Name: Archaeoglobus fulgidus VC-16
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 18096

Type strain:

Species: Archaeoglobus fulgidus

Strain Designation: VC-16

Culture col. no.: DSM 4304, ATCC 49558, JCM 9628, NBRC 100126

Strain history: DSM 4304 <-- K. O. Stetter VC-16.

NCBI tax ID(s): 224325 (strain), 2234 (species)

SI-ID 46110

ATCC 49558, DSM 4304, ATCC 49203, JCM 9628, NBRC 100126

Other strains from Archaeoglobus fulgidus

A. fulgidus Z, DSM 4139
A. fulgidus 7324, DSM 8774

Section

Archaeoglobus fulgidus VC-16 is an anaerobe, hyperthermophilic, Gram-negative archaeon that was isolated from submarine hot spring.

Gram-negative
anaerobe
hyperthermophilic
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	*Archaeoglobi*
	Order	*Archaeoglobales*
	Family	*Archaeoglobaceae*
	Genus	*Archaeoglobus*
	Species	**Archaeoglobus fulgidus**
	Full Scientific Name (LPSN)	Archaeoglobus fulgidus Stetter 1988

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	negative Confidence in %99.991

Information on culture and growth conditions Culture and growth conditions

[Ref.: #1648]

Culture medium

ARCHAEOGLOBUS MEDIUM (DSMZ Medium 399)

[Ref.: #1648]

Culture medium growth

[Ref.: #1648]

Culture medium link

Medium recipe at MediaDive

[Ref.: #1648]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #1648]			growth	85 °C
[Ref.: #67770]			growth	80 °C

[Ref.: #1648]	Temperature range	hyperthermophilic
[Ref.: #67770]	Temperature range	hyperthermophilic
[Ref.: #69480]	Temperature range	thermophilic Confidence in %98.702

Information on physiology and metabolism Physiology and metabolism

[Ref.: #1648]	Oxygen tolerance	anaerobe
[Ref.: #69480]	Oxygen tolerance	anaerobe Confidence in %98.675

[Ref.: #69480]

Ability of spore formation

no Confidence in %99.738

[Ref.: #1648]

Name of produced compound

isocitrate dehydrogenase

[Ref.: #67770]

Observation

quinones: MK-7(H₁₄)

