Natrinema pallidum (DSM 3751, ATCC 43214, NCMB 777)

Name: Natrinema pallidum (DSM 3751, ATCC 43214, NCMB 777)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 5889

Type strain

Strain Designation 2

Variant Isotype of BacDive ID 5890

Culture col. no. DSM 3751 ATCC 43214 NCMB 777 2 JCM 8980 7 more

NCBI tax ID(s) 1227495 69527

Special Collections DSMZ JCM CIP

Links

Natrinema pallidum 2 is a mesophilic, Gram-negative, rod-shaped prokaryote that was isolated from salted cod fish.

Gram-negative rod-shaped mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 41713

ATCC 43214,NCMB 777,NCMB 2152,CIP 106292,DSM 3751,IAM 13167,JCM 8980,NCIMB 777,DSM 670,IFO 14716,NBRC 14716,CGMCC 1.1959,CGMCC 1.2379,JCM 20854,DSM 15623

@ref 20215

Last LPSN update 2025-12-16 09:48:10

Domain Methanobacteriati

Phylum Methanobacteriota

Class Halobacteria

Order Halobacteriales

Family Natrialbaceae

Genus Natrinema

Species Natrinema pallidum

Full scientific name Natrinema pallidum McGenity et al. 1998

BacDive ID	Other strains from **Natrinema pallidum** (1)	Type strain
5890	N. pallidum DSM 15623, CIP 106292, JCM 8980, NCIMB 777, ... (type strain)

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Motility
121513	negative	rod-shaped

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
1462	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
1462	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
40286	MEDIUM 330 - for Natrinema pallidum		Distilled water make up to (1000.000 ml);Sodium chloride (200.000 g);Potassium chloride (2.000 g);ManganeseII chloride tetrahydrate (0.360 mg);Magnesium sulphate heptahydrate (20.000 g);Agar (20.000 g);Yeast extract (5.000 g);Ferrous chloride tetrahydrate
121513	CIP Medium 330	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
1462	positive	growth	37	mesophilic
40286	positive	growth	37	mesophilic
67770	positive	growth	37	mesophilic
121513	positive	growth	30-45
121513	negative	growth	5
121513	negative	growth	15
121513	negative	growth	25

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	aerobe	90.3

Observation

67770

Observationquinones: MK-8, MK-8(H₂)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
121513	16947 ChEBI	citrate	-	carbon source
121513	4853 ChEBI	esculin	-	hydrolysis
121513	606565 ChEBI	hippurate	-	hydrolysis
121513	15792 ChEBI	malonate	-	assimilation

Antibiotic resistance

@ref	Metabolite	Is antibiotic	Is sensitive	Is resistant
121513	0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)

Metabolite production

@ref	Chebi-ID	Metabolite	Production
121513	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Methylred-test
121513	15688 ChEBI	acetoin	-
121513	17234 ChEBI	glucose		-

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	-	3.1.3.2	from API zym
121513	alcohol dehydrogenase	-	1.1.1.1
68382	alkaline phosphatase	+	3.1.3.1	from API zym
68382	alpha-chymotrypsin	-	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68382	alpha-galactosidase	-	3.2.1.22	from API zym
68382	alpha-glucosidase	-	3.2.1.20	from API zym
68382	alpha-mannosidase	-	3.2.1.24	from API zym
68382	beta-galactosidase	-	3.2.1.23	from API zym
121513	beta-galactosidase	-	3.2.1.23
68382	beta-glucosidase	-	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
121513	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
68382	esterase (C 4)	-		from API zym
68382	esterase lipase (C 8)	+		from API zym
121513	gamma-glutamyltransferase	-	2.3.2.2
121513	gelatinase	-
68382	leucine arylamidase	-	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
121513	lysine decarboxylase	-	4.1.1.18
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
121513	ornithine decarboxylase	-	4.1.1.17
121513	phenylalanine ammonia-lyase	-	4.3.1.24
68382	trypsin	-	3.4.21.4	from API zym
121513	tryptophan deaminase	-
121513	urease	-	3.5.1.5
68382	valine arylamidase	-		from API zym

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
121513	-	+	-	+	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2
#Host	#Fishes
#Condition	#Saline

Isolation

@ref	Sample type	Isolation date
1462	salted cod fish
67770	Salted cod
121513	Salted fish and hides	1962

Taxonmaps

69479

Global distribution of 16S sequence JF421973 (>99% sequence identity) for Natrinema from Microbeatlas

Aquatic Samples	34
Soil Samples	4
Animal Samples
Plant Samples	1
Total Samples	39

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
1462	1	Risk group (German classification) According to TRBA 466
121513	1	Risk group (French classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	ASM33761v1 assembly for Natrinema pallidum DSM 3751	contig	GCA_000337615	1227495.3	2529293001	1227495	55.14

