Environmental DNA analysis (eDNA) has revolutionized the field of biomonitoring in the past years. Various sources have been shown to contain eDNA of diverse organisms, for example, water, soil, gut content and plant surfaces. Here we show that dried plant material is a highly promising source for arthropod community eDNA. We designed a metabarcoding assay to enrich diverse arthropod communities while preventing amplification of plant DNA. Using this assay, we analysed various commercially produced teas and herbs. These samples recovered ecologically and taxonomically diverse arthropod communities, a total of over a thousand species in more than 20 orders, many of them specific to their host plant and its geographical origin. Atypically for eDNA, arthropod DNA in dried plants shows very high temporal stability, opening up plant archives as a source for historical arthropod eDNA. Considering these results, dried plant material appears excellently suited as a novel tool to monitor arthropods and arthropod–plant interactions, detect agricultural pests and identify the geographical origin of imported plant material. The simplicity of our approach and the ability to detect highly diverse arthropod communities from all over the world in tea bags also highlights its utility for outreach purposes and to raise awareness about biodiversity.

Our limited knowledge about the ecological drivers of global arthropod decline highlights the urgent need for more effective biodiversity monitoring approaches. Monitoring of arthropods is commonly performed using passive trapping devices, which reliably recover diverse communities, but provide little ecological information on the sampled taxa. Especially the manifold interactions of arthropods with plants are barely understood. A promising strategy to overcome this shortfall is environmental DNA (eDNA) metabarcoding from plant material on which arthropods leave DNA traces through direct or indirect interactions. However, the accuracy of this approach has not been sufficiently tested. In four experiments, we exhaustively test the comparative performance of plant‐derived eDNA from surface washes of plants and homogenized plant material against traditional monitoring approaches. We show that the recovered communities of plant‐derived eDNA and traditional approaches only partly overlap, with eDNA recovering various additional taxa. This suggests eDNA as a useful complementary tool to traditional monitoring. Despite the differences in recovered taxa, estimates of community α‐ and β‐diversity between both approaches are well correlated, highlighting the utility of eDNA as a broad scale tool for community monitoring. Last, eDNA outperforms traditional approaches in the recovery of plant‐specific arthropod communities. Unlike traditional monitoring, eDNA revealed fine‐scale community differentiation between individual plants and even within plant compartments. Especially specialized herbivores are better recovered with eDNA. Our results highlight the value of plant‐derived eDNA analysis for large‐scale biodiversity assessments that include information about community‐level interactions.

Molecular gut content analysis is a popular tool to study food web interactions and has recently been suggested as an alternative source for DNA‐based biomonitoring. However, the overabundant consumer's DNA often outcompetes that of its diet during PCR. Lineage‐specific primers are an efficient means to reduce consumer amplification while retaining broad specificity for dietary taxa. Here, we designed an amplicon sequencing assay to monitor the eukaryotic diet of mussels and other metazoan filter feeders and explore the utility of mussels as natural eDNA samplers to monitor planktonic communities. We designed several lineage‐specific rDNA primers with broad taxonomic suitability for eukaryotes. The primers were tested using DNA extracts of different limnic and marine mussel species and the results compared to eDNA water samples collected next to the mussel colonies. In addition, we analysed several 25‐year time series samples of mussels from German rivers. Our primer sets efficiently prevent the amplification of mussels and other metazoans. The recovered DNA reflects a broad dietary preference across the eukaryotic tree of life and considerable taxonomic overlap with filtered water samples. We also show the utility of a reversed version of our primers, which prevents amplification of nonmetazoan taxa from complex eukaryote community samples, by enriching fauna associated with the marine brown algae Fucus vesiculosus. Our protocol will enable large‐scale dietary analysis in metazoan filter feeders, facilitate aquatic food web analysis and allow surveying of aquacultures for pathogens. Moreover, we show that mussels and other aquatic filter feeders can serve as complementary DNA source for biomonitoring.

