Name: Novosphingobium lindaniclasticum DSM 25409
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 23267

Type strain:

Species: Novosphingobium lindaniclasticum

Culture col. no.: DSM 25409, CCM 7976, LE 124

Strain history: <- R. Lal, Univ. Delhi, Dept. Zoology, India; LE124

NCBI tax ID(s): 1329895 (species)

Section

Novosphingobium lindaniclasticum DSM 25409 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from hexachlorocylohexane dumpsite.

Gram-negative
rod-shaped
aerobe
mesophilic
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	*Erythrobacteraceae*
	Genus	*Novosphingobium*
	Species	**Novosphingobium lindaniclasticum**
	Full Scientific Name (LPSN)	Novosphingobium lindaniclasticum Saxena et al. 2013

Information on morphological and physiological properties Morphology

[Ref.: #30828]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.981

[Ref.: #30828]	Cell length	1.3 µm

[Ref.: #30828]	Cell width	0.7 µm

[Ref.: #30828]	Cell shape	rod-shaped

[Ref.: #30828]	Motility	no

[Ref.: #30828]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

	Temperatures	Kind of temperature		Temperature
[Ref.: #30828]			growth	25-32 °C
[Ref.: #30828]			optimum	28 °C

[Ref.: #30828]

Temperature range

mesophilic

	pH	Kind of pH		pH
[Ref.: #30828]			growth	6.0-9.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #30828]

Oxygen tolerance

aerobe

[Ref.: #30828]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %98
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.974

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #30828]		NaCl		growth	01-04	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #30828]	alanine ChEBI	+	carbon source
[Ref.: #30828]	arabinose ChEBI	+	carbon source
[Ref.: #30828]	fructose ChEBI	+	carbon source
[Ref.: #30828]	galactose ChEBI	+	carbon source
[Ref.: #30828]	glucose ChEBI	+	carbon source
[Ref.: #30828]	histidine ChEBI	+	carbon source
[Ref.: #30828]	malate ChEBI	+	carbon source
[Ref.: #30828]	maltose ChEBI	+	carbon source
[Ref.: #30828]	mannose ChEBI	+	carbon source
[Ref.: #30828]	nitrate ChEBI	+	reduction
[Ref.: #30828]	proline ChEBI	+	carbon source
[Ref.: #30828]	serine ChEBI	+	carbon source
[Ref.: #30828]	sucrose ChEBI	+	carbon source
[Ref.: #30828]	trehalose ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #30828]		indole ChEBI	yes

	Physiological tests	Metabolite	Indole test
[Ref.: #30828]		indole ChEBI	+

	Enzyme	Enzyme activity	EC number
[Ref.: #30828]	catalase	+	1.11.1.6
[Ref.: #30828]	cytochrome oxidase	+	1.9.3.1
[Ref.: #30828]	urease	+	3.5.1.5

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

[Ref.: #19347]	Sample type/isolated from	hexachlorocylohexane (HCH) dumpsite
[Ref.: #19347]	Geographic location (country and/or sea, region)	Uttar Pradesh, Lucknow
[Ref.: #19347]	Country	India
[Ref.: #19347]	Country ISO 3 Code	IND
[Ref.: #19347]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Engineered	#Built environment	-
#Engineered	#Contamination	-

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence JN687581 (>99% sequence identity) for Novosphingobium lindaniclasticum from Microbeatlas

Aquatic Samples	351
Soil Samples	303
Animal Samples	124
Plant Samples	96
Total Samples	874

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

[Ref.: #19347]

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.: #19347]	Novosphingobium lindaniclasticum LE124 16S ribosomal RNA gene, partial sequence	JN687581	1417	ENA	1096930 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Novosphingobium lindaniclasticum LE124	GCA_000445125	contig	GenBank	1096930 tax ID	*
[Ref.: #66792]	Novosphingobium lindaniclasticum LE124	1096930.3	wgs	PATRIC	1096930 tax ID	*
[Ref.: #66792]	Novosphingobium lindaniclasticum LE124	2558860244	draft	JGI IMG/M	1096930 tax ID	*

[Ref.: #19347]	GC-content	60.7 mol%	fluorimetric
[Ref.: #30828]	GC-content	60.7 mol%

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Novosphingobium lindaniclasticum LE124 PATRIC: 1096930.3
[Ref.: #69481]	spore-forming	no	98	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Novosphingobium lindaniclasticum LE124 PATRIC: 1096930.3
[Ref.: #69480]	motile	yes	69.692	no
[Ref.: #69480]	flagellated	no	87.578	yes
[Ref.: #69480]	gram-positive	no	97.816	yes
[Ref.: #69480]	anaerobic	no	98.423	yes
[Ref.: #69480]	aerobic	yes	91.255	yes
[Ref.: #69480]	halophile	no	97.104	no
[Ref.: #69480]	spore-forming	no	92.84	yes
[Ref.: #69480]	glucose-util	yes	90.299	yes
[Ref.: #69480]	thermophile	no	99.031	no
[Ref.: #69480]	glucose-ferment	no	92.609	no

Availability in culture collections External links

[Ref.: #19347]

Culture collection no.

DSM 25409, CCM 7976, LE 124

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Novosphingobium lindaniclasticum sp. nov., a hexachlorocyclohexane (HCH)-degrading bacterium isolated from an HCH dumpsite.	Saxena A, Anand S, Dua A, Sangwan N, Khan F, Lal R	Int J Syst Evol Microbiol	10.1099/ijs.0.045443-0	2012	*
Genetics	Genome Sequence of Novosphingobium lindaniclasticum LE124T, Isolated from a Hexachlorocyclohexane Dumpsite.	Saxena A, Nayyar N, Sangwan N, Kumari R, Khurana JP, Lal R	Genome Announc	10.1128/genomeA.00715-13	2013	*

References

#19347

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 25409

#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 )

#30828

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 #27158 (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) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#27158

IJSEM 2160 2013 ( DOI 10.1099/ijs.0.045443-0 , PubMed 23104365 )

* These data were automatically processed and therefore are not curated

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Novosphingobium lindaniclasticum LE124

Novosphingobium lindaniclasticum LE124

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