Name: Pedobacter psychrotolerans V5RD
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 133008

Type strain:

Species: Pedobacter psychrotolerans

Strain Designation: V5RD

Culture col. no.: DSM 103236, CGMCC 1.15644

Strain history: <- P. Manandhar, Chinese Acad. Sci. (CAS), Beijing; V5RD

NCBI tax ID(s): 1843235 (species)

Section

Pedobacter psychrotolerans V5RD is an aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and has a light-pink pigmentation.

colony-forming
Gram-negative
pigmented
rod-shaped
aerobe
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	07-12-2022 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Bacteroidota*
	Class	*Sphingobacteriia*
	Order	*Sphingobacteriales*
	Family	*Sphingobacteriaceae*
	Genus	*Pedobacter*
	Species	**Pedobacter psychrotolerans**
	Full Scientific Name (PNU)	Pedobacter psychrotolerans Manandhar et al. 2016

Information on morphological and physiological properties Morphology

[Ref.: #24993]	Gram stain	negative
[Ref.: #24993]	Cell length	1.6 µm
[Ref.: #24993]	Cell width	0.8 µm
[Ref.: #24993]	Cell shape	rod-shaped
[Ref.: #24993]	Motility	no

[Ref.: #24993]	Colony color	light-pink
[Ref.: #24993]	Colony shape	circular
[Ref.: #24993]	Incubation period	3 days
[Ref.: #24993]	Cultivation medium used	R2A agar (Reasoner's 2A agar)

[Ref.: #24993]	Pigment production	yes
[Ref.: #24993]	Pigmentation color	light-pink

Information on culture and growth conditions Culture and growth conditions

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Culture medium

TSA (Trypticase soy agar)

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Culture medium growth

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Culture medium

Reasoner's 2A agar (R2A)

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Culture medium growth

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Culture medium

R2A MEDIUM (DSMZ Medium 830)

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Culture medium growth

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Culture medium link

Medium recipe provided by DSMZ

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Culture medium composition

expand / minimize

		Temperature
[Ref.: #24796]	growth	28 °C
[Ref.: #24993]	growth	0.0-30.0 °C
[Ref.: #24993]	optimum	10 °C

[Ref.: #24796]	Temperature range	mesophilic
[Ref.: #24993]	Temperature range	psychrophilic

	pH	Kind of pH		pH	pH range
[Ref.: #24993]			optimum	9
[Ref.: #24993]			growth	5.0-10.0	alkaliphile

Information on physiology and metabolism Physiology and metabolism

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Oxygen tolerance

aerobe

	Salt		Salt conc.
[Ref.: #24993]	NaCl	growth	1	%(w/v)
[Ref.: #24993]	NaCl	maximum	3	%(w/v)
[Ref.: #24993]	NaCl	growth	0.0-3.0	%(w/v)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #24993]	adipate ChEBI	-	assimilation
[Ref.: #24993]	D-glucose ChEBI	-	fermentation
[Ref.: #24993]	D-glucose ChEBI	+	assimilation
[Ref.: #24993]	D-mannitol ChEBI	-	assimilation
[Ref.: #24993]	D-mannose ChEBI	+	assimilation
[Ref.: #24993]	decanoate ChEBI	-	assimilation
[Ref.: #24993]	esculin ChEBI	+	hydrolysis
[Ref.: #24993]	gelatin ChEBI	-	hydrolysis
[Ref.: #24993]	L-arabinose ChEBI	+	assimilation
[Ref.: #24993]	malate ChEBI	+	assimilation
[Ref.: #24993]	maltose ChEBI	+	assimilation
[Ref.: #24993]	N-acetylglucosamine ChEBI	+	assimilation
[Ref.: #24993]	nitrate ChEBI	-	reduction
[Ref.: #24993]	phenylacetate ChEBI	-	assimilation
[Ref.: #24993]	potassium gluconate ChEBI	-	assimilation
[Ref.: #24993]	sodium citrate ChEBI	-	assimilation
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite
[Ref.: #24993]		indole ChEBI

