Strain identifier
BacDive ID: 18096
Type strain: 
Species: Archaeoglobus fulgidus
Strain Designation: VC-16
Strain history: DSM 4304 <-- K. O. Stetter VC-16.
NCBI tax ID(s): 224325 (strain), 2234 (species)
version 8.1 (current version)
General
@ref: 1648
BacDive-ID: 18096
DSM-Number: 4304
keywords: genome sequence, 16S sequence, Archaea, anaerobe, hyperthermophilic, Gram-negative
description: Archaeoglobus fulgidus VC-16 is an anaerobe, hyperthermophilic, Gram-negative archaeon that was isolated from submarine hot spring.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 224325 | strain |
| 2234 | species |
strain history
| @ref | history |
|---|---|
| 1648 | <- K.O. Stetter, VC-16 |
| 67770 | DSM 4304 <-- K. O. Stetter VC-16. |
doi: 10.13145/bacdive18096.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/archaea
- keyword: phylum/methanobacteriota
- domain: Archaea
- phylum: Methanobacteriota
- class: Archaeoglobi
- order: Archaeoglobales
- family: Archaeoglobaceae
- genus: Archaeoglobus
- species: Archaeoglobus fulgidus
- full scientific name: Archaeoglobus fulgidus Stetter 1988
@ref: 1648
domain: Archaea
phylum: Euryarchaeota
class: Archaeoglobi
order: Archaeoglobales
family: Archaeoglobaceae
genus: Archaeoglobus
species: Archaeoglobus fulgidus
full scientific name: Archaeoglobus fulgidus Stetter 1988
strain designation: VC-16
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.991
Culture and growth conditions
culture medium
- @ref: 1648
- name: ARCHAEOGLOBUS MEDIUM (DSMZ Medium 399)
- growth: yes
- link: https://mediadive.dsmz.de/medium/399
- composition: Name: ARCHAEOGLOBUS MEDIUM (DSMZ Medium 399) Composition: MgCl2 x 6 H2O 3.95257 g/l NaHCO3 2.96443 g/l Na-L-lactate 1.48221 g/l Na2S x 9 H2O 0.494071 g/l Yeast extract 0.494071 g/l KCl 0.335968 g/l NH4Cl 0.247036 g/l K2HPO4 0.13834 g/l MgSO4 x 7 H2O 0.0296443 g/l Nitrilotriacetic acid 0.0148221 g/l NaCl 0.00988142 g/l MnSO4 x H2O 0.00494071 g/l Fe(NH4)2(SO4)2 x 7 H2O 0.00197628 g/l CoSO4 x 7 H2O 0.00177866 g/l ZnSO4 x 7 H2O 0.00177866 g/l FeSO4 x 7 H2O 0.000988142 g/l CaCl2 x 2 H2O 0.000988142 g/l Sodium resazurin 0.000494071 g/l NiCl2 x 6 H2O 0.000296443 g/l AlK(SO4)2 x 12 H2O 0.000197628 g/l CuSO4 x 5 H2O 9.88142e-05 g/l Na2MoO4 x 2 H2O 9.88142e-05 g/l H3BO3 9.88142e-05 g/l Na2WO4 x 2 H2O 3.95257e-06 g/l Na2SeO3 x 5 H2O 2.96443e-06 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range | confidence |
|---|---|---|---|---|---|
| 1648 | positive | growth | 85 | hyperthermophilic | |
| 67770 | positive | growth | 80 | hyperthermophilic | |
| 69480 | thermophilic | 98.702 |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 1648 | anaerobe | |
| 69480 | anaerobe | 98.675 |
spore formation
- @ref: 69480
- spore formation: no
- confidence: 99.738
compound production
- @ref: 1648
- compound: isocitrate dehydrogenase
observation
- @ref: 67770
- observation: quinones: MK-7(H14)
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 1648 | submarine hot spring | Vulcano island | Italy | ITA | Europe |
| 67770 | Hot sediments of marine hydrothermal system | Vulcano | Italy | ITA | Europe |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Marine |
| #Environmental | #Aquatic | #Thermal spring |
| #Condition | #Thermophilic (>45°C) |
taxonmaps
- @ref: 69479
- File name: preview.99_187140.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_17856;96_68819;97_89461;98_121737;99_187140&stattab=map
- Last taxonomy: Archaeoglobus fulgidus subclade
- 16S sequence: Y00275
- Sequence Identity:
- Total samples: 95
- soil counts: 3
- aquatic counts: 91
- animal counts: 1
Safety information
risk assessment
- @ref: 1648
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 67770 | Archaeoglobus fulgidus strain VC-16 16S ribosomal RNA gene | X05567 | 1492 | ena | 224325 |
| 67770 | Archaeoglobus fulgidus (VC-16) DNA for 16S ribosomal RNA | Y00275 | 1492 | ena | 224325 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Archaeoglobus fulgidus DSM 4304 | GCA_000008665 | complete | ncbi | 224325 |
| 66792 | Archaeoglobus fulgidus VC-16, DSM 4304 | 638154502 | complete | img | 224325 |
| 66792 | Archaeoglobus fulgidus DSM 4304 | 224325.10 | complete | patric | 224325 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 1648 | 46.0 | |
| 67770 | 46 | thermal denaturation, midpoint method (Tm) |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | yes | 61 | no |
