Name: Halogeometricum borinquense PR3
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 5873

Type strain:

Species: Halogeometricum borinquense

Strain Designation: PR3

Culture col. no.: DSM 11551, ATCC 700274, JCM 10706, CGMCC 1.6168, KCTC 4070

Strain history: ATCC 700274 <-- R. Montalvo-Rodríguez PR3.

NCBI tax ID(s): 469382 (strain), 60847 (species)

Section

Halogeometricum borinquense PR3 is a mesophilic archaeon that was isolated from solar salterns.

mesophilic
16S sequence
Archaea
genome sequence

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

	Last LPSN update	07-12-2022 (DD-MM-YYYY)
	Domain	"Archaea"
	Phylum	"Euryarchaeota"
	Class	Halobacteria
	Order	*Haloferacales*
	Family	*Haloferacaceae*
	Genus	*Halogeometricum*
	Species	**Halogeometricum borinquense**
	Full Scientific Name (PNU)	Halogeometricum borinquense Montalvo-Rodríguez et al. 1998

Information on morphological and physiological properties Morphology

[Ref.: #69480]

Gram stain

negative Confidence in %99.991

Multimedia content

[Ref.: #66793]

Caption:

electron microscopic image

[Ref.: #66793]

Intellectual property rights:

Information on culture and growth conditions Culture and growth conditions

[Ref.: #4413]

Culture medium

HALOBACTERIA MEDIUM (DSMZ Medium 372)

[Ref.: #4413]

Culture medium growth

[Ref.: #4413]

Culture medium link

Medium recipe provided by DSMZ

[Ref.: #4413]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #4413]			growth	37 °C
[Ref.: #67770]			growth	37 °C

