Genomes of Neutrophilic Sulfur-Oxidizing Chemolithoautotrophs Representing 9 Proteobacterial Species From 8 Genera

Abstract

Even in the current era of metagenomics, the interpretation of nucleotide sequence data is primarily dependent on knowledge obtained from a limited number of microbes isolated in pure culture. Thus, it is of fundamental importance to expand the variety of strains available in pure culture, to make reliable connections between physiological characteristics and genomic information. In this study, two sulfur oxidizers that potentially represent two novel species were isolated and characterized. They were subjected to whole-genome sequencing together with 7 neutrophilic and chemolithoautotrophic sulfur-oxidizing bacteria. The genes for sulfur oxidation in the obtained genomes were identified and compared with those of isolated sulfur oxidizers in the classes Betaproteobacteria and Gammaproteobacteria . Although the combinations of these genes in the respective genomes are diverse, typical combinations corresponding to three types of core sulfur oxidation pathways were identified. Each pathway involves one of three specific sets of proteins, SoxCD, DsrABEFHCMKJOP, and HdrCBAHypHdrCB. All three core pathways contain the SoxXYZAB proteins, and a cytoplasmic sulfite oxidase encoded by soeABC is a conserved component in the core pathways lacking SoxCD. Phylogenetically close organisms share same core sulfur oxidation pathway, but a notable exception was observed in the family ‘ Sulfuricellaceae ’. In this family, some strains have either core pathway involving DsrABEFHCMKJOP or HdrCBAHypHdrCB, while others have both pathways. A proteomics analysis showed that proteins constituting the core pathways were produced at high levels. While hypothesized function of HdrCBAHypHdrCB is similar to that of Dsr system, both sets of proteins were detected with high relative abundances in the proteome of a strain possessing genes for these proteins. In addition to the genes for sulfur oxidation, those for arsenic metabolism were searched for in the sequenced genomes. As a result, two strains belonging to the families Thiobacillaceae and Sterolibacteriaceae were observed to harbor genes encoding ArxAB, a type of arsenite oxidase that has been identified in a limited number of bacteria. These findings were made with the newly obtained genomes, including those from 6 genera from which no genome sequence of an isolated organism was previously available. These genomes will serve as valuable references to interpret nucleotide sequences.

Sulfuriferula nivalis sp. nov., a sulfur oxidizer isolated from snow and emended description of Sulfuriferula plumbiphila

“…This value is clearly lower than the previously reported value estimated by melting temperature and HPLC-based methods, 66 % [2]. In the genomes of SGTM T and S. plumbiphila Gro7 T , genes involved in the Sox-Hdr-Soe pathway defined by Watanabe et al [6] were identified. They lack dsrAB genes required for sulfur oxidation via the Sox-Dsr-Soe pathway and soxCD genes for the cSox pathway.…”

“…A previous study has shown that S. plumbiphila Gro7 T has phylogenetically distinct copies of the aprBA genes that belong to lineages I and II respectively [14]. In genomes of sulfur-oxidizing betaproteobacteria, the aprBA genes generally coexist with the dsrAB genes [6]. Inspection of the complete genome sequence confirmed that S. plumbiphila Gro7 T has these two sets of the aprBA genes in fact, although it lacks the dsrAB genes.…”

“…In all strains, the most, second most, and third most abundant fatty acids are C 16 : 1 , C 16 : 0 and C 12 : 0 , respectively. Genomic features (including DNA G+C content calculated from genome sequence) of strains 2 and 4 were cited from [6], and those of strains 1 and 3 were obtained in this study.…”

“…The common major cellular fatty acids of these three genera are C 16 : 1 and C 16 : 0 [3]. Despite their close relatedness, there are considerable variations in sulfur oxidation pathways among strains belonging to these genera, as revealed by a comparative genomic analysis [6]. The comparative analysis did not include S. plumbiphila, because its genome was not available at that time.…”

“…From these linear contigs, chromosome and plasmids were manually reconstructed based on sequence alignment. The resulting genome sequence was annotated with DFAST [11], and then genes involved in sulfur oxidation were identified as described previously [6]. Overall genome relatedness indices, values of the average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) were calculated by using on-line tools as described below.…”