Toward shotgun metagenomic approaches for microbial source tracking sewage spills based on laboratory mesocosms
Toward shotgun metagenomic approaches for microbial source tracking sewage spills based on laboratory mesocosms
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DOI：
10.1016/j.watres.2021.117993
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发表时间：
2022-02-15
期刊：
影响因子：
12.8
通讯作者：
Konstantinidis，Konstantinos T.
中科院分区：
文献类型：
--
作者：
Lindner，Blake G.;Suttner，Brittany;Konstantinidis，Konstantinos T.
人们对与未经处理的城市污水(污水)有关的微生物群落的基因组多样性知之甚少，包括是否存在污水特有的微生物种群，以及如何利用这些种群改进受污染水域的来源归属和分配。在这里，我们使用位于美国佐治亚州亚特兰大的三个污水处理厂的进水来扰乱实验室淡水中观系统，模拟污水污染事件，并在7天的观察期内用鸟枪式元基因组学跟踪这些中观系统。我们描述了15个丰富的非冗余细菌元基因组组装基因组(MAG)，它们普遍存在于所有污水接种中，但在我们的分析检测极限下，却不存在于未受干扰的淡水对照中。跟踪这些MAG所代表的种群的动态显示了不同的衰减动力学，这取决于(推断的)表型，例如，在充气良好的培养条件下，厌氧菌比好氧菌衰减得更快。值得注意的是，这些人群中的一部分表现出与常见标志物肠球菌和HF183相似的衰退模式。尽管这些种群有明显的衰退，但在整个孵化过程中，β-内酰胺酶编码基因的丰度仍然高于对照。最后，我们构建了代表几种不同粪便来源的基因组文库，并概述了一种利用这些文库利用鸟枪元基因组数据在多个可能的来源中识别和分配污染信号的生物信息学方法。
Little is known about the genomic diversity of the microbial communities associated with raw municipal wastewater (sewage), including whether microbial populations specific to sewage exist and how such populations could be used to improve source attribution and apportioning in contaminated waters. Herein, we used the influent of three wastewater treatment plants in Atlanta, Georgia (USA) to perturb laboratory freshwater mesocosms, simulating sewage contamination events, and followed these mesocosms with shotgun metagenomics over a 7-day observational period. We describe 15 abundant non-redundant bacterial metagenome-assembled genomes (MAGs) ubiquitous within all sewage inocula yet absent from the unperturbed freshwater control at our analytical limit of detection. Tracking the dynamics of the populations represented by these MAGs revealed varied decay kinetics, depending on (inferred) phenotypes, e.g., anaerobes decayed faster than aerobes under the well-aerated incubation conditions. Notably, a portion of these populations showed decay patterns similar to those of common markers,Enterococcusand HF183. Despite the apparent decay of these populations, the abundance of β-lactamase encoding genes remained high throughout incubation relative to the control. Lastly, we constructed genomic libraries representing several different fecal sources and outline a bioinformatic approach which leverages these libraries for identifying and apportioning contamination signal among multiple probable sources using shotgun metagenomic data.