Staphylothermus marinus (DSM 3639, F1, JCM 9404)

Name: Staphylothermus marinus (DSM 3639, F1, JCM 9404)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 4201

Type strain

Strain Designation F1

Culture col. no. DSM 3639 F1 JCM 9404 ATCC 43588

NCBI tax ID(s) 399550 2280

Special Collections DSMZ JCM

History <- K.O. Stetter and G. Fiala, F1 DSM 3639 <-- K. O. Stetter and G. Fiala F1.

Links

Staphylothermus marinus F1 is an anaerobe archaeon that was isolated from geothermally heated marine sediment.

anaerobe genome sequence 16S sequence Archaea

Name and taxonomic classification

SI-ID 47743

ATCC 43588,DSM 3639,JCM 9404

@ref 20215

Last LPSN update 2026-02-09 11:18:40

Domain Archaea

Phylum Thermoproteota

Class Thermoprotei

Order Desulfurococcales

Family Desulfurococcaceae

Genus Staphylothermus

Species Staphylothermus marinus

Full scientific name Staphylothermus marinus Stetter and Fiala 1986

BacDive ID	Other strains from **Staphylothermus marinus** (1)	Type strain
4202	S. marinus Al2, DSM 3666

Morphology

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
1429	PYROCOCCUS MEDIUM (DSMZ Medium 377)		Medium recipe at MediaDive	Name: PYROCOCCUS MEDIUM (DSMZ Medium 377) Composition: Sulfur 30.0 g/l Peptone 5.0 g/l MgCl2 x 6 H2O 2.75 g/l Yeast extract 1.0 g/l KH2PO4 0.5 g/l Na2S x 9 H2O 0.5 g/l KCl 0.33 g/l NaBr 0.05 g/l MgSO4 x 7 H2O 0.03 g/l Nitrilotriacetic acid 0.015 g/l NaCl 0.01 g/l (NH4)2SO4 0.01 g/l SrCl2 x 6 H2O 0.007 g/l Citric acid 0.005 g/l MnSO4 x H2O 0.005 g/l CoSO4 x 7 H2O 0.0018 g/l ZnSO4 x 7 H2O 0.0018 g/l CaCl2 x 2 H2O 0.001 g/l FeSO4 x 7 H2O 0.001 g/l Sodium resazurin 0.0005 g/l NiCl2 x 6 H2O 0.0003 g/l AlK(SO4)2 x 12 H2O 0.0002 g/l CuSO4 x 5 H2O 0.0001 g/l Na2MoO4 x 2 H2O 0.0001 g/l H3BO3 0.0001 g/l KI 5e-05 g/l Na2WO4 x 2 H2O 4e-06 g/l Na2SeO3 x 5 H2O 3e-06 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
1429	positive	growth	88
67770	positive	growth	90

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
1429	anaerobe
125438	anaerobe	93.039

