A guide to minimize contamination issues in microbiome restoration studies

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.