Where are the bees? Tracking down which flowers they pollinate
Researchers at the UEA and Earlham Institute (EI) have developed a new method to quickly identify sources of bee pollen in order to understand which flowers are important to bees.
Bees are in great decline in the United Kingdom and Europe, as are the wildflowers on which they depend.
Bees play an essential role in our ecosystems and one third of our food depends on their pollination. In economic terms alone, bee pollination is estimated at £265 billion worldwide each year.
The main risks to bees include the widespread use of pesticides in agriculture, pests, diseases and climate change, and especially the loss of valuable biodiversity that poses an additional threat to bees and other wild pollinators.
One way to increase their numbers is to plant the right wildflowers, providing better habitat for pollinators to disperse, nest and breed.
However, it is not clear which plant species are most valued by different pollinators, including bees, and how this could change over time and under different environmental conditions.
In agriculture, farmers want to know that pollinators visit the plants they need. Historically, scientists used optical microscopy to identify individual pollen grains collected by bees, which was a long and impractical method.
To get a more accurate understanding without the need for laborious manual pollen inspection, scientists have developed a rapid analytical method called "Reverse Metagenomics" (RevMet) that can identify the plants that individual bees visit using the MinION, a portable DNA sequencer from Oxford Nanopore Technologies.
The portability of the equipment involved means that this type of analysis could be done on site, where bees are collected and sampled, allowing us to better understand where bees are looking for pollen nationally.
Ned Peel, a PhD student who conducted the research within EI's Leggett group, said: "It is important to note that from a mixed pollen sample, in addition to being able to determine the plant species that bees have visited, we can also measure the relative amounts of each type of pollen. This type of analysis can be applied not only to the conservation of pollinators, but also to the sustainable improvement of crop production that depends on pollinators."
Expensive and inefficient manual methods for measuring pollen and other genomic methods, such as metabolic coding, have already been developed, but they do not accurately measure the amount of each type of pollen found in a sample.
Professor Douglas Yu, from the School of Biological Sciences at the UEA, initially developed the RevMet method. He said, "In standard metagenomics, short portions of DNA from mixed samples are compared to whole genomes, which can be costly to produce. We discovered that we could perform the analysis using "reference skims" instead.
"To make a reference skimming, we do a really cheap sequencing that should only partially cover the entire genome of the plant and does not need to be assembled.
"To support our tests, we quickly generated scum from 49 species of wild plants in the United Kingdom. The assembly of these genomes would have taken us months of work and would have required a lot of money. With our method, pollen is sequenced separately with MinION, which generates long DNA sequences. We then used the 49 reference skims to identify each of the long readings of local plant species."
This technique makes it possible to reliably differentiate the species in a mixed sample according to the amount of DNA present in each species. The results showed that honey bees and two bumblebee species have a high preference for one plant species per foraging trip.
The reverse metagenomics pipeline can apply to issues other than which plants bees like to pollinate; we can also understand whether some wildflowers compete with agricultural flowers for pollination or pollinator behaviour on large areas and on different types of land.
The method could also be used to study other mixed samples, such as herbivorous manure, for diet and air analysis, to identify airborne allergen pollen and crop pathogens.
"Semi-quantitative characterization of mixed pollen samples using MinION sequencing and Reverse Metagenomics (RevMet)" is published in Methods in Ecology and Evolution on August 7, 2019.
