Hyphomicrobium denitrificans (DSM 1869, X)

Name: Hyphomicrobium denitrificans (DSM 1869, X)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 6184

Type strain

Strain Designation X

Culture col. no. DSM 1869 X

NCBI tax ID(s) 53399

Special Collections DSMZ

Links

Hyphomicrobium denitrificans X is a mesophilic prokaryote of the family Hyphomicrobiaceae.

mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 125568

ATCC 51888,NCIMB 11706,DSM 1869,NCIB 11706

@ref 20215

Last LPSN update 2025-12-16 09:48:15

Domain Pseudomonadati

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Hyphomicrobiales

Family Hyphomicrobiaceae

Genus Hyphomicrobium

Species Hyphomicrobium denitrificans

Full scientific name Hyphomicrobium denitrificans Urakami et al. 1995

Morphology

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
915	HYPHOMICROBIUM STRAIN X MEDIUM (DSMZ Medium 166)		Medium recipe at MediaDive	Name: HYPHOMICROBIUM STRAIN X MEDIUM (DSMZ Medium 166) Composition: Agar 15.0 g/l Methylamine hydrochloride 3.4 g/l K2HPO4 1.55 g/l (NH4)2SO4 1.0 g/l NaH2PO4 x H2O 0.5 g/l MgSO4 x 7 H2O 0.2 g/l Na2-EDTA 0.01 g/l ZnSO4 x 7 H2O 0.0044 g/l CaCl2 x 2 H2O 0.001108 g/l MnCl2 x 4 H2O 0.001012 g/l FeSO4 x 7 H2O 0.001 g/l CoCl2 x 6 H2O 0.000322 g/l CuSO4 x 5 H2O 0.000314 g/l (NH4)6Mo7O24 x 4 H2O 0.00022 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
915	positive	growth	28	mesophilic

Physiology and metabolism

Compound production

@ref	Compound
915	dimethylamine dehydrogenase
915	methanol dehydrogenase

Isolation, sampling and environmental information

Isolation

@ref	Country	Country ISO 3 Code	Continent
915	Netherlands	NLD	Europe

Taxonmaps

69479

Global distribution of 16S sequence Y14308 (>99% sequence identity) for Hyphomicrobium denitrificans from Microbeatlas

Aquatic Samples	958
Soil Samples	841
Animal Samples	335
Plant Samples	179
Total Samples	2313

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
915	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
915	ASM14314v1 assembly for Hyphomicrobium denitrificans ATCC 51888	complete	GCA_000143145	582899.7	648028034	582899	98.2

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	Hyphomicrobium denitrificans partial 16S rRNA gene	AJ854111	1242		53399
20218	Hyphomicrobium denitrificans partial 16S rRNA gene, strain DSM 1869	Y14308	1446		53399

Genome-based predictions

Literature

Topic	Title	Authors	Journal	DOI	Year
	Safety of pyrroloquinoline quinone disodium salt as a novel food pursuant to Regulation (EC) No 258/97.	EFSA Panel on Dietetic Products, Nutrition and Allergies (NDA), Turck D, Bresson JL, Burlingame B, Dean T, Fairweather-Tait S, Heinonen M, Hirsch-Ernst KI, Mangelsdorf I, McArdle HJ, Naska A, Neuhauser-Berthold M, Nowicka G, Pentieva K, Sanz Y, Siani A, Sjodin A, Stern M, Tome D, Vinceti M, Willatts P, Engel KH, Marchelli R, Poting A, Poulsen M, Schlatter JR, de Sesmaisons A, Van Loveren H.	EFSA J	10.2903/j.efsa.2017.5058	2017
Enzymology	Quantitative detection of the nosZ gene, encoding nitrous oxide reductase, and comparison of the abundances of 16S rRNA, narG, nirK, and nosZ genes in soils.	Henry S, Bru D, Stres B, Hallet S, Philippot L.	Appl Environ Microbiol	10.1128/aem.00231-06	2006
Enzymology	Differences in hyporheic-zone microbial community structure along a heavy-metal contamination gradient.	Feris K, Ramsey P, Frazar C, Moore JN, Gannon JE, Holben WE.	Appl Environ Microbiol	10.1128/aem.69.9.5563-5573.2003	2003
Enzymology	Relative abundances of proteobacterial membrane-bound and periplasmic nitrate reductases in selected environments.	Bru D, Sarr A, Philippot L.	Appl Environ Microbiol	10.1128/aem.00643-07	2007
	Microbial community diversity associated with carbon and nitrogen cycling in permeable shelf sediments.	Hunter EM, Mills HJ, Kostka JE.	Appl Environ Microbiol	10.1128/aem.03007-05	2006
	Diversity and structure of hyphomicrobium populations in a sewage treatment plant and its adjacent receiving lake.	Holm NC, Gliesche CG, Hirsch P.	Appl Environ Microbiol	10.1128/aem.62.2.522-528.1996	1996
Phylogeny	Characterization of nitrifying, denitrifying, and overall bacterial communities in permeable marine sediments of the northeastern Gulf of Mexico.	Mills HJ, Hunter E, Humphrys M, Kerkhof L, McGuinness L, Huettel M, Kostka JE.	Appl Environ Microbiol	10.1128/aem.02692-07	2008
Phylogeny	Quantification of Hyphomicrobium populations in activated sludge from an industrial wastewater treatment system as determined by 16S rRNA analysis.	Layton AC, Karanth PN, Lajoie CA, Meyers AJ, Gregory IR, Stapleton RD, Taylor DE, Sayler GS	Appl Environ Microbiol	10.1128/AEM.66.3.1167-1174.2000	2000

References

#915	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 1869
#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 )
#20218	Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )
#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 .
#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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Hyphomicrobium denitrificans (DSM 1869, X)

Name and taxonomic classification

Morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Compound production

Isolation, sampling and environmental information

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000143145

16S sequences

Genome-based predictions

Literature

Literature

References

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