Haloferax denitrificans (DSM 4425, ATCC 35960, S1)

Name: Haloferax denitrificans (DSM 4425, ATCC 35960, S1)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 5930

Type strain

Strain Designation S1

Culture col. no. DSM 4425 ATCC 35960 S1 JCM 8864 CGMCC 1.2198 2 more

NCBI tax ID(s) 662478 35745

Special Collections DSMZ JCM

Links

Haloferax denitrificans S1 is a mesophilic prokaryote that was isolated from solar saltern.

mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 41391

ATCC 35960,DSM 4425,JCM 8864,NCIMB 13115,VKM B-1754,AS 1.2198,CGMCC 1.2149,AS 1.219,CGMCC 1.2198

@ref 20215

Last LPSN update 2025-12-16 09:48:11

Domain Methanobacteriati

Phylum Methanobacteriota

Class Halobacteria

Order Halobacteriales

Family Haloferacaceae

Genus Haloferax

Species Haloferax denitrificans

Full scientific name Haloferax denitrificans (Tomlinson et al. 1986) Tindall et al. 1989

Synonyms (1)

Halobacterium denitrificans

Morphology

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
1664	HALOBACTERIA MEDIUM (DSMZ Medium 372)		Medium recipe at MediaDive	Name: HALOBACTERIA MEDIUM (DSMZ Medium 372) Composition: NaCl 200.0 g/l MgSO4 x 7 H2O 20.0 g/l Agar 20.0 g/l Yeast extract 5.0 g/l Casamino acids 5.0 g/l Na3-citrate 3.0 g/l KCl 2.0 g/l Na glutamate 1.0 g/l FeCl2 x 4 H2O 0.036 g/l MnCl2 x 4 H2O 0.00036 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
1664	positive	growth	37	mesophilic
67770	positive	growth	37	mesophilic

Physiology and metabolism

Spore formation

@ref	Spore formation	Confidence
125439		95.9

Observation

67770

Observationquinones: MK-8, MK-8(H₂)

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2
#Condition	#Saline

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
1664	solar saltern	San Francisco Bay	USA	USA	North America
67770	Saltern in the southern portion of the San Francisco Bay

Taxonmaps

69479

Global distribution of 16S sequence D14128 (>99% sequence identity) for Haloferax from Microbeatlas

Aquatic Samples	7
Soil Samples	1
Animal Samples
Plant Samples
Total Samples	8

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
1664	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	Haloferax denitrificans S1	complete			2508501014	662478	92.17
67770	ASM33779v1 assembly for Haloferax denitrificans ATCC 35960	contig	GCA_000337795	662478.6	2534682141	662478	74.65

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	Haloferax denitrificans gene for 16S rRNA, complete sequence, strain: JCM 8864	AB663374	1473		662478
1664	Haloferax denitrificans gene for 16S rRNA, strain: ATCC35960	D14128	1469		662478

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Haloferax denitrificans ATCC 35960
NCBI: GCA_000337795

