Using environmental DNA (eDNA) to elucidate the role of habitat upon the transmission of pollinator disease

昆虫传粉者是全球生态系统的组成部分，对未来的粮食安全至关重要。英国和世界范围内的传粉者数量正在下降。减少的原因普遍是农业集约化、入侵物种的形成、疾病和气候变化。然而，昆虫数量减少的方向、强度和原因是高度可变的，需要证据来量化驱动这些过程的机制。一个关键话题是新出现的传染病（EID）的作用以及潜在的疾病从管理种群蔓延到野生种群。蜜蜂（Apis mellifera）是全世界主要的受管理授粉物种，并且还用于生产蜂蜜、蜂蜡和皇家浆。由于蜜蜂在很远的距离上觅食，它们在广阔的空间尺度上整合栖息地资源的信息，并与c。250种野生蜜蜂。在英国，养蜂作为一种爱好正在迅速发展，超过29，000名养蜂人管理着大约126，000个蜂群。因此，养蜂人代表了研究该物种的一个有价值的国家网络，这是UKCEH国家蜂蜜监测计划（NHMS）目前正在利用的一种资源。https://honey-monitoring.ac.uk/这项公民科学计划应用分子技术来确定蜂蜜的花组成，从而在景观尺度上测量传粉者资源。结合存档数据与野生传粉者的采样，这个学生将开发新的技术来调查蜜蜂与他们的景观，野生传粉者的竞争，并暴露于种间疾病传播的相互作用。环境DNA（eDNA）的研究利用分子技术来调查特定环境中包含的遗传物质。当研究特定的分类学相关基因时，就有可能辨别出组成样本的植物物种--这种技术被称为植物元条形码。除了分类信息外，eDNA还包含蜜蜂的遗传物质以及它们可能接触过的任何病原体。UKCEH的试点工作能够成功检测来自已知蜜蜂病原体的蜂蜜中的DNA：蜜蜂微孢子虫，Melissococcus plutonius和类芽孢杆菌幼虫。所开发的检测方法需要对蜂蜜分别进行每种病原体的筛选，因此成本高且耗时。然而，eDNA的测序具有同时筛选多种病原体的潜力，并且还允许发现另外的病原体，否则这些病原体将无法被检测到。通过结合尖端的现场和实验室技术，该项目将探索使用新兴的测序技术来调查关键问题：新兴和现有技术如何比较传粉者觅食活动的记录？常见的蜜蜂病原体可以在eDNA中检测到吗？蜜蜂是一个很好的哨兵物种，探索管理和野生传粉者的相互作用？传粉者之间是否有任何共同的植物特征，这些特征是否与潜在的疾病传播场所有关？这个奖学金将能够借鉴UKCEH，阅读和BBKA团队的经验，并获得经验丰富的公民科学家养蜂人的大型网络。这种独特的布局确保了学生能够利用额外的现有元数据和样本，否则学生不可能在单个博士学位期间生成。该博士通过实验室工作和与BBKA专家合作建立的深入实地实验相结合来研究其目标。总体目标是了解蜜蜂如何与其他传粉媒介及其环境相互作用，从而确定疾病传播的潜在途径，以及这如何影响传粉媒介减少的趋势。

Insect pollinators are an integral component of global ecosystems, and vital to future food security. UK and Worldwide pollinator populations are declining. Declines are widely attributed to agricultural intensification, the establishment of invasive species, disease and climate change. However, the direction, strength and causes of insect declines are highly variable, and evidence is needed to quantify the mechanisms driving these processes. One key topic is the role of emerging infectious diseases (EIDs) and potential disease spill over from managed to wild populations. The honey bee (Apis mellifera) is the dominant managed pollinator species worldwide, and is additionally used for the production of honey, bees wax and royal jelly. Since honeybees forage over large distances, they integrate information on habitat resources over vast spatial scales, and interact with c. 250 native wild bee species. Beekeeping as a hobby in the UK is rapidly growing with over 29,000 beekeepers managing around 126,000 colonies. Consequently, beekeepers represent a valuable national network for the study of this species, a resource currently being utilised by the UKCEH National Honey Monitoring Scheme (NHMS), https://honey-monitoring.ac.uk/. This citizen science scheme applies molecular techniques to determine the floral composition of honey, thereby measuring pollinator resources at landscape scales. Combing archived data with the sampling of wild pollinators this studentship will develop new techniques to investigate honeybee interactions with their landscape, wild pollinator competition, and exposure to inter-species disease transmission.The study of environmental DNA (eDNA) utilises molecular technologies to investigate the genetic material contained within a given environment. When specific taxonomically relevant genes are studied it's possible to discern the plant species from which a sample is composed - a technique known as plant metabarcoding. In addition to taxonomic information eDNA also contains genetic material from bees and any pathogens to which they may have been exposed. Pilot work at UKCEH was able to successfully detect DNA in honey derived from known bee pathogens: Nosema apis, Melissococcus plutonius and Paenibacillus larvae. The developed assays require that honey is screened for each pathogen separately, and therefore is costly and time consuming. However, the sequencing of eDNA holds the potential to simultaneously screen for multiple pathogens and further, allows for the discovery of additional pathogens which would otherwise be undetected. Through a combination of cutting-edge field and laboratory techniques this project will explore the use of emerging sequencing technologies to investigate key questions: How do emerging and existing technologies compare as a record of pollinator foraging activity? Can common bee pathogens be detected in eDNA? Are honeybees a good sentinel species to explore managed and wild pollinator interactions? Do any common plant signatures occur between pollinators, and are these linked to potential disease transmission sites? This studentship will be able to draw upon the experience of the UKCEH, Reading and BBKA teams and has access to a large network of highly experienced citizen scientist beekeepers. This unique placement ensures that the student is able draw on additional existing metadata and samples which would otherwise be impossible for a student to generate over the duration of a single PhD. This PhD investigates its aims through a combination of laboratory work and in-depth field experiments set up in partnership with experts from the BBKA. The overall aim is to understand how honeybees interact with other pollinators and their environment, thereby identifying potential routes of disease transmission, and how this influences trends in pollinator decline.