Halobacterium salinarum (DSM 671, CCUG 24034, R1)

Name: Halobacterium salinarum (DSM 671, CCUG 24034, R1)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 5911

Type strain

Strain Designation R1

Culture col. no. DSM 671 CCUG 24034 R1 JCM 9409 ATCC 29341 1 more

NCBI tax ID(s) 2242

Special Collections DSMZ CCUG JCM

Links

Halobacterium salinarum R1 is an aerobe, mesophilic prokaryote of the family Halobacteriaceae.

aerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 92941

ATCC 29341,CCUG 24034,DSM 671,JCM 9409,NCIMB 2080,CGMCC 1.2368

@ref 20215

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

Domain Methanobacteriati

Phylum Methanobacteriota

Class Halobacteria

Order Halobacteriales

Family Halobacteriaceae

Genus Halobacterium

Species Halobacterium salinarum

Full scientific name Halobacterium salinarum corrig. (Harrison and Kennedy 1922) Elazari-Volcani 1957 (Approved Lists 1980)

Synonyms (9)

Halobacterium halobium
"Halobacter cutirubrum"
Halobacterium cutirubrum
"Bacterium halobium"
Halobacterium piscisalsi
Halobacterium salinarium
"Pseudomonas salinaria"
"Halobacter salinaria"
"Serratia cutirubra"

BacDive ID	Other strains from **Halobacterium salinarum** (14)	Type strain
5912	H. salinarum 91-R6, DSM 3754, ATCC 33171, JCM 8978, NCMB ... (type strain)
5908	H. salinarum 1, DSM 668, ATCC 19700
5909	H. salinarum 63-R2, DSM 669, ATCC 33170, NRC 34001, JCM ...
5910	H. salinarum DSM 670, JCM 20854, ATCC 43214, IAM 13167, ...
23038	H. salinarum DS21, GRB, DSM 22414
100563	H. salinarum ST033385(HKI),
24073	H. salinarum GRB-mut326-P577, DSM 21899, MUT mut326, MUT ...
134335	H. salinarum HPC1-2, BCC 24372, JCM 14661, PCU 302
161096	H. salinarum JCM 10927
162900	H. salinarum JCM 20370, IAM 12046
165991	H. salinarum JCM 9118, CCM 2148
165992	H. salinarum JCM 9119, CCM 2088
165993	H. salinarum JCM 9120, CCM 2090
165994	H. salinarum JCM 9121, CCM 2084

Morphology

Cell morphology

@ref	Motility	Confidence
125438		90.333

Colony morphology

47906

Incubation period4 days

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
354	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
354	HALOBACTERIUM MEDIUM (DSMZ Medium 97)		Medium recipe at MediaDive	Name: HALOBACTERIUM MEDIUM (DSMZ Medium 97) Composition: NaCl 250.0 g/l Agar 20.0 g/l MgSO4 x 7 H2O 20.0 g/l Yeast extract 10.0 g/l Casamino acids 7.5 g/l Na3-citrate 3.0 g/l KCl 2.0 g/l FeSO4 x 7 H2O 0.05 g/l MnSO4 x H2O 0.0002 g/l Distilled water

Culture temp

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

Physiology and metabolism

Oxygen tolerance

47906

Oxygen toleranceaerobe

Spore formation

@ref	Spore formation	Confidence
125439		90.1

Observation

67770

Observationquinones: MK-8, MK-8(H₂)

Isolation, sampling and environmental information

Taxonmaps

69479

Global distribution of 16S sequence M11583 (>99% sequence identity) for Halobacterium salinarum from Microbeatlas

Aquatic Samples	26
Soil Samples	5
Animal Samples	2
Plant Samples
Total Samples	33

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
354	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	ASM6902v1 assembly for Halobacterium salinarum R1 DSM 671 = R1	complete	GCA_000069025	478009.20	641522631	478009	98.53
66792	Halobacterium salinarum R1, DSM 671	complete			2596583691	478009	87.07

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
67770	Halobacterium halobium 16S rRNA gene, complete cds	M11583	1473		2242

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Halobacterium salinarum R1, DSM 671
IMG: 641522631

