Name: Natrinema pallidum 2
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 5889

Type strain:

Species: Natrinema pallidum

Strain Designation: 2

Variant: Isotype of BacDive ID 5890

Culture col. no.: DSM 3751, ATCC 43214, NCMB 777, JCM 8980, CGMCC 1.3707, CGMCC 1.6163, CIP 106292, NCIMB 777, IAM 13167, NRC 34020, Delft 9

Strain history: CIP <- 1999, NCIMB <- C.W.F. McClare <- D.J. Kushner: strain Delft9 <- J.F.W. Holtz: strain 2, Halobacterium halobium

NCBI tax ID(s): 1227495 (strain), 69527 (species)

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

Other strains from Natrinema pallidum

N. pallidum DSM 15623, CIP 106292, JCM 8980, ... (type strain)

Section

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

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

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Archaea"
	Phylum	*Methanobacteriota*
	Class	*Halobacteria*
	Order	*Natrialbales*
	Family	*Natrialbaceae*
	Genus	*Natrinema*
	Species	**Natrinema pallidum**
	Full Scientific Name (LPSN)	Natrinema pallidum McGenity et al. 1998

Information on morphological and physiological properties Morphology

[Ref.: #121513]	Gram stain	negative

[Ref.: #121513]	Cell shape	rod-shaped

[Ref.: #121513]	Motility	no

Information on culture and growth conditions Culture and growth conditions

[Ref.: #1462]

Culture medium

HALOBACTERIA MEDIUM (DSMZ Medium 372)

[Ref.: #1462]

Culture medium growth

[Ref.: #1462]

Culture medium link

Medium recipe at MediaDive

[Ref.: #1462]

Culture medium composition

expand / minimize

[Ref.: #1462]

Culture medium

HALOBACTERIUM MEDIUM (DSMZ Medium 97)

[Ref.: #1462]

Culture medium growth

[Ref.: #1462]

Culture medium link

Medium recipe at MediaDive

[Ref.: #1462]

Culture medium composition

expand / minimize

[Ref.: #40286]

Culture medium

MEDIUM 330 - for Natrinema pallidum

[Ref.: #40286]

Culture medium growth

[Ref.: #40286]

Culture medium composition

expand / minimize

[Ref.: #121513]

Culture medium

CIP Medium 330

[Ref.: #121513]

Culture medium growth

[Ref.: #121513]

Culture medium link

Medium recipe provided by DSMZ

	Kind of temperature		Temperature
[Ref.: #1462]		growth	37 °C
[Ref.: #40286]		growth	37 °C
[Ref.: #67770]		growth	37 °C
[Ref.: #121513]		growth	30-45 °C
[Ref.: #121513]	no	growth	5 °C
[Ref.: #121513]	no	growth	15 °C
[Ref.: #121513]	no	growth	25 °C

[Ref.: #1462]	Temperature range	mesophilic
[Ref.: #40286]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic
[Ref.: #121513]	Temperature range	psychrophilic
[Ref.: #121513]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #67770]

Observation

quinones: MK-8, MK-8(H₂)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #121513]	citrate ChEBI	-	carbon source
[Ref.: #121513]	esculin ChEBI	-	hydrolysis
[Ref.: #121513]	hippurate ChEBI	-	hydrolysis
[Ref.: #121513]	malonate ChEBI	-	assimilation

	Antibiotica	Metabolite	Antibiotic sensitivity	Antibiotic resistance
[Ref.: #121513]		0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)	yes	no

	Metabolite production	Metabolite	Production
[Ref.: #121513]		indole ChEBI	no

	Physiological tests	Metabolite	Voges-Proskauer-test	Methylred-test
[Ref.: #121513]		acetoin ChEBI	-
[Ref.: #121513]		glucose ChEBI		-

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	-	3.1.3.2	* from API zym
[Ref.: #121513]	alcohol dehydrogenase	-	1.1.1.1
[Ref.: #68382]	alkaline phosphatase	+	3.1.3.1	* from API zym
[Ref.: #68382]	alpha-chymotrypsin	-	3.4.21.1	* from API zym
[Ref.: #68382]	alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #68382]	alpha-galactosidase	-	3.2.1.22	* from API zym
[Ref.: #68382]	alpha-glucosidase	-	3.2.1.20	* from API zym
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #121513]	beta-galactosidase	-	3.2.1.23
[Ref.: #68382]	beta-galactosidase	-	3.2.1.23	* from API zym
[Ref.: #68382]	beta-glucosidase	-	3.2.1.21	* from API zym
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #121513]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #68382]	esterase (C 4)	-		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #121513]	gamma-glutamyltransferase	-	2.3.2.2
[Ref.: #121513]	gelatinase	-
[Ref.: #68382]	leucine arylamidase	-	3.4.11.1	* from API zym
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #121513]	lysine decarboxylase	-	4.1.1.18
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #121513]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #121513]	phenylalanine ammonia-lyase	-	4.3.1.24
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #121513]	tryptophan deaminase	-
[Ref.: #121513]	urease	-	3.5.1.5
[Ref.: #68382]	valine arylamidase	-		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® zym:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #121513]	9374	-	+	-	+	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #1462]	Sample type/isolated from	salted cod fish

[Ref.: #67770]	Sample type/isolated from	Salted cod

[Ref.: #121513]	Sample type/isolated from	Salted fish and hides
[Ref.: #121513]	Isolation date	1962
* marker position based on {}

Isolation sources categories

#Host	#Fishes	-
#Condition	#Saline	-

What are isolation sources categories?

[Ref.: #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

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #1462]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #121513]	Biosafety level	1	Risk group (French classification)

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #1462]	Natrinema pallidum partial 16S rRNA gene, strain DSM 3751T	LN681405	1458	ENA	69527 tax ID
[Ref.: #1462]	Halobacterium halobium NCIMB 777 16S rRNA gene	AJ002949	1463	ENA	69527 tax ID
[Ref.: #1462]	Natrinema pallidum gene for 16S ribosomal RNA, partial sequence, strain: JCM 8980	AB477230	1434	ENA	69527 tax ID
[Ref.: #1462]	Natrinema pallidum strain JCM 8980 16S ribosomal RNA gene, partial sequence	JF421973	1474	ENA	69527 tax ID
[Ref.: #20218]	Natrinema pallidum gene for 16S rRNA, complete sequence, strain: JCM 8980	AB663463	1474	ENA	69527 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Natrinema pallidum DSM 3751	GCA_000337615	contig	GenBank	1227495 tax ID
[Ref.: #66792]	Natrinema pallidum DSM 3751	2529293001	draft	JGI IMG/M	1227495 tax ID	*
[Ref.: #66792]	Natrinema pallidum DSM 3751	1227495.3	wgs	PATRIC	1227495 tax ID	*

Availability in culture collections External links

[Ref.: #1462]

Culture collection no.

DSM 3751, ATCC 43214, NCMB 777, JCM 8980, CGMCC 1.3707, CGMCC 1.6163, CIP 106292, NCIMB 777, IAM 13167, NRC 34020, Delft 9

[Ref.: #75369]	SI-ID 41713	*
[Ref.: #75370]	SI-ID 312364	*

Literature:

Topic	Title	Authors	Journal	DOI	Year
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	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	*
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	*

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;

#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;

#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 .

#75369

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID41713.1 )

#75370

#121513 Collection of Institut Pasteur ; Curators of the CIP; CIP 106292
* These data were automatically processed and therefore are not curated

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