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Natrinema pallidum gene for 16S rRNA, complete sequence, strain: JCM 8980	AB663463	1474	69527
1462	Natrinema pallidum partial 16S rRNA gene, strain DSM 3751T	LN681405	1458	69527
1462	Halobacterium halobium NCIMB 777 16S rRNA gene	AJ002949	1463	69527
1462	Natrinema pallidum gene for 16S ribosomal RNA, partial sequence, strain: JCM 8980	AB477230	1434	69527
1462	Natrinema pallidum strain JCM 8980 16S ribosomal RNA gene, partial sequence	JF421973	1474	69527

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Natrinema pallidum DSM 3751
NCBI: GCA_000337615

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	88.80	no
125439	motility	BacteriaNetⓘ	yes	59.30	no
125439	gram_stain	BacteriaNetⓘ	negative	84.60	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	90.30	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	High quality draft genome sequence of an extremely halophilic archaeon Natrinema altunense strain AJ2^T.	Cheng H, Huo YY, Hu J, Xu XW, Wu M.	Stand Genomic Sci	10.1186/s40793-017-0237-3	2017
Metabolism	Dihydroxyacetone metabolism in Haloferax volcanii.	Ouellette M, Makkay AM, Papke RT.	Front Microbiol	10.3389/fmicb.2013.00376	2013
Genetics	The haloarchaeal MCM proteins: bioinformatic analysis and targeted mutagenesis of the beta7-beta8 and beta9-beta10 hairpin loops and conserved zinc binding domain cysteines.	Kristensen TP, Maria Cherian R, Gray FC, MacNeill SA.	Front Microbiol	10.3389/fmicb.2014.00123	2014
	Production of Poly(3-Hydroxybutyrate) by Haloarcula, Halorubrum, and Natrinema Haloarchaeal Genera Using Starch as a Carbon Source.	Karray F, Ben Abdallah M, Baccar N, Zaghden H, Sayadi S.	Archaea	10.1155/2021/8888712	2021
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
	Evolutionary insights into provirus-encoded CRISPR-Cas systems in halophilic archaea.	Naki D, Gophna U.	Microlife	10.1093/femsml/uqaf033	2025
	Genomic Analysis of Haloarchaea from Diverse Environments, including Permian Halite, Reveals Diversity of Ultraviolet Radiation Survival and DNA Photolyase Gene Variants.	Nag S, DasSarma P, Crowley DJ, Hamawi R, Tepper S, Anton BP, Guzman D, DasSarma S.	Microorganisms	10.3390/microorganisms11030607	2023
	Phylogenomics of Haloarchaea: The Controversy of the Genera Natrinema-Haloterrigena.	de la Haba RR, Minegishi H, Kamekura M, Shimane Y, Ventosa A.	Front Microbiol	10.3389/fmicb.2021.740909	2021
	Life in the brine of Lunenburg, Germany: unveiling microorganisms associated with Zechstein salt deposits.	Runzheimer K, Schwab L, Engel D, Schaudinn C, Laue M, Rebrosova K, Beblo-Vranesevic K, Azizah M, Leuko S.	Front Microbiol	10.3389/fmicb.2025.1625916	2025
Metabolism	Production of Polyhydroxyalkanoates by Two Halophilic Archaeal Isolates from Chott El Jerid Using Inexpensive Carbon Sources.	Ben Abdallah M, Karray F, Sayadi S.	Biomolecules	10.3390/biom10010109	2020
Enzymology	Carotenoid analysis of halophilic archaea by resonance Raman spectroscopy.	Marshall CP, Leuko S, Coyle CM, Walter MR, Burns BP, Neilan BA.	Astrobiology	10.1089/ast.2006.0097	2007
	Physiological and genomic insights into abiotic stress of halophilic archaeon Natrinema altunense 4.1R isolated from a saline ecosystem of Tunisian desert.	Najjari A, Boussetta A, Youssef N, Linares-Pasten JA, Mahjoubi M, Belloum R, Sghaier H, Cherif A, Ouzari HI.	Genetica	10.1007/s10709-023-00182-0	2023
Metabolism	Is there a common water-activity limit for the three domains of life?	Stevenson A, Cray JA, Williams JP, Santos R, Sahay R, Neuenkirchen N, McClure CD, Grant IR, Houghton JD, Quinn JP, Timson DJ, Patil SV, Singhal RS, Anton J, Dijksterhuis J, Hocking AD, Lievens B, Rangel DE, Voytek MA, Gunde-Cimerman N, Oren A, Timmis KN, McGenity TJ, Hallsworth JE.	ISME J	10.1038/ismej.2014.219	2015
	Rhizosphere-dwelling halophilic archaea: a potential candidate for alleviating salinity-associated stress in agriculture.	Naitam MG, Ramakrishnan B, Grover M, Kaushik R.	Front Microbiol	10.3389/fmicb.2023.1212349	2023
	Diversity of Lysis-Resistant Bacteria and Archaea in the Polyextreme Environment of Salar de Huasco.	Corona Ramirez A, Cailleau G, Fatton M, Dorador C, Junier P.	Front Microbiol	10.3389/fmicb.2022.826117	2022
