Background In light of the current biodiversity crisis, DNA barcoding is developing into an essential tool to quantify state shifts in global ecosystems. Current barcoding protocols often rely on short amplicon sequences, which yield accurate identification of biological entities in a community but provide limited phylogenetic resolution across broad taxonomic scales. However, the phylogenetic structure of communities is an essential component of biodiversity. Consequently, a barcoding approach is required that unites robust taxonomic assignment power and high phylogenetic utility. A possible solution is offered by sequencing long ribosomal DNA (rDNA) amplicons on the MinION platform (Oxford Nanopore Technologies). Findings Using a dataset of various animal and plant species, with a focus on arthropods, we assemble a pipeline for long rDNA barcode analysis and introduce a new software (MiniBar) to demultiplex dual indexed Nanopore reads. We find excellent phylogenetic and taxonomic resolution offered by long rDNA sequences across broad taxonomic scales. We highlight the simplicity of our approach by field barcoding with a miniaturized, mobile laboratory in a remote rainforest. We also test the utility of long rDNA amplicons for analysis of community diversity through metabarcoding and find that they recover highly skewed diversity estimates. Conclusions Sequencing dual indexed, long rDNA amplicons on the MinION platform is a straightforward, cost-effective, portable, and universal approach for eukaryote DNA barcoding. Although bulk community analyses using long-amplicon approaches may introduce biases, the long rDNA amplicons approach signifies a powerful tool for enabling the accurate recovery of taxonomic and phylogenetic diversity across biological communities.

Environmental DNA (eDNA) metabarcoding promises to be a cost- and time-efficient monitoring tool to detect interactions of arthropods with plants. However, observation-based verification of the eDNA-derived data is still required to confirm the reliability of those detections, i.e., to verify whether the arthropods have previously interacted with the plant. Here, we conducted a comparative analysis of the performance of eDNA metabarcoding and video camera observations to detect arthropod communities associated with sunflowers (Helianthus annuus, L.). We compared the taxonomic composition, interaction type, and diversity by testing for an effect of arthropod interaction time and occupancy on successful taxon recovery by eDNA. We also tested if prewashing of the flowers successfully removed eDNA deposition from before the video camera recording, thus enabling a reset of the community for standardized monitoring. We find that eDNA and video camera observations recovered distinct communities, with about a quarter of the arthropod families overlapping. However, the overlapping taxa comprised ~90% of the interactions observed by the video camera. Interestingly, eDNA metabarcoding recovered more unique families than the video cameras, but approximately two-thirds of those unique observations were of rare species. The eDNA-derived families were biased toward plant sap-suckers, showing that such species may deposit more eDNA than, for example, transient pollinators. We also find that prewashing of the flower heads did not suffice to remove all eDNA traces, suggesting that eDNA on plants may be more temporally stable than previously thought. Our work highlights the great potential of eDNA as a tool to detect plant-arthropod interactions, particularly for specialized and frequently interacting taxa.