	Enzyme	Enzyme activity	EC number
[Ref.: #24993]	acid phosphatase	+	3.1.3.2
[Ref.: #24993]	alkaline phosphatase	+	3.1.3.1
[Ref.: #24993]	alpha-chymotrypsin	+	3.4.21.1
[Ref.: #24993]	alpha-fucosidase	+	3.2.1.51
[Ref.: #24993]	alpha-galactosidase	+	3.2.1.22
[Ref.: #24993]	alpha-glucosidase	+	3.2.1.20
[Ref.: #24993]	alpha-mannosidase	-	3.2.1.24
[Ref.: #24993]	arginine dihydrolase	-	3.5.3.6
[Ref.: #24993]	beta-galactosidase	+	3.2.1.23
[Ref.: #24993]	beta-glucosidase	+	3.2.1.21
[Ref.: #24993]	beta-glucuronidase	+	3.2.1.31
[Ref.: #24993]	catalase	+	1.11.1.6
[Ref.: #24993]	cytochrome oxidase	+	1.9.3.1
[Ref.: #24993]	esterase (C 4)	+
[Ref.: #24993]	esterase Lipase (C 8)	+
[Ref.: #24993]	leucine arylamidase	+	3.4.11.1
[Ref.: #24993]	N-acetyl-beta-glucosaminidase	+	3.2.1.52
[Ref.: #24993]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #24993]	trypsin	+	3.4.21.4
[Ref.: #24993]	urease	-	3.5.1.5
[Ref.: #24993]	valine arylamidase	+
	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.: #24796]	Sample type/isolated from	soil
[Ref.: #24796]	Geographic location (country and/or sea, region)	Qinghai-Tibetan Plateau, Damxung county (29.83° N, 90.75° E)
[Ref.: #24796]	Country	China
[Ref.: #24796]	Country ISO 3 Code	CHN
[Ref.: #24796]	Continent	Asia
[Ref.: #24796]	Geographic location	29.8300°/90.7500°

[Ref.: #24993]	Enrichment culture	R2A agar (Reasoner's 2A agar)
[Ref.: #24993]	Enrichment culture duration	4-7 days
[Ref.: #24993]	Enrichment culture temperature	10 ̊C
* marker position based on {}

Isolation sources categories

#Environmental

#Terrestrial

#Soil

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence KU535673 (>99% sequence identity) for Pedobacter psychrotolerans subclade from Microbeatlas

Aquatic Samples	414
Soil Samples	512
Animal Samples	630
Plant Samples	1085
Total Samples	2641

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

[Ref.: #24796]

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.: #24796]	Pedobacter psychrotolerans strain V5RD 16S ribosomal RNA gene, partial sequence	KU535673	1423	ENA	1843235 tax ID

Genome sequence information:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Assembly level (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Pedobacter psychrotolerans DSM 103236	GCA_004340665	scaffold	GenBank	1843235 tax ID	*
[Ref.: #66792]	Pedobacter psychrotolerans CGMCC 1.15644	GCA_014643495	scaffold	GenBank	1843235 tax ID	*
[Ref.: #66792]	Pedobacter psychrotolerans strain CGMCC 1.15644	1843235.6	wgs	PATRIC	1843235 tax ID	*
[Ref.: #66792]	Pedobacter psychrotolerans strain DSM 103236	1843235.3	wgs	PATRIC	1843235 tax ID	*
[Ref.: #66792]	Pedobacter psychrotolerans DSM 103236	2802428854	draft	JGI IMG/M	1843235 tax ID	*
[Ref.: #66792]	Salmonella enterica BCW_2524	GCA_002036785	contig	PATRIC	28901 tax ID	*

[Ref.: #24993]	GC-content	37.4 mol%	genome sequence analysis
[Ref.: #24796]	GC-content	37.40 mol%	sequence analysis

Availability in culture collections External links

[Ref.: #24796]

Culture collection no.

DSM 103236, CGMCC 1.15644

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Pedobacterpsychrotolerans sp. nov., isolated from soil.	Manandhar P, Zhang G, Lama A, Hu Y, Gao F	Int J Syst Evol Microbiol	10.1099/ijsem.0.001391	2016	*

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 )

#24796

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 103236

#24993

P. Z. Manandhar, Gengxin,Lama, Arun,Hu, Yilun,Gao, Feng: Pedobacter psychrotolerans sp. nov., isolated from soil. IJSEM 66: 4560 - 4566 2016 ( DOI 10.1099/ijsem.0.001391 , PubMed 27498823 )

#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) .

#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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