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.

近三十年来，高通量测序技术和生物信息学方法的进步极大地提高了我们探索微生物及其功能的能力——包括那些尚未完全分离培养的微生物。基因组解析的宏基因组方法使强大的功能预测能够以越来越高的保真度与特定的分类群联系起来。此外，整个社区基因表达调查和代谢物分析的相关发展已经允许在特定环境设置中直接调查社区规模的功能。这些进步使微生物组科学从描述性研究转向机械和预测框架，以设计和利用微生物群落以实现预期的有益结果。研究活性污泥、厌氧消化和饮用水分配系统的水工程师、微生物学家和微生物生态学家已应用各种（元）组学技术将微生物群落动力学和生理学与整体过程参数和系统性能联系起来。然而，对于那些希望首次应用这些最先进实践的人来说，开发基于组学的新方法的快速发展可能令人生畏。在这里，我们回顾了现代基因组解析的宏基因组方法如何应用于从实验室规模的生物反应器到全面系统的各种水工程应用。我们描述了跨工程水系统的集成组学分析以及将这些见解与建模方法相结合的基础。最后，我们总结了新兴的基于组学的技术，我们认为这些技术将成为水工程应用的强大工具。总的来说，我们为专门从事水工程的微生物生态学家提供了一个框架，将尖端的组学方法应用于他们的研究问题，以获得新的功能见解。随着对水和能源资源的需求增加，在工程水系统中成功采用预测框架可以实现更经济和环境可持续的生物过程。