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Capabilities and limitations of using DNA metabarcoding to study plant-pollinator interactions

Citation

Arstingstall, Katherine et al. (2021), Capabilities and limitations of using DNA metabarcoding to study plant-pollinator interactions, Dryad, Dataset, https://doi.org/10.5061/dryad.xwdbrv1dr

Abstract

Many pollinator populations are experiencing declines, emphasizing the need for a better understanding of the complex relationship between bees and flowering plants. Using DNA metabarcoding to describe plant-pollinator interactions eliminates many challenges associated with traditional methods and has the potential to reveal a more comprehensive understanding of foraging behavior and pollinator life history. Here we use DNA metabarcoding of ITS2 and rbcL gene regions to identify plant species present in pollen loads of 404 bees from three habitats in eastern Oregon. Our specific objectives were to 1) determine whether plant species identified using DNA metabarcoding are consistent with plant species identified using observations, 2) compare characterizations of diet breadth derived from foraging observations to those based on plant species assignments obtained using DNA metabarcoding, and 3) compare plant species assignments produced by DNA metabarcoding using a “regional” reference database to those produced using a “local” database. At the three locations, 31-86% of foraging observations were consistent with DNA metabarcoding data, 8-50% of diet breadth characterizations based on observations differed from those based on DNA metabarcoding data, and 22-25% of plant species detected using the regional database were not known to occur in the study area in question. Plant-pollinator networks produced from DNA metabarcoding data had higher sampling completeness and significantly lower specialization than networks based on observations. Here, we examine some strengths and limitations of using DNA metabarcoding to identify plant species present in bee pollen loads, make ecological inferences about foraging behavior, and provide guidance for future research.

Methods

Native bees were sampled by handnetting, pollen loads were isolated individually from each bee, DNA was extracted from pollen loads, PCR was using to amplify the rbcL gene and ITS2 gene region, and a bioinformatics pipeline was used to determine which plant species were present in each pollen load. We compared plant species assignments obtained using regional and local reference databases. 

Usage Notes

This file contains plant species assignments obtained using DNA metabarcoding with both local and regional reference databases for 404 native bee pollen loads. Bees were collected by handnetting in 2018 from 8 sites at Threemile Canyon Farms, 10 sites at USFS Starkey Experimental Forest and Range, and 7 sites at TNC's Zumwalt Prairie Preserve. This dataset includes sampling location, month captured, and a foraging observation for each individual bee.