Wallace James C, Youngblood Jessica E, Port Jesse A, Cullen Alison C, Smith Marissa N, Workman Tomomi, Faustman Elaine M
Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington, United States of America.
Environmental Toxicology, Amec Foster Wheeler, Lynnwood, Washington, United States of America.
PLoS One. 2018 Feb 13;13(2):e0192412. doi: 10.1371/journal.pone.0192412. eCollection 2018.
Whole-metagenome sequencing (WMS) has emerged as a powerful tool to assess potential public health risks in marine environments by measuring changes in microbial community structure and function in uncultured bacteria. In addition to monitoring public health risks such as antibiotic resistance determinants, it is essential to measure predictors of microbial variation in order to identify natural versus anthropogenic factors as well as to evaluate reproducibility of metagenomic measurements.This study expands our previous metagenomic characterization of Puget Sound by sampling new nearshore environments including the Duwamish River, an EPA superfund site, and the Hood Canal, an area characterized by highly variable oxygen levels. We also resampled a wastewater treatment plant, nearshore and open ocean sites introducing a longitudinal component measuring seasonal and locational variations and establishing metagenomics sampling reproducibility. Microbial composition from samples collected in the open sound were highly similar within the same season and location across different years, while nearshore samples revealed multi-fold seasonal variation in microbial composition and diversity. Comparisons with recently sequenced predominant marine bacterial genomes helped provide much greater species level taxonomic detail compared to our previous study. Antibiotic resistance determinants and pollution and detoxification indicators largely grouped by location showing minor seasonal differences. Metal resistance, oxidative stress and detoxification systems showed no increase in samples proximal to an EPA superfund site indicating a lack of ecosystem adaptation to anthropogenic impacts. Taxonomic analysis of common sewage influent families showed a surprising similarity between wastewater treatment plant and open sound samples suggesting a low-level but pervasive sewage influent signature in Puget Sound surface waters. Our study shows reproducibility of metagenomic data sampling in multiple Puget Sound locations while establishing baseline measurements of antibiotic resistance determinants, pollution and detoxification systems. Combining seasonal and longitudinal data across these locations provides a foundation for evaluating variation in future studies.
全基因组测序（WMS）已成为一种强大的工具，可通过测量未培养细菌中微生物群落结构和功能的变化来评估海洋环境中的潜在公共卫生风险。除了监测抗生素耐药性决定因素等公共卫生风险外，测量微生物变异的预测指标对于识别自然因素与人为因素以及评估宏基因组测量的可重复性也至关重要。本研究通过对新的近岸环境进行采样，扩展了我们之前对普吉特海湾的宏基因组特征描述，这些新环境包括美国环境保护局（EPA）指定的超级基金污染场地杜瓦米什河，以及一个以氧含量高度变化为特征的区域胡德运河。我们还对一个污水处理厂、近岸和公海站点进行了重新采样，引入了一个纵向成分，以测量季节和位置变化，并建立宏基因组采样的可重复性。在不同年份的同一季节和位置，从开阔海域采集的样本中的微生物组成高度相似，而近岸样本显示微生物组成和多样性存在多倍的季节变化。与最近测序的主要海洋细菌基因组进行比较，与我们之前的研究相比，有助于提供更详细的物种水平分类信息。抗生素耐药性决定因素以及污染和解毒指标在很大程度上按位置分组，显示出较小的季节差异。金属抗性、氧化应激和解毒系统在靠近EPA超级基金污染场地的样本中没有增加，这表明生态系统对人为影响缺乏适应性。对常见污水流入菌群的分类分析表明，污水处理厂和开阔海域样本之间存在惊人的相似性，这表明普吉特海湾表层水体中存在低水平但普遍存在的污水流入特征。我们的研究表明，在普吉特海湾的多个地点进行宏基因组数据采样具有可重复性，同时建立了抗生素耐药性决定因素、污染和解毒系统的基线测量。结合这些地点的季节和纵向数据为评估未来研究中的变化提供了基础。
