Many restoration ecology studies now incorporate an environmental microbiome component, made possible mainly via advanced DNA sequencing technologies. Environmental microbiomes are important for successful restoration as they support many ecosystem functions and services that are a target of restoration interventions. However, since microbes are ubiquitous in most environments, including laboratories and researchers, there are contamination risks. If these risks are not adequately managed, the conclusions drawn from these microbiome restoration studies could be compromised. Here, we provide a user guide for restoration ecologists on how to navigate microbiome contamination risks at each stage of a study, from planning and sampling to data analysis and publishing. The two main categories of contamination we discuss are cross-contamination—contamination between samples—and external contamination—contamination from reagents and environmental sources. We also consider the impact of batch effects, where sampling and/or processing order could leave a signal in the data. Without adequate control, these contamination issues can undermine the results of microbiome restoration studies. We hope that this guide will help minimize the effect of contamination and improve the quality of data and studies going forward.

中文翻译：

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在微生物组恢复研究中尽量减少污染问题的指南

现在，许多恢复生态学研究都纳入了环境微生物组成分，这主要是通过先进的 DNA 测序技术实现的。环境微生物组对于成功恢复很重要，因为它们支持作为恢复干预目标的许多生态系统功能和服务。然而，由于微生物在包括实验室和研究人员在内的大多数环境中无处不在，因此存在污染风险。如果这些风险没有得到充分管理，从这些微生物组恢复研究中得出的结论可能会受到影响。在这里，我们为恢复生态学家提供了一份用户指南，了解如何在研究的每个阶段（从规划和采样到数据分析和发布）应对微生物组污染风险。我们讨论的两大类污染是交叉污染——样品之间的污染——和外部污染——来自试剂和环境来源的污染。我们还考虑了批次效应的影响，其中采样和/或处理顺序可能会在数据中留下信号。如果没有适当的控制，这些污染问题会破坏微生物组恢复研究的结果。我们希望本指南将有助于最大限度地减少污染的影响，并提高数据和研究的质量。