Meta-omics-derived structure, function, and activity of mixed microbial communities driving biological nutrient removal and recovery

Improved process design and operation of systems engineered for the biological removal and recovery of carbon, nitrogen, and phosphorus from waste streams requires an understanding of the mixed microbial communities employed. While traditional microbiology techniques have been used to characterize the metabolic capability and activity of some organisms responsible for nutrient cycling, the metabolism of novel organisms and dynamics of complex microbial communities have been insufficiently revealed. The development and increased commercial availability of next-generation sequencing technology over the last 5-7 years has led to immense data-gathering capabilities from biological systems at the DNA ((meta)genomics), RNA ((meta)transcriptomics), and protein ((meta)proteomics) levels. However, the application of next-generation sequencing and bioinformatics to engineered biological processes remains rare, and major gaps still exist in the reference databases and metabolic understanding of single organisms (genomics) and mixed communities (metagenomics) driving biological nutrient removal and recovery in wastewater and food waste. This dissertation therefore had several major objectives: (1) Improving understanding of microbial conversion of food waste to volatile fatty acids; (2) Surveying pilot- and full-scale global biological nitrogen removal communities; (3) Application of mainstream deammonification; and (4) Adding to the sparse genomic reference database related to enhanced biological phosphorus removal (EBPR). The model of acidogenesis and acetogenesis from food waste was significantly expanded, and used to link shifts in microbial community structure and functional potential, caused by varying reactor operating conditions, to the production and speciation of volatile fatty acids for a variety of endpoint uses. Unexpected trends in the microbial ecology and functional potential of global full-scale systems were also uncovered, indicating opportunity for further enhancement of nitrogen removal through microbial community selection as a response to increasingly stringent nitrogen discharge permit levels. At the lab-scale, energy- and cost-saving anaerobic ammonia oxidation (anammox) was successfully applied as an alternative to conventional biological nitrogen removal under suboptimal mainstream wastewater conditions without constant bioaugmentation. Lastly, the annotation of PAO and GAO metagenomes from highly enriched cultures for which long-term morphological, physiological, and performance data were available allowed for increased confidence in the resulting genetic insights into the anaerobic metabolism and denitrification capabilities of these organisms. A systems biology approach to the analysis of engineered bioprocesses provided insights on microbial community structure and functional capabilities which were previously unavailable and unattainable. Ultimately, the work reported here will lead to better diagnoses of underlying issues in problematic bioreactors and smarter design of new wastewater and food waste treatment options.