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	95.90	no
125439	motility	BacteriaNetⓘ	yes	64.30	no
125439	gram_stain	BacteriaNetⓘ	negative	86.70	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	54.80	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Production, characterization, and genomic insights of a human lectin-binding exopolysaccharide from Haloarcula japonica strain SST1.	Ghevondyan D, Hakobyan A, Margaryan A, Finore I, Cattaneo A, Chiodo F, Birkeland NK, Poli A, Panosyan H.	Sci Rep	10.1038/s41598-025-18462-4	2025
Phylogeny	Highly diverse nirK genes comprise two major clades that harbour ammonium-producing denitrifiers.	Helen D, Kim H, Tytgat B, Anne W.	BMC Genomics	10.1186/s12864-016-2465-0	2016
Metabolism	The Halophile protein database.	Sharma N, Farooqi MS, Chaturvedi KK, Lal SB, Grover M, Rai A, Pandey P.	Database (Oxford)	10.1093/database/bau114	2014
Metabolism	Dihydroxyacetone metabolism in Haloferax volcanii.	Ouellette M, Makkay AM, Papke RT.	Front Microbiol	10.3389/fmicb.2013.00376	2013
	Comparative Analysis of Surface Layer Glycoproteins and Genes Involved in Protein Glycosylation in the Genus Haloferax.	Shalev Y, Soucy SM, Papke RT, Gogarten JP, Eichler J, Gophna U.	Genes (Basel)	10.3390/genes9030172	2018
Transcriptome	Sequencing of seven haloarchaeal genomes reveals patterns of genomic flux.	Lynch EA, Langille MG, Darling A, Wilbanks EG, Haltiner C, Shao KS, Starr MO, Teiling C, Harkins TT, Edwards RA, Eisen JA, Facciotti MT.	PLoS One	10.1371/journal.pone.0041389	2012
Metabolism	Anaerobic Growth of Haloarchaeon Haloferax volcanii by Denitrification Is Controlled by the Transcription Regulator NarO.	Hattori T, Shiba H, Ashiki K, Araki T, Nagashima YK, Yoshimatsu K, Fujiwara T.	J Bacteriol	10.1128/jb.00833-15	2016
Enzymology	Exopolysaccharides from Marine and Marine Extremophilic Bacteria: Structures, Properties, Ecological Roles and Applications.	Casillo A, Lanzetta R, Parrilli M, Corsaro MM.	Mar Drugs	10.3390/md16020069	2018
Phylogeny	Quantifying homologous replacement of loci between haloarchaeal species.	Williams D, Gogarten JP, Papke RT.	Genome Biol Evol	10.1093/gbe/evs098	2012
Phylogeny	Unusually High Archaeal Diversity in a Crystallizer Pond, Pomorie Salterns, Bulgaria, Revealed by Phylogenetic Analysis.	Kambourova M, Tomova I, Boyadzhieva I, Radchenkova N, Vasileva-Tonkova E.	Archaea	10.1155/2016/7459679	2016
Enzymology	Wide distribution among halophilic archaea of a novel polyhydroxyalkanoate synthase subtype with homology to bacterial type III synthases.	Han J, Hou J, Liu H, Cai S, Feng B, Zhou J, Xiang H.	Appl Environ Microbiol	10.1128/aem.01117-10	2010
Metabolism	Denitrifying haloarchaea within the genus Haloferax display divergent respiratory phenotypes, with implications for their release of nitrogenous gases.	Torregrosa-Crespo J, Pire C, Martinez-Espinosa RM, Bergaust L.	Environ Microbiol	10.1111/1462-2920.14474	2019
Metabolism	Anaerobic Metabolism in Haloferax Genus: Denitrification as Case of Study.	Torregrosa-Crespo J, Martinez-Espinosa RM, Esclapez J, Bautista V, Pire C, Camacho M, Richardson DJ, Bonete MJ.	Adv Microb Physiol	10.1016/bs.ampbs.2016.02.001	2016
Metabolism	Perchlorate and halophilic prokaryotes: implications for possible halophilic life on Mars.	Oren A, Elevi Bardavid R, Mana L.	Extremophiles	10.1007/s00792-013-0594-9	2014
	The microbiome of Riccia liverworts is an important reservoir for microbial diversity in temporary agricultural crusts.	Wicaksono WA, Semler B, Poltl M, Berg C, Berg G, Cernava T.	Environ Microbiome	10.1186/s40793-023-00501-0	2023
Metabolism	d-Ribose Catabolism in Archaea: Discovery of a Novel Oxidative Pathway in Haloarcula Species.	Johnsen U, Sutter JM, Reinhardt A, Pickl A, Wang R, Xiang H, Schonheit P.	J Bacteriol	10.1128/jb.00608-19	2020
