Rhodanobacter denitrificans (DSM 24678, JCM 17642, 116-2)

Name: Rhodanobacter denitrificans (DSM 24678, JCM 17642, 116-2)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 17526

Type strain

Strain Designation 116-2

Culture col. no. DSM 24678 JCM 17642 116-2

NCBI tax ID(s) 666685

Special Collections DSMZ JCM

Links

Rhodanobacter denitrificans 116-2 is a mesophilic prokaryote that was isolated from uranium and nitrate contaminated subsurface groundwater.

mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 398244

JCM 17642,DSM 24678

@ref 20215

Last LPSN update 2025-12-16 09:51:07

Domain Pseudomonadati

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Lysobacterales

Family Rhodanobacteraceae

Genus Rhodanobacter

Species Rhodanobacter denitrificans

Full scientific name Rhodanobacter denitrificans Prakash et al. 2012

BacDive ID	Other strains from **Rhodanobacter denitrificans** (1)	Type strain
17525	R. denitrificans 2APBS1, DSM 23569, JCM 17641 (type strain)

Morphology

Cell morphology

@ref	Gram stain	Confidence
125439	negative	99.6
125439		90.3

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
17729	REACTIVATION WITH LIQUID MEDIUM 830 (DSMZ Medium 830c)		Medium recipe at MediaDive	Name: REACTIVATION WITH LIQUID MEDIUM 830 (DSMZ Medium 830c) Composition: Agar 15.0 g/l Yeast extract 0.5 g/l Proteose peptone 0.5 g/l Casamino acids 0.5 g/l Glucose 0.5 g/l Starch 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
17729	positive	growth	28	mesophilic
67770	positive	growth	30	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	98.2

Spore formation

@ref	Spore formation	Confidence
125439		99.2

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2
#Engineered	#Contamination
#Environmental	#Aquatic

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
17729	uranium and nitrate contaminated subsurface groundwater	Oak Ridge, Integrated Field Research Center	USA	USA	North America
67770	Groundwater of the Oak Ridge Integrated Field Research Challenge (OR-IFRC) site	Oak Ridge, TN	USA	USA	North America

Taxonmaps

69479

Global distribution of 16S sequence JF719061 (>99% sequence identity) for Rhodanobacter from Microbeatlas

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

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
17729	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	NCBI tax ID	Score
124043	ASM2156063v1 assembly for Rhodanobacter denitrificans DSM-24678	complete	GCA_021560635	666685.119	666685	97.99
66792	Rh24678 assembly for Rhodanobacter denitrificans 116-2	contig	GCA_000264355		666685	9.85

Genome browser: GCA_021560635

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
17729	Rhodanobacter denitrificans strain 116-2 16S ribosomal RNA gene, partial sequence; and 16S-23S ribosomal RNA intergenic spacer, complete sequence	JF719061	2100		666685

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Rhodanobacter denitrificans 116-2
NCBI: GCA_000264355

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	99.20	no
125439	motility	BacteriaNetⓘ	yes	90.30	no
125439	gram_stain	BacteriaNetⓘ	negative	99.60	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.20	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Metabolism	Genome sequences for six Rhodanobacter strains, isolated from soils and the terrestrial subsurface, with variable denitrification capabilities.	Kostka JE, Green SJ, Rishishwar L, Prakash O, Katz LS, Marino-Ramirez L, Jordan IK, Munk C, Ivanova N, Mikhailova N, Watson DB, Brown SD, Palumbo AV, Brooks SC.	J Bacteriol	10.1128/jb.00871-12	2012
Phylogeny	Denitrifying bacteria from the genus Rhodanobacter dominate bacterial communities in the highly contaminated subsurface of a nuclear legacy waste site.	Green SJ, Prakash O, Jasrotia P, Overholt WA, Cardenas E, Hubbard D, Tiedje JM, Watson DB, Schadt CW, Brooks SC, Kostka JE.	Appl Environ Microbiol	10.1128/aem.06435-11	2012
Metabolism	A putative multicopper oxidase, IoxA, is involved in iodide oxidation by Roseovarius sp. strain A-2.	Shiroyama K, Kawasaki Y, Unno Y, Amachi S	Biosci Biotechnol Biochem	10.1080/09168451.2015.1052767	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

#17729	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 24678
#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 )
#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;
#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 .
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

Rate our new design

Content

About us

Rhodanobacter denitrificans (DSM 24678, JCM 17642, 116-2)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_021560635

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

Help

Social Media