New chemicals fuel the evolution of microbial biodegradation

Most known chemicals originate from humans, thousands enter industrial usage annually, and new chemicals pose a continuous challenge to microbial evolution. The evolution of microbes to biodegrade new chemicals is crucial in protecting human and ecosystem health. New chemical biodegradation requires the evolution of new enzymes and metabolic pathways to meet the challenge. The rate of this process is determined by the structures of the new chemicals and preexisting enzymes, and the available metabolic pathways of the host microbe. Existing metabolism evolved over billions of years in response to naturally occurring chemicals. Natural petroleum is one example. Its diverse chemical structures have provided a training ground for microbial evolution. Similarly, studies on the biodegradation of petroleum have elucidated mechanisms that microbes have recruited to degrade industrial chemicals. Such studies have also led to the concepts of co-oxidation, co-metabolism, and enzyme promiscuity, which underlie new enzyme evolution. The focus of the present review is on evolutionary adaptations leading to the microbial biodegradation of non-polymeric industrial organic molecules. The greatest challenges to microbes and evolution are chemicals synthesized to resist biodegradation. A major current example is for per- and polyfluorinated alkyl substances, often known as PFAS. Most recently, directed evolution and artificial intelligence are being applied to the problems posed by highly resistant chemicals.