Halogeometricum pallidum (KCTC 4017, JCM 14848, BZ256)

Name: Halogeometricum pallidum (KCTC 4017, JCM 14848, BZ256)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 134312

Type strain

Strain Designation BZ256

Culture col. no. KCTC 4017 JCM 14848 BZ256

NCBI tax ID(s) 1227487 411361

Special Collections JCM KCTC Literature strains

History K. N. Savage BZ256. <- Kristen N Savage, Univ. of Oklahoma, USA

Links

Halogeometricum pallidum BZ256 is an aerobe, Gram-negative, coccus-shaped archaeon that was isolated from freshwater .

Gram-negative coccus-shaped aerobe genome sequence 16S sequence Archaea

Name and taxonomic classification

SI-ID 286074

KCTC 4017,JCM 14848

@ref 20215

Last LPSN update 2026-02-09 11:32:09

Domain Archaea

Phylum Methanobacteriota

Class Halobacteria

Order Halobacteriales

Family Haloferacaceae

Genus Halogeometricum

Species Halogeometricum pallidum

Full scientific name Halogeometricum pallidum (Savage et al. 2008) Qiu et al. 2013

Synonyms (1)

Halosarcina pallida

Morphology

Cell morphology

@ref	Gram stain	Cell width	Cell shape	Motility
32375	negative	0.9 µm	coccus-shaped
67771			coccus-shaped

Pigmentation

32375

Productionyes

Culture and growth conditions

Culture temp

@ref	Growth	Type	Temperature (°C)
32375	positive	growth	25-45
32375	positive	optimum	30
67770	positive	growth	37
67771	positive	growth	37

Culture pH

@ref	Ability	Type	PH	PH range
32375	positive	optimum	6.5
32375	positive	growth	5-8.5	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
32375	aerobe
67771	aerobe

Spore formation

@ref	Spore formation	Confidence
125439		92.4

Halophily

@ref	Salt	Growth	Tested relation	Concentration
32375	NaCl	positive	growth	9.86-24.94 %
32375	NaCl	positive	optimum	17.98 %

Observation

32375

Observationaggregates in clumps

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
32375	30089 ChEBI	acetate	+	carbon source
32375	35391 ChEBI	aspartate	+	carbon source
32375	28757 ChEBI	fructose	+	carbon source
32375	28260 ChEBI	galactose	+	carbon source
32375	17234 ChEBI	glucose	+	carbon source
32375	29987 ChEBI	glutamate	+	carbon source
32375	17754 ChEBI	glycerol	+	carbon source
32375	15428 ChEBI	glycine	+	carbon source
32375	27570 ChEBI	histidine	+	carbon source
32375	24996 ChEBI	lactate	+	carbon source
32375	17716 ChEBI	lactose	+	carbon source
32375	25115 ChEBI	malate	+	carbon source
32375	17632 ChEBI	nitrate	+	reduction
32375	28044 ChEBI	phenylalanine	+	carbon source
32375	15361 ChEBI	pyruvate	+	carbon source
32375	17814 ChEBI	salicin	+	carbon source
32375	30911 ChEBI	sorbitol	+	carbon source
32375	30031 ChEBI	succinate	+	carbon source
32375	17992 ChEBI	sucrose	+	carbon source
32375	27082 ChEBI	trehalose	+	carbon source

Metabolite production

@ref	Chebi-ID	Metabolite	Production
32375	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
32375	35581 ChEBI	indole	+

Enzymes

@ref	Value	Activity	Ec
32375	catalase	+	1.11.1.6
32375	cytochrome oxidase	+	1.9.3.1