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	hydrogen production	100	5 of 5
[Ref.: #66794]	methanofuran biosynthesis	100	5 of 5
[Ref.: #66794]	ubiquinone biosynthesis	100	7 of 7
[Ref.: #66794]	ribulose monophosphate pathway	100	2 of 2
[Ref.: #66794]	factor 420 biosynthesis	100	5 of 5
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	88.89	8 of 9
[Ref.: #66794]	gluconeogenesis	87.5	7 of 8
[Ref.: #66794]	propanol degradation	85.71	6 of 7
[Ref.: #66794]	methanogenesis from CO2	83.33	10 of 12
[Ref.: #66794]	flavin biosynthesis	80	12 of 15
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	valine metabolism	77.78	7 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	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]	vitamin B12 metabolism	76.47	26 of 34
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	C4 and CAM-carbon fixation	75	6 of 8
[Ref.: #66794]	NAD metabolism	72.22	13 of 18
[Ref.: #66794]	glutamate and glutamine metabolism	71.43	20 of 28
[Ref.: #66794]	lipid metabolism	70.97	22 of 31
[Ref.: #66794]	propionate fermentation	70	7 of 10
[Ref.: #66794]	4-hydroxyphenylacetate degradation	70	7 of 10
[Ref.: #66794]	sulfate reduction	69.23	9 of 13
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	formaldehyde oxidation	66.67	2 of 3
[Ref.: #66794]	serine metabolism	66.67	6 of 9
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	methane metabolism	66.67	2 of 3
[Ref.: #66794]	purine metabolism	65.96	62 of 94
[Ref.: #66794]	alanine metabolism	65.52	19 of 29
[Ref.: #66794]	glycolysis	64.71	11 of 17
[Ref.: #66794]	pyrimidine metabolism	64.44	29 of 45
[Ref.: #66794]	heme metabolism	64.29	9 of 14
[Ref.: #66794]	oxidative phosphorylation	63.74	58 of 91
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	arginine metabolism	62.5	15 of 24
[Ref.: #66794]	leucine metabolism	61.54	8 of 13
[Ref.: #66794]	urea cycle	61.54	8 of 13
[Ref.: #66794]	threonine metabolism	60	6 of 10
[Ref.: #66794]	phenylacetate degradation (aerobic)	60	3 of 5
[Ref.: #66794]	vitamin K metabolism	60	3 of 5
[Ref.: #66794]	lysine metabolism	59.52	25 of 42
[Ref.: #66794]	reductive acetyl coenzyme A pathway	57.14	4 of 7
[Ref.: #66794]	citric acid cycle	57.14	8 of 14
[Ref.: #66794]	polyamine pathway	56.52	13 of 23
[Ref.: #66794]	nitrate assimilation	55.56	5 of 9
[Ref.: #66794]	d-mannose degradation	55.56	5 of 9
[Ref.: #66794]	non-pathway related	55.26	21 of 38
[Ref.: #66794]	pentose phosphate pathway	54.55	6 of 11
[Ref.: #66794]	histidine metabolism	51.72	15 of 29
[Ref.: #66794]	lactate fermentation	50	2 of 4
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	toluene degradation	50	2 of 4
[Ref.: #66794]	cis-vaccenate biosynthesis	50	1 of 2
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	1,4-dihydroxy-6-naphthoate biosynthesis	50	3 of 6
[Ref.: #66794]	Entner Doudoroff pathway	50	5 of 10
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	50	1 of 2
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	sulfopterin metabolism	50	2 of 4
[Ref.: #66794]	glycolate and glyoxylate degradation	50	3 of 6
[Ref.: #66794]	acetate fermentation	50	2 of 4
[Ref.: #66794]	glycogen biosynthesis	50	2 of 4
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	50	6 of 12
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	selenocysteine biosynthesis	50	3 of 6
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	isoprenoid biosynthesis	50	13 of 26
[Ref.: #66794]	methionine metabolism	50	13 of 26
[Ref.: #66794]	tryptophan metabolism	47.37	18 of 38
[Ref.: #66794]	proline metabolism	45.45	5 of 11
[Ref.: #66794]	glutathione metabolism	42.86	6 of 14
[Ref.: #66794]	cardiolipin biosynthesis	42.86	3 of 7
[Ref.: #66794]	tyrosine metabolism	42.86	6 of 14
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	coenzyme M biosynthesis	40	4 of 10
[Ref.: #66794]	elloramycin biosynthesis	40	2 of 5
[Ref.: #66794]	myo-inositol biosynthesis	40	4 of 10
[Ref.: #66794]	ethylmalonyl-CoA pathway	40	2 of 5
[Ref.: #66794]	degradation of hexoses	38.89	7 of 18
[Ref.: #66794]	carnitine metabolism	37.5	3 of 8
[Ref.: #66794]	ketogluconate metabolism	37.5	3 of 8
[Ref.: #66794]	degradation of pentoses	35.71	10 of 28
[Ref.: #66794]	cyanate degradation	33.33	1 of 3
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	lipid A biosynthesis	33.33	3 of 9
[Ref.: #66794]	cysteine metabolism	33.33	6 of 18
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	benzoyl-CoA degradation	28.57	2 of 7
[Ref.: #66794]	mevalonate metabolism	28.57	2 of 7
[Ref.: #66794]	tetrahydrofolate metabolism	28.57	4 of 14
[Ref.: #66794]	chlorophyll metabolism	27.78	5 of 18
[Ref.: #66794]	vitamin B6 metabolism	27.27	3 of 11
[Ref.: #66794]	metabolism of disaccharids	27.27	3 of 11
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	cholesterol biosynthesis	27.27	3 of 11
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	biotin biosynthesis	25	1 of 4
[Ref.: #66794]	vitamin E metabolism	25	1 of 4
[Ref.: #66794]	alginate biosynthesis	25	1 of 4
[Ref.: #66794]	dTDPLrhamnose biosynthesis	25	2 of 8
[Ref.: #66794]	CMP-KDO biosynthesis	25	1 of 4
[Ref.: #66794]	catecholamine biosynthesis	25	1 of 4
[Ref.: #66794]	ppGpp biosynthesis	25	1 of 4
[Ref.: #66794]	degradation of sugar acids	24	6 of 25
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	23.08	3 of 13
[Ref.: #66794]	4-hydroxymandelate degradation	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.: #1648]	Sample type/isolated from	submarine hot spring
[Ref.: #1648]	Geographic location (country and/or sea, region)	Vulcano island
[Ref.: #1648]	Country	Italy
[Ref.: #1648]	Country ISO 3 Code	ITA
[Ref.: #1648]	Continent	Europe

