Comparative genomics of the sulfur-reducing bacterial family Desulfurellaceae. Desulfurella amilsii genome

Desulfurella amilsii, an acidotolerant sulfur reducer, was recently isolated from sediments of an extreme acid environment, Tinto River. Here we report its draft genome sequence and compare it to the available genome sequences from the Desulfurellaceae family comprised by the thermophilic sulfur-reducing bacterial genera, Desulfurella and Hippea, which inhabit terrestrial environments and submarine hot vents, respectively. D. amilsii genome consists of 2 Mbp with a G+C content of 33.98%. A total of 2136 genes were predicted, from which 2087 are protein-coding and 49 are RNA genes. Pairwise comparison of the available genomes sequences of Desulfurellaceae family revealed that two described species, D. acetivorans and D. multipotens, might be merged since they showed 98.58% identity in the average nucleotide and 88.1% of their DNA hybridize in silico, which surpass the estimated 95% and 70% thresholds, respectively. Comparative analyses of the gene sets of D. amilsii, D. acetivorans, H. maritima, H. alviniae, H. medeae and H. jasoniae were performed. The 2136 genes of D. amilsii were shown to assign into 1661 orthologous genes clusters, from which 1141 are common to all the species in the family, 1633 are shared within the Desulfurella genus and 35 are unique from the D. amilsii species. Genes encoding for sulfide dehydrogenase are present in all the analysed sequences, while only Hippea species present the genes encoding for polysulfide reductase, both enzymes involved in sulfur reduction process mediated by polysulfide. In D. amilsii, however, in addition to sulfide dehydrogenase, the enzyme sulfur reductase, involved in elemental sulfur reduction by attachment, is also encoded. The presence of sulphur reductase arouses the possibility of elemental sulfur reduction by attachment when D. amilsii faces acidic conditions, where polysulfide is not available. Thiosulfate reductase is encoded in both genera, but in vivo analysis showed thiosulfate reduction occurring only in D. amilsii. Complete pathway for acetate oxidation via the citric acid cycle is present in D. amilsii genome, also present in D. acetivorans and H. maritima, while the genes encoding for those enzymes were not present in H. jasoniae and H. alviniae. Fatty acid degradation via the β-oxidation pathway is revealed in all the genomes, as genes encoding for resistance to acidic conditions, oxygen stress and metals resistance. Analysis of available genomes of the Desulfurellaceae family has provided an insight on the mechanisms, helping in the elucidation of the genomic diversity in the group. Further studies need to be performed to address remaining questions about the active pathways active and how environmental conditions interfere with them.