Abstract
Honey bees are large-scale monitoring tools due to their extensive environmental exploration. In their activities and from the hive ecosystem complex, they get in close contact with many organisms whose traces can be transferred into the honey, which can represent an interesting reservoir of environmental DNA (eDNA) signatures and information useful to analyse the honey bee hologenome complexity. In this study, we tested a deep shotgun sequencing approach of honey DNA coupled with a specifically adapted bioinformatic pipeline. This methodology was applied to a few honey samples pointing out DNA sequences from 191 organisms spanning different kingdoms or phyla (viruses, bacteria, plants, fungi, protozoans, arthropods, mammals). Bacteria included the largest number of species. These multi-kingdom signatures listed common hive and honey bee gut microorganisms, honey bee pathogens, parasites and pests, which resembled a complex interplay that might provide a general picture of the honey bee pathosphere. Based on the Apis mellifera filamentous virus genome diversity (the most abundant detected DNA source) we obtained information that could define the origin of the honey at the apiary level. Mining Apis mellifera sequences made it possible to identify the honey bee subspecies both at the mitochondrial and nuclear genome levels.
Highlights
Traditional biomonitoring approaches used to obtain information on living organisms for ecological and epidemiological studies are based on appropriately designed sampling strategies that rely on the direct identification and collection of biological specimens from the organisms under investigation in a defined area or context[1]
For contigs presenting more than one alignment over different entries, we considered the whole set of hits presenting statistics equal to the top one
Honey bees have proven to be useful bioindicators to detect, measure and track the source and origin of pollutants in agricultural and urban landscapes[8,77]. During their foraging and explorations activities, honey bees get exposed to chemicals and to the biological components of an environment, whose traces can be transferred into the hives and can be retrieved from the honey, the main hive product[7,9,78,79]
Summary
Traditional biomonitoring approaches used to obtain information on living organisms for ecological and epidemiological studies are based on appropriately designed sampling strategies that rely on the direct identification and collection of biological specimens from the organisms under investigation in a defined area or context[1]. Computational effort was proportional to the limited number of sequenced reads (hundreds of thousands), that were enough to detect interesting signatures from arthropods, plants, fungi, bacteria and viruses characterizing the analysed honey samples[10]. In this methodological study, we applied for the first time a high depth shotgun sequencing approach of honey DNA, combined with a designed bioinformatic pipeline, to describe in more detail the complex ecosystems of the honey bee colony superorganism using its agroecological recovered DNA. The obtained results provided new insights on the honey bee hologenome complexity that might be useful for many different applications
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