The bug in a teacup—monitoring arthropod–plant associations with environmental DNA from dried plant material

Abstract

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.

Environmental DNA from archived leaves reveals widespread temporal turnover and biotic homogenization in forest arthropod communities

“…While this primer pair is known to have taxonomic biases for certain arthropod groups ( Piñol et al, 2015 ), it is still widely used as an efficient and reliable marker for community analysis ( Thomsen and Sigsgaard, 2019 ; Eitzinger et al, 2021 ). Recently, we designed a novel and highly degenerate primer pair by modifying two degenerate metabarcoding primers ( Gibson et al, 2014 ; Leray et al, 2013 ), which allows the suppression of plant amplification ( NoPlantF_270/mICOIintR_W ; Supplementary file 1 ; Krehenwinkel et al, 2022 ). To ensure the reproducibility of the diversity patterns recovered from our original ZBJ-ArtF1c/ZBJ-ArtR2c dataset, we additionally processed eleven complete ESB time series (174 samples) for this novel primer pair and compared results for species composition, α - and β -diversity.…”

Unravelling bird nest arthropod community structure using metabarcoding

“…Dust is known to be a good source of plant eDNA (Lennartz et al 2021), but can also be used to detect arthropods (Krehenwinkel et al 2022) and vertebrates (Lynggaard et al 2022). In comparison to metabarcoding results obtained from bulk samples of terrestrial or aquatic arthropods (Gleason et al, 2021;Steinke et al, 2021), the number of high-quality reads obtained from the different sample types in this study, is low.…”

“…Dust is known to be a good source of plant eDNA (Lennartz et al . 2021), but can also be used to detect arthropods (Krehenwinkel et al . 2022) and vertebrates (Lynggaard et al .…”

“…Provided that we employed a combination of primers and bioinformatic processing, which is well established for arthropod metabarcoding, there are three main reasons for this turnout: i) the DNA of Arthropoda and Chordata contained in dust samples is difficult to amplify because it's likely only a fraction of the plant and microorganism DNA contained in theses samples. Under such conditions, selecting a primer pair which is less prone to amplify plant, fungal, and microbial DNA is crucial (Elbrecht et al, 2019, Krehenwinkel et al 2022. ii) Much of the target DNA in the dust and in arthropod remains is likely old and degraded; it gradually accumulated during the breeding season and was exposed to decay processes.…”

Collective and harmonized high throughput barcoding of insular arthropod biodiversity: Toward a Genomic Observatories Network for islands

“…However, larger arthropod samples, such as aggregating arthropod samples by plant species (Rego et al, 2019; Ribeiro et al, 2005), can be coupled to wocDNA metabarcoding. Recently, environmental DNA metabarcoding from plant material offers promise as an additional tool to recover arthropod‐plant interactions (Krehenwinkel et al, 2022; Thomsen & Sigsgaard, 2019). Barcode reference sequences for taxonomic assignment will be desirable, but even in their absence, ecological networks can still be established with higher‐level taxonomic assignment.…”