Towards all-inclusive community ecology via DNA metabarcoding

An exhaustive assessment of biodiversity is a major challenge of ecological research, and molecular approaches such as the metabarcoding of environmental DNA are boosting our ability to perform biodiversity inventories. Are we actually able to assess the whole community, to unravel the intricate interactions between organisms and the impacts of global changes on the different trophic levels? The majority of metabarcoding papers published in the last years used just one or two markers and analyzed a limited number of taxonomic groups. Nevertheless, approaches are emerging that might allow “all-taxa biological inventories”. Exhaustive biodiversity assessments can be attempted by combining a large number of specific primers, by exploiting the power of universal primers, or by combining specific and universal primers to obtain good information on key taxa while limiting the overlooked biodiversity. Multiplexes of primers and shotgun sequencing may provide a better coverage of biodiversity compared to standard metabarcoding, but still require major methodological advances. We identify the strengths and limitations of different approaches, and suggest new development lines that might improve broad scale biodiversity analyses in the near future.