	Utilization of Sugarcane Bagasse by Halogeometricum borinquense Strain E3 for Biosynthesis of Poly(3-hydroxybutyrate-co-3-hydroxyvalerate).	Salgaonkar BB, Braganca JM.	Bioengineering (Basel)	10.3390/bioengineering4020050	2017
	Halocin SH10 production by an extreme haloarchaeon Natrinema sp. BTSH10 isolated from salt pans of South India.	Karthikeyan P, Bhat SG, Chandrasekaran M.	Saudi J Biol Sci	10.1016/j.sjbs.2013.02.002	2013
Phylogeny	Diversity, taxonomy, and evolution of archaeal viruses of the class Caudoviricetes.	Liu Y, Demina TA, Roux S, Aiewsakun P, Kazlauskas D, Simmonds P, Prangishvili D, Oksanen HM, Krupovic M.	PLoS Biol	10.1371/journal.pbio.3001442	2021
Enzymology	Prokaryotic diversity in Aran-Bidgol salt lake, the largest hypersaline playa in Iran.	Makhdoumi-Kakhki A, Amoozegar MA, Kazemi B, Pasic L, Ventosa A.	Microbes Environ	10.1264/jsme2.me11267	2012
Metabolism	Isolation and Molecular Identification of Auxotrophic Mutants to Develop a Genetic Manipulation System for the Haloarchaeon Natrinema sp. J7-2.	Lv J, Wang S, Wang Y, Huang Y, Chen X.	Archaea	10.1155/2015/483194	2015
	Evolution of rhodopsin ion pumps in haloarchaea.	Sharma AK, Walsh DA, Bapteste E, Rodriguez-Valera F, Ford Doolittle W, Papke RT.	BMC Evol Biol	10.1186/1471-2148-7-79	2007
Phylogeny	Archaeal diversity at the great salt plains of Oklahoma described by cultivation and molecular analyses.	Caton TM, Caton IR, Witte LR, Schneegurt MA.	Microb Ecol	10.1007/s00248-009-9507-y	2009
Metabolism	Glycerol enhances fungal germination at the water-activity limit for life.	Stevenson A, Hamill PG, Medina A, Kminek G, Rummel JD, Dijksterhuis J, Timson DJ, Magan N, Leong SL, Hallsworth JE.	Environ Microbiol	10.1111/1462-2920.13530	2017
Genetics	Phylogenetically driven sequencing of extremely halophilic archaea reveals strategies for static and dynamic osmo-response.	Becker EA, Seitzer PM, Tritt A, Larsen D, Krusor M, Yao AI, Wu D, Madern D, Eisen JA, Darling AE, Facciotti MT.	PLoS Genet	10.1371/journal.pgen.1004784	2014
Genetics	Identification, Characterization, and Application of the Replicon Region of the Halophilic Temperate Sphaerolipovirus SNJ1.	Wang Y, Sima L, Lv J, Huang S, Liu Y, Wang J, Krupovic M, Chen X	J Bacteriol	10.1128/JB.00131-16	2016
Metabolism	Preparation of poly(3-hydroxybutyrate-co-hydroxyvalerate) films from halophilic archaea and their potential use in drug delivery.	Danis O, Ogan A, Tatlican P, Attar A, Cakmakci E, Mertoglu B, Birbir M	Extremophiles	10.1007/s00792-015-0735-4	2015
Phylogeny	Proposal of a new halobacterial genus Natrinema gen. nov., with two species Natrinema pellirubrum nom. nov. and Natrinema pallidum nom. nov.	McGenity TJ, Gemmell RT, Grant WD	Int J Syst Bacteriol	10.1099/00207713-48-4-1187	1998
Phylogeny	Natrinema versiforme sp. nov., an extremely halophilic archaeon from Aibi salt lake, Xinjiang, China.	Xin H, Itoh T, Zhou P, Suzuki K, Kamekura M, Nakase T.	Int J Syst Evol Microbiol	10.1099/00207713-50-3-1297	2000
Genetics	Non-contiguous finished genome sequence and description of Halopiger goleamassiliensis sp. nov.	Ikram HI, Catherine R, Caroline M, Didier R, Hocine H, Christelle D.	Stand Genomic Sci	10.4056/sigs.4618288	2014
Phylogeny	Natrinema ejinorense sp. nov., isolated from a saline lake in Inner Mongolia, China.	Castillo AM, Gutierrez MC, Kamekura M, Xue Y, Ma Y, Cowan DA, Jones BE, Grant WD, Ventosa A	Int J Syst Evol Microbiol	10.1099/ijs.0.64421-0	2006

References

#1462	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 3751
#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 )
#40286	; Curators of the CIP;
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68382	Automatically annotated from API zym .
#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 .
#121513	Collection of Institut Pasteur ; Curators of the CIP; CIP 106292
#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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Natrinema pallidum (DSM 3751, ATCC 43214, NCMB 777)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Observation

Metabolite utilization

Antibiotic resistance

Metabolite production

Metabolite tests

Enzymes

API zym

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000337615

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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