Department of Bacteriology, University of Wisconsin - Madison, Madison, WI, USA.
Department of Biotechnology, Delft University of Technology, Delft, the Netherlands.
Water Res. 2021 Oct 15;205:117608. doi: 10.1016/j.watres.2021.117608. Epub 2021 Aug 27.
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.
在过去的近三十年中，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——包括那些尚未在纯培养中分离出来的微生物。基因组解析宏基因组学方法使我们能够将强大的功能预测与特定的分类群以越来越高的保真度联系起来。此外，整个群落基因表达调查和代谢物分析相关技术的发展，使得在特定的环境背景下对群落尺度的功能进行直接调查成为可能。这些进展使微生物组科学从描述性研究转向了设计和利用微生物群落以获得预期有益结果的机制和预测框架。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经应用了各种（宏）组学技术，将微生物群落动态和生理学与整体过程参数和系统性能联系起来。然而，新的基于组学的方法的快速发展可能会让那些首次尝试应用这些最先进技术的人望而却步。在这里，我们回顾了现代基因组解析宏基因组学方法如何应用于从实验室规模的生物反应器到全规模系统的各种水工程应用。我们描述了工程水系统中跨组学分析的方法和基础，并将这些见解与建模方法相结合。最后，我们总结了新兴的基于组学的技术，我们相信这些技术将成为水工程应用的有力工具。总的来说，我们为专注于水工程的微生物生态学家提供了一个框架，使他们能够将最先进的组学方法应用于他们的研究问题，以获得新的功能见解。在工程水系统中成功采用预测框架可以使生物过程更具经济和环境可持续性，因为对水和能源资源的需求不断增加。
