Strain OK10^T (= DSM 16294 = ATCC BAA-671 = JCM 11897) is the type strain of Sulfurimonas autotrophica [1], which is the type species of its genus Sulfurimonas [1,2]. Together with S. paralvinellae and S. denitrificans, the latter of which was formerly classified as Thiomicrospira denitrificans [3]. There are currently three validly named species in the genus Sulfurimonas [4,5]. The autotrophic and mixotrophic sulfur-oxidizing bacteria such as the members of the genus Sulfurimonas are believed to contribute significantly to the global sulfur cycle [6]. The genus name derives from the Latin word ‘sulphur’, and the Greek word ‘monas’, meaning a unit, in order to indicate a “sulfur-oxidizing rod” [1]. The species epithet derives from the Greek word ‘auto’, meaning self, and from the Greek adjective ‘trophicos’ meaning nursing, tending or feeding, in order to indicate its autotrophy [1]. S. autotrophica strain OK10^T, like S. paralvinellae strain GO25^T (= DSM 17229), was isolated from the surface of a deep-sea hydrothermal sediment on the Hatoma Knoll in the Mid-Okinawa Trough hydrothermal field [1,2]. Thus, the members of the genus Sulfurimonas appear to be free living, whereas the other members of the family Helicobacteraceae, the genera Helicobacter and Wolinella, appear to be strictly associated with the human stomach and the bovine rumen, respectively. Here we present a summary classification and a set of features for S. autotrophica OK10^T, together with the description of the complete genomic sequencing and annotation.

There exist currently no experimental reports that indicate further cultivated strains of this species. The type strains of S. denitrificans and S. paralvinellae share 93.5% and 96.3% 16S rRNA gene sequence similarity with strain OK10^T. Further analysis also revealed that strain OK10^T shares high similarity (99.1%) with the uncultured clone sequence PVB-12 (U15104) obtained from a microbial mat near the deep-sea hydrothermal vent in the Loihi Seamont, Hawaii [7]. This further corroborates the distribution of S. autotrophica in hydrothermal vents. The 16S rRNA gene sequence similarities of strain OK10^T to metagenomic libraries (env_nt) were 87% or less, indicating the absence of further members of the species in the environments screened so far (status August 2010).

Figure 1 shows the phylogenetic neighborhood of S. autotrophica OK10^T in a 16S rRNA based tree. The sequences of the four 16S rRNA gene copies in the genome differ from each other by up to four nucleotides, and differ by up to three nucleotides from the previously published sequence (AB088431).

Figure 1 Phylogenetic tree highlighting the position of S. autotrophica OK10T relative to the type strains of the other species within the genus and the type strains of the other genera within the order Campylobacterales. The tree was inferred from 1,327 aligned characters [8,9] of the 16S rRNA gene sequence under the maximum likelihood criterion [10] and rooted in accordance with current taxonomy [11]. The branches are scaled in terms of the expected number of substitutions per site. Numbers above branches are support values from 350 bootstrap replicates [12] if larger than 60%. Lineages with type strain genome sequencing projects registered in GOLD [13] are shown in blue, published genomes in bold [14,15], such as the recently published GEBA genomes from Sulfurospirillum deleyianum [16] and Arcobacter nitrofigilis [17].

The cells of strain OK10^T are Gram-negative, occasionally slightly curved rods of 1.5–2.5 × 0.5-1.0 µm (Figure 2 and Table 1) [1]. On solid medium, the cells form white colonies [1]. Under optimal conditions, the generation time of S. autotrophica strain OK10^T is approximately 1.4 h [1,2]. The reductive tricarboxylic acid (rTCA) cycle for autotrophic CO₂ fixation is present in strain OK10^T, as shown by PCR amplification of the respective genes [28]. Moreover, the activities of several rTCA key enzymes (ACL, ATP dependent citrate lyase; POR, pyruvate:acceptor oxidoreductase; OGOR, 2-oxoglutarase:accecptor oxidoreductase; ICDH, isocytrate dehydrogenase) have been determined, also in comparison to S. paralvinellae and S. denitrificans [28]. There were no enzyme activities for the phosphoenolpyruvate and ribulose 1,5-bisphosphate (Calvin-Benson) pathways detected in strain OK10^T [28], though the latter is apparently active in S. thermophila [28]. Also, soluble hydrogenase activity was not found in strain OK10^T [28]. With respect to sulfur oxidation, enzyme activity for SOR (sulfite oxidoreductase) but not for APSR (adenosine 5′-phosphate sulfate reductase) and TSO (thiosulfate-oxidizing enzymes) were detected [28]. A detailed comparison of these enzyme activities to S. paralvinellae and S. denitrificans is given in Takai et al. [28]. Elemental sulfur, thiosulfate or sulfide is utilized as the sole electron donor for chemolithoautotrophic growth with O₂ as electron acceptor. Thereby thiosulfate is oxidized to sulfate [1]. Organic substrates and H₂ are not utilized as electron donors and only oxygen is utilized as an electron acceptor [28]. Strain OK10^T requires 4% sea salt for growth [1] and is not able to reduce nitrate [2].

Figure 2 Scanning electron micrograph of S. autotrophica OK10T

The genome consists of a 2,153,198 bp long chromosome with a 35.2% GC content (Table 3 and Figure 3). Of the 2,220 genes predicted, 2,165 were protein-coding genes, and 55 RNAs; seven pseudogenes were also identified. The majority of the protein-coding genes (69.1%) were assigned with a putative function while the remaining ones were annotated as hypothetical proteins. The distribution of genes into COGs functional categories is presented in Table 4.

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