Identifying Bacteria Responsible for Non-Sulphate-Based Hydrogen Sulphide Production in Aquaculture

The unintended microbiological production of hydrogen sulphide (H₂S) poses a significant challenge in engineered systems, including sewage treatment plants, landfills and aquaculture systems. Although sulphur-rich amino acids and other substrates conducive to non-sulphate-based H₂S production are frequently present, the capacity and potential of various microorganisms to perform sulphate-free H₂S production remain unclear. In this study, we identify the identity, activity and genomic characteristics of bacteria that degrade cysteine to produce H₂S in anaerobic enrichment bioreactors seeded with material from aquaculture systems. Our comparison with canonical sulphate-reducing bacteria reveals that both sulphur sources contribute to microbial H₂S production, with cysteine facilitating a more rapid process compared to sulphate. 16S rRNA amplicon sequencing and metagenomic analysis identified four bacterial families—Dethiosulfatibacteraceae, Fusobacteriaceae, Vibrionaceae and Desulfovibrionaceae—as central to non-sulphate H₂S production. Metagenome- and metatranscriptome-assembled genomes elucidated the primary cysteine degradation pathway mediated by cysteine desulphidase cyuA and indicated that some bacteria may also utilise cysteine as a carbon source in sulphate-based H₂S production.