Pratt School of Engineering, Department of Civil and Environmental Engineering, Duke University, Durham, NC 27713, United States.
Nicholas School of the Environment, Duke University, Durham, NC 27713, United States.
J Hazard Mater. 2019 Oct 15;378:120859. doi: 10.1016/j.jhazmat.2019.120859. Epub 2019 Jul 2.
Bioremediation is a sustainable treatment strategy which remains challenging to implement especially in heterogeneous environments such as soil and sediment. Herein, we present a novel precision bioremediation framework that integrates amplicon based metagenomic analysis and chemical profiling. We applied this approach to samples obtained at a site contaminated with polycyclic aromatic hydrocarbons (PAHs). Geobacter spp. were identified as biostimulation targets because they were one of the most abundant genera and previously identified to carry relevant degradative genes. Mycobacterium and Sphingomonads spp. were identified as bioaugmentation and genetic bioaugmentation targets, respectively, due to their positive associations with PAHs and their high abundance and species diversity at all sampling locations. Overall, this case study suggests this framework can help identify bacterial targets for precision bioremediation. However, it is imperative that we continue to build our databases as the power of metagenomic based approaches remains limited to microorganisms currently in our databases.
生物修复是一种可持续的处理策略，但在土壤和沉积物等非均相环境中实施仍然具有挑战性。在此，我们提出了一种新的精准生物修复框架，该框架结合了基于扩增子的宏基因组分析和化学分析。我们将该方法应用于多环芳烃（PAHs）污染场地的样品。由于 Geobacter spp. 是最丰富的属之一，并且之前被鉴定为携带相关降解基因，因此被确定为生物刺激的目标。由于 Mycobacterium 和 Sphingomonads spp. 与 PAHs 呈正相关，并且在所有采样地点的丰度和物种多样性都很高，因此被确定为生物增强和遗传生物增强的目标。总体而言，这项案例研究表明，该框架可以帮助确定精准生物修复的细菌目标。然而，我们必须继续构建我们的数据库，因为基于宏基因组的方法的能力仍然受到我们数据库中现有微生物的限制。
