Strain P8^T (=DSM 12710 = JCM 10830) is the type strain of the species Staphylothermus hellenicus. It was isolated from a shallow hydrothermal vent at Palaeochori Bay near the island of Milos, Greece [1]. There is one other validly named species in the genus, S. marinus, for which a complete genome sequence has been determined and published [2,3]. The S. hellenicus genome is the ninth to be published from the order Desulfurococcales in the phylum Crenarchaeota. The only other genus in the Desulfurococcales for which two species have been sequenced is Desulfurococcus. Figure 1 shows the phylogenetic position of S. hellenicus with respect to the other species in the order Desulfurococcales.

Figure 1 Phylogenetic tree highlighting the position of S. hellenicus relative to the type strains of the other species within the order Desulfurococcales. The tree was inferred from 1,333 aligned characters [4,5] of the 16S rRNA gene sequence under the maximum likelihood (ML) criterion [6]. Rooting was done initially using the midpoint method [7] and then checked for its agreement with the current classification (Table 1). The branches are scaled in terms of the expected number of substitutions per site. Numbers adjacent to the branches are support values from 1,000 ML bootstrap replicates [8] (left) and from 1,000 maximum parsimony bootstrap replicates [9] (right) if larger than 60%. Lineages with type strain genome sequencing projects registered in GOLD [10] are labeled with one asterisk, those listed as 'Complete and Published' with two asterisks.

S. hellenicus was isolated from sediment at Palaeochori Bay, Milos, Greece [1]. For isolation, 1 ml of sediment was added to half-strength SME medium [11] with 2% elemental sulfur and incubated at 90°C under H₂/CO₂. Colonies were isolated on plates with the same medium and with 1% Phytagel and 2-3% sodium alginate added [1]. S. hellenicus is a regular-shaped coccus (Figure 2) which can form large aggregates of up to fifty cells, similar to S. marinus [1,12]. No flagella were observed and cells were nonmotile. The temperature range for growth of S. hellenicus is 70-90°C, with an optimum at 85°C [1]. The salinity range was from 2% to 8% NaCl, and the optimum was 4% NaCl [1]. The pH range for growth was from 4.5 to 7.5. The optimum pH was 6.0 [1]. S. hellenicus is a strict anaerobe, and can grow under H₂/CO₂ or N₂/CO₂ [1]. It is a heterotroph which grows well on yeast extract but poorly on peptone [1]. Many carbon sources were tested, but no growth was observed, showing that a complex nutrient source is required [1]. Elemental sulfur was required for growth [1]. The features of the organism are listed in Table 1.

Figure 2 Scanning electron micrograph of S. hellenicus P8T.

The genome includes one chromosome and no plasmids, for a total size of 1,580,437 bp (Table 3 and Figure 3). This genome size is close to the average for Desulfurococcales. The GC percentage is 36.8%, which is lower than most of the Desulfurococcales. A total of 1,716 genes were identified: 48 RNA genes and 1,668 protein-coding genes. There are 69 pseudogenes, comprising 4.1% of the protein-coding genes. About 62% of predicted genes begin with ATG, 30% begin with TTG, and 7% begin with GTG. There is one copy of each ribosomal RNA. Table 4 shows the distribution of genes in COG categories.

Figure 3 Graphical circular map of the chromosome. From outside to the center: Genes on forward strand (colored by COG categories), genes on reverse strand (colored by COG categories), RNA genes (tRNAs green, rRNAs red, other RNAs black), GC content, and GC skew.

The genome of S. hellenicus is slightly larger than the genome of S. marinus (1.58 Mbp vs. 1.57 Mbp), and the number of protein-coding genes is also larger (1668 vs. 1610). However, the number of pseudogenes is also higher in S. hellenicus (69 vs. 40). Some of the COG categories show different numbers of genes between the two organisms. S. hellenicus has 25 additional genes that do not belong to COGs. S. hellenicus has greater numbers of genes involved in cell wall biogenesis (39 vs. 23), nucleotide transport and metabolism (44 vs. 39) and carbohydrate transport and metabolism (79 vs. 72), while S. marinus has greater numbers of genes in the categories of energy production and conversion (92 vs. 79) and inorganic ion transport and metabolism (85 vs. 67).

The genes involved in cell wall metabolism that are in S. hellenicus but not in S. marinus are genes involved in nucleotide-sugar metabolism and glycosyltransferases, suggesting that S. hellenicus may have a greater variety of sugars attached to glycolipids and glycoproteins. Most of the additional S. hellenicus genes are located within a region of fifty genes on the chromosome (Shell_0865-Shell_0915) that is not present in S. marinus. The additional genes in S. hellenicus involved in nucleotide metabolism include adenylosuccinate synthase, adenylosuccinate lyase, and GMP synthase. Both S. hellenicus and S. marinus lack de novo purine synthesis, but the presence of these three additional enzymes suggests that S. hellenicus may be able to synthesize AMP and GMP from IMP, while S. marinus is unable to do so. The additional genes in carbohydrate transport and metabolism include nucleotide-sugar modifying enzymes that were also included in cell wall metabolism, but they also include a probable β-1,4-endoglucanase (cellulase) from glycosyl hydrolase family 5.

The genes found in S. marinus but not in S. hellenicus belong to the categories of energy production and conversion, and inorganic ion transport and metabolism. They include proteins related to subunits of multisubunit cation:proton antiporters and proteins related to subunits of NADH dehydrogenase and formate hydrogen lyase. These proteins are similar to subunits of mbh, a multisubunit membrane-bound hydrogenase from Pyrococcus furiosus [35], and mbx, a multisubunit complex of unknown function that probably has a role in sulfur reduction, also from P. furiosus [36]. S. marinus has three operons related to mbh and mbx, while S. hellenicus has only one, suggesting that the three operons may be redundant in function in S. marinus. Since S. marinus and S. hellenicus lack other enzymes involved in sulfur reduction, it is possible that these mbh/mbx-related operons play a role in sulfur reduction in these organisms.