Name: Halorhabdus tiamatea SARL4B
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 5882

Type strain:

Species: Halorhabdus tiamatea

Strain Designation: SARL4B

Culture col. no.: DSM 18392, JCM 14471

Strain history: A. Antunes SARL4B.

NCBI tax ID(s): 1033806 (strain), 430914 (species)

SI-ID 323967

DSM 18392, JCM 14471

Section

Halorhabdus tiamatea SARL4B is an anaerobe, thermophilic, Gram-negative archaeon that was isolated from brine–sediment interface of the Shaban Deep.

Gram-negative
rod-shaped
anaerobe
thermophilic
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	*Halobacteriales*
	Family	*Haloarculaceae*
	Genus	*Halorhabdus*
	Species	**Halorhabdus tiamatea**
	Full Scientific Name (LPSN)	Halorhabdus tiamatea Antunes et al. 2008

Information on morphological and physiological properties Morphology

[Ref.: #32325]	Gram stain	negative

[Ref.: #32325]	Cell length	4.5 µm

[Ref.: #32325]	Cell width	0.75 µm

[Ref.: #32325]	Cell shape	rod-shaped

[Ref.: #32325]	Motility	no

[Ref.: #32325]

Pigment production

Information on culture and growth conditions Culture and growth conditions

[Ref.: #7521]

Culture medium

HALOBACTERIA MEDIUM (DSMZ Medium 372)

[Ref.: #7521]

Culture medium growth

[Ref.: #7521]

Culture medium link

Medium recipe at MediaDive

[Ref.: #7521]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #7521]	growth	45 °C
[Ref.: #32325]	growth	15-55 °C
[Ref.: #32325]	optimum	45 °C
[Ref.: #67770]	growth	37 °C

[Ref.: #7521]	Temperature range	thermophilic
[Ref.: #32325]	Temperature range	thermophilic
[Ref.: #67770]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #32325]			optimum	6.75
[Ref.: #32325]			growth	5.5-8.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #7521]	Oxygen tolerance	anaerobe
[Ref.: #32325]	Oxygen tolerance	anaerobe

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #32325]		NaCl		growth	10-30	%
[Ref.: #32325]		NaCl		optimum	27	%

[Ref.: #67770]

Observation

quinones: MK-8(VIII-H₂)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #32325]	esculin ChEBI	+	hydrolysis
[Ref.: #32325]	fructose ChEBI	+	carbon source
[Ref.: #32325]	galactose ChEBI	+	carbon source
[Ref.: #32325]	glucose ChEBI	+	carbon source
[Ref.: #32325]	proline ChEBI	+	carbon source

	Enzyme	Enzyme activity	EC number
[Ref.: #32325]	alpha-galactosidase	+	3.2.1.22
[Ref.: #32325]	catalase	+	1.11.1.6
[Ref.: #32325]	gelatinase	+