[Ref.: #67770]	Sample type/isolated from	Hot sediments of marine hydrothermal system
[Ref.: #67770]	Geographic location (country and/or sea, region)	Vulcano
[Ref.: #67770]	Country	Italy
[Ref.: #67770]	Country ISO 3 Code	ITA
[Ref.: #67770]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Marine
#Environmental	#Aquatic	#Thermal spring
#Condition	#Thermophilic (>45°C)	-

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence Y00275 (>99% sequence identity) for Archaeoglobus fulgidus subclade from Microbeatlas

Aquatic Samples	91
Soil Samples	3
Animal Samples	1
Plant Samples
Total Samples	95

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

[Ref.: #1648]

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]	Archaeoglobus fulgidus (VC-16) DNA for 16S ribosomal RNA	Y00275	1492	ENA	224325 tax ID
[Ref.: #67770]	Archaeoglobus fulgidus strain VC-16 16S ribosomal RNA gene	X05567	1492	ENA	224325 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Archaeoglobus fulgidus DSM 4304	GCA_000008665	complete	GenBank	224325 tax ID	*
[Ref.: #66792]	Archaeoglobus fulgidus VC-16, DSM 4304	638154502	complete	JGI IMG/M	224325 tax ID	*
[Ref.: #66792]	Archaeoglobus fulgidus DSM 4304	224325.10	complete	PATRIC	224325 tax ID	*

[Ref.: #1648]	GC-content	46.0 mol%
[Ref.: #67770]	GC-content	46 mol%	thermal denaturation, midpoint method (Tm)

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Archaeoglobus fulgidus DSM 4304 DSM 4304 NCBI: GCA_000008665.1
[Ref.: #69481]	spore-forming	yes	61	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Archaeoglobus fulgidus DSM 4304 DSM 4304 NCBI: GCA_000008665.1
[Ref.: #69480]	motile	no	86.343	no
[Ref.: #69480]	flagellated	no	97.002	no
[Ref.: #69480]	gram-positive	no	97.893	no
[Ref.: #69480]	anaerobic	yes	97.611	yes
[Ref.: #69480]	halophile	no	83.912	no
[Ref.: #69480]	spore-forming	no	93.981	no
[Ref.: #69480]	glucose-util	yes	72.287	no
[Ref.: #69480]	aerobic	no	95.966	yes
[Ref.: #69480]	thermophile	yes	99.742	yes
[Ref.: #69480]	glucose-ferment	no	77.068	no

Availability in culture collections External links

[Ref.: #1648]

Culture collection no.

DSM 4304, ATCC 49558, JCM 9628, NBRC 100126

[Ref.: #87084]

SI-ID 46110

Literature:

Only first 10 entries are displayed. Click here to see all.

