Print Email Facebook Twitter Prospects for multi-omics in the microbial ecology of water engineering Title Prospects for multi-omics in the microbial ecology of water engineering Author McDaniel, Elizabeth A. (University of Wisconsin-Madison) Wahl, S.A. (TU Delft BT/Industriele Microbiologie) Ishii, Shun'ichi (Japan Agency for Marine-Earth Science and Technologies (JAMSTEC)) Pinto, Ameet (Northeastern University) Ziels, Ryan (University of British Columbia) Nielsen, Per Halkjær (Aalborg University) McMahon, Katherine D. (University of Wisconsin-Madison) Williams, Rohan B.H. (National University of Singapore) Date 2021 Abstract 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, related developments in both whole community gene expression surveys and metabolite profiling have permitted for 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. Water engineers, microbiologists, and microbial ecologists studying activated sludge, anaerobic digestion, and drinking water distribution systems have applied various (meta)omics techniques for connecting microbial community dynamics and physiologies to overall process parameters and system performance. However, the rapid pace at which new omics-based approaches are developed can appear daunting to those looking to apply these state-of-the-art practices for the first time. 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. Subject Metabolic modelingMetabolomicsMetagenomicsMetaproteomicsMetatranscriptomicsMicrobial ecologyWater engineering To reference this document use: http://resolver.tudelft.nl/uuid:bdb2e10a-5ddc-45e2-965d-3f53ac3b5bf0 DOI https://doi.org/10.1016/j.watres.2021.117608 Embargo date 2023-09-20 ISSN 0043-1354 Source Water Research, 205 Part of collection Institutional Repository Document type review Rights © 2021 Elizabeth A. McDaniel, S.A. Wahl, Shun'ichi Ishii, Ameet Pinto, Ryan Ziels, Per Halkjær Nielsen, Katherine D. McMahon, Rohan B.H. Williams Files PDF WR_MEWE_review_paper.pdf 1.38 MB Close viewer /islandora/object/uuid:bdb2e10a-5ddc-45e2-965d-3f53ac3b5bf0/datastream/OBJ/view