Complete genome sequence of Staphylothermus marinus Stetter and Fiala 1986 type strain F1
© The Author(s) 2009
Published: 29 September 2009
Staphylothermus marinus Fiala and Stetter 1986 belongs to the order Desulfurococcales within the archaeal phylum Crenarchaeota. S. marinus is a hyperthermophilic, sulfur-dependent, anaerobic heterotroph. Strain F1 was isolated from geothermally heated sediments at Vulcano, Italy, but S. marinus has also been isolated from a hydrothermal vent on the East Pacific Rise. We report the complete genome of S. marinusstrain F1, the type strain of the species. This is the fifth reported complete genome sequence from the order Desulfurococcales.
KeywordsArchaea Desulfurococcales sulfur-reducing hyperthermophile
Classification and features
S. marinus is a nonmotile coccus with a diameter of 0.5–1.0 µm. At low nutrient concentrations it forms clumps of up to 100 cells, while at higher nutrient concentrations single cells or pairs of cells are observed. At high concentrations of yeast extract, giant cells with a diameter of up to 15µm are formed . The optimum and maximum growth temperatures also depend on the nutrient concentration. At low nutrient concentration the optimum growth temperature is 85°C and the maximum is 92°C, while at higher nutrient concentration the optimum growth temperature is 92°C and the maximum is 98°C . The optimum pH for growth is 6.5, but growth is observed within a range of 4.5 to 8.5.
S. marinus is a heterotroph, growing on complex media but not on simple carbohydrates or amino acids. Elemental sulfur is required for growth, and it can not be substituted by other sulfur compounds . In the absence of sulfur, cells can survive while producing hydrogen . Metabolic products are CO2, H2S, acetate, and isovalerate, suggesting a metabolism similar to that of Pyrococcus species .
Classification and general features of S. marinus F1 according to the MIGS recommendations .
Species Staphylothermus marinus
marine geothemally heated areas
geothermally heated sediment
Genome sequencing and annotation
Genome project history
Genome sequencing project information.
3kb, 6kb and 40kb (fosmid)
less than one error per 50kb
Gene calling method
GenBank date of release
NCBI project ID
IMG Taxon ID
Source material identifier
Tree of Life
Growth conditions and DNA isolation
The methods for DNA isolation, genome sequencing and assembly for this genome have previously been published .
Protein-coding genes were identified using a combination of Critica  and Glimmer  followed by a round of manual curation using the JGI GenePRIMP pipeline . The predicted CDSs were translated and used to search the National Center for Biotechnology Information (NCBI) nonredundant database, UniProt, TIGRFam, Pfam, PRIAM, KEGG, COG, and InterPro databases. The tRNAScan-SE tool  was used to find tRNA genes. Additional gene prediction analysis and manual functional annotation was performed within the Integrated Microbial Genomes Expert Review (IMG-ER) platform .
% of total
Genome size (bp)
DNA coding region (bp)
DNA G+C content (bp)
Number of replicons
Genes with function prediction
Genes in paralog clusters
Genes assigned to COGs
Genes assigned Pfam domains
Genes with signal peptides
Genes with transmembrane helices
Numbers of genes associated with the general COG functional categories.
Amino acid transport and metabolism
Carbohydrate transport and metabolism
Cell cycle control, cell division, chromosome partitioning
Cell wall/membrane/envelope biogenesis
Chromatin structure and dynamics
Coenzyme transport and metabolism
Energy production and conversion
General function prediction only
Inorganic ion transport and metabolism
Intracellular trafficking, secretion, and vesicular transport
Lipid transport and metabolism
Nucleotide transport and metabolism
Posttranslational modification, protein turnover, chaperones
RNA processing and modification
Replication, recombination and repair
Secondary metabolites biosynthesis, transport and catabolism
Signal transduction mechanisms
Translation, ribosomal structure and biogenesis
Not in COGs
Insights from genome sequence
The genome of S. marinus has several novel features compared to other Crenarchaeota. It is the first crenarchaeote found to have a sodium ion-translocating decarboxylase, which is probably involved in energy generation from amino acid degradation . In addition it is the first crenarchaeote found to have proteins related to multisubunit cation/proton antiporters, although the S. marinus proteins probably do not function as antiporters. These antiporter-related proteins belong to larger operons similar to the mbh and mbx operons of Pyrococcus furiosus [24,25], therefore, they may play a role in sulfur reduction or hydrogen production. S. marinus appears to use different proteins for sulfur reduction than the other anaerobic, sulfur-reducing Crenarchaeota. Both Thermofilum pendens and Hyperthermus butylicus appear to have molybdenum-containing sulfur/polysulfide reductases and NADPH:sulfur oxidoreductases, but these are not present in S. marinus 
This work was performed under the auspices of the US Department of Energy’s Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344, and Los Alamos National Laboratory under contract No. DE-AC02-06NA25396. M. L. was supported by the Department of Energy under contract DE-AC05-000R22725.
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