A decade after environmental scientists integrated high-throughput sequencing technologies in their toolbox, the genomics-based monitoring of anthropogenic impacts on the biodiversity and functioning of ecosystems is yet to be implemented by regulatory frameworks. Despite the broadly acknowledged potential of environmental genomics to this end, technical limitations and conceptual issues still stand in the way of its broad application by end-users. In addition, the multiplicity of potential implementation strategies may contribute to a perception that the routine application of this methodology is premature or “in development”, hence restraining regulators from binding these tools into legal frameworks. Here, we review recent implementations of environmental genomics-based methods, applied to the biomonitoring of ecosystems. By taking a general overview, without narrowing our perspective to particular habitats or groups of organisms, this paper aims to compare, review and discuss the strengths and limitations of four general implementation strategies of environmental genomics for monitoring: (a) Taxonomy-based analyses focused on identification of known bioindicators or described taxa; (b) De novo bioindicator analyses; (c) Structural community metrics including inferred ecological networks; and (d) Functional community metrics (metagenomics or metatranscriptomics). We emphasise the utility of the three latter strategies to integrate meiofauna and microorganisms that are not traditionally utilised in biomonitoring because of difficult taxonomic identification. Finally, we propose a roadmap for the implementation of environmental genomics into routine monitoring programmes that leverage recent analytical advancements, while pointing out current limitations and future research needs.

中文翻译：

---

由环境基因组学支持的生态系统监测：回顾当前战略及其实施路线图

在环境科学家将高通量测序技术集成到他们的工具箱中十年后，监管框架尚未实施基于基因组学的人为对生物多样性和生态系统功能影响的监测。尽管环境基因组学在这方面的潜力得到了广泛认可，但技术限制和概念问题仍然阻碍了最终用户的广泛应用。此外，潜在实施策略的多样性可能会让人认为这种方法的常规应用为时过早或“正在开发中”，从而限制监管机构将这些工具绑定到法律框架中。在这里，我们回顾了最近应用于生态系统生物监测的基于环境基因组学的方法的实施。通过总体概述，本文旨在比较、回顾和讨论用于监测的环境基因组学的四种一般实施策略的优点和局限性，而不是将我们的视角缩小到特定的栖息地或生物群体：（a）基于分类学的分析识别已知的生物指示剂或所描述的分类单元；(b) 从头生物指示剂分析；(c) 结构群落指标，包括推断的生态网络；(d) 功能群落指标（宏基因组学或宏转录组学）。我们强调后三种策略在整合小型动物和微生物方面的实用性，这些策略由于分类学鉴定困难而传统上不用于生物监测。最后，我们提出了将环境基因组学实施到常规监测计划中的路线图，利用最新的分析进展，同时指出当前的局限性和未来的研究需求。