Name: Diaphorobacter nitroreducens SL-205
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 130259

Type strain:

Species: Diaphorobacter nitroreducens

Strain Designation: SL-205

Culture col. no.: DSM 29460, ACCC 19739, JCM 30411

Strain history: T. Qiu; Beijing Agro-Biotechnol. Res. Center, China; SL-205.

NCBI tax ID(s): 164759 (species)

SI-ID 399216

DSM 29460

Special Collections

DSMZ
JCM

Other strains from Diaphorobacter nitroreducens

Section

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

Gram-negative
mesophilic
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	09-12-2024 (DD-MM-YYYY)
	Domain	*Bacteria*
	Phylum	*Pseudomonadota*
	Class	*Betaproteobacteria*
	Order	*Burkholderiales*
	Family	*Comamonadaceae*
	Genus	*Diaphorobacter*
	Species	**Diaphorobacter nitroreducens**
	Full Scientific Name (LPSN)	Diaphorobacter nitroreducens Khan and Hiraishi 2003

Synonym

Diaphorobacter polyhydroxybutyrativorans

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	negative Confidence in %98

Multimedia content

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Intellectual property rights:

Information on culture and growth conditions Culture and growth conditions

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Culture medium

LB (Luria-Bertani) MEDIUM (DSMZ Medium 381)

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Culture medium growth

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Culture medium link

Medium recipe provided by DSMZ

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Culture medium

NUTRIENT AGAR (DSMZ Medium 1)

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Culture medium growth

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Culture medium link

Medium recipe provided by DSMZ

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Culture medium

TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)

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Culture medium growth

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Culture medium link

Medium recipe at MediaDive

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Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #21576]			growth	28 °C
[Ref.: #67770]			growth	28 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #69481]

Ability of spore formation

no Confidence in %100

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68369]	adipate ChEBI	+	assimilation	* from API 20NE
[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.: #68369]	L-arabinose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	malate ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	maltose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	N-acetylglucosamine ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	nitrate ChEBI	+	reduction	* from API 20NE
[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.: #68369]	arginine dihydrolase	-	3.5.3.6	* from API 20NE
[Ref.: #68369]	beta-glucosidase	-	3.2.1.21	* from API 20NE
[Ref.: #68369]	cytochrome oxidase	+	1.9.3.1	* from API 20NE
[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.: #21576]	28048	+	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	+	+	-	-	+

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

[Ref.: #21576]	Sample type/isolated from	biofilm of a denitrifying reactor using PHBV as carbon source
[Ref.: #21576]	Geographic location (country and/or sea, region)	Beijing, Fangshan District
[Ref.: #21576]	Country	China
[Ref.: #21576]	Country ISO 3 Code	CHN
[Ref.: #21576]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Biofilms of a denitrifying reactor
* marker position based on {}

Isolation sources categories

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

What are isolation sources categories?

[Ref.: #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

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

[Ref.: #21576]

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.: #21576]	Diaphorobacter nitroreducens strain SL-205 16S ribosomal RNA gene, partial sequence	JX974341	1428	GenBank ENA	1546149 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Diaphorobacter nitroreducens SL-205	GCA_002214645	complete	GenBank ENA	164759 tax ID

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GC-content

66.8 mol%

thermal denaturation, midpoint method (Tm)

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

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Diaphorobacter nitroreducens SL-205 NCBI: GCA_002214645.1
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	100	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Diaphorobacter nitroreducens SL-205 NCBI: GCA_002214645.1
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	98	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	96.75	no
[Ref.: #69480]	aerobic	aerobicⓘ	yes	81.219	no
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	89.644	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	96.445	no
[Ref.: #69480]	flagellated	motile2+ⓘ	yes	84.111	no

Availability in culture collections External links

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Culture collection no.

DSM 29460, ACCC 19739, JCM 30411

[Ref.: #88798]

SI-ID 399216

Literature:

	Title	Authors	Journal	DOI	Year
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	*
	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	*

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 .

#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 )

#88798

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-ID399216.1 )

* These data were automatically processed and therefore are not curated

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