Name: Sphingomonas difficilis 1PNM-26
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 141166

Type strain:

Species: Sphingomonas difficilis

Strain Designation: 1PNM-26

Culture col. no.: GDMCC 1.664, KCTC 42758, DSM 27573

Strain history: <- Guangda Feng, South China Agricultural Univ.

NCBI tax ID(s): 1141888 (species)

SI-ID 402663

DSM 27573

Special Collections

Section

When using BacDive for research please cite our paper

Sphingomonas difficilis 1PNM-26 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from From abandoned lead-zinc ore in Meizhou.

Gram-negative
rod-shaped
aerobe
16S sequence
Bacteria

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

	Last LPSN update	09-12-2024 (DD-MM-YYYY)
	Domain	*Bacteria*
	Phylum	*Pseudomonadota*
	Class	*Alphaproteobacteria*
	Order	*Sphingomonadales*
	Family	*Sphingomonadaceae*
	Genus	*Sphingomonas*
	Species	**Sphingomonas difficilis**
	Full Scientific Name (LPSN)	Sphingomonas difficilis Feng et al. 2017

Information on morphological and physiological properties Morphology

[Ref.: #44085]	Gram stain	negative

[Ref.: #44085]	Cell shape	rod-shaped

[Ref.: #44085]	Motility	no

[Ref.: #44085]	Colony size	1-2 mm
[Ref.: #44085]	Colony color	orange
[Ref.: #44085]	Incubation period	4 days
[Ref.: #44085]	Cultivation medium used	R2A agar

Information on culture and growth conditions Culture and growth conditions

[Ref.: #44085]

Culture medium

PYE

[Ref.: #44085]

Culture medium growth

[Ref.: #44085]

Culture medium

Reasoner's 2A agar (R2A)

[Ref.: #44085]

Culture medium growth

[Ref.: #64988]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #64988]

Culture medium growth

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Culture medium link

Medium recipe at MediaDive

[Ref.: #64988]

Culture medium composition

expand / minimize

[Ref.: #44085]

Culture medium

Liquid media

[Ref.: #44085]

Culture medium growth

[Ref.: #44085]

Culture medium

Nutrient agar (NA)

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Culture medium growth

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Culture medium

Trypticase Soy Agar (TSA)

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Culture medium growth

		Temperature
[Ref.: #44085]	growth	20-35 °C
[Ref.: #44085]	optimum	28-30 °C
[Ref.: #64988]	growth	28 °C
[Ref.: #67771]	growth	30 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #44085]	Oxygen tolerance	aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe

[Ref.: #44085]

Ability of spore formation

[Ref.: #44085]

Halophily / tolerance level

non-halophilic

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #44085]		NaCl		growth	0-1	%(w/v)
[Ref.: #44085]		NaCl		optimum	0	%(w/v)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #44085]	adipate ChEBI	-	assimilation
[Ref.: #44085]	citrate ChEBI	-	assimilation
[Ref.: #44085]	D-mannitol ChEBI	-	assimilation
[Ref.: #44085]	D-mannose ChEBI	-	assimilation
[Ref.: #44085]	decanoate ChEBI	-	assimilation
[Ref.: #44085]	esculin ChEBI	+	hydrolysis
[Ref.: #44085]	gelatin ChEBI	-	hydrolysis
[Ref.: #44085]	gluconate ChEBI	-	assimilation
[Ref.: #44085]	glucose ChEBI	-	assimilation
[Ref.: #44085]	glucose ChEBI	-	fermentation
[Ref.: #44085]	L-arabinose ChEBI	-	assimilation
[Ref.: #44085]	malate ChEBI	-	assimilation
[Ref.: #44085]	maltose ChEBI	-	assimilation
[Ref.: #44085]	N-acetylglucosamine ChEBI	-	assimilation
[Ref.: #44085]	nitrate ChEBI	-	reduction
[Ref.: #44085]	phenylacetate ChEBI	-	assimilation
[Ref.: #44085]	starch ChEBI	-	hydrolysis
[Ref.: #44085]	tween 40 ChEBI	+	hydrolysis
[Ref.: #44085]	tween 80 ChEBI	-	hydrolysis
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #44085]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #44085]	arginine dihydrolase	-	3.5.3.6
[Ref.: #44085]	beta-galactosidase	+	3.2.1.23
[Ref.: #44085]	catalase	+	1.11.1.6
[Ref.: #44085]	cytochrome oxidase	+	1.9.3.1
[Ref.: #44085]	urease	-	3.5.1.5

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

[Ref.: #67771]	Sample type/isolated from	From abandoned lead-zinc ore in Meizhou
[Ref.: #67771]	Geographic location (country and/or sea, region)	Guangdong Province
[Ref.: #67771]	Country	China
[Ref.: #67771]	Country ISO 3 Code	CHN
[Ref.: #67771]	Continent	Asia

[Ref.: #44085]	Sample type/isolated from	abandoned lead-zinc mine
[Ref.: #44085]	Geographic location (country and/or sea, region)	Meizhou, Guangdong Province
[Ref.: #44085]	Country	China
[Ref.: #44085]	Country ISO 3 Code	CHN
[Ref.: #44085]	Continent	Asia
[Ref.: #44085]	Geographic location	24.3622°/116.2760°
[Ref.: #44085]	Enrichment culture	R2A

[Ref.: #64988]	Sample type/isolated from	abandoned lead-zinc ore
[Ref.: #64988]	Geographic location (country and/or sea, region)	Guangdong Province, Meizhou (24° 21' 44'' N 116° 16' 34'' E)
[Ref.: #64988]	Country	China
[Ref.: #64988]	Country ISO 3 Code	CHN
[Ref.: #64988]	Continent	Asia
[Ref.: #64988]	Geographic location	24.3622°/116.2760°
* marker position based on {}

Isolation sources categories

#Engineered	#Other	#Mine
#Engineered	#Contamination	#Heavy metal

What are isolation sources categories?

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

[Ref.: #64988]

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.: #64988]	Sphingomonas difficilis strain 1PNM-26 16S ribosomal RNA gene, partial sequence	JQ608334	1434	GenBank ENA	1141888 tax ID

[Ref.: #64988]

GC-content

66.3 mol%

high performance liquid chromatography (HPLC)

Availability in culture collections External links

[Ref.: #64988]

Culture collection no.

GDMCC 1.664, KCTC 42758, DSM 27573

[Ref.: #96876]

SI-ID 402663

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Sphingomonas difficilis sp. nov., a difficultly cultivable bacterium that grows on solid but not in liquid medium, isolated from an abandoned lead-zinc mine.	Feng GD, Xiong X, Zhu HH, Li HP	Int J Syst Evol Microbiol	10.1099/ijsem.0.002461	2017	*

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 )

#44085

Guang-Da Feng, Xiong Xiong, Hong-Hui Zhu and Hua-Ping Li: Sphingomonas difficilis sp. nov., a difficultly cultivable bacterium that grows on solid but not in liquid medium, isolated from an abandoned lead–zinc mine. IJSEM 67: 5273 - 5278 2017 ( DOI 10.1099/ijsem.0.002461 , PubMed 29091024 )

#64988

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 27573

#67771 Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;

#96876

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-ID402663.1 )

* These data were automatically processed and therefore are not curated

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