Topic	Title	Authors	Journal	DOI	Year
Enzymology	Structural and Kinetic Characterization of Hyperthermophilic NADH-Dependent Persulfide Reductase from Archaeoglobus fulgidus.	Shabdar S, Anaclet B, Castineiras AG, Desir N, Choe N, Crane EJ 3rd, Sazinsky MH	Archaea	10.1155/2021/8817136	2021	*
Enzymology	The serine, threonine, and/or tyrosine-specific protein kinases and protein phosphatases of prokaryotic organisms: a family portrait.	Shi L, Potts M, Kennelly PJ	FEMS Microbiol Rev	10.1111/j.1574-6976.1998.tb00369.x	1998	*
Enzymology	Spectroscopic studies on APS reductase isolated from the hyperthermophilic sulfate-reducing archaebacterium Archaeglobus fulgidus.	Lampreia J, Fauque G, Speich N, Dahl C, Moura I, Truper HG, Moura JJ	Biochem Biophys Res Commun	10.1016/s0006-291x(05)81424-x	1991	*
Metabolism	5'-Methylbenzimidazolyl-cobamides are the corrinoids from some sulfate-reducing and sulfur-metabolizing bacteria.	Krautler B, Kohler HP, Stupperich E	Eur J Biochem	10.1111/j.1432-1033.1988.tb14303.x	1988	*
Enzymology	Vitamin contents of archaebacteria.	Noll KM, Barber TS	J Bacteriol	10.1128/jb.170.9.4315-4321.1988	1988	*
Metabolism	Assessment of the Carbon Monoxide Metabolism of the Hyperthermophilic Sulfate-Reducing Archaeon Archaeoglobus fulgidus VC-16 by Comparative Transcriptome Analyses.	Hocking WP, Roalkvam I, Magnussen C, Stokke R, Steen IH	Archaea	10.1155/2015/235384	2015	*
Metabolism	Improved enantioselectivity of thermostable esterase from Archaeoglobus fulgidus toward (S)-ketoprofen ethyl ester by directed evolution and characterization of mutant esterases.	Kim J, Kim S, Yoon S, Hong E, Ryu Y	Appl Microbiol Biotechnol	10.1007/s00253-015-6422-7	2015	*
Metabolism	Anaerobic oxidation of long-chain n-alkanes by the hyperthermophilic sulfate-reducing archaeon, Archaeoglobus fulgidus.	Khelifi N, Amin Ali O, Roche P, Grossi V, Brochier-Armanet C, Valette O, Ollivier B, Dolla A, Hirschler-Rea A	ISME J	10.1038/ismej.2014.58	2014	*
Metabolism	Phenylalanine catabolism in Archaeoglobus fulgidus VC-16.	Parthasarathy A, Kahnt J, Chowdhury NP, Buckel W	Arch Microbiol	10.1007/s00203-013-0925-3	2013	*
Proteome	The crystal structure of the AF2331 protein from Archaeoglobus fulgidus DSM 4304 forms an unusual interdigitated dimer with a new type of alpha + beta fold.	Wang S, Kirillova O, Chruszcz M, Gront D, Zimmerman MD, Cymborowski MT, Shumilin IA, Skarina T, Gorodichtchenskaia E, Savchenko A, Edwards AM, Minor W	Protein Sci	10.1002/pro.251	2009	*
Metabolism	Temperature effect on the sulfur isotope fractionation during sulfate reduction by two strains of the hyperthermophilic Archaeoglobus fulgidus.	Mitchell K, Heyer A, Canfield DE, Hoek J, Habicht KS	Environ Microbiol	10.1111/j.1462-2920.2009.02002.x	2009	*
Phylogeny	Nucleotide triplet based molecular phylogeny of class I and class II aminoacyl t-RNA synthetase in three domain of life process: bacteria, archaea, and eukarya.	Mondal UK, Das B, Ghosh TC, Sen A, Bothra AK	J Biomol Struct Dyn	10.1080/07391102.2008.10507247	2008	*
Enzymology	Cloning and characterization of thermostable esterase from Archaeoglobus fulgidus.	Kim SB, Lee W, Ryu YW	J Microbiol	10.1007/s12275-007-0185-5	2008	*
Enzymology	Heat shock response of Archaeoglobus fulgidus.	Rohlin L, Trent JD, Salmon K, Kim U, Gunsalus RP, Liao JC	J Bacteriol	10.1128/JB.187.17.6046-6057.2005	2005	*
Enzymology	The putative lipase, AF1763, from Archaeoglobus fulgidusis is a carboxylesterase with a very high pH optimum.	Rusnak M, Nieveler J, Schmid RD, Petri R	Biotechnol Lett	10.1007/s10529-005-5621-1	2005	*
Cultivation	A variant of the hyperthermophile Archaeoglobus fulgidus adapted to grow at high salinity.	Goncalves LG, Huber R, da Costa MS, Santos H	FEMS Microbiol Lett	10.1111/j.1574-6968.2003.tb11523.x	2003	*
Enzymology	Dissimilatory ATP sulfurylase from the hyperthermophilic sulfate reducer Archaeoglobus fulgidus belongs to the group of homo-oligomeric ATP sulfurylases.	Sperling D, Kappler U, Wynen A, Dahl C, Truper HG	FEMS Microbiol Lett	10.1111/j.1574-6968.1998.tb13007.x	1998	*
Phylogeny	A possible biochemical missing link among archaebacteria.	Achenbach-Richter L, Stetter KO, Woese CR	Nature	10.1038/327348a0	1987	*
	Rate and Extent of Growth of a Model Extremophile, Archaeoglobus fulgidus, Under High Hydrostatic Pressures.	Oliver GC, Cario A, Rogers KL	Front Microbiol	10.3389/fmicb.2020.01023	2020	*

References

#1648

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 4304

#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 )

#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;

#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 .

#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 )

#87084

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-ID46110.1 )

* These data were automatically processed and therefore are not curated

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Archaeoglobus fulgidus DSM 4304 DSM 4304

Archaeoglobus fulgidus DSM 4304 DSM 4304

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