Gut content metabarcoding has provided important insights into the food web ecology of spiders, the most dominant terrestrial arthropod predators. In small invertebrates, like spiders, gut content analysis is often performed on whole body DNA extracts of individual predators, from which prey sequences are selectively enriched and sequenced. Since many spider species are generalist predators, large numbers of samples comprising individual spider specimens must be analysed to recover an exhaustive image of a spider species' prey spectrum, which is costly and time‐consuming. Pooled processing of bulk samples of multiple specimens has been suggested to reduce the necessary workload and cost while still recovering a representative estimate of the prey diversity. However, it is still unclear if pooling approaches lead to bias in recovering the prey spectrum and if the results are comparable with data from individually processed spiders. Here, we test the effects of metabarcoding pooled spider gut content on the recovered taxonomic diversity and composition of prey. Using a newly adapted primer pair, which efficiently enriches COI barcode sequences of diverse arthropod prey groups while suppressing spider amplification, we test if pooling leads to reduced taxonomic diversity or skewed estimates of prey composition. Our results show that pooling and individual processing recover highly correlated taxonomic diversity and composition of prey. The only exception are very rare prey items which were less well recovered by pooling. Our results support pooling as a cost‐effective and time‐efficient approach to recover the diet of generalist predators for population‐level studies of spider trophic interactions.

Detecting the imprints of global environmental change on biological communities is a paramount task for ecological research. But a lack of standardized long-term biomonitoring data prevents a deeper understanding of biodiversity change in the Anthropocene. Novel sources of data for analysing biodiversity change across time and space are urgently needed. By metabarcoding highly standardized biota samples from a long-term pollution monitoring archive in Germany, we here analyse four decades of community diversity for tens of thousands of species across the tree of life. The archived samples—tree leaves, marine macroalgae, and marine and limnic mussels—represent natural community DNA samplers, preserving a taxonomically diverse imprint of their associated biodiversity at the time of collection. We find no evidence for universal diversity declines at the local scale. Instead, a gradual compositional turnover emerges as a universal pattern of temporal biodiversity change in Germany’s terrestrial and aquatic ecosystems. This turnover results in biotic homogenization in most terrestrial and marine communities. Limnic communities, in contrast, rather differentiate across space, probably due to the immigration of different invasive species into different sites. Our study highlights the immense promise of alternative sample sources to provide standardized time series data of biodiversity change in the Anthropocene.

Plant–animal interactions (PAIs) are critical in natural and agricultural ecosystems, mediating energy flow with both positive and negative interactions. Traditional methods of tracking PAIs, such as morphological identification and camera trapping, are limited in speed and scalability, posing challenges for comprehensive biodiversity monitoring. Recently, environmental DNA (eDNA) metabarcoding has emerged as a promising technique for detecting species interactions non‐destructively. This pilot study explores the application of eDNA metabarcoding to investigate frugivorous interactions involving 18 partially consumed and three intact fruits of each Carica papaya and Ananas comosus . Metabarcoding of mitochondrial COI gene fragments generated 796,234 paired‐end reads representing 117 ASVs spanning diverse taxonomic groups, including Metazoans, Protozoans, Algae, Fungi, and Bacteria. After filtering for animal taxa, 41 ASVs were retained, dominated by Arthropoda (~97%). Major frugivores included Drosophila , Zaprionus , and Bactrocera species. Additional detections included beetles, ants, parasitoid wasps, and vertebrates such as Acridotheres javanicus , Callosciurus erythraeus , and Bandicota indica . Moreover, consumed fruits showed high insect (~90%–95%) and mammal (~4%–5%) DNA, while intact fruits were dominated by rotifers (~75%–80%). Distinct communities were found between pineapple and papaya, with 15 and 11 unique ASVs, respectively, and only one ASV was unique to intact fruits. Alpha and beta diversity analyses confirmed the differences in community structure between fruit types. Despite the limited sample size, our findings demonstrate the potential of fruit‐surface eDNA to monitor frugivory and species interactions. Future studies should scale this approach across seasons and crop types to assess its potential in long‐term biodiversity and pest management monitoring.