Laboratoire de Génie Biologique, Earth and Life Institute, Université Catholique de Louvain, Place Croix du Sud 2, boite L7.05.19, 1348 Louvain-la-Neuve, Belgium.
Laboratoire de Génie Biologique, Earth and Life Institute, Université Catholique de Louvain, Place Croix du Sud 2, boite L7.05.19, 1348 Louvain-la-Neuve, Belgium; School of Life Sciences and Biotechnology, Yachay Tech University, 100119 San Miguel de Urcuquí, Ecuador.
Biotechnol Adv. 2016 Dec;34(8):1413-1426. doi: 10.1016/j.biotechadv.2016.10.006. Epub 2016 Nov 5.
Polluted environments are a reservoir of microbial species able to degrade or to convert pollutants to harmless compounds. The proper management of microbial resources requires a comprehensive characterization of their genetic pool to assess the fate of contaminants and increase the efficiency of bioremediation processes. Metagenomics offers appropriate tools to describe microbial communities in their whole complexity without lab-based cultivation of individual strains. After a decade of use of metagenomics to study microbiomes, the scientific community has made significant progress in this field. In this review, we survey the main steps of metagenomics applied to environments contaminated with organic compounds or heavy metals. We emphasize technical solutions proposed to overcome encountered obstacles. We then compare two metagenomic approaches, i.e. library-based targeted metagenomics and direct sequencing of metagenomes. In the former, environmental DNA is cloned inside a host, and then clones of interest are selected based on (i) their expression of biodegradative functions or (ii) sequence homology with probes and primers designed from relevant, already known sequences. The highest score for the discovery of novel genes and degradation pathways has been achieved so far by functional screening of large clone libraries. On the other hand, direct sequencing of metagenomes without a cloning step has been more often applied to polluted environments for characterization of the taxonomic and functional composition of microbial communities and their dynamics. In this case, the analysis has focused on 16S rRNA genes and marker genes of biodegradation. Advances in next generation sequencing and in bioinformatic analysis of sequencing data have opened up new opportunities for assessing the potential of biodegradation by microbes, but annotation of collected genes is still hampered by a limited number of available reference sequences in databases. Although metagenomics is still facing technical and computational challenges, our review of the recent literature highlights its value as an aid to efficiently monitor the clean-up of contaminated environments and develop successful strategies to mitigate the impact of pollutants on ecosystems.
受污染的环境是微生物物种的储存库，这些微生物能够降解或转化污染物为无害化合物。要想妥善管理微生物资源，就需要全面描述其基因库，以评估污染物的归宿，并提高生物修复过程的效率。宏基因组学提供了适当的工具来描述微生物群落的整体复杂性，而无需对单个菌株进行基于实验室的培养。在使用宏基因组学研究微生物组的十年后，科学界在这一领域取得了重大进展。在这篇综述中，我们调查了应用于受有机化合物或重金属污染环境的宏基因组学的主要步骤。我们强调了为克服遇到的障碍而提出的技术解决方案。然后，我们比较了两种宏基因组学方法，即基于文库的靶向宏基因组学和宏基因组的直接测序。在前者中，环境 DNA 被克隆到宿主中，然后根据（i）其生物降解功能的表达或（ii）与从相关的、已知序列设计的探针和引物的序列同源性，选择有兴趣的克隆。到目前为止，通过对大型克隆文库进行功能筛选，在发现新基因和降解途径方面取得了最高分。另一方面，无需克隆步骤的宏基因组直接测序更常用于受污染环境，以表征微生物群落的分类和功能组成及其动态。在这种情况下，分析集中在 16S rRNA 基因和生物降解的标记基因上。下一代测序和测序数据的生物信息学分析的进步为评估微生物的生物降解潜力开辟了新的机会，但收集基因的注释仍然受到数据库中可用参考序列数量有限的阻碍。尽管宏基因组学仍然面临技术和计算方面的挑战，但我们对最近文献的综述强调了它作为一种有效监测受污染环境清理和开发成功策略以减轻污染物对生态系统影响的辅助工具的价值。