[Ref.: #4413]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.942

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	vitamin K metabolism	100	5 of 5
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	flavin biosynthesis	100	15 of 15
[Ref.: #66794]	denitrification	100	2 of 2
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	pantothenate biosynthesis	100	6 of 6
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	enterobactin biosynthesis	100	3 of 3
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	citric acid cycle	92.86	13 of 14
[Ref.: #66794]	vitamin B1 metabolism	92.31	12 of 13
[Ref.: #66794]	starch degradation	90	9 of 10
[Ref.: #66794]	propionate fermentation	90	9 of 10
[Ref.: #66794]	threonine metabolism	90	9 of 10
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	isoleucine metabolism	87.5	7 of 8
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	87.5	7 of 8
[Ref.: #66794]	tetrahydrofolate metabolism	85.71	12 of 14
[Ref.: #66794]	propanol degradation	85.71	6 of 7
[Ref.: #66794]	ethylmalonyl-CoA pathway	80	4 of 5
[Ref.: #66794]	gallate degradation	80	4 of 5
[Ref.: #66794]	factor 420 biosynthesis	80	4 of 5
[Ref.: #66794]	Entner Doudoroff pathway	80	8 of 10
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	phenylacetate degradation (aerobic)	80	4 of 5
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	glutamate and glutamine metabolism	78.57	22 of 28
[Ref.: #66794]	NAD metabolism	77.78	14 of 18
[Ref.: #66794]	molybdenum cofactor biosynthesis	77.78	7 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	77.78	7 of 9
[Ref.: #66794]	valine metabolism	77.78	7 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	77.78	7 of 9
[Ref.: #66794]	phenylalanine metabolism	76.92	10 of 13
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	C4 and CAM-carbon fixation	75	6 of 8
[Ref.: #66794]	gluconeogenesis	75	6 of 8
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	biotin biosynthesis	75	3 of 4
[Ref.: #66794]	pyrimidine metabolism	73.33	33 of 45
[Ref.: #66794]	purine metabolism	72.34	68 of 94
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	glutathione metabolism	71.43	10 of 14
[Ref.: #66794]	vitamin B12 metabolism	70.59	24 of 34
[Ref.: #66794]	myo-inositol biosynthesis	70	7 of 10
[Ref.: #66794]	leucine metabolism	69.23	9 of 13
[Ref.: #66794]	histidine metabolism	68.97	20 of 29
[Ref.: #66794]	tryptophan metabolism	68.42	26 of 38
[Ref.: #66794]	lipid metabolism	67.74	21 of 31
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	serine metabolism	66.67	6 of 9
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	selenocysteine biosynthesis	66.67	4 of 6
[Ref.: #66794]	glycolate and glyoxylate degradation	66.67	4 of 6
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	alanine metabolism	65.52	19 of 29
[Ref.: #66794]	oxidative phosphorylation	64.84	59 of 91
[Ref.: #66794]	glycolysis	64.71	11 of 17
[Ref.: #66794]	heme metabolism	64.29	9 of 14
[Ref.: #66794]	pentose phosphate pathway	63.64	7 of 11
[Ref.: #66794]	ketogluconate metabolism	62.5	5 of 8
[Ref.: #66794]	dTDPLrhamnose biosynthesis	62.5	5 of 8
[Ref.: #66794]	arginine metabolism	62.5	15 of 24
[Ref.: #66794]	methionine metabolism	61.54	16 of 26
[Ref.: #66794]	3-chlorocatechol degradation	60	3 of 5
[Ref.: #66794]	lipoate biosynthesis	60	3 of 5
[Ref.: #66794]	cellulose degradation	60	3 of 5
[Ref.: #66794]	reductive acetyl coenzyme A pathway	57.14	4 of 7
[Ref.: #66794]	tyrosine metabolism	57.14	8 of 14
[Ref.: #66794]	lysine metabolism	57.14	24 of 42
[Ref.: #66794]	cysteine metabolism	55.56	10 of 18
[Ref.: #66794]	d-mannose degradation	55.56	5 of 9
[Ref.: #66794]	d-xylose degradation	54.55	6 of 11
[Ref.: #66794]	cholesterol biosynthesis	54.55	6 of 11
[Ref.: #66794]	degradation of sugar acids	52	13 of 25
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	50	1 of 2
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	resorcinol degradation	50	1 of 2
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	non-pathway related	50	19 of 38
[Ref.: #66794]	degradation of sugar alcohols	50	8 of 16
[Ref.: #66794]	coenzyme M biosynthesis	50	5 of 10
[Ref.: #66794]	vitamin E metabolism	50	2 of 4
[Ref.: #66794]	sulfate reduction	46.15	6 of 13
[Ref.: #66794]	isoprenoid biosynthesis	46.15	12 of 26
[Ref.: #66794]	proline metabolism	45.45	5 of 11
[Ref.: #66794]	arachidonic acid metabolism	44.44	8 of 18
[Ref.: #66794]	nitrate assimilation	44.44	4 of 9
[Ref.: #66794]	androgen and estrogen metabolism	43.75	7 of 16
[Ref.: #66794]	aclacinomycin biosynthesis	42.86	3 of 7
[Ref.: #66794]	mevalonate metabolism	42.86	3 of 7
[Ref.: #66794]	ubiquinone biosynthesis	42.86	3 of 7
[Ref.: #66794]	methanogenesis from CO2	41.67	5 of 12
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
[Ref.: #66794]	carotenoid biosynthesis	40.91	9 of 22
[Ref.: #66794]	phenol degradation	40	8 of 20
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	glycine betaine biosynthesis	40	2 of 5
[Ref.: #66794]	4-hydroxyphenylacetate degradation	40	4 of 10
[Ref.: #66794]	creatinine degradation	40	2 of 5
[Ref.: #66794]	hydrogen production	40	2 of 5
[Ref.: #66794]	degradation of pentoses	39.29	11 of 28
[Ref.: #66794]	urea cycle	38.46	5 of 13
[Ref.: #66794]	vitamin B6 metabolism	36.36	4 of 11
[Ref.: #66794]	4-hydroxymandelate degradation	33.33	3 of 9
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	lipid A biosynthesis	33.33	3 of 9
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	sulfoquinovose degradation	33.33	1 of 3
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	phenylpropanoid biosynthesis	30.77	4 of 13
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	ascorbate metabolism	27.27	6 of 22
[Ref.: #66794]	metabolism of disaccharids	27.27	3 of 11
[Ref.: #66794]	3-phenylpropionate degradation	26.67	4 of 15
[Ref.: #66794]	polyamine pathway	26.09	6 of 23
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	alginate biosynthesis	25	1 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	25	1 of 4
[Ref.: #66794]	catecholamine biosynthesis	25	1 of 4
[Ref.: #66794]	degradation of hexoses	22.22	4 of 18
		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.: #4413]	Sample type/isolated from	solar salterns
[Ref.: #4413]	Geographic location (country and/or sea, region)	Cabor Rojo
[Ref.: #4413]	Country	Puerto Rico
[Ref.: #4413]	Country ISO 3 Code	PRI
[Ref.: #4413]	Continent	Middle and South America

