Honey DNA analysis enhances human understanding of bees and environment

Scientists from Biomedical Sciences Research Center Alexander Fleming in Greece have come up with a method to detect and identify DNA traces in honey – revealing the species that honey bees interact with.

Led by researcher Dr Solenn Patalano, the team “monitor[ed] the variability of bee diets across the year, reveal[ed] bee microbiota in a non-invasive way, and identif[ied] pathogenic species they are confronted by,” a news release notes.

The study was published in the journal Molecular Ecology Resources. The news release suggests that it may “revolutionise the way we understand honey bee ecological niches.”

Why is it important to understand honey bee ecological niches?

An organism’s ecological niche is defined by an intricate balance of interactions and adjustments to other species coexisting within the same habitat. Honey bees pollinate trees and flowers, and are an integral part of the ecological balance of agriculture and human society. They make use of a vast array of flowering plant species for their own food resources and growth.

Yet honey bee colonies are weakened when environmental conditions support the proliferation of pathogenic species, for example Varroa mites that attack and feed on the honey bees Apis cerana and Apis mellifera. The study uses Apis mellifera hives.

The habitats that honey bees live in can vary and may undergo changes during the seasons. The “species dynamics of the honey bee ecological niche are  inextricably linked” with these habitats and their seasonal changes.

Bee ecological niches are becoming more vulnerable day by day because of “the increasing restructuring of agricultural areas and the effects of climate change.” If we were to better comprehend the dynamics of interactions between bees and the cohabiting species, this knowledge would assist us in identifying risk periods and zones for the insects.

“This is extremely important in rural and agricultural environments, where species interactions influence the productivity of crops. It's compelling how much of our food and survival depends on the proper functioning of tiny insects!” commented Anastasios Galanis, the first author of the study.

Environmental plant diversity reflected in the product: honey

Honey bees make honey by collecting nectar and pollen from flowering plants, then regurgitating it into cells of their hive, waiting for water to evaporate.

The authors write: “Owing to their foraging and honey production activities, honeybees form complex relationships with species across all domains, such as plants, viruses, bacteria (symbiotic and pathogenic), and other hive pests, making honey a valuable biomonitoring tool for assessing their ecological niche.”

As a result of these complex relationships, honey comes into contact with a plethora of organisms and therefore contains DNA from various species, called eDNA (environmental DNA), including plants, the gut bacteria of bees and potential hive pathogens as identified by their DNA.

The researchers used a method called ‘direct-shotgun metagenomics’, which relies on the sequencing and comprehensive identification of the environmental DNA fragments found in the hives used in the research. Galanis explains it as such: "The design and testing of a bioinformatic pipeline tuned for honey metagenomic data allows us to increase sensitivity and specificity; thus, we can be quite confident about the identification of certain species".

The researchers analysed samples of honey from an apiary installed on the property surrounding the BSRC ‘Alexander Fleming’ in Vari (Attica region, Greece). They were able to pinpoint more than 40 species of plants from the area surrounding the hives in the honey.

"What was very striking”, said Dr. Patalano, “is to see how variable the abundance of plant eDNA is over the seasons, reflecting perfectly the behavioural foraging adaptations that follow plant flowering."

Researchers also compared the different samples of honey by the use of melissopalynology (using the shape of pollen grains for characterisation). The two analyses fit in together to provide a more comprehensive understanding of bees, and the study brought into light that the metagenomic approach also reveals non-pollen seeking behaviour, “such as the foraging of pine honeydew, an important food resource for the survival of bees in early autumn.”

The ecological niche of bees goes beyond plants. When the researchers went through the honey samples, they found “an even greater number of bacterial eDNA species, the vast majority of which emanates from microorganisms considered to be harmless and which comprise the core species of the bee microbiome.”

“Like the human gut microbiome, the gut microbiome of the bee is an important element of their health,” Dr. Patalano explains. “We already know that environmental stressors, such as pesticides, can seriously damage gut microbial communities and increase the risk of bee diseases. But how this works remains largely unknown.”

The researchers were able to study the gut microbiome variation of bees by the honey metagenomics method which allowed for the insects to remain alive.

The researchers also sought alleged pathogens presented as eDNA. They were able to extract Varroa mite eDNA in honey that showed signs of hive contamination. The method could one day be used to “monitor and anticipate disease and pathogens” in large scale studies.

"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. Our challenge is to build biomonitoring strategies in order to identify the fittest ecological niches for all pollinators", concludes Dr. Patalano.