Diaphorobacter nitroreducens (DSM 29460, ACCC 19739, SL-205)

Name: Diaphorobacter nitroreducens (DSM 29460, ACCC 19739, SL-205)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 130259

Type strain

Strain Designation SL-205

Culture col. no. DSM 29460 ACCC 19739 SL-205 JCM 30411

NCBI tax ID(s) 164759

Special Collections DSMZ JCM

History <- T. Qiu, Beijing Academy of Agriculture and Forestry Science; SL-205 <- L. Iili, Beijing Academy of Agriculture and Forestry Science T. Qiu; Beijing Agro-Biotechnol. Res. Center, China; SL-205.

Links

Diaphorobacter nitroreducens SL-205 is a bacterium that was isolated from biofilm of a denitrifying reactor using PHBV as carbon source.

genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 399216

DSM 29460

@ref 20215

Last LPSN update 2026-02-09 11:31:10

Domain Bacteria

Phylum Pseudomonadota

Class Betaproteobacteria

Order Burkholderiales

Family Comamonadaceae

Genus Diaphorobacter

Species Diaphorobacter nitroreducens

Full scientific name Diaphorobacter nitroreducens Khan and Hiraishi 2003

Synonyms (1)

Diaphorobacter polyhydroxybutyrativorans

BacDive ID	Other strains from **Diaphorobacter nitroreducens** (1)	Type strain
2956	D. nitroreducens NA10B, DSM 15985, CIP 107294, JCM 11421 (type strain)

Morphology

Cell morphology

@ref	Gram stain	Confidence
125439	negative	99.3
125438	negative	98

Multimedia

@ref:	21576
multimedia content:	DSM_29460.jpg
multimedia.multimedia content:	https://www.dsmz.de/microorganisms/photos/DSM_29460.jpg
intellectual property rights:	© Leibniz-Institut DSMZ
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
21576	LB (Luria-Bertani) MEDIUM (DSMZ Medium 381)	Medium recipe at MediaDive	Name: LB (Luria-Bertani) MEDIUM (DSMZ Medium 381) Composition: Agar 20.0 g/l NaCl 10.0 g/l Tryptone 10.0 g/l Yeast extract 5.0 g/l Distilled water
21576	NUTRIENT AGAR (DSMZ Medium 1)	Medium recipe at MediaDive	Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
21576	TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)	Medium recipe at MediaDive	Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
21576	positive	growth	28
67770	positive	growth	28

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	95.1

Spore formation

@ref	Spore formation	Confidence
125439		98.5

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68369	17128 ChEBI	adipate	+	assimilation	from API 20NE
68369	29016 ChEBI	arginine	-	hydrolysis	from API 20NE
68369	17634 ChEBI	D-glucose	-	assimilation	from API 20NE
68369	17634 ChEBI	D-glucose	-	fermentation	from API 20NE
68369	16899 ChEBI	D-mannitol	-	assimilation	from API 20NE
68369	16024 ChEBI	D-mannose	-	assimilation	from API 20NE
68369	27689 ChEBI	decanoate	-	assimilation	from API 20NE
68369	4853 ChEBI	esculin	-	hydrolysis	from API 20NE
68369	5291 ChEBI	gelatin	-	hydrolysis	from API 20NE
68369	24265 ChEBI	gluconate	+	assimilation	from API 20NE
68369	30849 ChEBI	L-arabinose	-	assimilation	from API 20NE
68369	25115 ChEBI	malate	+	assimilation	from API 20NE
68369	17306 ChEBI	maltose	-	assimilation	from API 20NE
68369	59640 ChEBI	N-acetylglucosamine	-	assimilation	from API 20NE
68369	17632 ChEBI	nitrate	+	reduction	from API 20NE
68369	27897 ChEBI	tryptophan	-	energy source	from API 20NE
68369	16199 ChEBI	urea	-	hydrolysis	from API 20NE

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68369	35581 ChEBI	indole		from API 20NE

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
68369	35581 ChEBI	indole	-	from API 20NE

Enzymes

@ref	Value	Activity	Ec
68369	arginine dihydrolase	-	3.5.3.6	from API 20NE
68369	beta-glucosidase	-	3.2.1.21	from API 20NE
68369	cytochrome oxidase	+	1.9.3.1	from API 20NE
68369	gelatinase	-		from API 20NE
68369	urease	-	3.5.1.5	from API 20NE

