Honeybees are prolific pollinators that play an extremely important role in maintaining the health of ecosystems. However, many threats such as climate change, pesticides and pathogens have increased the need for conservation efforts and programs to monitor the health and activity of these valuable species. Researchers from the Biomedical Sciences Research Center Alexander Fleming have now developed an optimized method to understand the ecological niche of honeybees by noninvasively studying the environmental DNA (eDNA) left behind in honey.
Honey can be a valuable source of information about the activity and health of bee populations, as it contains traces of the plants they forage, pathogens and gut microbiota. The researchers worked to improve strategies for evaluating this eDNA, by determining optimal DNA extraction methods for honey and leveraging direct shotgun metagenomics (direct-SM) to sequence eDNA fragments. The team tailored a simple Na-OH-based extraction method to the honey matrix and direct-SM method, and further designed a specialized bioinformatic pipeline for honey metagenomic data allowing them to increase the sensitivity and specificity of their analysis, said first author Anastasios Galanis.
The researchers used their optimized method to analyze several honey samples from an apiary located in a typical Mediterranean landscape, and were able to identify more than 40 species of plants reflecting the botanical diversity surrounding the hives. The team was able to observe how the abundance of plant DNA varied over the seasons, which reflected the bees’ foraging adaptations following plant flowering, said corresponding author Solenn Patalano. The information about foraging behavior obtained from the honey was also compared to that gained from melissopalynology, which involves evaluating the shape of the pollen grains found in the honey. The results from both methods were found to be consistent and showed how the methods can be used together to monitor foraging activity.
The researchers further identified an even greater number of bacterial species representing the bee gut microbiome, which plays an important role in an organism’s health. The identification of this bacterial eDNA showed that the method could be used to monitor gut microbiota without sacrificing bees, and could be used to detect the impact of environmental stressors, like pesticides, that can alter the gut microbiome. Additionally, the team identified eDNA from Varroa mites, which correlated with a mite infestation observed at the hives. The method could thus potentially be used to monitor similar parasites and other pathogens and anticipate outbreaks of disease among bee populations. This study was published in Molecular Ecology Resources.
“In the future, this work might also have very important implications for humans. If we want to ensure ecosystem services, such as fruit and vegetable pollination, while maintaining species biodiversity, we also need to safeguard bee health,” said Patalano. “Our challenge is to build biomonitoring strategies in order to identify the fittest ecological niches for all pollinators.”