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Advances in high-throughput sequencing technologies and bioinformaticsapproaches over almost the last three decades have substantially increased ourability to explore microorganisms and their functions-including those that haveyet to be cultivated in pure isolation. Genome-resolved metagenomic approacheshave enabled linking powerful functional predictions to specific taxonomicalgroups with increasing fidelity. Additionally, whole community gene expressionsurveys and metabolite profiling have permitted direct surveys ofcommunity-scale functions in specific environmental settings. These advanceshave allowed for a shift in microbiome science away from descriptive studiesand towards mechanistic and predictive frameworks for designing and harnessingmicrobial communities for desired beneficial outcomes. Here, we review howmodern genome-resolved metagenomic approaches have been applied to a variety ofwater engineering applications from lab-scale bioreactors to full-scalesystems. We describe integrated omics analysis across engineered water systemsand the foundations for pairing these insights with modeling approaches.Lastly, we summarize emerging omics-based technologies that we believe will bepowerful tools for water engineering applications. Overall, we provide aframework for microbial ecologists specializing in water engineering to applycutting-edge omics approaches to their research questions to achieve novelfunctional insights. Successful adoption of predictive frameworks in engineeredwater systems could enable more economically and environmentally sustainablebioprocesses as demand for water and energy resources increases.

Prospects for Multi-omics in the Microbial Ecology of Water Engineering