Name: Chryseobacterium frigidisoli PB4
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 24035

Type strain:

Species: Chryseobacterium frigidisoli

Strain Designation: PB4

Culture col. no.: DSM 26000, LMG 27025

Strain history: <- D. Wagner, Alfred Wegener Inst. Polar and Marine Res. (AWI) in the Helmholtz Association, Res. Unit Potsdam, Germany; PB4 <- L. Padur, AWI Potsdam, Germany

NCBI tax ID(s): 1125876 (species)

SI-ID 380503

LMG 27025, DSM 26000

Section

Chryseobacterium frigidisoli PB4 is an aerobe, psychrophilic, Gram-negative bacterium that was isolated from sandy dry permafrost from a glacier forefield.

Gram-negative
rod-shaped
aerobe
psychrophilic
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	*Bacteroidota*
	Class	*Flavobacteriia*
	Order	*Flavobacteriales*
	Family	*Weeksellaceae*
	Genus	*Chryseobacterium*
	Species	**Chryseobacterium frigidisoli**
	Full Scientific Name (LPSN)	Chryseobacterium frigidisoli Bajerski et al. 2013

Synonym

Halpernia frigidisoli

Information on morphological and physiological properties Morphology

[Ref.: #30891]	Gram stain	negative

[Ref.: #30891]	Cell length	2.75 µm

[Ref.: #30891]	Cell width	0.45 µm

[Ref.: #30891]	Cell shape	rod-shaped

[Ref.: #30891]	Motility	no

[Ref.: #30891]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #20930]

Culture medium

NUTRIENT AGAR (DSMZ Medium 1)

[Ref.: #20930]

Culture medium growth

[Ref.: #20930]

Culture medium link

Medium recipe at MediaDive

[Ref.: #20930]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #20930]	growth	20 °C
[Ref.: #30891]	growth	0-25 °C
[Ref.: #30891]	optimum	20 °C

[Ref.: #20930]	Temperature range	psychrophilic
[Ref.: #30891]	Temperature range	psychrophilic

	pH	Kind of pH		pH
[Ref.: #30891]			optimum	6.5
[Ref.: #30891]			growth	5.5-8.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #30891]

Oxygen tolerance

aerobe

[Ref.: #30891]

Ability of spore formation

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #30891]		NaCl		growth	0-5	%
[Ref.: #30891]		NaCl		optimum	0.5	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #30891]	cellobiose ChEBI	+	carbon source
[Ref.: #30891]	fructose ChEBI	+	carbon source
[Ref.: #30891]	galactose ChEBI	+	carbon source
[Ref.: #30891]	glucose ChEBI	+	carbon source
[Ref.: #30891]	glycerol ChEBI	+	carbon source
[Ref.: #30891]	glycogen ChEBI	+	carbon source
[Ref.: #30891]	L-arabitol ChEBI	+	carbon source
[Ref.: #30891]	lactose ChEBI	+	carbon source
[Ref.: #30891]	maltose ChEBI	+	carbon source
[Ref.: #30891]	mannitol ChEBI	+	carbon source
[Ref.: #30891]	mannose ChEBI	+	carbon source
[Ref.: #30891]	melibiose ChEBI	+	carbon source
[Ref.: #30891]	N-acetylglucosamine ChEBI	+	carbon source
[Ref.: #30891]	raffinose ChEBI	+	carbon source
[Ref.: #30891]	rhamnose ChEBI	+	carbon source
[Ref.: #30891]	ribitol ChEBI	+	carbon source
[Ref.: #30891]	ribose ChEBI	+	carbon source
[Ref.: #30891]	salicin ChEBI	+	carbon source
[Ref.: #30891]	sorbitol ChEBI	+	carbon source
[Ref.: #30891]	sucrose ChEBI	+	carbon source
[Ref.: #30891]	trehalose ChEBI	+	carbon source
[Ref.: #30891]	xylitol ChEBI	+	carbon source
[Ref.: #30891]	xylose ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #30891]		indole ChEBI	yes

	Physiological tests	Metabolite	Indole test
[Ref.: #30891]		indole ChEBI	+

	Enzyme	Enzyme activity	EC number
[Ref.: #30891]	catalase	+	1.11.1.6
[Ref.: #30891]	cytochrome oxidase	+	1.9.3.1
[Ref.: #30891]	gelatinase	+

