Name: Duganella radicis Sac-41
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 133834

Type strain:

Species: Duganella radicis

Strain Designation: Sac-41

Culture col. no.: KCTC 22382, NCIMB 14476

NCBI tax ID(s): 551988 (species)

Section

Duganella radicis Sac-41 is an aerobe, Gram-negative, motile bacterium that was isolated from plant associated.

Gram-negative
motile
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	*Betaproteobacteria*
	Order	*Burkholderiales*
	Family	*Oxalobacteraceae*
	Genus	*Duganella*
	Species	**Duganella radicis**
	Full Scientific Name (LPSN)	Duganella radicis Madhaiyan et al. 2013

Information on morphological and physiological properties Morphology

[Ref.: #30627]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.997

[Ref.: #30627]	Cell length	1.2 µm

[Ref.: #30627]	Cell width	0.35 µm

[Ref.: #30627]	Cell shape	rod-shaped

[Ref.: #30627]	Motility	yes
[Ref.: #69480]	Motility	yes Confidence in %97.303

[Ref.: #30627]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

	Temperatures	Kind of temperature		Temperature
[Ref.: #30627]			growth	15-37 °C
[Ref.: #30627]			optimum	30 °C

[Ref.: #30627]

Temperature range

mesophilic

	pH	Kind of pH		pH
[Ref.: #30627]			optimum	7.2
[Ref.: #30627]			growth	04-10

Information on physiology and metabolism Physiology and metabolism

[Ref.: #30627]

Oxygen tolerance

aerobe

[Ref.: #30627]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.986

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #30627]	alpha-cyclodextrin ChEBI	+	carbon source
[Ref.: #30627]	arabinose ChEBI	+	carbon source
[Ref.: #30627]	asparagine ChEBI	+	carbon source
[Ref.: #30627]	aspartate ChEBI	+	carbon source
[Ref.: #30627]	cellobiose ChEBI	+	carbon source
[Ref.: #30627]	dextrin ChEBI	+	carbon source
[Ref.: #30627]	ethanol ChEBI	+	carbon source
[Ref.: #30627]	formate ChEBI	+	carbon source
[Ref.: #30627]	fructose ChEBI	+	carbon source
[Ref.: #30627]	fucose ChEBI	+	carbon source
[Ref.: #30627]	galactose ChEBI	+	carbon source
[Ref.: #30627]	gluconate ChEBI	+	carbon source
[Ref.: #30627]	glucose ChEBI	+	carbon source
[Ref.: #30627]	glucuronamide ChEBI	+	carbon source
[Ref.: #30627]	glutamate ChEBI	+	carbon source
[Ref.: #30627]	glycogen ChEBI	+	carbon source
[Ref.: #30627]	histidine ChEBI	+	carbon source
[Ref.: #30627]	L-alaninamide ChEBI	+	carbon source
[Ref.: #30627]	lactate ChEBI	+	carbon source
[Ref.: #30627]	lactose ChEBI	+	carbon source
[Ref.: #30627]	maltose ChEBI	+	carbon source
[Ref.: #30627]	mannose ChEBI	+	carbon source
[Ref.: #30627]	methyl pyruvate ChEBI	+	carbon source
[Ref.: #30627]	nitrate ChEBI	+	reduction
[Ref.: #30627]	quinate ChEBI	+	carbon source
[Ref.: #30627]	raffinose ChEBI	+	carbon source
[Ref.: #30627]	succinate ChEBI	+	carbon source
[Ref.: #30627]	sucrose ChEBI	+	carbon source
[Ref.: #30627]	threonine ChEBI	+	carbon source
[Ref.: #30627]	trehalose ChEBI	+	carbon source
[Ref.: #30627]	tween 40 ChEBI	+	carbon source
[Ref.: #30627]	tween 80 ChEBI	+	carbon source
[Ref.: #30627]	urocanic acid ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #30627]		catalase	+	1.11.1.6

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

[Ref.: #30627]	Sample type/isolated from	plant associated
* marker position based on {}

Isolation sources categories

#Host

#Plants

What are isolation sources categories?

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.: #30627]	Duganella radicis strain Sac-41 16S ribosomal RNA gene, partial sequence	EU672807	1402	GenBank	551988 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Duganella radicis KCTC 22382	GCA_009720825	contig	GenBank	551988 tax ID	*
[Ref.: #66792]	Duganella radicis strain KCTC 22382	551988.3	wgs	PATRIC	551988 tax ID	*

[Ref.: #30627]

GC-content

54.9 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: Duganella radicis strain KCTC 22382 PATRIC: 551988.3
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Duganella radicis strain KCTC 22382 PATRIC: 551988.3
[Ref.: #69480]	gram-positive	no	98.092	no
[Ref.: #69480]	anaerobic	no	99.098	no
[Ref.: #69480]	halophile	no	94.641	no
[Ref.: #69480]	spore-forming	no	94.042	no
[Ref.: #69480]	glucose-util	yes	91.105	no
[Ref.: #69480]	thermophile	no	99.333	yes
[Ref.: #69480]	aerobic	yes	93.887	yes
[Ref.: #69480]	motile	yes	88.111	no
[Ref.: #69480]	flagellated	yes	70.636	no
[Ref.: #69480]	glucose-ferment	no	88.718	no

Availability in culture collections External links

[Ref.: #30627]

Culture collection no.

KCTC 22382, NCIMB 14476

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Duganella rivus sp. nov., Duganella fentianensis sp. nov., Duganella qianjiadongensis sp. nov. and Massilia guangdongensis sp. nov., isolated from subtropical streams in China and reclassification of all species within genus Pseudoduganella.	Lu HB, Cai ZP, Yang YG, Xu MY	Antonie Van Leeuwenhoek	10.1007/s10482-020-01422-5	2020	*
Phylogeny	Duganella sacchari sp. nov. and Duganella radicis sp. nov., two novel species isolated from rhizosphere of field-grown sugar cane.	Madhaiyan M, Poonguzhali S, Saravanan VS, Hari K, Lee KC, Lee JS	Int J Syst Evol Microbiol	10.1099/ijs.0.040584-0	2012	*
Phylogeny	Duganella alba sp. nov., Duganella aquatilis sp. nov., Duganella margarita sp. nov. and Duganella levis sp. nov., isolated from subtropical streams in China.	Lu H, Deng T, Liu F, Wang Y, Yang X, Xu M	Int J Syst Evol Microbiol	10.1099/ijsem.0.004234	2020	*
Phylogeny	Duganella ginsengisoli sp. nov., isolated from ginseng soil.	Zhang J, Kim YJ, Hoang VA, Lan Nguyen N, Wang C, Kang JP, Wang D, Yang DC	Int J Syst Evol Microbiol	10.1099/ijsem.0.000669	2015	*

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 )

#30627

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 #26958 (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) .

#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 )

#26958

IJSEM 1126 2013 ( DOI 10.1099/ijs.0.040584-0 , PubMed 22753524 )

* These data were automatically processed and therefore are not curated

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Duganella radicis strain KCTC 22382

Duganella radicis strain KCTC 22382

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