| motile | no | 86.343 | no |
| flagellated | no | 97.002 | no |
| gram-positive | no | 97.893 | no |
| anaerobic | yes | 97.611 | yes |
| halophile | no | 83.912 | no |
| spore-forming | no | 93.981 | no |
| glucose-util | yes | 72.287 | no |
| aerobic | no | 95.966 | yes |
| thermophile | yes | 99.742 | yes |
| glucose-ferment | no | 77.068 | no |
External links
@ref: 1648
culture collection no.: DSM 4304, ATCC 49558, JCM 9628, NBRC 100126
straininfo link
- @ref: 87084
- straininfo: 46110
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Enzymology | 1659811 | 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 | Archaea/*enzymology, Binding Sites, Electron Spin Resonance Spectroscopy, Hot Temperature, Oxidation-Reduction, Oxidoreductases/chemistry/isolation & purification/*metabolism, *Oxidoreductases Acting on Sulfur Group Donors, Spectrophotometry, Sulfates/metabolism | Stress |
| Enzymology | 3137215 | Vitamin contents of archaebacteria. | Noll KM, Barber TS | J Bacteriol | 10.1128/jb.170.9.4315-4321.1988 | 1988 | Archaea, Bacteria, Biological Assay, Biotin/analysis, Coenzymes/analysis, Escherichia coli, Lactobacillus casei/growth & development, Niacin/analysis, Pantothenic Acid/analysis, Pyridoxine/analysis, Riboflavin/analysis, Thioctic Acid/analysis, Vitamins/*analysis | |
| Metabolism | 3416881 | 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 | Bacteria/*analysis/metabolism, Chemical Phenomena, Chemistry, Chromatography, High Pressure Liquid, Corrinoids, Magnetic Resonance Spectroscopy, Sulfur/metabolism, Vitamin B 12/analysis/*isolation & purification | Enzymology |
| Enzymology | 9627961 | 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 | Amino Acid Sequence, Archaeoglobus fulgidus/*enzymology/genetics, Electrophoresis, Polyacrylamide Gel, Genes, Archaeal/genetics, Molecular Sequence Data, Phylogeny, Sequence Alignment, Sulfate Adenylyltransferase/analysis/*classification/genetics | Phylogeny |
| Enzymology | 9862122 | 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 | Amino Acid Sequence, Archaeal Proteins/*genetics, Archaeoglobus fulgidus/enzymology/genetics, Bacillus subtilis/enzymology/genetics, Bacterial Proteins/*genetics, Borrelia burgdorferi Group/enzymology/genetics, Cyanobacteria/enzymology/genetics, Escherichia coli/enzymology/genetics, Haemophilus influenzae/enzymology/genetics, Helicobacter pylori/enzymology/genetics, Methanobacterium/enzymology/genetics, Methanococcus/enzymology/genetics, Molecular Sequence Data, Mycoplasma/enzymology/genetics, Open Reading Frames/*genetics, Phosphoprotein Phosphatases/*genetics, Protein Serine-Threonine Kinases/*genetics, Protein-Tyrosine Kinases/*genetics, Sequence Alignment | Genetics |
| Phylogeny | 11540893 | A possible biochemical missing link among archaebacteria. | Achenbach-Richter L, Stetter KO, Woese CR | Nature | 10.1038/327348a0 | 1987 | Archaea/*classification/genetics/metabolism, Archaeoglobus/*classification/genetics/metabolism, Base Sequence, Biological Evolution, Methane/metabolism, Methanococcus, Molecular Sequence Data, Phenotype, *Phylogeny, *RNA, Archaeal, RNA, Ribosomal, 16S/*analysis, Sequence Analysis, RNA, *Sequence Homology, Nucleic Acid, Sulfolobus, Sulfur/metabolism, Thermococcus | Metabolism |
| Cultivation | 12586398 | 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 | Acetates, Adaptation, Physiological, Archaeoglobus fulgidus/drug effects/*growth & development/isolation & purification/metabolism, Culture Media, Glutamates/biosynthesis, Glycerophosphates/biosynthesis, *Hot Temperature, Inositol Phosphates/biosynthesis, Osmotic Pressure, Sodium Chloride/*pharmacology | Stress |
| Enzymology | 16086253 | 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 | Archaeal Proteins/genetics/*metabolism, Archaeoglobus/*enzymology, Carboxylesterase/genetics/*metabolism, Cloning, Molecular, Electrophoresis, Polyacrylamide Gel, Escherichia coli/genetics, Hydrogen-Ion Concentration, Kinetics, Lipase/genetics/*metabolism, Plasmids/genetics, Recombinant Proteins/isolation & purification/metabolism, Sequence Analysis, DNA, Substrate Specificity, Temperature | Metabolism |