[Ref.: #67770]	Sample type/isolated from	Solar saltern
[Ref.: #67770]	Geographic location (country and/or sea, region)	Cabo Rojo
[Ref.: #67770]	Country	Puerto Rico
[Ref.: #67770]	Country ISO 3 Code	PRI
[Ref.: #67770]	Continent	North America
* marker position based on {}

Isolation sources categories

#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.: #4413]

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.: #67770]	Halogeometricum borinquense 16S ribosomal RNA gene, complete sequence	AF002984	1451	ENA	469382 tax ID

Genome sequence information:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Halogeometricum borinquense DSM 11551 DSM 11551	GCA_000337855	contig	GenBank	469382 tax ID
[Ref.: #67770]	Halogeometricum borinquense DSM 11551, complete genome	CP001690		ENA	469382 tax ID
[Ref.: #66792]	Halogeometricum borinquense DSM 11551	469382.19	wgs	PATRIC	469382 tax ID	*
[Ref.: #66792]	Halogeometricum borinquense PR3, DSM 11551	649633053	complete	JGI IMG/M	469382 tax ID	*
[Ref.: #66792]	Halogeometricum borinquense PR3, DSM 11551	2537561588	draft	JGI IMG/M	469382 tax ID	*
[Ref.: #66792]	Halogeometricum borinquense DSM 11551 strain PR 3	469382.37	plasmid	PATRIC	469382 tax ID	*

[Ref.: #4413]	GC-content	59.0 mol%
[Ref.: #67770]	GC-content	59 mol%	high performance liquid chromatography (HPLC)

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Halogeometricum borinquense DSM 11551 PR 3 NCBI: GCA_000172995.2
[Ref.: #69480]	gram-positive	no	99.991	yes
[Ref.: #69480]	anaerobic	no	95.887	no
[Ref.: #69480]	spore-forming	no	99.942	yes
[Ref.: #69480]	thermophile	no	94.015	no
[Ref.: #69480]	motile	no	59.256	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Halogeometricum borinquense DSM 11551 PR 3 NCBI: GCA_000172995.2
[Ref.: #69481]	spore-forming	no	100	no

Availability in culture collections External links

[Ref.: #4413]

Culture collection no.

DSM 11551, ATCC 700274, JCM 10706, CGMCC 1.6168, KCTC 4070

[Ref.: #20218]

Associated Passport(s) in StrainInfo

302620, 117778

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Taxonomic study of the genera Halogeometricum and Halosarcina: transfer of Halosarcina limi and Halosarcina pallida to the genus Halogeometricum as Halogeometricum limi comb. nov. and Halogeometricum pallidum comb. nov., respectively.	Qiu XX, Zhao ML, Han D, Zhang WJ, Dyall-Smith ML, Cui HL	Int J Syst Evol Microbiol	10.1099/ijs.0.055038-0	2013	*
Cultivation	Organic solvent tolerance of halophilic archaea.	Usami R, Fukushima T, Mizuki T, Inoue A, Yoshida Y, Horikoshi K	Biosci Biotechnol Biochem	10.1271/bbb.67.1809	2003	*
Phylogeny	Halogeometricum borinquense gen. nov., sp. nov., a novel halophilic archaeon from Puerto Rico.	Montalvo-Rodriguez R, Vreeland RH, Oren A, Kessel M, Betancourt C, Lopez-Garriga J	Int J Syst Bacteriol	10.1099/00207713-48-4-1305	1998	*

References

#4413

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 11551

#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) .

#66793

Mukherjee et al.: GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life. 35: 676 - 683 2017 ( DOI 10.1038/nbt.3886 , PubMed 28604660 )

#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;

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

* These data were automatically processed and therefore are not curated

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Halogeometricum borinquense DSM 11551 PR 3

Halogeometricum borinquense DSM 11551 PR 3

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