A metabolic framework for microbial thiocyanate degradation from meta-omics

Thiocyanate (SCN^-), an environmental toxin produced in gold mining effluents, can be biologically treated using microbial consortia. SCN^- biodegradation produces sulfate, ammonium, and carbon dioxide. We performed the first metagenomic analysis of such a consortium and suggested that the critical members are autotrophic populations whose growth depends on SCN^- and the sulfide and ammonium its breakdown generates. Most important were three dominant Thiobacillus spp. whose genomes harbor a key operon for SCN^- degradation as well as sulfur oxidation genes. Initial isolation-based studies of the system were conducted using only rich media, thereby missing the importance of Thiobacillus. Our findings were consistent with clone library-based studies, but they also clearly show the limitations of such fingerprinting methods in predicting the metabolic potential of key organisms.

A follow-up experiment assessed the effect on the consortium of increasing SCN^- loadings over time and also addressed the potential for nitrogen removal by members of this consortium. Deep metagenomic sequencing of samples from this experiment yielded 157 bacterial genomes including 31 seen in the initial study, numerous mobile elements, and several eukaryotic sequences. Metaproteomic data confirmed expression of the key genes involved in SCN^- degradation, ammonium oxidation, nitrite oxidation, and denitrification. The relative abundances of several key species shifted over time and a decline in the dominant Thiobacillus species coincided with a drop in reactor performance. This work provides an organism-level framework describing the mechanisms underlying SCN^- degradation, and offers suggestions for improving efficiency and nitrogen removal and decreasing operational costs of SCN-degrading bioreactors.