Capabilities and limitations of using DNA metabarcoding to study plant-pollinator interactions

Many pollinator populations are experiencing declines, emphasizing the need for a better understanding of the complex relationship between bees and flowering plants. Using DNA metabarcoding to describe plant-pollinator interactions eliminates many challenges associated with traditional methods and has the potential to reveal a more comprehensive understanding of foraging behavior and pollinator life history. Here we use DNA metabarcoding of ITS2 and rbcL gene regions to identify plant species present in pollen loads of 404 bees from three habitats in eastern Oregon. Our specific objectives were to 1) determine whether plant species identified using DNA metabarcoding are consistent with plant species identified using observations, 2) compare characterizations of diet breadth derived from foraging observations to those based on plant species assignments obtained using DNA metabarcoding, and 3) compare plant species assignments produced by DNA metabarcoding using a “regional” reference database to those produced using a “local” database. At the three locations, 31-86% of foraging observations were consistent with DNA metabarcoding data, 8-50% of diet breadth characterizations based on observations differed from those based on DNA metabarcoding data, and 22-25% of plant species detected using the regional database were not known to occur in the study area in question. Plant-pollinator networks produced from DNA metabarcoding data had higher sampling completeness and significantly lower specialization than networks based on observations. Here, we examine some strengths and limitations of using DNA metabarcoding to identify plant species present in bee pollen loads, make ecological inferences about foraging behavior, and provide guidance for future research.

诸多传粉者类群正面临种群衰退，凸显出深入解析蜜蜂与显花植物间复杂互作关系的迫切需求。利用DNA元条形码（DNA metabarcoding）开展植物-传粉者互作研究，可规避诸多传统方法面临的挑战，且有望更全面地揭示觅食行为与传粉者生活史特征。本研究针对俄勒冈州东部3类生境中的404份蜜蜂花粉团样本，通过靶向ITS2与rbcL基因区域的DNA元条形码技术，对样本携带花粉中的植物物种进行鉴定。本研究的具体目标包括：1）验证通过DNA元条形码技术鉴定的植物物种与野外观察所得结果是否一致；2）对比基于觅食观察推导得到的食性广度特征，与通过DNA元条形码物种鉴定结果得到的食性广度特征；3）对比分别使用"regional"参考数据库与"local"参考数据库，通过DNA元条形码技术得到的植物物种鉴定结果。在3个采样点中，31%~86%的觅食观察结果与DNA元条形码数据一致；基于野外观察得到的食性广度特征中，有8%~50%与DNA元条形码推导结果存在差异；通过区域级参考数据库检测到的植物物种中，有22%~25%未被记录分布于本研究区域内。相较于基于野外观察构建的植物-传粉者网络，由DNA元条形码数据生成的网络具有更高的采样完整性，且专业化程度显著更低。本研究探讨了利用DNA元条形码技术鉴定蜜蜂花粉团样本内植物物种、推导觅食行为相关生态学推论的优势与局限，并为后续研究提供参考方向。