Anaerobic digestion (AD) is a microbial process that converts organic waste into biogas and nutrient-rich digestate. We study the microbial communities and their responses to different operating conditions in both high-solid and wet AD systems, including conditions with high ammonia concentrations and process disturbances. Metagenomic and 16S sequencing are used to characterize microbial community composition and functional potential, while metatranscriptomics is used to investigate which microorganisms and metabolic pathways are actively responding to specific conditions. Current projects include studies of ammonia inhibition in high-solid AD and microbial responses to elevated propionate levels in wet AD systems.