What students do

Our work involves three areas: Reactor Operations, Environmental Testing, Molecular Assays, and Bioinformatics. Students work in one or several of these areas.

Reactor Operations

Designing, constructing, operating, and maintaining biological reactors (bioreactors) at multiple scales is a key function of our lab. Bioreactors create controlled environments that we can manipulate to impact the microbiomes contained within. As environmental engineers, we are often looking for a "knob" that we can turn to direct a microbiome to perform a desirable conversion process. While most of the reactors we run are bioreactors, we also use chemical and physical processes to manipulate and control microbiomes.

Environmental Testing

Environmental tests allow us to assess changes in the reactor environment and monitor conversion processes performed by microbiomes. These tests include measuring the organic matter (typically measured as chemical oxygen demand), nutrients, and specific transformation products, such as volatile fatty acids. Some of these tests rely on commercially available kits and others rely on chromatography.

Molecular Assays

Molecular assays include DNA and protein sequencing, which allow us to gain further insights into microbiomes. These analysis can be characterized into several subareas with varying levels of complexity: PCR/qPCR/rt-qPCR, 16S Amplicon Sequencing, Metagenomics, Metatranscriptomics and Metaproteomics.


Bioinformaticians use computers to analyze large datasets generated from sequencing and other biological analyses. Students learn how to code using some combination of bash, perl, python, julia, and matlab. Our bionformatics work includes analyzing 16S amplicon sequencing data, assembling and binning metagenomes, annotating genomes, reconstructing metabolic networks, analyzing gene expression data, conducting phylogenetic analyses, and metabolic modeling. We often rely on supercomputers for our data analyses and it's not uncommon for our computing jobs to last multiple weeks.