Nitrobacter winogradskyi (DSM 10237, ATCC 25391, 255)

Name: Nitrobacter winogradskyi (DSM 10237, ATCC 25391, 255)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 1796

Type strain

Strain Designation 255, Nb-255

Culture col. no. DSM 10237 ATCC 25391 255 Nb-255

NCBI tax ID(s) 913

Special Collections DSMZ

History <- E. Spiek <- E. Bock

Links

Nitrobacter winogradskyi 255 is a bacterium of the family Nitrobacteraceae.

genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 38533

ATCC 25391,DSM 10237,NCIMB 11846,LMG 19030,ICMP 13140,CIP 104748

@ref 20215

Last LPSN update 2026-02-09 11:18:11

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Hyphomicrobiales

Family Nitrobacteraceae

Genus Nitrobacter

Species Nitrobacter winogradskyi

Full scientific name Nitrobacter winogradskyi Winslow et al. 1917 (Approved Lists 1980)

BacDive ID	Other strains from **Nitrobacter winogradskyi** (1)	Type strain
145156	N. winogradskyi CCUG 27769, IFO 14297, NBRC 14297, ATCC 14123

Morphology

Cell morphology

@ref	Gram stain	Confidence
125438	negative	96.328
125439	negative	98.6

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
3860	MIXOTROPHIC NITROBACTER MEDIUM (DSMZ Medium 756a)		Medium recipe at MediaDive	Name: MIXOTROPHIC NITROBACTER MEDIUM (DSMZ Medium 756a) Composition: NaNO2 2.0 g/l Yeast extract 1.5 g/l Peptone 1.5 g/l Na-pyruvate 0.55 g/l NaCl 0.5 g/l KH2PO4 0.15 g/l MgSO4 x 7 H2O 0.05 g/l CaCO3 0.007 g/l FeSO4 x 7 H2O 9.73e-05 g/l H3BO3 4.94e-05 g/l ZnSO4 x 7 H2O 4.31e-05 g/l (NH4)6Mo7O24 3.71e-05 g/l MnSO4 x H2O 3.38e-05 g/l CuSO4 x 5 H2O 2.5e-05 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
3860	positive	growth	28

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	aerobe	98.1

Spore formation

@ref	Spore formation	Confidence
125439		98.2

Isolation, sampling and environmental information

Taxonmaps

69479

Global distribution of 16S sequence NR_074324 (>99% sequence identity) for Nitrobacter from Microbeatlas

Aquatic Samples	1315
Soil Samples	5887
Animal Samples	625
Plant Samples	1158
Total Samples	8985

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
3860	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
66792	ASM1272v1 assembly for Nitrobacter winogradskyi Nb-255	complete	GCA_000012725	323098.6	637000193	323098	98.65

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
3860	Nitrobacter winogradskyi strain Nb-255 16S ribosomal RNA, partial sequence	NR_074324	1490		913

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Nitrobacter winogradskyi Nb-255
PATRIC: 323098.6

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	98.20	no
125439	motility	BacteriaNetⓘ	yes	75.50	no
125439	gram_stain	BacteriaNetⓘ	negative	98.60	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	98.10	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Nitrobacter winogradskyi Nb-255
PATRIC: 323098.6

