  Advances in high-throughput sequencing technologies and bioinformatics
approaches over almost the last three decades have substantially increased our
ability to explore microorganisms and their functions-including those that have
yet to be cultivated in pure isolation. Genome-resolved metagenomic approaches
have enabled linking powerful functional predictions to specific taxonomical
groups with increasing fidelity. Additionally, whole community gene expression
surveys and metabolite profiling have permitted direct surveys of
community-scale functions in specific environmental settings. These advances
have allowed for a shift in microbiome science away from descriptive studies
and towards mechanistic and predictive frameworks for designing and harnessing
microbial communities for desired beneficial outcomes. Here, we review how
modern genome-resolved metagenomic approaches have been applied to a variety of
water engineering applications from lab-scale bioreactors to full-scale
systems. We describe integrated omics analysis across engineered water systems
and the foundations for pairing these insights with modeling approaches.
Lastly, we summarize emerging omics-based technologies that we believe will be
powerful tools for water engineering applications. Overall, we provide a
framework for microbial ecologists specializing in water engineering to apply
cutting-edge omics approaches to their research questions to achieve novel
functional insights. Successful adoption of predictive frameworks in engineered
water systems could enable more economically and environmentally sustainable
bioprocesses as demand for water and energy resources increases.
