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

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.