Complete genome sequence of the sulfur compounds oxidizing chemolithoautotroph Sulfuricurvum kujiense type strain (YK-1T)

Abstract

Sulfuricurvum kujiense Kodama and Watanabe 2004 is the type species of the monotypic genus Sulfuricurvum, which belongs to the family Helicobacteraceae in the class Epsilonproteobacteria. The species is of interest because it is frequently found in crude oil and oil sands where it utilizes various reduced sulfur compounds such as elemental sulfur, sulfide and thiosulfate as electron donors. Members of the species do not utilize sugars, organic acids or hydrocarbons as carbon and energy sources. This genome sequence represents the type strain of the only species in the genus Sulfuricurvum. The genome, which consists of a circular chromosome of 2,574,824 bp length and four plasmids of 118,585 bp, 71,513 bp, 51,014 bp, and 3,421 bp length, respectively, harboring a total of 2,879 protein-coding and 61 RNA genes and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

A Proposed Genus Boundary for the Prokaryotes Based on Genomic Insights

“…They can be classified into a single genus according to the POCP genus classification standard. Consistent with this conclusion, these two strains have similar genome sizes (2.2 Mb and 2.8 Mb, respectively) (25,26). Both strains are facultatively anaerobic, can oxidize sulfur, and have the ability to grow autotrophically (27,28).…”

The complete genome sequence for putative H2‐ and S‐oxidizer Candidatus Sulfuricurvum sp., assembled de novo from an aquifer‐derived metagenome

“…A bacterium isolated from an underground crude oil storage cavity in Japan, S. kujiense , was the closest cultivated relative in all cases (Kodama and Watanabe, ; Figs B–C and ) and shares 98.5% 16S rRNA gene sequence identity with RIFRC‐1 (1494/1516 nucleotide match). Therefore, RIFRC‐1 represents a novel Sulfuricurvum species (Stackebrandt and Ebers, ), which is further supported by the nucleotide identities of total, conserved and protein coding fractions shared by the S. kujiense genome (Han et al ., ) and RIFRC‐1 (Table ), as these are below the thresholds that correlate with DNA‐DNA hybridization values of 70% (Goris et al ., ). These nucleotide identities are also consistent with those derived from bacteria within the same genus (Goris et al ., ).…”

“…However, divergence of these genomes is evident owing to differences in nucleotide identities (Table ), and a large amount of genomic rearrangements resulting from translocations and inversions (Figs and ). The genome size and gene content of RIFRC‐1 is smaller than that of S. kujiense (Table ; Han et al ., ), and RIFRC‐1 has a lower estimated proportion of duplicated genes compared with S. kujiense (Table ). Most putative gene redundancies are among genes of unknown function, and many are among genes for virulence, transcriptional regulators, ABC transporters or diguanylate cyclase (involved in biofilm formation).…”

The Family Helicobacteraceae

“…Sulfuricurvum is a monotypic genus of the family Helicobacteraceae (Han et al 2012). Sulfuricurvum kujiense (N.L.…”

“…S. kujiense does not grow on sugars, organic acids or hydrocarbons as carbon and energy sources (Kodama and Watanabe 2004). The genome of S. kujiense YK-1 (DNA coding region: 93.04 %; G+C content: 44.56 mol%) consists of a circular chromosome 2,574,824 bp in size and four plasmids 118,585 bp, 71,513 bp, 51,014 bp, and 3,421 bp in size, harboring a total of 2,879 protein-coding and 61 RNA genes (Han et al 2012 (Inagaki et al 2003). S. autotrophica are motile short rods which possess a single polar flagellum and grow chemolithoautotrophically with elemental sulfur, sulfide and thiosulfate (oxygen as electron acceptor) at 10-40 C (optimum 25 C) and pH 4.5-9.0 (optimum pH 6.5) (Inagaki et al 2003).…”