Environmental DNA metabarcoding of wild flowers reveals diverse communities of terrestrial arthropods

Abstract

Terrestrial arthropods comprise the most species‐rich communities on Earth, and grassland flowers provide resources for hundreds of thousands of arthropod species. Diverse grassland ecosystems worldwide are threatened by various types of environmental change, which has led to decline in arthropod diversity. At the same time, monitoring grassland arthropod diversity is time‐consuming and strictly dependent on declining taxonomic expertise. Environmental DNA (eDNA) metabarcoding of complex samples has demonstrated that information on species compositions can be efficiently and non‐invasively obtained. Here, we test the potential of wild flowers as a novel source of arthropod eDNA. We performed eDNA metabarcoding of flowers from several different plant species using two sets of generic primers, targeting the mitochondrial genes 16S rRNA and COI. Our results show that terrestrial arthropod species leave traces of DNA on the flowers that they interact with. We obtained eDNA from at least 135 arthropod species in 67 families and 14 orders, together representing diverse ecological groups including pollinators, parasitoids, gall inducers, predators, and phytophagous species. Arthropod communities clustered together according to plant species. Our data also indicate that this experiment was not exhaustive, and that an even higher arthropod richness could be obtained using this eDNA approach. Overall, our results demonstrate that it is possible to obtain information on diverse communities of insects and other terrestrial arthropods from eDNA metabarcoding of wild flowers. This novel source of eDNA represents a vast potential for addressing fundamental research questions in ecology, obtaining data on cryptic and unknown species of plant‐associated arthropods, as well as applied research on pest management or conservation of endangered species such as wild pollinators.

Establishing arthropod community composition using metabarcoding: Surprising inconsistencies between soil samples and preservative ethanol and homogenate from Malaise trap catches

“…The COI marker, even one associated with a highly degenerate primer pair like the one we used, is not sufficient to detect all insect biodiversity. Thus, our results are consistent with those of other studies advocating for complementary multi‐marker approaches in metabarcoding of insect communities (Clarke et al, ; Deagle et al, ; Kaunisto et al, ; Thomsen & Sigsgaard, ) and other taxa (Holman et al, ; Wangensteen et al, ).…”

“…The COI marker, even one associated with a highly degenerate primer pair like the one we used, is not sufficient to detect all insect biodiversity. Thus, our results are consistent with those of other studies advocating for complementary multi-marker approaches in metabarcoding of insect communities (Clarke et al, 2014;Deagle et al, 2014;Kaunisto et al, 2017;Thomsen & Sigsgaard, 2019) and other taxa (Holman et al, 2018;Wangensteen et al, 2018). F I G U R E 6 Least-squares means (with standard errors) from the fitted model of log-ratio between the read counts of the same taxon from the same sample, as recorded from ethanol versus tissue homogenate, as a function of the (left) size and (right) sclerotization of insect families.…”

Raccoons foster the spread of freshwater and terrestrial microorganisms—Mammals as a source of microbial eDNA

“…Currently, the concept of eDNA is more frequently associated with analyses of extracellular (or extraorganismal) macrobial DNA that is shed into the environment by the target species, for example, in the form of faeces, urine or hair (Ibáñez de Aldecoa, Zafra, & González‐Pastor, ; Levy‐Booth et al, ). However, the array of eDNA sources has been widening, recently encompassing flowers (Thomsen & Sigsgaard, ), blood‐feeding sand flies and mosquitoes (Kocher et al, ) and leeches (Schnell et al, ). Analysed samples may contain different combinations of extra‐ and intracellular DNA.…”

High-throughput sequencing for community analysis: the promise of DNA barcoding to uncover diversity, relatedness, abundances and interactions in spider communities

“…However, terrestrial organisms can also be detected using eDNA, for example from soil DNA extractions. Arthropods were recently shown to leave eDNA traces on wildflowers (Thomsen and Sigsgaard 2019). Thus, by washing eDNA off of plants, it may be possible to reconstruct associated arthropod communities.…”