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

Abstract

A major limitation of current reports on insect declines is the lack of standardized, long-term, and taxonomically broad time series. Here, we demonstrate the utility of environmental DNA from archived leaf material to characterize plant-associated arthropod communities. We base our work on several multi-decadal leaf time series from tree canopies in four land use types, which were sampled as part of a long-term environmental monitoring program across Germany. Using these highly standardized and well-preserved samples, we analyze temporal changes in communities of several thousand arthropod species belonging to 23 orders using metabarcoding and quantitative PCR. Our data do not support widespread declines of α-diversity or genetic variation within sites. Instead, we find a gradual community turnover, which results in temporal and spatial biotic homogenization, across all land use types and all arthropod orders. Our results suggest that insect decline is more complex than mere α-diversity loss, but can be driven by β-diversity decay across space and time.

Plant‐derived environmental DNA complements diversity estimates from traditional arthropod monitoring methods but outperforms them detecting plant–arthropod interactions

“…Moreover, eDNA outperformed vegetation beating in recovering plant-arthropod interactions, an approach frequently used to identify plant-specific arthropod communities (Graham et al, 2022). As expected, both beating and plant-derived eDNA yielded a broad spectrum of ecological groups, including predators, parasitoids and herbivores (Johnson et al, 2023;Krehenwinkel, Weber, Broekmann, 2022;Thomsen & Sigsgaard, 2019). However, in our experiment, only eDNA was able to consistently differentiate specific arthropod communities between individual plant species.…”

“…PCR amplification, Index PCR and amplicon checks on all samples were conducted as described in Krehenwinkel, Weber, Broekmann, et al. (2022) using the primer combination fNoPlantF_270 (forward primer, RGCHTTYCCHCGWATAAAYAAYATAAG) and mlCOIintR_W (reverse primer, GRGGRTAWACWGTTCAWCCWGTNCC) in one PCR replicate, with a fragment length of 116 bp of the COI gene (Krehenwinkel, Weber, Künzel, & Kennedy, 2022). Illumina Truseq libraries were prepared using dual index PCRs as described in Lange et al.…”

“…Therefore, the diverse arthropod community that resides inside leaf tissue may be omitted by surface washes. A possible alternative to surface washes is the homogenization of whole plant compartments and DNA isolation from the ground plant material (Krehenwinkel, Weber, Broekmann, et al., 2022; Krehenwinkel, Weber, Künzel, & Kennedy, 2022), which possibly recovers more endophytic species.…”

It's raining species: Rainwash eDNA metabarcoding as a minimally invasive method to assess tree canopy invertebrate diversity

“…The stunned, falling insects are caught in collection hoops and can be identified by morphological assessment (Floren et al, 2022; Pedley et al, 2016) or bulk sample DNA metabarcoding (Creedy et al, 2019). Another approach is branch bagging and clipping (i.e., covering the branch in a cloth or bag and cutting the branch), which has the advantage of directly correlating species richness or density with plant or leaf biomass (Krehenwinkel et al, 2022). One of the challenges with bagging and clipping is that only the low canopy can be sampled unless it is done by a tree climber, and that sample sizes are hence often small.…”

BeeDNA: Microfluidic environmental DNA metabarcoding as a tool for connecting plant and pollinator communities

“…Here, only one flower per plant was sampled with each sampling method, but plant‐associated arthropods may not have interacted with this particular flower. Since this study was conceived, alternative strategies for eDNA detection of terrestrial insects have been successfully trialed, such as eDNA aggregation via water (Valentin et al, 2020), airborne eDNA (Roger et al, 2022), and eDNA deposited on leaves (Krehenwinkel et al, 2022). These approaches may circumvent the need for biological replication and invasive sampling of flowers but require extensive validation against the current sampling strategies of swabbing flowers and/or whole flower head harvest for pollinator eDNA used here and by Thomsen and Sigsgaard (2019).…”