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	cellulose degradation	100	5 of 5
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	denitrification	100	2 of 2
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	glycogen metabolism	100	5 of 5
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	vitamin K metabolism	100	5 of 5
[Ref.: #66794]	ceramide biosynthesis	100	1 of 1
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	phenylacetate degradation (aerobic)	100	5 of 5
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	teichoic acid biosynthesis	100	1 of 1
[Ref.: #66794]	palmitate biosynthesis	95.45	21 of 22
[Ref.: #66794]	starch degradation	90	9 of 10
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	88.89	8 of 9
[Ref.: #66794]	lipid A biosynthesis	88.89	8 of 9
[Ref.: #66794]	C4 and CAM-carbon fixation	87.5	7 of 8
[Ref.: #66794]	tetrahydrofolate metabolism	85.71	12 of 14
[Ref.: #66794]	photosynthesis	85.71	12 of 14
[Ref.: #66794]	pentose phosphate pathway	81.82	9 of 11
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	CO2 fixation in Crenarchaeota	77.78	7 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	77.78	7 of 9
[Ref.: #66794]	serine metabolism	77.78	7 of 9
[Ref.: #66794]	NAD metabolism	77.78	14 of 18
[Ref.: #66794]	leucine metabolism	76.92	10 of 13
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	flavin biosynthesis	73.33	11 of 15
[Ref.: #66794]	cysteine metabolism	72.22	13 of 18
[Ref.: #66794]	ubiquinone biosynthesis	71.43	5 of 7
[Ref.: #66794]	propanol degradation	71.43	5 of 7
[Ref.: #66794]	reductive acetyl coenzyme A pathway	71.43	5 of 7
[Ref.: #66794]	heme metabolism	71.43	10 of 14
[Ref.: #66794]	lipid metabolism	70.97	22 of 31
[Ref.: #66794]	purine metabolism	70.21	66 of 94
[Ref.: #66794]	propionate fermentation	70	7 of 10
[Ref.: #66794]	Entner Doudoroff pathway	70	7 of 10
[Ref.: #66794]	phenylalanine metabolism	69.23	9 of 13
[Ref.: #66794]	alanine metabolism	68.97	20 of 29
[Ref.: #66794]	non-pathway related	68.42	26 of 38
[Ref.: #66794]	glutamate and glutamine metabolism	67.86	19 of 28
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	66.67	2 of 3
[Ref.: #66794]	enterobactin biosynthesis	66.67	2 of 3
[Ref.: #66794]	pyrimidine metabolism	66.67	30 of 45
[Ref.: #66794]	d-mannose degradation	66.67	6 of 9
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	glycolysis	64.71	11 of 17
[Ref.: #66794]	citric acid cycle	64.29	9 of 14
[Ref.: #66794]	tyrosine metabolism	64.29	9 of 14
[Ref.: #66794]	histidine metabolism	62.07	18 of 29
[Ref.: #66794]	methionine metabolism	61.54	16 of 26
[Ref.: #66794]	tryptophan metabolism	60.53	23 of 38
[Ref.: #66794]	methylglyoxal degradation	60	3 of 5
[Ref.: #66794]	threonine metabolism	60	6 of 10
[Ref.: #66794]	glycine betaine biosynthesis	60	3 of 5
[Ref.: #66794]	glutathione metabolism	57.14	8 of 14
[Ref.: #66794]	phenylpropanoid biosynthesis	53.85	7 of 13
[Ref.: #66794]	lysine metabolism	52.38	22 of 42
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	suberin monomers biosynthesis	50	1 of 2
[Ref.: #66794]	dTDPLrhamnose biosynthesis	50	4 of 8
[Ref.: #66794]	ketogluconate metabolism	50	4 of 8
[Ref.: #66794]	isoleucine metabolism	50	4 of 8
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	carotenoid biosynthesis	50	11 of 22
[Ref.: #66794]	cis-vaccenate biosynthesis	50	1 of 2
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	vitamin B1 metabolism	46.15	6 of 13
[Ref.: #66794]	isoprenoid biosynthesis	46.15	12 of 26
[Ref.: #66794]	proline metabolism	45.45	5 of 11
[Ref.: #66794]	vitamin B6 metabolism	45.45	5 of 11
[Ref.: #66794]	d-xylose degradation	45.45	5 of 11
[Ref.: #66794]	valine metabolism	44.44	4 of 9
[Ref.: #66794]	degradation of sugar acids	44	11 of 25
[Ref.: #66794]	oxidative phosphorylation	42.86	39 of 91
[Ref.: #66794]	cardiolipin biosynthesis	42.86	3 of 7
[Ref.: #66794]	mevalonate metabolism	42.86	3 of 7
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	D-cycloserine biosynthesis	40	2 of 5
[Ref.: #66794]	lipoate biosynthesis	40	2 of 5
[Ref.: #66794]	coenzyme M biosynthesis	40	4 of 10
[Ref.: #66794]	O-antigen biosynthesis	40	2 of 5
[Ref.: #66794]	sulfate reduction	38.46	5 of 13
[Ref.: #66794]	metabolism of disaccharids	36.36	4 of 11
[Ref.: #66794]	arachidonic acid metabolism	33.33	6 of 18
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	octane oxidation	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	allantoin degradation	33.33	3 of 9
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	glycolate and glyoxylate degradation	33.33	2 of 6
[Ref.: #66794]	degradation of pentoses	32.14	9 of 28
[Ref.: #66794]	ascorbate metabolism	31.82	7 of 22
[Ref.: #66794]	degradation of sugar alcohols	31.25	5 of 16
[Ref.: #66794]	urea cycle	30.77	4 of 13
[Ref.: #66794]	myo-inositol biosynthesis	30	3 of 10
[Ref.: #66794]	arginine metabolism	29.17	7 of 24
[Ref.: #66794]	degradation of hexoses	27.78	5 of 18
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	androgen and estrogen metabolism	25	4 of 16
[Ref.: #66794]	biotin biosynthesis	25	1 of 4
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	carnitine metabolism	25	2 of 8
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	23.08	3 of 13
[Ref.: #66794]	polyamine pathway	21.74	5 of 23
		Only first 10 entries are displayed. Click here to see all.