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	cyanate degradation	100	3 of 3
[Ref.: #66794]	vitamin K metabolism	100	5 of 5
[Ref.: #66794]	factor 420 biosynthesis	100	5 of 5
[Ref.: #66794]	glycogen metabolism	100	5 of 5
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	ethanol fermentation	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	isoleucine metabolism	87.5	7 of 8
[Ref.: #66794]	flavin biosynthesis	86.67	13 of 15
[Ref.: #66794]	photosynthesis	85.71	12 of 14
[Ref.: #66794]	ubiquinone biosynthesis	85.71	6 of 7
[Ref.: #66794]	heme metabolism	85.71	12 of 14
[Ref.: #66794]	pantothenate biosynthesis	83.33	5 of 6
[Ref.: #66794]	hydrogen production	80	4 of 5
[Ref.: #66794]	threonine metabolism	80	8 of 10
[Ref.: #66794]	cellulose degradation	80	4 of 5
[Ref.: #66794]	starch degradation	80	8 of 10
[Ref.: #66794]	valine metabolism	77.78	7 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	77.78	7 of 9
[Ref.: #66794]	chorismate metabolism	77.78	7 of 9
[Ref.: #66794]	vitamin B1 metabolism	76.92	10 of 13
[Ref.: #66794]	phenylalanine metabolism	76.92	10 of 13
[Ref.: #66794]	purine metabolism	75.53	71 of 94
[Ref.: #66794]	ppGpp biosynthesis	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	ketogluconate metabolism	75	6 of 8
[Ref.: #66794]	C4 and CAM-carbon fixation	75	6 of 8
[Ref.: #66794]	gluconeogenesis	75	6 of 8
[Ref.: #66794]	pyrimidine metabolism	73.33	33 of 45
[Ref.: #66794]	methionine metabolism	73.08	19 of 26
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	Entner Doudoroff pathway	70	7 of 10
[Ref.: #66794]	non-pathway related	68.42	26 of 38
[Ref.: #66794]	serine metabolism	66.67	6 of 9
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	NAD metabolism	66.67	12 of 18
[Ref.: #66794]	glycolate and glyoxylate degradation	66.67	4 of 6
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	enterobactin biosynthesis	66.67	2 of 3
[Ref.: #66794]	molybdenum cofactor biosynthesis	66.67	6 of 9
[Ref.: #66794]	glycolysis	64.71	11 of 17
[Ref.: #66794]	glutamate and glutamine metabolism	64.29	18 of 28
[Ref.: #66794]	d-xylose degradation	63.64	7 of 11
[Ref.: #66794]	pentose phosphate pathway	63.64	7 of 11
[Ref.: #66794]	oxidative phosphorylation	62.64	57 of 91
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	sulfate reduction	61.54	8 of 13
[Ref.: #66794]	methylglyoxal degradation	60	3 of 5
[Ref.: #66794]	phenylacetate degradation (aerobic)	60	3 of 5
[Ref.: #66794]	3-chlorocatechol degradation	60	3 of 5
[Ref.: #66794]	degradation of sugar acids	60	15 of 25
[Ref.: #66794]	carotenoid biosynthesis	59.09	13 of 22
[Ref.: #66794]	alanine metabolism	58.62	17 of 29
[Ref.: #66794]	arginine metabolism	58.33	14 of 24
[Ref.: #66794]	propanol degradation	57.14	4 of 7
[Ref.: #66794]	tetrahydrofolate metabolism	57.14	8 of 14
[Ref.: #66794]	reductive acetyl coenzyme A pathway	57.14	4 of 7
[Ref.: #66794]	degradation of sugar alcohols	56.25	9 of 16
[Ref.: #66794]	d-mannose degradation	55.56	5 of 9
[Ref.: #66794]	cysteine metabolism	55.56	10 of 18
[Ref.: #66794]	histidine metabolism	55.17	16 of 29
[Ref.: #66794]	metabolism of disaccharids	54.55	6 of 11
[Ref.: #66794]	proline metabolism	54.55	6 of 11
[Ref.: #66794]	leucine metabolism	53.85	7 of 13
[Ref.: #66794]	degradation of pentoses	53.57	15 of 28
[Ref.: #66794]	lipid metabolism	51.61	16 of 31
[Ref.: #66794]	4-hydroxyphenylacetate degradation	50	5 of 10
[Ref.: #66794]	coenzyme M biosynthesis	50	5 of 10
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	50	1 of 2
[Ref.: #66794]	selenocysteine biosynthesis	50	3 of 6
[Ref.: #66794]	lactate fermentation	50	2 of 4
[Ref.: #66794]	adipate degradation	50	1 of 2
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	isoprenoid biosynthesis	50	13 of 26
[Ref.: #66794]	glutathione metabolism	50	7 of 14
[Ref.: #66794]	tryptophan metabolism	47.37	18 of 38
[Ref.: #66794]	CO2 fixation in Crenarchaeota	44.44	4 of 9
[Ref.: #66794]	nitrate assimilation	44.44	4 of 9
[Ref.: #66794]	citric acid cycle	42.86	6 of 14
[Ref.: #66794]	mevalonate metabolism	42.86	3 of 7
[Ref.: #66794]	tyrosine metabolism	42.86	6 of 14
[Ref.: #66794]	methanogenesis from CO2	41.67	5 of 12
[Ref.: #66794]	lysine metabolism	40.48	17 of 42
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	phenol degradation	40	8 of 20
[Ref.: #66794]	gallate degradation	40	2 of 5
[Ref.: #66794]	metabolism of amino sugars and derivatives	40	2 of 5
[Ref.: #66794]	arachidonic acid metabolism	38.89	7 of 18
[Ref.: #66794]	degradation of hexoses	38.89	7 of 18
[Ref.: #66794]	urea cycle	38.46	5 of 13
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	38.46	5 of 13
[Ref.: #66794]	dTDPLrhamnose biosynthesis	37.5	3 of 8
[Ref.: #66794]	vitamin B6 metabolism	36.36	4 of 11
[Ref.: #66794]	cholesterol biosynthesis	36.36	4 of 11
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	36.36	4 of 11
[Ref.: #66794]	ascorbate metabolism	36.36	8 of 22
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	33.33	4 of 12
[Ref.: #66794]	sulfoquinovose degradation	33.33	1 of 3
[Ref.: #66794]	4-hydroxymandelate degradation	33.33	3 of 9
[Ref.: #66794]	androgen and estrogen metabolism	31.25	5 of 16
[Ref.: #66794]	phenylpropanoid biosynthesis	30.77	4 of 13
[Ref.: #66794]	myo-inositol biosynthesis	30	3 of 10
[Ref.: #66794]	aclacinomycin biosynthesis	28.57	2 of 7
[Ref.: #66794]	polyamine pathway	26.09	6 of 23
[Ref.: #66794]	biotin biosynthesis	25	1 of 4
[Ref.: #66794]	butanoate fermentation	25	1 of 4
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	carnitine metabolism	25	2 of 8
[Ref.: #66794]	vitamin E metabolism	25	1 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	25	1 of 4
[Ref.: #66794]	catecholamine biosynthesis	25	1 of 4
[Ref.: #66794]	sulfopterin metabolism	25	1 of 4
[Ref.: #66794]	lipid A biosynthesis	22.22	2 of 9
		Only first 10 entries are displayed. Click here to see all.

