The development of metabarcoding as a method for community ecology began with microbial studies over a decade ago, which have revealed the extensive diversity of bacteria and archaea on our planet and demonstrated the potential of metabarcoding for global biodiversity syntheses (Bates et al., 2013; Thompson et al., 2017). Although the integration and meta-analysis of microbial community data from independent studies is still challenging (e.g. Ramirez-Gonzalez et al., 2013), the success of international consortia such as the Earth Microbiome Project (EMP, Gilbert et al., 2010, 2014) has promoted the development of a harmonised framework for data generation and analyses within microbial eDNA research (see e.g. Tedersoo et al., 2015).