DNA metabarcoding of saproxylic beetles - Streamlining species identification for large-scale forest biomonitoring

Forest ecosystems host most of the terrestrial biodiversity on Earth. Climate change scenarios predict an increase in the intensity and frequency of severe summer droughts, high temperatures, and infestations of pathogens and insects, causing high mortality of some keystone tree species. These changes will affect forestry policies and practices, strongly impacting biodiversity. Understanding the responses of biodiversity to forest decline is therefore essential to developing new climate-smart management options. Biomonitoring of forest insects relies on techniques involving laborious and expensive sampling procedures. For instance, the study of indicators such as saproxylic beetles is strongly impeded by their high abun- dance and diversity, and by the deficit in taxonomists able to identify them. Here, we propose and test the use of metabarcoding for bulk samples of saproxylic beetles, in combination with the assembly of a relevant barcode reference library, as a mean to streamline identification. Results: Using a set of three primer pairs targeting short fragments within the cytochrome c oxidase subunit I (COI) barcode, we analyzed through metabarcoding a set of 32 bulk samples of saproxylic beetles collected in France, containing hundreds of specimens that were all initially counted and identified using morphology. To test the efficiency of non-destructive analyses, we also sequenced libraries of amplicons directly obtained from the ethanol used for preserving the samples. Identifying the resulting reads with a newly assembled barcode library, we successfully recovered most species present in each of the samples. Furthermore, our samples were selected to take into account a variety of conditions and parameters possibly affecting the results (species diversity, relative abundance and biomass, sampling medium, and preservation method). Significance: The use of DNA metabarcoding to monitor forest biodiversity can significantly improve our capacity to measure, understand, and anticipate the impact of global changes on forests, thus enhancing conservation strategies and the sustainability of silvicultural practices.