	Enrichment culture duration	11 days
[Ref.: #44035]	Enrichment culture temperature	15 ̊C
[Ref.: #44035]	Isolation/enrichment procedure	serially diluted (100µl) in 0.85 %(w/v) NaCl

[Ref.: #67770]	Sample type/isolated from	Terrestrial soil collected on King George Island
[Ref.: #67770]	Country	Antarctica
[Ref.: #67770]	Country ISO 3 Code	ATA
[Ref.: #67770]	Continent	Antarctica

[Ref.: #67771]	Sample type/isolated from	From terrestrial soil
[Ref.: #67771]	Country	Republic of Korea
[Ref.: #67771]	Country ISO 3 Code	KOR
[Ref.: #67771]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Climate	#Cold	#Polar
#Environmental	#Terrestrial	#Soil

What are isolation sources categories?

[Ref.: #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

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.: #44035]	16S rRNA gene sequence	KT163920		GenBank

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Cypionkella psychrotolerans PAMC 27389	GCA_001294535	contig	GenBank	1678131 tax ID

[Ref.: #44035]

GC-content

60.1 mol%

genome sequence analysis

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Cypionkella psychrotolerans PAMC 27389 NCBI: GCA_001294535.1
[Ref.: #69480]	motile	no	82.756	yes
[Ref.: #69480]	flagellated	no	97.104	no
[Ref.: #69480]	gram-positive	no	98.086	yes
[Ref.: #69480]	anaerobic	no	99.313	no
[Ref.: #69480]	aerobic	yes	91.863	no
[Ref.: #69480]	halophile	no	87.339	no
[Ref.: #69480]	spore-forming	no	96.426	no
[Ref.: #69480]	glucose-util	yes	87.718	no
[Ref.: #69480]	thermophile	no	99.458	yes
[Ref.: #69480]	glucose-ferment	no	80.321	yes

Availability in culture collections External links

[Ref.: #44035]

Culture collection no.

PAMC 27389, JCM 30764, KCTC 42640

Literature:

Topic	Title	Authors	Journal	DOI	Year
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 .

#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) .

* These data were automatically processed and therefore are not curated

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