Metagenomics; Transcriptomics; Proteomics; Stable Isotope Probing; Nanopore Sequencing

In order to effectively manage and engineer microbiomes for resource recovery, we need to not only know what microbes are present in different engineered ecosystems, but also what they are doing and how they are doing it. Such information can be used to inform new process-level models that help to predict carbon and nutrient flows through engineered water systems, providing a platform for improved engineering designs. 

We utilize a suite of molecular microbiology techniques to probe microbial ecophysiology in water microbiomes. Our group commonly utilizes stable isotope probing (SIP) techniques to label DNA, RNA, and proteins to track the growth of microorganisms in engineered water systems. We couple such techniques to multi-omics (e.g. metagenomics, metatranscriptomics, metaproteomics). We also are developing new protocols for the use of long-read sequencing in metagenome and amplicon sequencing. Ultimately, we utilize this molecular information to inform strategies to optimize engineered systems for enhanced resource recovery from waste streams.