Honey as a Source of Environmental DNA for the Detection and Monitoring of Honey Bee Pathogens and Parasites

Abstract

Environmental DNA (eDNA) has been proposed as a powerful tool to detect and monitor cryptic, elusive, or invasive organisms. We recently demonstrated that honey constitutes an easily accessible source of eDNA. In this study, we extracted DNA from 102 honey samples (74 from Italy and 28 from 17 other countries of all continents) and tested the presence of DNA of nine honey bee pathogens and parasites (Paenibacillus larvae, Melissococcus plutonius, Nosema apis, Nosema ceranae, Ascosphaera apis,Lotmaria passim, Acarapis woodi, Varroa destructor, and Tropilaelaps spp.) using qualitative PCR assays. All honey samples contained DNA from V. destructor, confirming the widespread diffusion of this mite. None of the samples gave positive amplifications for N. apis, A. woodi, and Tropilaelaps spp. M. plutonius was detected in 87% of the samples, whereas the other pathogens were detected in 43% to 57% of all samples. The frequency of Italian samples positive for P. larvae was significantly lower (49%) than in all other countries (79%). The co-occurrence of positive samples for L. passim and A. apis with N. ceranae was significant. This study demonstrated that honey eDNA can be useful to establish monitoring tools to evaluate the sanitary status of honey bee populations.

Honey Bee Health

“…Ribani et al used environmental DNA (eDNA) to monitor honey bee pathogens and parasites, demonstrating that V. destructor is widespread and L. passim and A. apis with N. ceranae occurr frequently together [ 4 ].…”

Distribution of the Main Apis mellifera Mitochondrial DNA Lineages in Italy Assessed Using an Environmental DNA Approach

“…Honey DNA is usually highly degraded and only short DNA fragments can be easily amplified by PCR from this template [ 51 , 52 , 53 , 54 , 55 ]; that means that the informativity of the obtained mtDNA amplicons is limited by the sequence information contained in a short fragment, which, in our case, was constituted by a part of the COI-COII intergenic spacer, including the 3′-end of the tRNALeu gene and the non-coding P and Q regions [ 26 , 51 , 56 ]. As a consequence, it was not possible to obtain a more detailed classification within the main branches of the A, C and M lineages.…”

“…We recently developed a simple end-point PCR method to discriminate the main three mtDNA lineages (A, C and M) of A. mellifera , using honey as a source of environmental DNA (eDNA), which also contains traces of the DNA of the honey bees that have produced it [ 51 ]. This is a cost-effective method that simplifies the collection of useful specimens, such as the honey, which, however, can be analyzed by investigating small DNA fragments, due to the highly degraded DNA that it contains [ 52 , 53 , 54 ]. The method gives the possibility to analyze more than one colony at the same time, considering that the honey that is prepared by the beekeepers is usually a mixture obtained from several colonies, or is even derived by different apiaries of the same beekeeper [ 51 , 53 , 54 ].…”

“…This is a cost-effective method that simplifies the collection of useful specimens, such as the honey, which, however, can be analyzed by investigating small DNA fragments, due to the highly degraded DNA that it contains [ 52 , 53 , 54 ]. The method gives the possibility to analyze more than one colony at the same time, considering that the honey that is prepared by the beekeepers is usually a mixture obtained from several colonies, or is even derived by different apiaries of the same beekeeper [ 51 , 53 , 54 ]. Therefore, honey can be used to obtain a quite extensive population-wide picture of the presence of genetic features in a vast geographic area.…”

Application of Next Generation Semiconductor-Based Sequencing for the Identification of Apis mellifera Complementary Sex Determiner (csd) Alleles from Honey DNA

“…Honey is a unique source of environmental DNA (eDNA) as it contains traces of all the organisms that directly or indirectly contributed to produce it or were part of the hive environment where it was produced [30][31][32][33][34][35][36][37][38]. Therefore, honey also contains the DNA of the honey bees that produced it [33].…”