Genetics	Function-Based Rhizosphere Assembly along a Gradient of Desiccation in the Former Aral Sea.	Wicaksono WA, Egamberdieva D, Berg C, Mora M, Kusstatscher P, Cernava T, Berg G.	mSystems	10.1128/msystems.00739-22	2022
	Biosynthesis of silver nanoparticles using Haloferax sp. NRS1: image analysis, characterization, in vitro thrombolysis and cytotoxicity.	Tag HM, Saddiq AA, Alkinani M, Hagagy N.	AMB Express	10.1186/s13568-021-01235-3	2021
	Unraveling Anaerobic Metabolisms in a Hypersaline Sediment.	Solchaga JI, Busalmen JP, Nercessian D.	Front Microbiol	10.3389/fmicb.2022.811432	2022
Metabolism	Reduction of perchlorate and nitrate by salt tolerant bacteria.	Okeke BC, Giblin T, Frankenberger WT.	Environ Pollut	10.1016/s0269-7491(01)00288-3	2002
Enzymology	Haloferax mediterranei, an Archaeal Model for Denitrification in Saline Systems, Characterized Through Integrated Physiological and Transcriptional Analyses.	Torregrosa-Crespo J, Pire C, Bergaust L, Martinez-Espinosa RM.	Front Microbiol	10.3389/fmicb.2020.00768	2020
	Exploring the potentials of halophilic prokaryotes from a solar saltern for synthesizing nanoparticles: The case of silver and selenium.	Abdollahnia M, Makhdoumi A, Mashreghi M, Eshghi H.	PLoS One	10.1371/journal.pone.0229886	2020
	Potential Applications of Some Indigenous Bacteria Isolated from Polluted Areas in the Treatment of Brewery Effluents.	Oljira T, Muleta D, Jida M.	Biotechnol Res Int	10.1155/2018/9745198	2018
Enzymology	Purification and properties of a dissimilatory nitrate reductase from Haloferax denitrificans.	Hochstein LI, Lang F.	Arch Biochem Biophys	10.1016/0003-9861(91)90210-a	1991
	[Amplification of 16S rDNAs from halobacteria by means of PCR technique].	Zhou P, Xu Y, Ma Y, Liu H.	Wei Sheng Wu Xue Bao		1994
Enzymology	Properties of a thermostable nitrate reductase from the hyperthermophilic archaeon Pyrobaculum aerophilum.	Afshar S, Johnson E, de Vries S, Schroder I.	J Bacteriol	10.1128/jb.183.19.5491-5495.2001	2001
Metabolism	Pathways of carbon assimilation and ammonia oxidation suggested by environmental genomic analyses of marine Crenarchaeota.	Hallam SJ, Mincer TJ, Schleper C, Preston CM, Roberts K, Richardson PM, DeLong EF.	PLoS Biol	10.1371/journal.pbio.0040095	2006
Genetics	Structural studies on the acidic exopolysaccharide from Haloferax denitrificans ATCC 35960.	Parolis LA, Parolis H, Paramonov NA, Boan IF, Anton J, Rodriguez-Valera F	Carbohydr Res	10.1016/s0008-6215(99)00111-1	1999
Metabolism	Transfer of Halobacterium denitrificans (Tomlinson, Jahnke, and Hochstein) to the genus Haloferax as Haloferax denitrificans comb. nov.	Tindall BJ, Tomlinson GA, Hochstein LI	Int J Syst Bacteriol	10.1099/00207713-39-3-359	1989
Phylogeny	Haloferax profundi sp. nov. and Haloferax marisrubri sp. nov., Isolated from the Discovery Deep Brine-Seawater Interface in the Red Sea.	Zhang G, Dong X, Sun Y, Antunes A, Hikmawan T, Haroon MF, Wang J, Stingl U	Microorganisms	10.3390/microorganisms8101475	2020
Phylogeny	Haloferax chudinovii sp. nov., a halophilic archaeon from Permian potassium salt deposits.	Saralov AI, Baslerov RV, Kuznetsov BB	Extremophiles	10.1007/s00792-013-0534-8	2013
Metabolism	Halobacterium denitrificans sp. nov., an extremely halophilic denitrifying bacterium.	Tomlinson GA, Jahnke LL, Hochstein LI	Int J Syst Bacteriol	10.1099/00207713-36-1-66	1986

References

#1664	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 4425
#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 )
#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 .
#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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Haloferax denitrificans (DSM 4425, ATCC 35960, S1)

Name and taxonomic classification

Morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Spore formation

Observation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000337795

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

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