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	ceramide biosynthesis	100	1 of 1
66794	palmitate biosynthesis	100	22 of 22
66794	suberin monomers biosynthesis	100	2 of 2
66794	factor 420 biosynthesis	100	5 of 5
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	formaldehyde oxidation	100	3 of 3
66794	denitrification	100	2 of 2
66794	valine metabolism	100	9 of 9
66794	methylglyoxal degradation	100	5 of 5
66794	adipate degradation	100	2 of 2
66794	coenzyme A metabolism	100	4 of 4
66794	aerobactin biosynthesis	100	1 of 1
66794	starch degradation	100	10 of 10
66794	folate polyglutamylation	100	1 of 1
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	flavin biosynthesis	93.33	14 of 15
66794	citric acid cycle	92.86	13 of 14
66794	vitamin B1 metabolism	92.31	12 of 13
66794	propionate fermentation	90	9 of 10
66794	Entner Doudoroff pathway	90	9 of 10
66794	threonine metabolism	90	9 of 10
66794	chorismate metabolism	88.89	8 of 9
66794	CO2 fixation in Crenarchaeota	88.89	8 of 9
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	isoleucine metabolism	87.5	7 of 8
66794	propanol degradation	85.71	6 of 7
66794	ubiquinone biosynthesis	85.71	6 of 7
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	tetrahydrofolate metabolism	85.71	12 of 14
66794	phenylalanine metabolism	84.62	11 of 13
66794	NAD metabolism	83.33	15 of 18
66794	pantothenate biosynthesis	83.33	5 of 6
66794	glutamate and glutamine metabolism	82.14	23 of 28
66794	vitamin K metabolism	80	4 of 5
66794	phenylacetate degradation (aerobic)	80	4 of 5
66794	cellulose degradation	80	4 of 5
66794	glycogen metabolism	80	4 of 5
66794	ethylmalonyl-CoA pathway	80	4 of 5
66794	purine metabolism	79.79	75 of 94
66794	molybdenum cofactor biosynthesis	77.78	7 of 9
66794	pyrimidine metabolism	77.78	35 of 45
66794	lipid metabolism	77.42	24 of 31
66794	leucine metabolism	76.92	10 of 13
66794	alanine metabolism	75.86	22 of 29
66794	ketogluconate metabolism	75	6 of 8
66794	glycogen biosynthesis	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	sulfopterin metabolism	75	3 of 4
66794	C4 and CAM-carbon fixation	75	6 of 8
66794	gluconeogenesis	75	6 of 8
66794	vitamin B12 metabolism	73.53	25 of 34
66794	photosynthesis	71.43	10 of 14
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	heme metabolism	71.43	10 of 14
66794	histidine metabolism	68.97	20 of 29
66794	non-pathway related	68.42	26 of 38
66794	degradation of sugar acids	68	17 of 25
66794	cyanate degradation	66.67	2 of 3
66794	octane oxidation	66.67	2 of 3
66794	serine metabolism	66.67	6 of 9
66794	arginine metabolism	66.67	16 of 24
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	d-mannose degradation	66.67	6 of 9
66794	enterobactin biosynthesis	66.67	2 of 3
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	selenocysteine biosynthesis	66.67	4 of 6
66794	tryptophan metabolism	65.79	25 of 38
66794	glycolysis	64.71	11 of 17
66794	tyrosine metabolism	64.29	9 of 14
66794	pentose phosphate pathway	63.64	7 of 11
66794	metabolism of disaccharids	63.64	7 of 11
66794	proline metabolism	63.64	7 of 11
66794	dTDPLrhamnose biosynthesis	62.5	5 of 8
66794	creatinine degradation	60	3 of 5
66794	3-chlorocatechol degradation	60	3 of 5
66794	4-hydroxyphenylacetate degradation	60	6 of 10
66794	myo-inositol biosynthesis	60	6 of 10
66794	gallate degradation	60	3 of 5
66794	phenol degradation	60	12 of 20
66794	methionine metabolism	57.69	15 of 26
66794	lysine metabolism	57.14	24 of 42
66794	glutathione metabolism	57.14	8 of 14
66794	degradation of sugar alcohols	56.25	9 of 16
66794	cysteine metabolism	55.56	10 of 18
66794	nitrate assimilation	55.56	5 of 9
66794	oxidative phosphorylation	54.95	50 of 91
66794	vitamin B6 metabolism	54.55	6 of 11
66794	urea cycle	53.85	7 of 13
66794	CDP-diacylglycerol biosynthesis	50	1 of 2
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	ribulose monophosphate pathway	50	1 of 2
66794	alginate biosynthesis	50	2 of 4
66794	cyclohexanol degradation	50	2 of 4
66794	kanosamine biosynthesis II	50	1 of 2
66794	ethanol fermentation	50	1 of 2
66794	butanoate fermentation	50	2 of 4
66794	phenylmercury acetate degradation	50	1 of 2
66794	glycine metabolism	50	5 of 10
66794	resorcinol degradation	50	1 of 2
66794	carotenoid biosynthesis	50	11 of 22
66794	degradation of pentoses	50	14 of 28
66794	androgen and estrogen metabolism	50	8 of 16
66794	3-phenylpropionate degradation	46.67	7 of 15
66794	degradation of hexoses	44.44	8 of 18
66794	arachidonic acid metabolism	44.44	8 of 18
66794	mevalonate metabolism	42.86	3 of 7
66794	methanogenesis from CO2	41.67	5 of 12
66794	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
66794	ascorbate metabolism	40.91	9 of 22
66794	hydrogen production	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	coenzyme M biosynthesis	40	4 of 10
66794	glycine betaine biosynthesis	40	2 of 5
66794	lipoate biosynthesis	40	2 of 5
66794	bacilysin biosynthesis	40	2 of 5
66794	polyamine pathway	39.13	9 of 23
66794	cholesterol biosynthesis	36.36	4 of 11
66794	isoprenoid biosynthesis	34.62	9 of 26
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	4-hydroxymandelate degradation	33.33	3 of 9
66794	methane metabolism	33.33	1 of 3
66794	lipid A biosynthesis	33.33	3 of 9
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	sulfoquinovose degradation	33.33	1 of 3
66794	IAA biosynthesis	33.33	1 of 3
66794	phenylpropanoid biosynthesis	30.77	4 of 13
66794	phosphatidylethanolamine bioynthesis	30.77	4 of 13
66794	sulfate reduction	30.77	4 of 13
66794	aclacinomycin biosynthesis	28.57	2 of 7
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	d-xylose degradation	27.27	3 of 11
66794	peptidoglycan biosynthesis	26.67	4 of 15
66794	carnitine metabolism	25	2 of 8
66794	biotin biosynthesis	25	1 of 4
66794	CMP-KDO biosynthesis	25	1 of 4
66794	catecholamine biosynthesis	25	1 of 4
66794	vitamin E metabolism	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	toluene degradation	25	1 of 4
66794	bile acid biosynthesis, neutral pathway	23.53	4 of 17