API 20NE

@ref	Reduction of nitratesNO3	TRP	GLU_ Ferm	ADH (Arg)	URE	ESC	GEL	PNPG	GLU_ Assim	ARA	MNE	MAN	NAG	MAL	GNT	CAP	ADI	MLT	CIT	PAC	OX
21576	+	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	+	+	-	-	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Industrial	#Machines and devices
#Engineered	#Laboratory	#Lab enrichment
#Environmental	#Biofilm	-

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
21576	biofilm of a denitrifying reactor using PHBV as carbon source	Beijing, Fangshan District	China	CHN	Asia
67770	Biofilms of a denitrifying reactor

Taxonmaps

69479

Global distribution of 16S sequence JX974341 (>99% sequence identity) for Diaphorobacter nitroreducens from Microbeatlas

Aquatic Samples	6609
Soil Samples	4505
Animal Samples	8073
Plant Samples	2013
Total Samples	21200

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
21576	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	ASM221464v1 assembly for Diaphorobacter nitroreducens SL-205	complete	GCA_002214645	164759.5	2757320913	164759	99.22

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
21576	Diaphorobacter nitroreducens strain SL-205 16S ribosomal RNA gene, partial sequence	JX974341	1428		1546149

GC content

@ref	GC-content (mol%)	Method
21576	66.8	thermal denaturation, midpoint method (Tm)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Diaphorobacter nitroreducens SL-205
NCBI: GCA_002214645

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	98.50	no
125439	motility	BacteriaNetⓘ	yes	83.20	no
125439	gram_stain	BacteriaNetⓘ	negative	99.30	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	95.10	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Diaphorobacter nitroreducens SL-205
NCBI: GCA_002214645.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.00	no
125438	anaerobic	anaerobicⓘ	no	96.75	no
125438	aerobic	aerobicⓘ	yes	81.22	no
125438	spore-forming	spore-formingⓘ	no	89.64	no
125438	thermophilic	thermophileⓘ	no	96.45	no
125438	flagellated	motile2+ⓘ	yes	84.11	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Enhancement of Bacterial Survival and Self-Healing Performance in Mortars After Exposure to Negative Temperature Using Alumina Hollow Spheres as Bacterial Carriers.	Wang YS, Zhou YZ, Wang XD, Zhang GZ.	Materials (Basel)	10.3390/ma18102245	2025
	Bioaugmentation with Diaphorobacter polyhydroxybutyrativorans to enhance nitrate removal in a poly (3-hydroxybutyrate-co-3-hydroxyvalerate)-supported denitrification reactor.	Zhang S, Sun X, Wang X, Qiu T, Gao M, Sun Y, Cheng S, Zhang Q	Bioresour Technol	10.1016/j.biortech.2018.04.115	2018
	Heterotrophic nitrification and aerobic denitrification by Diaphorobacter polyhydroxybutyrativorans SL-205 using poly(3-hydroxybutyrate-co-3-hydroxyvalerate) as the sole carbon source.	Zhang S, Sun X, Fan Y, Qiu T, Gao M, Wang X	Bioresour Technol	10.1016/j.biortech.2017.05.185	2017
Phylogeny	Diaphorobacter polyhydroxybutyrativorans Qiu et al. 2015 is a later heterotypic synonym of Diaphorobacter nitroreducens Khan and Hiraishi 2003.	Liu Y, Zhu HH	Int J Syst Evol Microbiol	10.1099/ijsem.0.003582	2019
Phylogeny	Pulveribacter suum gen. nov., sp. nov., isolated from a pig farm dust collector.	Heo J, Cho HY, Heo I, Hong SB, Kim JS, Kwon SW, Kim SJ	Int J Syst Evol Microbiol	10.1099/ijsem.0.003082	2019
Phylogeny	Diaphorobacter polyhydroxybutyrativorans sp. nov., a novel poly(3-hydroxybutyrate-co-3-hydroxyvalerate)-degrading bacterium isolated from biofilms.	Qiu T, Zuo Z, Gao J, Gao M, Han M, Sun L, Zhang L, Wang X	Int J Syst Evol Microbiol	10.1099/ijs.0.000353	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 )
#21576	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 29460
#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 .
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#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 )

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Diaphorobacter nitroreducens (DSM 29460, ACCC 19739, SL-205)

Name and taxonomic classification

Morphology

Cell morphology

Multimedia

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API 20NE

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_002214645

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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