HMS-S-S: A tool for the identification of Sulphur metabolism-related genes and analysis of operon structures in genome and metagenome assemblies.

Sulphur compounds are used in a variety of biological processes including respiration and photosynthesis. Sulphide and sulphur compounds of intermediary oxidation state can serve as electron donors for lithotrophic growth while sulphate, thiosulphate and sulphur are used as electron acceptors in anaerobic respiration. The biochemistry underlying the manifold transformations of inorganic sulphur compounds occurring in sulphur metabolizing prokaryotes is astonishingly complex and knowledge about it has immensely increased over the last years. The advent of next-generation sequencing approaches as well as the significant increase of data availability in public databases has driven focus of environmental microbiology to probing the metabolic capacity of microbial communities by analysis of this sequence data. To facilitate these analyses, we created HMS-S-S, a comprehensive equivalogous hidden Markov model (HMM)-supported tool. Protein sequences related to sulphur compound oxidation, reduction, transport and intracellular transfer are efficiently detected and related enzymes involved in dissimilatory sulphur oxidation as opposed to sulphur compound reduction can be confidently distinguished. HMM search results are coupled to corresponding genes, which allows analysis of co-occurrence, synteny and genomic neighbourhood. The HMMs were validated on an annotated test data set and by cross-validation. We also proved its performance by exploring meta-assembled genomes isolated from samples from environments with active sulphur cycling, including members of the cable bacteria, novel Acidobacteria and assemblies from a sulphur-rich glacier, and were able to replicate and extend previous reports.