活性污泥微生物群落宏组学研究进展

Advances in meta-omics research on activated sludge microbial community

摘要:

活性污泥是全球最常用的废水生物处理人工生态系统，微生物是驱动其污染净化能力的关键。活性污泥微生物群落所有物种与基因(简称“微生物组”)的研究先后经历了“显微镜观察和纯菌培养分离”(1915)、“PCR扩增-测序”(1994)和“高通量测序-宏组学分析”(2006)三个重要阶段的发展变迁。相应地，我们对活性污泥微生物组的认知经历了从最早对微型动物(如钟虫和轮虫)及其他微生物的形貌观察和纯种培养鉴定到今天对整个微生物组的全局多样性认识的飞跃。近13年来，基于高通量测序的宏组学方法被广泛应用于揭示活性污泥微生物群落组成结构和功能，我们现在充分意识到活性污泥微生物组蕴藏着大量不可培养新物种和基因多样性，驱动着各类污染物的降解与转化。目前，特异性分子标记基因的扩增子测序技术已经被广泛应用于揭示城市和工业废水处理活性污泥微生物组和典型功能种群(如硝化细菌和聚磷菌)的时空多样性和群落构建机制，进而为未来实现活性污泥微生物组功能的精准调控奠定理论基础。宏基因组学研究在群落、种群和个体基因组水平全面解析了活性污泥微生物组驱动的碳、氮、磷元素循环过程，以及有机微污染物的生物降解和转化机理。将来活性污泥微生物组学研究需要在“标准化的组学分析方法和绝对定量”“高通量培养组学”“高通量功能基因组学”和“多组学方法的结合及多种方法并用”4个方面取得实现精准生态基因组学所需的技术突破，以最大限度发掘活性污泥微生物组在污水处理与资源回收领域的生态学与工程学价值。

Abstract:

Activated sludge is the most popular artificial ecosystem for biotechnological wastewater treatment worldwide, and microorganisms are the key driver of its de-contamination ability of wastewater. The study of all species and genes of activated sludge microbial communities (referred to as ‘microbiome’) has undergone three major stages of tremendous development: microscopic observation and pure culture isolation (since 1915), PCR amplification and sequencing (since 1994), and high-throughput sequencing (HTS) and meta-omics (since 2006). Correspondingly, our understanding of the activated sludge microbiome has experienced the leap from the earliest observations of the morphology of micro-fauna (e.g. Vorticella and Rotifera) and other microorganisms to complete diversity profile of the entire microbiome nowadays. In the past 13 years, HTS-based meta-omics research has been widely used to reveal the structure and function of activated sludge microbiome. We have now fully realized that the activated sludge microbiome contains a large diversity of uncultivable new species and genes, driving the degradation and conversion of various pollutants. At present, amplicon sequencing analysis of specific molecular marker genes has been widely used to reveal the spatial and temporal diversity of urban and industrial wastewater treatment activated sludge microbiome, typical functional bacteria (e.g. nitrifying bacteria and polyphosphate-accumulating bacteria) and community assembly patterns, providing theoretical basis for achieving precise regulation of activated sludge microbiome functioning. Metagenomic studies have comprehensively revealed, the microbiome-driven carbon, nitrogen and phosphorus cycling in activated sludge and the biodegradation and transformation mechanisms of organic micro-pollutants at levels of community, population and individual genomes. Future research on the activated sludge microbiome is supposed to make breakthroughs in the following four technical aspects for the achievement of precision eco-genomics: i) standardized meta-omics approaches and absolute quantification, ii) high-throughput culture omics; iii) high-throughput functional metagenomics, and iv) integrated use of multi-omics methods and multiple methods, which are important for maximizing the ecological and engineering values of activated sludge microbiome in wastewater treatment and resource recovery.