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

[Ref.: #20930]	Sample type/isolated from	sandy dry permafrost from a glacier forefield
[Ref.: #20930]	Geographic location (country and/or sea, region)	Larsemann Hills (S 69°24', E 76°20')
[Ref.: #20930]	Continent	Australia and Oceania
[Ref.: #20930]	Geographic location	-69.4000°/76.3333°
* marker position based on {}

Isolation sources categories

#Environmental	#Terrestrial	#Glacier
#Environmental	#Terrestrial	#Permafrost
#Environmental	#Terrestrial	#Sandy

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence JN390676 (>99% sequence identity) for Chryseobacterium frigidisoli subclade from Microbeatlas

Aquatic Samples	153
Soil Samples	68
Animal Samples	200
Plant Samples	23
Total Samples	444

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #20930]

Biosafety level

Risk group (German classification)
According to TRBA 466

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.: #20930]	Chryseobacterium frigidisoli strain PB4 16S ribosomal RNA gene, partial sequence	JN390676	1301	ENA	1125876 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Halpernia frigidisoli DSM 26000	GCA_900113805	contig	GenBank	1125876 tax ID	*
[Ref.: #66792]	Chryseobacterium frigidisoli strain DSM 26000	1125876.4	wgs	PATRIC	1125876 tax ID	*
[Ref.: #66792]	Chryseobacterium frigidisoli DSM 26000	2684622856	draft	JGI IMG/M	1125876 tax ID	*

[Ref.: #20930]	GC-content	33.7 mol%	high performance liquid chromatography (HPLC)
[Ref.: #30891]	GC-content	33.7 mol%

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Chryseobacterium frigidisoli strain DSM 26000 PATRIC: 1125876.4
[Ref.: #69480]	motile	no	91.206	yes
[Ref.: #69480]	flagellated	no	96.797	no
[Ref.: #69480]	gram-positive	no	97.964	yes
[Ref.: #69480]	anaerobic	no	99.545	yes
[Ref.: #69480]	aerobic	yes	91.528	yes
[Ref.: #69480]	halophile	no	91.606	yes
[Ref.: #69480]	spore-forming	no	96.423	yes
[Ref.: #69480]	thermophile	no	99.652	yes
[Ref.: #69480]	glucose-util	yes	86.282	yes
[Ref.: #69480]	glucose-ferment	no	92.923	no

Availability in culture collections External links

[Ref.: #20930]

Culture collection no.

DSM 26000, LMG 27025

[Ref.: #88008]

SI-ID 380503

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Chryseobacterium frigidisoli sp. nov., a psychrotolerant species of the family Flavobacteriaceae isolated from sandy permafrost from a glacier forefield.	Bajerski F, Ganzert L, Mangelsdorf K, Padur L, Lipski A, Wagner D	Int J Syst Evol Microbiol	10.1099/ijs.0.046904-0	2013	*

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 )

#20930

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 26000

#30891

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 #27221 (see below)

#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) .

#66794

Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )

#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) .

#88008

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID380503.1 )

#27221

IJSEM 2666 2013 ( DOI 10.1099/ijs.0.046904-0 , PubMed 23291884 )

* These data were automatically processed and therefore are not curated

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Chryseobacterium frigidisoli strain DSM 26000

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