Name: Sphingobium ummariense RL-3
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 14190

Type strain:

Species: Sphingobium ummariense

Strain Designation: RL-3

Culture col. no.: DSM 22942, CCM 7431, MTCC 8599

Strain history: <- R. Lal, Univ. Delhi, Dept. Zoology, India; RL-3

NCBI tax ID(s): 420994 (species)

Section

Sphingobium ummariense RL-3 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from HCH-contaminated soil.

Gram-negative
rod-shaped
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	*Sphingomonadales*
	Family	*Sphingomonadaceae*
	Genus	*Sphingobium*
	Species	**Sphingobium ummariense**
	Full Scientific Name (LPSN)	Sphingobium ummariense Singh and Lal 2009

Information on morphological and physiological properties Morphology

[Ref.: #32571]	Gram stain	negative

[Ref.: #32571]	Cell shape	rod-shaped

[Ref.: #32571]	Motility	no

[Ref.: #32571]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

	Temperatures	Kind of temperature		Temperature
[Ref.: #32571]			growth	05-41 °C
[Ref.: #32571]			optimum	28 °C

[Ref.: #32571]

Temperature range

mesophilic

	pH	Kind of pH		pH
[Ref.: #32571]			optimum	7.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #32571]

Oxygen tolerance

aerobe

[Ref.: #32571]

Ability of spore formation

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #32571]		NaCl		optimum	01-02	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #32571]	arabinose ChEBI	+	carbon source
[Ref.: #32571]	esculin ChEBI	+	hydrolysis
[Ref.: #32571]	glucose ChEBI	+	carbon source
[Ref.: #32571]	sorbitol ChEBI	+	carbon source
[Ref.: #32571]	xylose ChEBI	+	carbon source

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #32571]		gelatinase	+
[Ref.: #32571]		urease	+	3.5.1.5

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

[Ref.: #16623]	Sample type/isolated from	HCH-contaminated soil
[Ref.: #16623]	Geographic location (country and/or sea, region)	Lucknow, Ummari village
[Ref.: #16623]	Country	India
[Ref.: #16623]	Country ISO 3 Code	IND
[Ref.: #16623]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Engineered	#Contamination	-
#Environmental	#Terrestrial	#Soil

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence EF207155 (>99% sequence identity) for Sphingobium ummariense subclade from Microbeatlas

Aquatic Samples	389
Soil Samples	190
Animal Samples	150
Plant Samples	98
Total Samples	827

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

[Ref.: #16623]

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.: #16623]	Sphingobium ummariense strain RL-3 16S ribosomal RNA gene, partial sequence	EF207155	1419	ENA	1346791 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Sphingobium ummariense RL-3	GCA_000447205	contig	GenBank	1346791 tax ID	*
[Ref.: #66792]	Sphingobium ummariense RL-3	1346791.3	wgs	PATRIC	1346791 tax ID	*
[Ref.: #66792]	Sphingobium ummariense RL-3	2571042663	draft	JGI IMG/M	1346791 tax ID	*

[Ref.: #16623]	GC-content	62.0 mol%	high performance liquid chromatography (HPLC)
[Ref.: #32571]	GC-content	62 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: Sphingobium ummariense RL-3 PATRIC: 1346791.3
[Ref.: #69480]	motile	yes	60.663	yes
[Ref.: #69480]	gram-positive	no	97.54	yes
[Ref.: #69480]	anaerobic	no	99.422	yes
[Ref.: #69480]	halophile	no	95.174	no
[Ref.: #69480]	spore-forming	no	94.414	yes
[Ref.: #69480]	thermophile	no	98.172	yes
[Ref.: #69480]	glucose-util	yes	92.56	no
[Ref.: #69480]	aerobic	yes	91.057	yes
[Ref.: #69480]	flagellated	no	87.264	yes
[Ref.: #69480]	glucose-ferment	no	93.203	no

Availability in culture collections External links

[Ref.: #16623]

Culture collection no.

DSM 22942, CCM 7431, MTCC 8599

Literature:

Only first 10 entries are displayed. Click here to see all.

Topic	Title	Authors	Journal	DOI	Year
Genetics	Draft Genome Sequence of Sphingobium ummariense Strain RL-3, a Hexachlorocyclohexane-Degrading Bacterium.	Kohli P, Dua A, Sangwan N, Oldach P, Khurana JP, Lal R	Genome Announc	10.1128/genomeA.00956-13	2013	*
Phylogeny	Sphingomonas formosensis sp. nov., a polycyclic aromatic hydrocarbon-degrading bacterium isolated from agricultural soil.	Lin SY, Shen FT, Lai WA, Zhu ZL, Chen WM, Chou JH, Lin ZY, Young CC	Int J Syst Evol Microbiol	10.1099/ijs.0.034728-0	2011	*
Phylogeny	Sphingobium wenxiniae sp. nov., a synthetic pyrethroid (SP)-degrading bacterium isolated from activated sludge in an SP-manufacturing wastewater treatment facility.	Wang BZ, Guo P, Zheng JW, Hang BJ, Li L, He J, Li SP	Int J Syst Evol Microbiol	10.1099/ijs.0.023309-0	2010	*
Phylogeny	Sphingobium vulgare sp. nov., isolated from freshwater sediment.	Baek SH, Lim JH, Lee ST	Int J Syst Evol Microbiol	10.1099/ijs.0.016816-0	2009	*
Phylogeny	Sphingobium faniae sp. nov., a pyrethroid-degrading bacterium isolated from activated sludge treating wastewater from pyrethroid manufacture.	Guo P, Wang BZ, Hang BJ, Li L, Li SP, He J	Int J Syst Evol Microbiol	10.1099/ijs.0.009795-0	2009	*
Phylogeny	Sphingobium ummariense sp. nov., a hexachlorocyclohexane (HCH)-degrading bacterium, isolated from HCH-contaminated soil.	Singh A, Lal R	Int J Syst Evol Microbiol	10.1099/ijs.0.65712-0	2009	*

References

#16623

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 22942

#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 )

#32571

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 #28786 (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) .

#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) .

#28786

IJSEM 162 2009 ( DOI 10.1099/ijs.0.65712-0 , PubMed 19126742 )

* These data were automatically processed and therefore are not curated

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