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	90.10	no
125439	motility	BacteriaNetⓘ	no	54.20	no
125439	gram_stain	BacteriaNetⓘ	positive	77.20	no
125439	oxygen_tolerance	BacteriaNetⓘ	facultative aerobe	67.00	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Halobacterium salinarum R1 DSM 671 = R1
NCBI: GCA_000069025.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	77.78	no
125438	anaerobic	anaerobicⓘ	no	85.22	yes
125438	aerobic	aerobicⓘ	yes	79.27	yes
125438	spore-forming	spore-formingⓘ	no	88.95	no
125438	thermophilic	thermophileⓘ	no	80.10	no
125438	flagellated	motile2+ⓘ	no	90.33	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Comparative Genomics of Halobacterium salinarum Strains Isolated from Salted Foods Reveals Protechnological Genes for Food Applications.	Fontana A, Falasconi I, Bellassi P, Fanfoni E, Puglisi E, Morelli L.	Microorganisms	10.3390/microorganisms11030587	2023
	Nutrient Removal and Recovery from Urine Using Bio-Mineral Formation Processes.	Colston RE, Nair A, Vale P, Hassard F, Stephenson T, Soares A.	ACS Sustain Resour Manag	10.1021/acssusresmgt.4c00025	2024
Genetics	Genome comparison reveals that Halobacterium salinarum 63-R2 is the origin of the twin laboratory strains NRC-1 and R1.	Pfeiffer F, Dyall-Smith M.	Microbiologyopen	10.1002/mbo3.1365	2023
	Surviving salt fluctuations: stress and recovery in Halobacterium salinarum, an extreme halophilic Archaeon.	Vauclare P, Natali F, Kleman JP, Zaccai G, Franzetti B.	Sci Rep	10.1038/s41598-020-59681-1	2020
Phylogeny	Halobacterium salinarum virus ChaoS9, a Novel Halovirus Related to PhiH1 and PhiCh1.	Dyall-Smith M, Palm P, Wanner G, Witte A, Oesterhelt D, Pfeiffer F.	Genes (Basel)	10.3390/genes10030194	2019
	Comparison of Miniaturized Raman Spectrometers for Discrimination of Carotenoids of Halophilic Microorganisms.	Jehlicka J, Culka A, Mana L, Oren A.	Front Microbiol	10.3389/fmicb.2019.01155	2019
Metabolism	The role of pH on the biological struvite production in digested sludge dewatering liquors.	Simoes F, Vale P, Stephenson T, Soares A.	Sci Rep	10.1038/s41598-018-25431-7	2018
Genetics	Deconstruction of archaeal genome depict strategic consensus in core pathways coding sequence assembly.	Pal A, Banerjee R, Mondal UK, Mukhopadhyay S, Bothra AK.	PLoS One	10.1371/journal.pone.0118245	2015
	Novel pili-like surface structures of Halobacterium salinarum strain R1 are crucial for surface adhesion.	Losensky G, Vidakovic L, Klingl A, Pfeifer F, Frols S.	Front Microbiol	10.3389/fmicb.2014.00755	2014
Genetics	Characterization of the mechanism of prolonged adaptation to osmotic stress of Jeotgalibacillus malaysiensis via genome and transcriptome sequencing analyses.	Yaakop AS, Chan KG, Ee R, Lim YL, Lee SK, Manan FA, Goh KM.	Sci Rep	10.1038/srep33660	2016
	Potential and limits of Raman spectroscopy for carotenoid detection in microorganisms: implications for astrobiology.	Jehlicka J, Edwards HG, Osterrothova K, Novotna J, Nedbalova L, Kopecky J, Nemec I, Oren A.	Philos Trans A Math Phys Eng Sci	10.1098/rsta.2014.0199	2014
Metabolism	Systems analysis of bioenergetics and growth of the extreme halophile Halobacterium salinarum.	Gonzalez O, Gronau S, Pfeiffer F, Mendoza E, Zimmer R, Oesterhelt D.	PLoS Comput Biol	10.1371/journal.pcbi.1000332	2009
	Variations in metabolic pathways create challenges for automated metabolic reconstructions: Examples from the tetrahydrofolate synthesis pathway.	de Crecy-Lagard V.	Comput Struct Biotechnol J	10.1016/j.csbj.2014.05.008	2014
Metabolism	Protein-DNA binding dynamics predict transcriptional response to nutrients in archaea.	Todor H, Sharma K, Pittman AM, Schmid AK.	Nucleic Acids Res	10.1093/nar/gkt659	2013