| Enzymology | 16109946 | 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 | Amino Acid Sequence, Archaeal Proteins/*genetics, Archaeoglobales/*genetics, Conserved Sequence, Gene Expression Regulation, Archaeal, Heat-Shock Proteins/*genetics, Kinetics, Molecular Sequence Data, Oligonucleotide Array Sequence Analysis, Open Reading Frames, Polymerase Chain Reaction, Sequence Alignment, Sequence Homology, Amino Acid, Sequence Homology, Nucleic Acid | Genetics |
| Enzymology | 18337701 | Cloning and characterization of thermostable esterase from Archaeoglobus fulgidus. | Kim SB, Lee W, Ryu YW | J Microbiol | 10.1007/s12275-007-0185-5 | 2008 | Amino Acid Sequence, Archaeal Proteins/antagonists & inhibitors/chemistry/*genetics/isolation & purification, Archaeoglobus fulgidus/*enzymology/genetics, Carboxylesterase/antagonists & inhibitors/*chemistry/*genetics/isolation & purification, *Cloning, Molecular, Enzyme Stability, Kinetics, Molecular Sequence Data, Nitrophenols/pharmacology, Organic Chemicals/pharmacology, Sequence Alignment, Sequence Analysis, Protein, Surface-Active Agents/pharmacology, Temperature | Phylogeny |
| Phylogeny | 18808198 | 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 | Amino Acyl-tRNA Synthetases/*genetics, Archaea/*genetics, Bacteria/*genetics, Base Sequence, *Eukaryotic Cells, Evolution, Molecular, Molecular Sequence Data, Nucleotides/*genetics, Phylogeny, RNA, Transfer/*genetics, Sequence Alignment | Genetics |
| Metabolism | 19624709 | 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 | Archaeoglobus fulgidus/growth & development/*metabolism, Chemical Fractionation, Extreme Heat, Sulfates/*metabolism, Sulfur Isotopes, Temperature | |
| Proteome | 19768810 | 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 | Archaeal Proteins/*chemistry/genetics/metabolism, Archaeoglobus fulgidus/*genetics, Computational Biology, Crystallography, X-Ray, *Models, Molecular, Protein Conformation, Protein Folding, Protein Multimerization/*genetics, Protein Structure, Tertiary/*genetics | Metabolism |
| Metabolism | 24096454 | Phenylalanine catabolism in Archaeoglobus fulgidus VC-16. | Parthasarathy A, Kahnt J, Chowdhury NP, Buckel W | Arch Microbiol | 10.1007/s00203-013-0925-3 | 2013 | Archaeoglobus fulgidus/classification/*enzymology/growth & development/metabolism, Enzymes/isolation & purification/metabolism, Fermentation, Oxidation-Reduction, Phenylalanine/*metabolism, Phylogeny, Sulfates/metabolism | Phylogeny |
| Metabolism | 24763368 | 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 | Alkanes/*metabolism, Anaerobiosis, Archaeal Proteins/chemistry/classification/genetics/metabolism, Archaeoglobus fulgidus/enzymology/genetics/growth & development/*metabolism, Fatty Acids/metabolism, Hot Temperature, Oxidation-Reduction, Phylogeny, Sulfates/metabolism | Phylogeny |
| Metabolism | 25661815 | 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 | Archaeoglobus fulgidus/*enzymology/genetics, *Directed Molecular Evolution, Enzyme Stability, Esterases/chemistry/genetics/*metabolism, Esters/*metabolism, Hot Temperature, Ketoprofen/*metabolism, Models, Molecular, Mutant Proteins/chemistry/genetics/metabolism, Polymerase Chain Reaction, Protein Conformation, Substrate Specificity | Enzymology |
| Metabolism | 26345487 | 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 | Archaeoglobus fulgidus/*genetics/growth & development/*metabolism, Carbon Monoxide/*metabolism, Energy Metabolism, *Gene Expression Profiling, Metabolic Networks and Pathways/genetics, Oxidation-Reduction, Sulfates/*metabolism | Transcriptome |
| 32595611 | 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 | |||
| Enzymology | 33776585 | 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 | *Archaeoglobus fulgidus, *NAD, Oxidoreductases, Shewanella, Sulfides |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 1648 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 4304) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-4304 | |||
| 20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | 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 | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
| 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. | https://microbeatlas.org/ | MicrobeAtlas 1.0 beta | |||
| 69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
| 87084 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID46110.1 | StrainInfo: A central database for resolving microbial strain identifiers |