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

昆虫传粉媒介是全球生态系统的重要组成部分，对未来的粮食安全至关重要。英国和全世界的传粉昆虫数量正在下降。农业集约化、入侵物种的出现、疾病和气候变化普遍导致了这种下降。然而，昆虫减少的方向、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。一个关键议题是新发传染病（eid）的作用以及从管理种群向野生种群的潜在疾病溢出。蜜蜂（Apis mellifera）是世界范围内主要的管理传粉者物种，并且还用于生产蜂蜜，蜂蜡和蜂王浆。由于蜜蜂在远距离上觅食，它们整合了大空间尺度上的栖息地资源信息，并与大约250种本地野生蜜蜂相互作用。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，这是目前由UKCEH国家蜂蜜监测计划（NHMS）利用的资源，https://honey-monitoring.ac.uk/。这个公民科学计划应用分子技术来确定蜂蜜的花卉组成，从而在景观尺度上测量传粉者资源。结合存档数据和野生传粉者的采样，这个学生将开发新的技术来研究蜜蜂与它们的景观的相互作用，野生传粉者的竞争，以及暴露于物种间疾病传播。环境DNA （eDNA）的研究利用分子技术来调查包含在给定环境中的遗传物质。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——一种被称为植物元条形码的技术。除了分类信息外，eDNA还包含蜜蜂和它们可能接触过的任何病原体的遗传物质。UKCEH的试点工作能够成功地检测出蜂蜜中的DNA，这些蜂蜜来自已知的蜜蜂病原体：apis小孢子虫、plutonius Melissococcus和Paenibacillus幼虫。开发的检测方法需要对蜂蜜中的每种病原体分别进行筛选，因此既昂贵又耗时。然而，eDNA的测序具有同时筛选多种病原体的潜力，并且进一步允许发现其他未被检测到的病原体。通过结合前沿的现场和实验室技术，该项目将探索新兴测序技术的使用，以调查关键问题：作为传粉媒介觅食活动的记录，新兴技术和现有技术的比较如何？常见的蜜蜂病原体能在eDNA中检测到吗？蜜蜂是一个很好的哨兵物种来探索管理和野生传粉者的相互作用吗？传粉媒介之间是否存在任何共同的植物特征？这些特征是否与潜在的疾病传播点有关？该学生将能够利用UKCEH， Reading和BBKA团队的经验，并可以访问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学生能够利用额外的现有元数据和样本，否则学生在单个博士学位期间无法生成这些数据和样本。该博士通过与BBKA专家合作建立的实验室工作和深入的现场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.