Abstract
The genome of Sulfolobus sp. A20 isolated from a hot spring in Costa Rica was sequenced. This circular genome of the strain is 2,688,317 bp in size and 34.8% in G+C content, and contains 2591 open reading frames (ORFs). Strain A20 shares ~95.6% identity at the 16S rRNA gene sequence level and <30% DNA-DNA hybridization (DDH) values with the most closely related known Sulfolobus species (i.e., Sulfolobus islandicus and Sulfolobus solfataricus), suggesting that it represents a novel Sulfolobus species. Comparison of the genome of strain A20 with those of the type strains of S. solfataricus, Sulfolobus acidocaldarius, S. islandicus, and Sulfolobus tokodaii, which were isolated from geographically separated areas, identified 1801 genes conserved among all Sulfolobus species analyzed (core genes). Comparative genome analyses show that central carbon metabolism in Sulfolobus is highly conserved, and enzymes involved in the Entner-Doudoroff pathway, the tricarboxylic acid cycle and the CO2 fixation pathways are predominantly encoded by the core genes. All Sulfolobus species encode genes required for the conversion of ammonium into glutamate/glutamine. Some Sulfolobus strains have gained the ability to utilize additional nitrogen source such as nitrate (i.e., S. islandicus strain REY15A, LAL14/1, M14.25, and M16.27) or urea (i.e., S. islandicus HEV10/4, S. tokodaii strain7, and S. metallicus DSM 6482). The strategies for sulfur metabolism are most diverse and least understood. S. tokodaii encodes sulfur oxygenase/reductase (SOR), whereas both S. islandicus and S. solfataricus contain genes for sulfur reductase (SRE). However, neither SOR nor SRE genes exist in the genome of strain A20, raising the possibility that an unknown pathway for the utilization of elemental sulfur may be present in the strain. The ability of Sulfolobus to utilize nitrate or sulfur is encoded by a gene cluster flanked by IS elements or their remnants. These clusters appear to have become fixed at a specific genomic site in some strains and lost in other strains during the course of evolution. The versatility in nitrogen and sulfur metabolism may represent adaptation of Sulfolobus to thriving in different habitats.
Highlights
Archaea of genus Sulfolobus are widespread in solfataric fields around the globe
Pairwise DNA-DNA hybridization (DDH) in silico between strain A20 and one of the tested Sulfolobus strains, including S. tokodaii str.7, S. acidocaldarius DSM 639, three S. solfataricus strains, and four S. islandicus strains, produces DDH values between 16.7 and 23.1% (Table 2), which are far below the 70% threshold proposed for species definition (Tindall et al, 2009). These results suggest that strain A20 represents a novel Sulfolobus species
The strain appears to be able to fix CO2 via the HP/HB cycle. It is capable of metabolizing glucose through a branched-ED pathway and the tricarboxylic acid (TCA) cycle, as are other Sulfolobus strains
Summary
Known Sulfolobus species were mostly isolated from the Northern hemisphere (Brock et al, 1972; Grogan et al, 1990; Huber and Stetter, 1991; Jan et al, 1999; Suzuki et al, 2002; Xiang et al, 2003; Guo et al, 2011; Mao and Grogan, 2012; Zuo et al, 2015). The complete genomes of 17 Sulfolobus strains belonging to four species have so far been deposited in GenBank These include a Sulfolobus tokodaii strain (str.7) (Kawarabayasi et al, 2001), three Sulfolobus solfataricus strains (She et al, 2001; McCarthy et al, 2015), four Sulfolobus acidocaldarius strains (Chen et al, 2005; Mao and Grogan, 2012), and nine Sulfolobus islandicus strains (Reno et al, 2009; Guo et al, 2011; Zhang et al, 2013). The genome of strain A20 was compared with all other available Sulfolobus genomes, and analyses of the pathways of carbon, nitrogen and sulfur metabolism in various Sulfolobus strains were performed
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