Spore formation

@ref	Spore formation	Confidence
125438		92.263

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	teichoic acid biosynthesis	100	1 of 1
66794	pantothenate biosynthesis	100	6 of 6
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	ribulose monophosphate pathway	100	2 of 2
66794	mannosylglycerate biosynthesis	100	2 of 2
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	flavin biosynthesis	93.33	14 of 15
66794	cellulose degradation	80	4 of 5
66794	starch degradation	80	8 of 10
66794	aspartate and asparagine metabolism	77.78	7 of 9
66794	molybdenum cofactor biosynthesis	77.78	7 of 9
66794	palmitate biosynthesis	77.27	17 of 22
66794	vitamin B1 metabolism	76.92	10 of 13
66794	glycolysis	76.47	13 of 17
66794	glycogen biosynthesis	75	3 of 4
66794	coenzyme A metabolism	75	3 of 4
66794	pyrimidine metabolism	68.89	31 of 45
66794	glutamate and glutamine metabolism	67.86	19 of 28
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	d-mannose degradation	66.67	6 of 9
66794	selenocysteine biosynthesis	66.67	4 of 6
66794	enterobactin biosynthesis	66.67	2 of 3
66794	serine metabolism	66.67	6 of 9
66794	formaldehyde oxidation	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	photosynthesis	64.29	9 of 14
66794	purine metabolism	62.77	59 of 94
66794	lipoate biosynthesis	60	3 of 5
66794	glycogen metabolism	60	3 of 5
66794	ubiquinone biosynthesis	57.14	4 of 7
66794	propanol degradation	57.14	4 of 7
66794	degradation of sugar alcohols	56.25	9 of 16
66794	oxidative phosphorylation	56.04	51 of 91
66794	NAD metabolism	55.56	10 of 18
66794	methionine metabolism	53.85	14 of 26
66794	lipid metabolism	51.61	16 of 31
66794	suberin monomers biosynthesis	50	1 of 2
66794	ethanol fermentation	50	1 of 2
66794	degradation of hexoses	50	9 of 18
66794	acetate fermentation	50	2 of 4
66794	CDP-diacylglycerol biosynthesis	50	1 of 2
66794	glycine metabolism	50	5 of 10
66794	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
66794	cis-vaccenate biosynthesis	50	1 of 2
66794	polyamine pathway	47.83	11 of 23
66794	sulfate reduction	46.15	6 of 13
66794	alanine metabolism	44.83	13 of 29
66794	non-pathway related	44.74	17 of 38
66794	cysteine metabolism	44.44	8 of 18
66794	valine metabolism	44.44	4 of 9
66794	glutathione metabolism	42.86	6 of 14
66794	tyrosine metabolism	42.86	6 of 14
66794	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
66794	propionate fermentation	40	4 of 10
66794	vitamin K metabolism	40	2 of 5
66794	hydrogen production	40	2 of 5
66794	3-chlorocatechol degradation	40	2 of 5
66794	phenylalanine metabolism	38.46	5 of 13
66794	urea cycle	38.46	5 of 13
66794	isoprenoid biosynthesis	38.46	10 of 26
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	37.5	3 of 8
66794	ketogluconate metabolism	37.5	3 of 8
66794	C4 and CAM-carbon fixation	37.5	3 of 8
66794	dolichyl-diphosphooligosaccharide biosynthesis	36.36	4 of 11
66794	pentose phosphate pathway	36.36	4 of 11
66794	metabolism of disaccharids	36.36	4 of 11
66794	lysine metabolism	35.71	15 of 42
66794	tryptophan metabolism	34.21	13 of 38
66794	lipid A biosynthesis	33.33	3 of 9
66794	CO2 fixation in Crenarchaeota	33.33	3 of 9
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	octane oxidation	33.33	1 of 3
66794	chlorophyll metabolism	33.33	6 of 18
66794	IAA biosynthesis	33.33	1 of 3
66794	sphingosine metabolism	33.33	2 of 6
66794	myo-inositol biosynthesis	30	3 of 10
66794	phenol degradation	30	6 of 20
66794	threonine metabolism	30	3 of 10
66794	arginine metabolism	29.17	7 of 24
66794	citric acid cycle	28.57	4 of 14
66794	cardiolipin biosynthesis	28.57	2 of 7
66794	mevalonate metabolism	28.57	2 of 7
66794	degradation of pentoses	28.57	8 of 28
66794	vitamin B6 metabolism	27.27	3 of 11
66794	peptidoglycan biosynthesis	26.67	4 of 15
66794	toluene degradation	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	gluconeogenesis	25	2 of 8
66794	sulfopterin metabolism	25	1 of 4
66794	biotin biosynthesis	25	1 of 4
66794	catecholamine biosynthesis	25	1 of 4
66794	ppGpp biosynthesis	25	1 of 4
66794	CMP-KDO biosynthesis	25	1 of 4
66794	methanogenesis from CO2	25	3 of 12
66794	butanoate fermentation	25	1 of 4
66794	isoleucine metabolism	25	2 of 8
66794	leucine metabolism	23.08	3 of 13
66794	phosphatidylethanolamine bioynthesis	23.08	3 of 13
66794	ascorbate metabolism	22.73	5 of 22
66794	nitrate assimilation	22.22	2 of 9
66794	histidine metabolism	20.69	6 of 29

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Marine
#Environmental	#Aquatic	#Sediment

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
1429	geothermally heated marine sediment	Vulcano island	Italy	ITA	Europe
67770	Geothermally heated sea floor at Vulcano		Italy	ITA	Europe

