Pollen DNA metabarcoding and related methods in global change ecology: prospects, challenges, and progress

Abstract

Anthropogenic activities are leading to changes in the environment at global scales, and understanding these changes requires rapid, high-throughput methods of assessment. Pollen DNA metabarcoding and related methods provide advantages in throughput and efficiency over traditional methods, such as microscopic identification of pollen and visual observation of plant-pollinator interactions. Pollen DNA metabarcoding is currently being applied to assessments of plant-pollinator interactions and their responses to land-use change such as increased agricultural intensity and urbanisation, surveillance of ecosystem change, and monitoring of spatiotemporal distribution of allergenic pollen. In combination with historical specimens, pollen DNA metabarcoding can compare contemporary and past ecosystems. Current technical challenges with pollen DNA metabarcoding include the need to understand the relationship between sequence read and species abundance, develop methods for determining confidence limits for detection and taxonomic classification, increase method standardisation, and improve of gaps in reference databases. Future research expanding the method to intraspecific identification, analysis of DNA in ancient pollen samples, and increased use of museum and herbarium specimens could open further avenues for research. Ongoing developments in sequencing technologies can accelerate progress towards these goals. Global ecological change is happening rapidly, and we anticipate that high-throughput methods such as pollen DNA metabarcoding are critical for assessing these changes and providing timely management recommendations to preserve biodiversity and the evolutionary and ecological processes that support it.

Temporal change in floral availability leads to periods of resource limitation and affects diet specificity in a generalist pollinator

“…The data obtained through DNA metabarcoding are considered semiquantitative, owing to the stochasticity of detecting rare taxa and potential biases in sampling, along with extraction, amplification and sequencing of DNA (Bell et al, 2022;. Relative read abundance was used for all analyses (Deagle et al, 2019), either using the proportion of taxa as a percentage or, for the models, the number of sequences, controlling for sequencing depth by setting the total number of sequences per sample as an offset (comparable to proportion) (Jones, Brennan, et al, 2021;.…”

“…Pollen DNA metabarcoding is a powerful tool for characterizing floral visitation by pollinators (reviewed in Bell et al, 2022;. The use of DNA metabarcoding for botanical identification of honey is well established (Hawkins et al, 2015;Milla et al, 2021;Valentini et al, 2010;Wirta et al, 2021), but few have applied this method to explore ecological questions related to honeybee foraging (de Vere et al, 2017;Jones, Brennan, et al, 2021;Lucek et al, 2019).…”