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Freshwater
#Environmental	#Aquatic	#Lake (large)
#Environmental	#Aquatic	#Pond (small)
#Environmental	#Aquatic	#River (Creek)

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
32375	freshwater (river, lake, pond)
67770	Zodletone Spring, a sulfide- and sulfur-rich spring	south-west Oklahoma	USA	USA	North America
67771	From Zodletone Spring, a sulfide- and sulfur-rich spring in south-western Oklahoma		USA	USA	North America

Taxonmaps

69479

Global distribution of 16S sequence HM185493 (>99% sequence identity) for Halogeometricum pallidum subclade from Microbeatlas

Aquatic Samples	3
Soil Samples	3
Animal Samples	3
Plant Samples
Total Samples	9

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67771	ASM33709v1 assembly for Halogeometricum pallidum JCM 14848	contig	GCA_000337095	1227487.5	2554235507	1227487	69.64

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
32375	Halosarcina pallida strain BZ256 16S ribosomal RNA gene, partial sequence	EF055454	1351	1227487
67770	Halosarcina pallida gene for 16S ribosomal RNA, partial sequence, strain: JCM 14848	AB477980	1433	1227487
67770	Halosarcina pallida strain BZ256 16S ribosomal RNA gene, partial sequence	HM185493	1473	1227487
67771	Halosarcina pallida gene for 16S rRNA, complete sequence, strain: JCM 14848	AB663429	1473	1227487

GC content

32375

GC-content (mol%)65.4

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Halogeometricum pallidum JCM 14848
NCBI: GCA_000337095

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	92.40	no
125439	motility	BacteriaNetⓘ	yes	61.60	no
125439	gram_stain	BacteriaNetⓘ	negative	86.30	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	79.10	no

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
Phylogeny	Halogeometricum rufum sp. nov., a halophilic archaeon from a marine solar saltern, and emended description of the genus Halogeometricum.	Cui HL, Yang X, Gao X, Li XY, Xu XW, Zhou YG, Liu HC, Zhou PJ	Int J Syst Evol Microbiol	10.1099/ijs.0.019463-0	2009
Phylogeny	Halosarcina pallida gen. nov., sp. nov., a halophilic archaeon from a low-salt, sulfide-rich spring.	Savage KN, Krumholz LR, Oren A, Elshahed MS	Int J Syst Evol Microbiol	10.1099/ijs.0.65398-0	2008

References

#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 )
#28603	IJSEM 856 2008 ( DOI 10.1099/ijs.0.65398-0 , PubMed 18398182 )
#32375	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 #28603
#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;
#67771	Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;
#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 .
#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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Halogeometricum pallidum (KCTC 4017, JCM 14848, BZ256)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_000337095

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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