Name: Rhodanobacter denitrificans 2APBS1
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 17525

Type strain:

Species: Rhodanobacter denitrificans

Strain Designation: 2APBS1

Culture col. no.: DSM 23569, JCM 17641

Strain history: J. E. Kostka 2APBS1.

NCBI tax ID(s): 666685 (species)

SI-ID 398151

DSM 23569

Other strains from Rhodanobacter denitrificans

R. denitrificans 116-2, DSM 24678, JCM 17642

Section

Rhodanobacter denitrificans 2APBS1 is a facultative anaerobe, mesophilic, Gram-negative bacterium that was isolated from subsurface sediment contaminated with uranium and nitrate.

Gram-negative
motile
rod-shaped
facultative anaerobe
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	*Gammaproteobacteria*
	Order	*Lysobacterales*
	Family	*Rhodanobacteraceae*
	Genus	*Rhodanobacter*
	Species	**Rhodanobacter denitrificans**
	Full Scientific Name (LPSN)	Rhodanobacter denitrificans Prakash et al. 2012

Information on morphological and physiological properties Morphology

[Ref.: #30428]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.986

[Ref.: #30428]	Cell shape	rod-shaped

[Ref.: #30428]	Motility	yes
[Ref.: #69480]	Motility	yes Confidence in %94.636

[Ref.: #30428]

Pigment production

yes

Multimedia content

[Ref.: #17289]

Intellectual property rights:

Information on culture and growth conditions Culture and growth conditions

[Ref.: #17289]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #17289]

Culture medium growth

[Ref.: #17289]

Culture medium link

Medium recipe at MediaDive

[Ref.: #17289]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #17289]	growth	30 °C
[Ref.: #30428]	growth	10-35 °C
[Ref.: #30428]	optimum	30 °C
[Ref.: #67770]	growth	30 °C

[Ref.: #17289]	Temperature range	mesophilic
[Ref.: #30428]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #30428]			optimum	6.5
[Ref.: #30428]			growth	04-08

Information on physiology and metabolism Physiology and metabolism

[Ref.: #30428]

Oxygen tolerance

facultative anaerobe

[Ref.: #30428]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.992

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #30428]		NaCl		growth	<2	%

[Ref.: #67770]

Observation

quinones: Q-8

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #30428]	3-hydroxybutyrate ChEBI	+	carbon source
[Ref.: #68369]	adipate ChEBI	-	assimilation	* from API 20NE
[Ref.: #30428]	arabinose ChEBI	+	carbon source
[Ref.: #68369]	arginine ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #68369]	D-glucose ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	D-glucose ChEBI	-	fermentation	* from API 20NE
[Ref.: #68369]	D-mannitol ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	D-mannose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	decanoate ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	esculin ChEBI	+	hydrolysis	* from API 20NE
[Ref.: #68369]	gelatin ChEBI	+	hydrolysis	* from API 20NE
[Ref.: #68369]	gluconate ChEBI	-	assimilation	* from API 20NE
[Ref.: #30428]	glucose ChEBI	+	carbon source
[Ref.: #30428]	glycogen ChEBI	+	carbon source
[Ref.: #68369]	L-arabinose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	malate ChEBI	-	assimilation	* from API 20NE
[Ref.: #30428]	maltose ChEBI	+	carbon source
[Ref.: #68369]	maltose ChEBI	+	assimilation	* from API 20NE
[Ref.: #30428]	N-acetylglucosamine ChEBI	+	carbon source
[Ref.: #68369]	N-acetylglucosamine ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	nitrate ChEBI	+	reduction	* from API 20NE
[Ref.: #30428]	ribose ChEBI	+	carbon source
[Ref.: #30428]	salicin ChEBI	+	carbon source
[Ref.: #68369]	tryptophan ChEBI	-	energy source	* from API 20NE
[Ref.: #68369]	urea ChEBI	-	hydrolysis	* from API 20NE
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #68369]		indole ChEBI	no	* from API 20NE

	Physiological tests	Metabolite	Indole test
[Ref.: #68369]		indole ChEBI	-	* from API 20NE

	Enzyme	Enzyme activity	EC number
[Ref.: #30428]	acid phosphatase	+	3.1.3.2
[Ref.: #30428]	alkaline phosphatase	+	3.1.3.1
[Ref.: #68369]	arginine dihydrolase	-	3.5.3.6	* from API 20NE
[Ref.: #68369]	beta-glucosidase	+	3.2.1.21	* from API 20NE
[Ref.: #30428]	catalase	+	1.11.1.6
[Ref.: #30428]	cytochrome oxidase	+	1.9.3.1
[Ref.: #68369]	cytochrome oxidase	+	1.9.3.1	* from API 20NE
[Ref.: #30428]	gelatinase	+
[Ref.: #68369]	gelatinase	+		* from API 20NE
[Ref.: #68369]	urease	-	3.5.1.5	* from API 20NE

