Natural formation of copper sulfide nanoparticles via microbially mediated organic sulfur mineralization in soil: Processes and mechanisms

Sulfur cycling is known to control the speciation and bioavailability of copper in the environment via inorganic sulfur oxidation and reduction. However, it remains unclear how the mineralization of organic sulfur and associated microbial processes affect Cu transformations. This study discovered a neglected mechanism that mediates Cu mobility and speciation via cysteine mineralization in a paddy soil. We provide evidence for a pathway of sulfide production from cysteine via indigenous soil microorganisms. The produced sulfide promotes the formation of copper sulfide nanoparticles, constituting an alternative copper sulfide formation mechanism that bypasses sulfate reduction. A bacterium isolated from the soil, named Bacillus sp. TR1, played a role in forming cell-associated copper sulfide nanoparticles. A metagenomics approach was applied to detect genes related to cysteine mineralization (dcyD, CTH, CBS, and sseA) and the associated microbes in the soil. The sseA gene was most abundant, and the microorganisms involved in cysteine mineralization were taxonomically diverse, including members of phyla Proteobacteria, Firmicutes, and Thaumarchaeota. Geobacter, Sulfuriferula, Nitrososphaera, Noviherbaspirillum, and Clostridium were the dominant genera with potential to metabolize cysteine to form copper sulfide nanoparticles. Our study not only provides initial molecular-level insights into the abundance, diversity, and metabolism of cysteine-mineralizing microorganisms but also highlights their important ecological functions in metal and sulfur biogeochemical cycles.