Nationwide Screening for Arthropod, Fungal, and Bacterial Pests and Pathogens of Honey Bees: Utilizing Environmental DNA from Honey Samples in Australia

The European honey bee (<i>Apis mellifera</i>) significantly contributes to Australian agriculture, especially in honey production and the pollination of key crops. However, managed bee populations are declining due to pathogens, agrochemicals, poor forage, climate change, and habitat loss. Major threats include bacteria, fungi, mites, and pests. With the increasing demand for pollination and the movement of bee colonies, monitoring these threats is essential. It has been demonstrated that honey constitutes an easily accessible source of environmental DNA. Environmental DNA in honey comes from all organisms that either directly or indirectly aid in its production and those within the hive environments. In this study, we extracted eDNA from 135 honey samples and tested for the presence of DNA for seven key honey bee pathogens and pests-<i>Paenibacillus larvae</i>, <i>Melissococcus plutonius</i> (bacterial pathogens), <i>Nosema apis</i>, <i>Nosema ceranae</i> (microsporidian fungi), <i>Ascosphaera apis</i> (fungal pathogen), <i>Aethina tumida</i>, and <i>Galleria mellonella</i> (arthropod pests) by using end-point singleplex and multiplex PCR assays. <i>N. ceranae</i> emerged as the most prevalent pathogen, present in 57% of the samples. This was followed by the pests <i>A. tumida</i> (40%) and <i>G. mellonella</i> (37%), and the pathogens <i>P. larvae</i> (21%), <i>N. apis</i> (19%), and <i>M. plutonius</i> (18%). <i>A. apis</i> was detected in a smaller proportion of the samples, with a prevalence of 5%. Additionally, 19% of the samples tested negative for all pathogens and pests analysed. The data outlines essential information about the prevalence of significant arthropod, fungal, and bacterial pathogens and pests affecting honey bees in Australia, which is crucial for protecting the nation's beekeeping industry.