Genetics	Genome information management and integrated data analysis with HaloLex.	Pfeiffer F, Broicher A, Gillich T, Klee K, Mejia J, Rampp M, Oesterhelt D.	Arch Microbiol	10.1007/s00203-008-0389-z	2008
Metabolism	Transcriptional control by two leucine-responsive regulatory proteins in Halobacterium salinarum R1.	Schwaiger R, Schwarz C, Furtwangler K, Tarasov V, Wende A, Oesterhelt D.	BMC Mol Biol	10.1186/1471-2199-11-40	2010
Metabolism	Identification of Archaea-specific chemotaxis proteins which interact with the flagellar apparatus.	Schlesner M, Miller A, Streif S, Staudinger WF, Muller J, Scheffer B, Siedler F, Oesterhelt D.	BMC Microbiol	10.1186/1471-2180-9-56	2009
Metabolism	Ubiquitous dissolved inorganic carbon assimilation by marine bacteria in the Pacific Northwest coastal ocean as determined by stable isotope probing.	DeLorenzo S, Brauer SL, Edgmont CA, Herfort L, Tebo BM, Zuber P.	PLoS One	10.1371/journal.pone.0046695	2012
	Regulated polyploidy in halophilic archaea.	Breuert S, Allers T, Spohn G, Soppa J.	PLoS One	10.1371/journal.pone.0000092	2006
Phylogeny	Phylogenetic analyses of some extremely halophilic archaea isolated from Dead Sea water, determined on the basis of their 16S rRNA sequences.	Arahal DR, Dewhirst FE, Paster BJ, Volcani BE, Ventosa A.	Appl Environ Microbiol	10.1128/aem.62.10.3779-3786.1996	1996
Metabolism	Dodecin is the key player in flavin homeostasis of archaea.	Grininger M, Staudt H, Johansson P, Wachtveitl J, Oesterhelt D.	J Biol Chem	10.1074/jbc.m808063200	2009
Metabolism	How do haloarchaea synthesize aromatic amino acids?	Gulko MK, Dyall-Smith M, Gonzalez O, Oesterhelt D.	PLoS One	10.1371/journal.pone.0107475	2014
	The protein interaction network of a taxis signal transduction system in a halophilic archaeon.	Schlesner M, Miller A, Besir H, Aivaliotis M, Streif J, Scheffer B, Siedler F, Oesterhelt D.	BMC Microbiol	10.1186/1471-2180-12-272	2012
	Molecular signature of hypersaline adaptation: insights from genome and proteome composition of halophilic prokaryotes.	Paul S, Bag SK, Das S, Harvill ET, Dutta C.	Genome Biol	10.1186/gb-2008-9-4-r70	2008
	Analysis of haloarchaeal twin-arginine translocase pathway reveals the diversity of the machineries.	Ghosh D, Boral D, Vankudoth KR, Ramasamy S.	Heliyon	10.1016/j.heliyon.2019.e01587	2019
Proteome	How to Cope With Heavy Metal Ions: Cellular and Proteome-Level Stress Response to Divalent Copper and Nickel in Halobacterium salinarum R1 Planktonic and Biofilm Cells.	Volkel S, Hein S, Benker N, Pfeifer F, Lenz C, Losensky G.	Front Microbiol	10.3389/fmicb.2019.03056	2019
	On the origin of prokaryotic "species": the taxonomy of halophilic Archaea.	DasSarma P, DasSarma S.	Saline Syst	10.1186/1746-1448-4-5	2008
	Imaging of protein crystals with two-photon microscopy.	Padayatti P, Palczewska G, Sun W, Palczewski K, Salom D.	Biochemistry	10.1021/bi201682q	2012
Enzymology	Analysis of the cytosolic proteome of Halobacterium salinarum and its implication for genome annotation.	Tebbe A, Klein C, Bisle B, Siedler F, Scheffer B, Garcia-Rizo C, Wolfertz J, Hickmann V, Pfeiffer F, Oesterhelt D	Proteomics	10.1002/pmic.200400910	2005

References

#354	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 671
#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 )
#47906	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 24034
#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 .
#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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Halobacterium salinarum (DSM 671, CCUG 24034, R1)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Observation

Isolation, sampling and environmental information

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000069025

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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