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	96.33	no
125438	anaerobic	anaerobicⓘ	no	89.20	no
125438	spore-forming	spore-formingⓘ	no	87.59	no
125438	aerobic	aerobicⓘ	yes	73.27	no
125438	thermophilic	thermophileⓘ	no	92.28	yes
125438	flagellated	motile2+ⓘ	yes	65.75	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Impact of Combined Exposure to Copper Nanoparticles, Copper Oxide Nanoparticles, and Pesticides on the Metabolic Activity of Nitrobacter winogradskyi.	Gajardo R, Rubilar O, Lopez-Mena E, Sanchez-Ante G, Fincheira P, Martinez M, Schoebitz M, Tighe-Neira R, Inostroza-Blancheteau C, Bardelhe L, Tortella-Fuentes G.	Int J Mol Sci	10.3390/ijms26136391	2025
Enzymology	Biochemical and structural characterization of chlorite dismutase enzyme from Pseudomonas aeruginosa.	Nokas DV, Panagiotopoulou EK, Kapogiannatos AI, Premetis GE, Labrou NE, Efthimiadou EK, Papageorgiou AC, Chronopoulou EG.	FEBS J	10.1111/febs.70151	2025
Enzymology	Establishing a co-culture aggregate of N-cycle bacteria to elucidate flocculation in biological wastewater treatment.	Parret L, Simoens K, Horemans B, De Vrieze J, Smets I.	Appl Microbiol Biotechnol	10.1007/s00253-025-13522-1	2025
	BIO-SPEC: An open-source bench-top parallel bioreactor system	Parret L, Simoens K, De Vrieze J, Smets I.	HardwareX		2025
	Conversion of monoculture cropland and open grassland to agroforestry alters the abundance of soil bacteria, fungi and soil-N-cycling genes.	Beule L, Corre MD, Schmidt M, Gobel L, Veldkamp E, Karlovsky P.	PLoS One	10.1371/journal.pone.0218779	2019
	Diversity of green-like and red-like ribulose-1,5-bisphosphate carboxylase/oxygenase large-subunit genes (cbbL) in differently managed agricultural soils.	Selesi D, Schmid M, Hartmann A.	Appl Environ Microbiol	10.1128/aem.71.1.175-184.2005	2005
	The Stochastic Assembly of Nitrobacter winogradskyi-Selected Microbiomes with Heterotrophs from Sewage Sludge or Grassland Soil.	Laanbroek HJ, Cassman NA, Keijzer RM, Kuramae EE.	Appl Environ Microbiol	10.1128/aem.00783-22	2022
Metabolism	Metabolic and Proteomic Responses to Salinity in Synthetic Nitrifying Communities of Nitrosomonas spp. and Nitrobacter spp.	Ilgrande C, Leroy B, Wattiez R, Vlaeminck SE, Boon N, Clauwaert P.	Front Microbiol	10.3389/fmicb.2018.02914	2018
	Development of Nitrogen Recycling Strategies for Bioregenerative Life Support Systems in Space.	Verbeelen T, Leys N, Ganigue R, Mastroleo F.	Front Microbiol	10.3389/fmicb.2021.700810	2021
Metabolism	A New Acyl-homoserine Lactone Molecule Generated by Nitrobacter winogradskyi.	Shen Q, Gao J, Liu J, Liu S, Liu Z, Wang Y, Guo B, Zhuang X, Zhuang G.	Sci Rep	10.1038/srep22903	2016
	Effects of Simulated Rare Earth Recycling Wastewaters on Biological Nitrification.	Fujita Y, Barnes J, Eslamimanesh A, Lencka MM, Anderko A, Riman RE, Navrotsky A.	Environ Sci Technol	10.1021/acs.est.5b01753	2015
Phylogeny	Analysis of Bacterial Communities in Partial Nitritation and Conventional Nitrification Systems for Nitrogen Removal.	Zhao Z, Luo J, Jin B, Zhang J, Li B, Ma B, An X, Zhang S, Shan B.	Sci Rep	10.1038/s41598-018-30532-4	2018
Metabolism	Effects of Bacterial Community Members on the Proteome of the Ammonia-Oxidizing Bacterium Nitrosomonas sp. Strain Is79.	Sedlacek CJ, Nielsen S, Greis KD, Haffey WD, Revsbech NP, Ticak T, Laanbroek HJ, Bollmann A.	Appl Environ Microbiol	10.1128/aem.01171-16	2016
Genetics	Complete genome sequence of Nitrobacter hamburgensis X14 and comparative genomic analysis of species within the genus Nitrobacter.	Starkenburg SR, Larimer FW, Stein LY, Klotz MG, Chain PS, Sayavedra-Soto LA, Poret-Peterson AT, Gentry ME, Arp DJ, Ward B, Bottomley PJ.	Appl Environ Microbiol	10.1128/aem.02311-07	2008
Metabolism	Nitrite as a stimulus for ammonia-starved Nitrosomonas europaea.	Laanbroek HJ, Bar-Gilissen MJ, Hoogveld HL.	Appl Environ Microbiol	10.1128/aem.68.3.1454-1457.2002	2002
Metabolism	Comparative analysis of nitrifying bacteria associated with freshwater and marine aquaria.	Hovanec TA, DeLong EF.	Appl Environ Microbiol	10.1128/aem.62.8.2888-2896.1996	1996
	Effects of Grazing by Flagellates on Competition for Ammonium between Nitrifying and Heterotrophic Bacteria in Soil Columns.	Verhagen FJ, Duyts H, Laanbroek HJ.	Appl Environ Microbiol	10.1128/aem.59.7.2099-2106.1993	1993
Metabolism	Influence of starvation on potential ammonia-oxidizing activity and amoA mRNA levels of Nitrosospira briensis.	Bollmann A, Schmidt I, Saunders AM, Nicolaisen MH.	Appl Environ Microbiol	10.1128/aem.71.3.1276-1282.2005	2005
Metabolism	Growth at low ammonium concentrations and starvation response as potential factors involved in niche differentiation among ammonia-oxidizing bacteria.	Bollmann A, Bar-Gilissen MJ, Laanbroek HJ.	Appl Environ Microbiol	10.1128/aem.68.10.4751-4757.2002	2002
	Effects of Grazing by Flagellates on Competition for Ammonium between Nitrifying and Heterotrophic Bacteria in Chemostats.	Verhagen FJ, Laanbroek HJ.	Appl Environ Microbiol	10.1128/aem.58.6.1962-1969.1992	1992
	Competition for Ammonium between Nitrifying and Heterotrophic Bacteria in Dual Energy-Limited Chemostats.	Verhagen FJ, Laanbroek HJ.	Appl Environ Microbiol	10.1128/aem.57.11.3255-3263.1991	1991
Biotechnology	Detection of Salmonella spp. in oysters by PCR.	Bej AK, Mahbubani MH, Boyce MJ, Atlas RM.	Appl Environ Microbiol	10.1128/aem.60.1.368-373.1994	1994
	Competition for Ammonium between Nitrifying and Heterotrophic Bacteria in Continuously Percolated Soil Columns.	Verhagen FJ, Duyts H, Laanbroek HJ.	Appl Environ Microbiol	10.1128/aem.58.10.3303-3311.1992	1992
Phylogeny	Distribution of Nitrosomonas europaea and Nitrobacter winogradskyi in an autotrophic nitrifying biofilm reactor as depicted by molecular analyses and mathematical modelling.	Montras A, Pycke B, Boon N, Godia F, Mergeay M, Hendrickx L, Perez J	Water Res	10.1016/j.watres.2007.10.025	2007
Genetics	Genome sequence of the chemolithoautotrophic nitrite-oxidizing bacterium Nitrobacter winogradskyi Nb-255.	Starkenburg SR, Chain PS, Sayavedra-Soto LA, Hauser L, Land ML, Larimer FW, Malfatti SA, Klotz MG, Bottomley PJ, Arp DJ, Hickey WJ	Appl Environ Microbiol	10.1128/AEM.72.3.2050-2063.2006	2006

References

#3860	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 10237
#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) .
#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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Nitrobacter winogradskyi (DSM 10237, ATCC 25391, 255)

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

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000012725

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

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