Taxonmaps

69479

Global distribution of 16S sequence X99560 (>99% sequence identity) for Staphylothermus marinus subclade from Microbeatlas

Aquatic Samples	1
Soil Samples
Animal Samples
Plant Samples
Total Samples	1

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
1429	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM1594v1 assembly for Staphylothermus marinus F1	complete	GCA_000015945	399550.11	640069332	399550	98.94

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	S.marinus 16S rRNA gene	X99560	1442		399550

GC content

@ref	GC-content (mol%)	Method
1429	35.0
67770	35.3	high performance liquid chromatography (HPLC)
67770	34.9	thermal denaturation, midpoint method (Tm)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Staphylothermus marinus F1, DSM 3639
IMG: 640069332

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	61.90	no
125439	motility	BacteriaNetⓘ	no	63.70	no
125439	gram_stain	BacteriaNetⓘ	positive	70.40	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	65.50	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Staphylothermus marinus F1 F1
NCBI: GCA_000015945.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	71.21	no
125438	anaerobic	anaerobicⓘ	yes	93.04	yes
125438	aerobic	aerobicⓘ	no	91.87	yes
125438	spore-forming	spore-formingⓘ	no	92.26	no
125438	thermophilic	thermophileⓘ	yes	85.55	yes
125438	flagellated	motile2+ⓘ	no	73.61	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	The structure of the Thermococcus gammatolerans McrB N-terminal domain reveals a new mode of substrate recognition and specificity among McrB homologs.	Hosford CJ, Bui AQ, Chappie JS.	J Biol Chem	10.1074/jbc.ra119.010188	2020
	Complete genome sequence of Staphylothermus marinus Stetter and Fiala 1986 type strain F1.	Anderson IJ, Sun H, Lapidus A, Copeland A, Glavina Del Rio T, Tice H, Dalin E, Lucas S, Barry K, Land M, Richardson P, Huber H, Kyrpides NC.	Stand Genomic Sci	10.4056/sigs.30527	2009
	Promiscuous behaviour of archaeal ribosomal proteins: implications for eukaryotic ribosome evolution.	Armache JP, Anger AM, Marquez V, Franckenberg S, Frohlich T, Villa E, Berninghausen O, Thomm M, Arnold GJ, Beckmann R, Wilson DN.	Nucleic Acids Res	10.1093/nar/gks1259	2013
Metabolism	Minimal sulfur requirement for growth and sulfur-dependent metabolism of the hyperthermophilic archaeon Staphylothermus marinus.	Hao X, Ma K.	Archaea	10.1155/2003/626017	2003
Metabolism	The Prodigal Compound: Return of Ribosyl 1,5-Bisphosphate as an Important Player in Metabolism.	Hove-Jensen B, Brodersen DE, Manav MC.	Microbiol Mol Biol Rev	10.1128/mmbr.00040-18	2019
Metabolism	Microbial communities with distinct denitrification potential in spruce and beech soils differing in nitrate leaching.	Barta J, Tahovska K, Santruckova H, Oulehle F.	Sci Rep	10.1038/s41598-017-08554-1	2017
	Keratin Degradation by Fervidobacterium pennavorans, a Novel Thermophilic Anaerobic Species of the Order Thermotogales.	Friedrich AB, Antranikian G.	Appl Environ Microbiol	10.1128/aem.62.8.2875-2882.1996	1996
Metabolism	The complete genome sequence of Staphylothermus marinus reveals differences in sulfur metabolism among heterotrophic Crenarchaeota.	Anderson IJ, Dharmarajan L, Rodriguez J, Hooper S, Porat I, Ulrich LE, Elkins JG, Mavromatis K, Sun H, Land M, Lapidus A, Lucas S, Barry K, Huber H, Zhulin IB, Whitman WB, Mukhopadhyay B, Woese C, Bristow J, Kyrpides N.	BMC Genomics	10.1186/1471-2164-10-145	2009

References

#1429	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 3639
#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) .
#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 .
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#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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Staphylothermus marinus (DSM 3639, F1, JCM 9404)

Name and taxonomic classification

Morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000015945

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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