API® 20NE:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Reduction of nitratesNO3	Indole productionTRP	Fermentation of D-glucoseGLU_ Ferm	Arginine dihydrolaseADH (Arg)	Urease/urea hydrolysisURE	Esculin hydrolysis/beta-GlucosidaseESC	Gelatinase/gelatin hydrolysisGEL	beta-GalactosidasePNPG	Assimilation of D-glucoseGLU_ Assim	Assimilation of L-arabinoseARA	Assimilation of D-mannoseMNE	Assimilation of D-mannitolMAN	Assimilation of N-acetyl-glucosamineNAG	Assimilation of maltoseMAL	Assimilation of gluconateGNT	Assimilation of capric acidCAP	Assimilation adipic acidADI	Assimilation of malic acidMLT	Assimilation of citric acidCIT	Assimilation of phenyl-acetic acidPAC	Cytochrome oxidaseOX
[Ref.: #17289]	24750	+	-	-	-	-	+	+	-	+	-	-	-	+	+	-	-	-	-	-	-	+

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

[Ref.: #17289]	Sample type/isolated from	subsurface sediment contaminated with uranium and nitrate
[Ref.: #17289]	Geographic location (country and/or sea, region)	TN, Oak Ridge Integrated Field Research site, borehole FW107
[Ref.: #17289]	Country	USA
[Ref.: #17289]	Country ISO 3 Code	USA
[Ref.: #17289]	Continent	North America

[Ref.: #67770]	Sample type/isolated from	Sediment of the Oak Ridge Integrated Field Research Challenge (OR-IFRC) site
[Ref.: #67770]	Geographic location (country and/or sea, region)	Oak Ridge, TN
[Ref.: #67770]	Country	USA
[Ref.: #67770]	Country ISO 3 Code	USA
[Ref.: #67770]	Continent	North America
* marker position based on {}

Isolation sources categories

#Engineered	#Contamination	-
#Environmental	#Terrestrial	#Sediment

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence JF719060 (>99% sequence identity) for Rhodanobacter from Microbeatlas

Aquatic Samples	515
Soil Samples	1614
Animal Samples	424
Plant Samples	459
Total Samples	3012

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

[Ref.: #17289]

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.: #17289]	Rhodanobacter denitrificans strain 2APBS1 16S ribosomal RNA gene, partial sequence	FJ851443	1419	ENA	666685 tax ID
[Ref.: #67770]	Rhodanobacter denitrificans strain 2APBS1 16S ribosomal RNA gene and 16S-23S ribosomal RNA intergenic spacer, complete sequence	JF719060	2125	ENA	666685 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Rhodanobacter denitrificans 2APBS1	GCA_000230695	complete	GenBank	666685 tax ID	*
[Ref.: #66792]	Rhodanobacter denitrificans 2APBS1	2506520041	complete	JGI IMG/M	666685 tax ID	*

[Ref.: #17289]	GC-content	67.5 mol%	sequence analysis
[Ref.: #30428]	GC-content	67.5 mol%
[Ref.: #67770]	GC-content	67.5 mol%	genome sequence analysis

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: Rhodanobacter denitrificans 2APBS1 NCBI: GCA_000230695.3
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Rhodanobacter denitrificans 2APBS1 NCBI: GCA_000230695.3
[Ref.: #69480]	motile	yes	80.802	no
[Ref.: #69480]	flagellated	no	80.868	no
[Ref.: #69480]	gram-positive	no	97.918	no
[Ref.: #69480]	anaerobic	no	98.423	no
[Ref.: #69480]	aerobic	yes	83.674	yes
[Ref.: #69480]	halophile	no	93.837	no
[Ref.: #69480]	spore-forming	no	95.22	yes
[Ref.: #69480]	glucose-util	yes	84.618	yes
[Ref.: #69480]	thermophile	no	98.469	yes
[Ref.: #69480]	glucose-ferment	no	90.773	yes

Availability in culture collections External links

[Ref.: #17289]

Culture collection no.

DSM 23569, JCM 17641

[Ref.: #86522]

SI-ID 398151

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Rhodanobacter rhizosphaerae sp. nov., isolated from soil of ginseng rhizosphere.	Cho GY, Lee JC, Whang KS	Int J Syst Evol Microbiol	10.1099/ijsem.0.001825	2017	*
Phylogeny	Rhodanobacter humi sp. nov., an acid-tolerant and alkalitolerant gammaproteobacterium isolated from forest soil.	Dahal RH, Kim J	Int J Syst Evol Microbiol	10.1099/ijsem.0.001786	2017	*
Phylogeny	Rhodanobacter aciditrophus sp. nov., an acidophilic bacterium isolated from mine wastewater.	Koh HW, Hong H, Min UG, Kang MS, Kim SG, Na JG, Rhee SK, Park SJ	Int J Syst Evol Microbiol	10.1099/ijsem.0.000614	2015	*
Phylogeny	Rhodanobacter denitrificans sp. nov., isolated from nitrate-rich zones of a contaminated aquifer.	Prakash O, Green SJ, Jasrotia P, Overholt WA, Canion A, Watson DB, Brooks SC, Kostka JE	Int J Syst Evol Microbiol	10.1099/ijs.0.035840-0	2011	*

References

#17289

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 23569

#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 )

#30428

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 #26764 (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) .

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#68369

Automatically annotated from API 20NE .

#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 )

#86522

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-ID398151.1 )

#26764

IJSEM 2457 2012 ( DOI 10.1099/ijs.0.035840-0 , PubMed 22140175 )

* These data were automatically processed and therefore are not curated

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