Using metabarcoding to reveal and quantify plant-pollinator interactions

Abstract

Given the ongoing decline of both pollinators and plants, it is crucial to implement effective methods to describe complex pollination networks across time and space in a comprehensive and high-throughput way. Here we tested if metabarcoding may circumvent the limits of conventional methodologies in detecting and quantifying plant-pollinator interactions. Metabarcoding experiments on pollen DNA mixtures described a positive relationship between the amounts of DNA from focal species and the number of trnL and ITS1 sequences yielded. The study of pollen loads of insects captured in plant communities revealed that as compared to the observation of visits, metabarcoding revealed 2.5 times more plant species involved in plant-pollinator interactions. We further observed a tight positive relationship between the pollen-carrying capacities of insect taxa and the number of trnL and ITS1 sequences. The number of visits received per plant species also positively correlated to the number of their ITS1 and trnL sequences in insect pollen loads. By revealing interactions hard to observe otherwise, metabarcoding significantly enlarges the spatiotemporal observation window of pollination interactions. By providing new qualitative and quantitative information, metabarcoding holds great promise for investigating diverse facets of interactions and will provide a new perception of pollination networks as a whole.

Counting with DNA in metabarcoding studies: How should we convert sequence reads to dietary data?

“…Conclusions from analyses of mock communities vary from no relationship to good correlations between the composition of the mixture and sequence reads (Edgar, ; Kimmerling et al., ; Pornon et al., ). One reason for these different conclusions is that the range of concentrations analysed varies considerably across studies, from nearly equal mixtures of a few taxa, to mixtures containing many taxa in very different abundances.…”

Methods for the extraction, storage, amplification and sequencing of DNA from environmental samples

“…A comparison of studies using these different gene regions strongly suggests that the trnL intron provides far greater resolution than lengths of rbcL suitable for metabarcoding with the current Illumina technology ). The plastid DNA region encompassing the chloroplast trnL intron and trnL-trnF intergenic spacer (used either together or each in isolation) have been used extensively in land plant systematics as well as some metabarcoding projects (Lang et al 2014;Pornon et al 2016;Yang et al 2016). Together the typical amplicon length of this region (c. 1 kb) is too great for current Illumina based metabarcoding techniques.…”

How Many Plant Species are There, Where are They, and at What Rate are They Going Extinct?

“…These methods enable taxonomic identifications of plant samples in which diagnostic characters are largely absent (e.g., roots in a soil sample, seeds from seed traps, or pollen), or for which few experts know the diagnostic characters. DNA metabarcoding has streamlined identifications of pollen for allergen monitoring (Kraaijeveld et al, 2015), plant-pollinator interactions Richardson et al, 2015aRichardson et al, , 2015bSickel et al, 2015;Pornon et al, 2016), and honey composition (Hawkins et al, 2015). The analysis of fragments of plant material in herbivore guts enables diet analysis (Valentini et al, 2009;Pompanon et al, 2012).…”