DNA Metabarcoding in Plant-Pollinator Interactions

DNA metabarcoding has become a pivotal technique for resolving the complexity of plant–pollinator interactions by combining targeted amplification of conserved genetic markers with high-throughput sequencing to identify the botanical origin of pollen grains carried by insect visitors. This molecular approach surpasses traditional microscopy and colour-based methods in taxonomic resolution, enabling detection of cryptic interactions and rare taxa across temporal and spatial scales. By reconstructing detailed pollen transport and visitation networks, metabarcoding provides insights into individual and community-level foraging specialisation, seasonal shifts in floral resource use and the impact of landscape composition on pollinator diets. Enhanced by multi-locus strategies and expansive reference libraries, modern workflows can achieve near-species-level assignment, while quantitative bioinformatic pipelines address biases in marker copy number and primer efficiency. Applications range from agroecosystem management and urban habitat design to conservation monitoring of wild pollinators. As environmental pressures intensify, DNA metabarcoding offers a robust framework to inform evidence-based strategies for pollinator health and ecosystem resilience.

Research from Nature Portfolio

Recent studies have applied DNA metabarcoding to managed honeybee colonies to elucidate selective foraging behaviour and network structure. In one investigation, analysis of hive-stored pollen and honey revealed that colonies exploit only a subset of available flowering genera for nectar and pollen, exhibiting greater selectivity for pollen sources and pronounced temporal shifts driven by phenology and site. Earlier work using metabarcoding of insect-collected pollen demonstrated detection of more than twice the number of plant species compared with observational surveys of flower visits, substantially expanding the known pollination network and highlighting widespread hidden interactions. Together, these findings underscore the capacity of DNA metabarcoding to refine ecological network models, quantify limitations of traditional methods and pinpoint essential floral resources for both managed and wild pollinators.

DNA Metabarcoding in Plant-Pollinator Interactions publication trend

The graph below shows the total number of articles in dna metabarcoding in plant-pollinator interactions across all publications each year (not limited to Nature Index journals).

Technical terms

DNA metabarcoding: A method that uses PCR amplification of barcode loci and high-throughput sequencing to identify multiple taxa within complex environmental samples.

High-throughput sequencing: Rapid, large-scale DNA sequencing technology that generates millions of sequence reads in parallel.

Marker gene (barcode locus): A conserved DNA region used to distinguish taxa, commonly ITS2, rbcL or trnL in plants.

Reference database: A curated collection of DNA barcode sequences from known taxa used to assign taxonomy to unknown environmental sequences.

Multi-locus approach: The use of two or more genetic markers in tandem to improve accuracy and resolution of taxonomic identification.

Pollination network: A representation of interactions between plant and pollinator species, often depicted as nodes (species) and links (interactions) to analyse community structure.

References

1. Pollen metabarcoding reveals a broad diversity of plant sources available to farmland flower visitors near tropical montane forest. Frontiers in Plant Science (2025).
2. Validating a multi-locus metabarcoding approach for characterizing mixed-pollen samples. Plant Methods (2023).
3. Honeybees’ foraging choices for nectar and pollen revealed by DNA metabarcoding. Scientific Reports (2023).
4. Using metabarcoding to reveal and quantify plant-pollinator interactions. Scientific Reports (2016).