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

[Ref.: #7521]	Sample type/isolated from	brine–sediment interface of the Shaban Deep
[Ref.: #7521]	Geographic location (country and/or sea, region)	Red Sea
[Ref.: #7521]	Country	Saudi Arabia
[Ref.: #7521]	Country ISO 3 Code	SAU
[Ref.: #7521]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Brine-sediment interface of the Shaban Deep in the northern Red Sea
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	-
#Condition	#Saline	-

What are isolation sources categories?

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

[Ref.: #7521]

Biosafety level

Risk group (German classification)
According to TRBA 466

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.: #7521]	Halorhabdus tiamatea strain SARL4B 16S ribosomal RNA gene, partial sequence	EF127229	1362	ENA	1033806 tax ID
[Ref.: #20218]	Halorhabdus tiamatea gene for 16S ribosomal RNA, partial sequence	AB576122	1472	ENA	1033806 tax ID	*
[Ref.: #20218]	Halorhabdus tiamatea gene for 16S rRNA, complete sequence, strain: JCM 14471	AB663399	1472	ENA	1033806 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Halorhabdus tiamatea SARL4B	GCA_000215915	contig	GenBank	1033806 tax ID
[Ref.: #66792]	Halorhabdus tiamatea SARL4B	2654588040	complete	JGI IMG/M	1033806 tax ID	*
[Ref.: #66792]	Halorhabdus tiamatea SARL4B	2562617191	draft	JGI IMG/M	1033806 tax ID	*
[Ref.: #66792]	Halorhabdus tiamatea SARL4B	1033806.12	complete	PATRIC	1033806 tax ID	*
[Ref.: #66792]	Halorhabdus tiamatea SARL4B	1033806.93	wgs	PATRIC	1033806 tax ID	*

[Ref.: #7521]	GC-content	61.7 mol%
[Ref.: #67770]	GC-content	61.7 mol%	high performance liquid chromatography (HPLC)

Availability in culture collections External links

[Ref.: #7521]

Culture collection no.

DSM 18392, JCM 14471

[Ref.: #75361]

SI-ID 323967

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Halorhabdus amylolytica sp. nov. and Halorhabdus salina sp. nov., isolated from hypersaline environments.	Wang R, Chen F, Wang J, Liu A, Ke L, Wan F, Chen S	Int J Syst Evol Microbiol	10.1099/ijsem.0.005346	2022	*
Phylogeny	Halorhabdus rudnickae sp. nov., a halophilic archaeon isolated from a salt mine borehole in Poland.	Albuquerque L, Kowalewicz-Kulbat M, Drzewiecka D, Staczek P, d'Auria G, Rossello-Mora R, da Costa MS	Syst Appl Microbiol	10.1016/j.syapm.2015.12.004	2015	*
Genetics	Halorhabdus tiamatea: proteogenomics and glycosidase activity measurements identify the first cultivated euryarchaeon from a deep-sea anoxic brine lake as potential polysaccharide degrader.	Werner J, Ferrer M, Michel G, Mann AJ, Huang S, Juarez S, Ciordia S, Albar JP, Alcaide M, La Cono V, Yakimov MM, Antunes A, Taborda M, da Costa MS, Hai T, Glockner FO, Golyshina OV, Golyshin PN, Teeling H	Environ Microbiol	10.1111/1462-2920.12393	2014	*
Phylogeny	Halorhabdus tiamatea sp. nov., a non-pigmented, extremely halophilic archaeon from a deep-sea, hypersaline anoxic basin of the Red Sea, and emended description of the genus Halorhabdus.	Antunes A, Taborda M, Huber R, Moissl C, Nobre MF, da Costa MS	Int J Syst Evol Microbiol	10.1099/ijs.0.65316-0	2008	*

References

#7521

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 18392

#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 )

#32325

Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #28559 (see below)

#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) .

#66794

Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#75361

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-ID323967.1 )

#28559

IJSEM 215 2008 ( DOI 10.1099/ijs.0.65316-0 , PubMed 18175711 )

* These data were automatically processed and therefore are not curated

Change proposal

You found an error in BacDive? Please tell us about it!

Note that changes will be reviewed and judged. If your changes are legitimate, changes will occur within the next BacDive update. Only proposed changes supported by the according reference will be reviewed. The BacDive team reserves the right to reject proposed changes.

Search for species Halorhabdus tiamatea in external resources:
SILVA
BRENDA
PANGAEA
StrainInfo
GBIF