Comparison of Short Generalist and Specific Markers to Assess the Diversity of Arthropods Using eDNA Metabarcoding

A large number of marker typologies have been developed for the metabarcoding of environmental DNA (eDNA). Generalist markers have been advocated for their ability to amplify many taxa simultaneously and produce exhaustive biodiversity assessments, while more specific markers have been proposed for their higher ability to detect and discriminate taxa within a more restricted group. Quantitative comparisons between generalist and specific markers are needed to assess their relative efficiency depending on study targets. Here we compared the performance of one generalist (Euka02, amplifying all eukaryotic groups), one intermediate (Arth02, amplifying arthropods), and two specific markers (Coll01 and Inse01, amplifying springtails and insects, respectively) for the assessment of springtails and insects diversity using eDNA metabarcoding. The four markers were used to analyze eDNA extracted from > 1200 soil samples collected in recently deglaciated terrains. We then assessed whether the different markers were able to detect community responses to key environmental drivers (soil temperature, time since glacier retreat, plant productivity, and topographic wetness). The two specific markers detected more taxa of both springtails and insects than the generalist markers; still the taxonomic richness and community dissimilarity were well correlated between generalist and specific markers. There was good overlap between the taxa identified by the specific markers and those identified by the generalist ones, but the specific markers often detected the taxa identified by the generalist markers, plus several additional ones. Both generalist and specific markers detected the impact of key environmental drivers on arthropods; still the specific markers showed the strongest power to detect relationships, and the most generalist marker was unable to identify the weaker relationships. Generalist markers efficiently provide an overall view of soil biodiversity; nevertheless complementing them with specific markers allows more detailed biodiversity measures, and provides a clearer picture of its response to environmental stressors.