Jones Kara S, Pilliod David S, Aunins Aaron W
U.S. Geological Survey Eastern Ecological Science Center, Leetown Research Laboratory, Kearneysville, West Virginia, USA.
U.S. Geological Survey Forest and Rangeland Ecosystem Science Center, Pacific Northwest Environmental DNA Laboratory, Boise, Idaho, USA.
Mol Ecol. 2025 Jul;34(14):e70003. doi: 10.1111/mec.70003. Epub 2025 Jun 25.
Limitations of traditional insect sampling methods have motivated the development and optimisation of new non-lethal methods capable of quantifying diverse arthropod communities. Environmental DNA (eDNA) metabarcoding using arthropod-specific primers has recently been investigated as a novel way to characterise arthropod communities from the DNA they deposit on the surface of plants. This sampling method has had demonstrated success, but pollinators-especially bees-are oddly underrepresented in these studies. To evaluate this inconsistency, we investigated the limitations of eDNA metabarcoding for bees and other pollinators. We compared pollinator diversity derived from eDNA extracted from flowers and DNA extracted from pulverised bulk samples of insects collected from vane traps deployed at the same sites using three metabarcoding primers, two of which target arthropods generally (COI-Jusino and 16S-Marquina) and one that targets bumblebees (Bombus spp., COI-Milam). Across methods, we detected 77 insect families from 9 orders. The COI-Jusino marker amplified the highest taxonomic diversity compared to 16S-Marquina and COI-Milam. More amplicon sequence variants (ASVs) were recovered from vane traps (blue: 1357, yellow: 1542) than flowers (245), but only 23% of families and 13% of genera were shared among methods, indicating that flowers and blue and yellow vane traps may each sample different parts of the available arthropod community. Of 29 flower samples with known bee visitations, only 10 samples had bee detections from eDNA, and incomplete reference databases hindered assignment to species. Although our study provides additional evidence for the usefulness of eDNA metabarcoding for characterising arthropod communities, significant challenges remain when using eDNA metabarcoding methods to identify and quantify pollinator communities, especially bees.
传统昆虫采样方法的局限性推动了新的非致死性方法的开发和优化，这些方法能够对多样的节肢动物群落进行量化。最近，使用节肢动物特异性引物的环境DNA（eDNA）宏条形码技术已被研究作为一种从节肢动物沉积在植物表面的DNA中表征节肢动物群落的新方法。这种采样方法已取得成功，但传粉者——尤其是蜜蜂——在这些研究中却奇怪地未得到充分体现。为了评估这种不一致性，我们研究了eDNA宏条形码技术在蜜蜂和其他传粉者方面的局限性。我们比较了从花朵中提取的eDNA以及从在同一地点设置的风向标诱捕器收集的昆虫粉碎后的大量样本中提取的DNA所获得的传粉者多样性，使用了三种宏条形码引物，其中两种通常针对节肢动物（COI-Jusino和16S-Marquina），一种针对熊蜂（熊蜂属，COI-Milam）。在所有方法中，我们从9个目中检测到了77个昆虫科。与16S-Marquina和COI-Milam相比，COI-Jusino标记扩增出的分类多样性最高。从风向标诱捕器（蓝色：1357，黄色：1542）中回收的扩增子序列变体（ASV）比从花朵中回收的（245）更多，但各方法之间仅共享了23%的科和13%的属，这表明花朵以及蓝色和黄色风向标诱捕器可能各自采样了可用节肢动物群落的不同部分。在29个已知有蜜蜂访花的样本中，只有10个样本通过eDNA检测到了蜜蜂，并且不完整的参考数据库阻碍了物种鉴定。尽管我们的研究为eDNA宏条形码技术在表征节肢动物群落方面的有用性提供了更多证据，但在使用eDNA宏条形码技术识别和量化传粉者群落，尤其是蜜蜂时，仍然存在重大挑战。
