Bioremediation Strategies Derived From Enzyme Studies

Bioremediation is powerful because of the great diversity of enzymes made by microbes. Traditionally, bioremediation has used mixed cultures of bacteria in natural or engineered enviornments, with the specific enzymes involved in biodegradation remaining undefined. As more enzymes are studied and DNA synthesis becomes cheaper, defined enzymes and microbial systems can be used more frequently. The research highlighted here uses well-characterized enzymes for which X-ray structures are available and uses them within robust microbial strains encapsulated in silica gels. The silica gel stabilizes enzymatic activites, facilitates storage and transport, and can be fabricated into spherical or fibrous biocatalyst materials. This approach has been demonstrated here with a range of bacteria, enzyme classes, and chemical compounds. One example is the use of native Pseudomonas strains expressing oxygenases, aldolases and hydrolases that mediate the biodegradation of aromatic hydrocarbons. Other studies have used E. coli strains expressing recombinant dehalogenases to bioremediate the herbicide atrazine. This research has been applied in an EPA-approved soil cleanup and within a drinking water treatment plant. Another commercial process under development uses a recombinant E. coli strain expressing cyanuric acid hydrolase to remove residual cyanuric acid from water. To facilitate these and other processes, we are developing enhanced capabilities for the computational modelling of enzyme substrate selectivity so that specific enzyme systems can be used more effectively to biodegrade single chemicals or multiple contaminant mixtures. As bioinformatics, enzyme modelling, and cell engineering become more efficient, we expect that the opportunities for designated-enzyme-based bioremediation strategies will increase dramatically.