Bee populations and other pollinators face multiple, synergistically acting threats, which have led to population declines, loss of local species richness and pollination services, and extinctions. However, our understanding of the degree, distribution and causes of declines is patchy, in part due to inadequate monitoring systems, with the challenge of taxonomic identification posing a major logistical barrier. Pollinator conservation would benefit from a high-throughput identification pipeline.
The UK's National Pollinator Strategy plans a large-scale bee monitoring programme. Traditional monitoring involves pinning individual bees and identifying them under a microscope. But the number of bees needed to track populations reliably over the whole country makes traditional methods unfeasible. New research shows how the process could become quicker, cheaper and more accurate. This would allow conservationists to detect where and when bee species are being lost, and importantly, whether conservation interventions are working.
The group of researchers from the UK and China used metagenomic mining and resequencing of mitochondrial genomes of bulk samples of wild bees. They assembled the mitogenomes of 48 UK bee species and then shotgun-sequenced total DNA extracted from 204 bees that had been collected in 10 pan-trap samples from farms in England and been morphologically identified to 33 species. Each sample data set was mapped against the 48 reference mitogenomes. The process did not require taxonomic experts (with the exception of the morphology-based identification for the proof of concept and still proved to be more accurate. Also, by skipping the PCR step through direct sequencing, the method was able to estimate the biomass contributed by each species, which opens the way to tracking population trajectories.
The big challenge is that there are hundreds of wild bee species per country, almost 300 in the UK alone. Even with the necessary expertise, it would be impossibly time-consuming to count and identify all the bees in each location. Large-scale bee monitoring programmes would really benefit from this type of DNA sequencing. The method can easily be scaled up to track more species, like the 1000 or so total pollinating insects in the UK. We can find out where species diversity or abundance is highest -- for example in the countryside or in city parks- and how species diversity is affected by farming methods -- for example, to see if habitat set-asides support more bees.