Many bacteria grow in slimy layers in freshwater streams known as biofilms. Stream biofilm communities can be considered as a ‘microbial skin’ that cycles nutrients and supports high levels of biodiversity as the base of aquatic foodwebs. Stream biofilms are constantly exposed to invading bacteria in run-off from plants and soil as well as anthropogenic chemicals from wastewater. The skin plays a critical role in maintaining the structure and function of stream ecosystems.
From previous field studies, we have sequenced the environmental DNA of stream biofilms involved in the biotransformation of pollutants including pharmaceuticals, insecticides, and artificial sweeteners. Many of these pollutants likely undergo hydrolytic degradation steps catalyzed by microbial enzymes produced in stream biofilms. In this project, we seek to identify and characterize enzymes that are involved in pollutant degradation. We use heterologous expression and in vivo and in vitro assays to screen candidate hydrolases from stream metagenomes. We further plan to use computational machine learning methods to train predictive models from our results. In the long-term, we aim for this work to shed light on the role of hydrolytic enzymes in stream biofilms to protect and restore aquatic ecosystems impacted by anthropogenic chemicals.