A PCR-based method for diet analysis in freshwater organisms using 18S rDNA barcoding on faeces
A PCR-based method for diet analysis in freshwater organisms using 18S rDNA barcoding on faeces
复制标题
DOI：
10.1111/j.1755-0998.2009.02795.x
复制
发表时间：
2010-01-01
影响因子：
7.7
通讯作者：
Gilles, Andre
中科院分区：
文献类型：
--
作者：
Corse, Emmanuel;Costedoat, Caroline;Gilles, Andre
粪便 DNA 条形码的开发代表了一种有前途的动物饮食分析方法。然而，目前的研究主要依赖于特定捕食者的猎物多样性的先验知识，而不是其潜在猎物物种的范围。考虑到硬骨鱼的摄食行为可能会随着环境的变化而演变，因此很难建立其猎物的详尽清单。在本文中，我们将 DNA 条形码方法扩展到饮食分析，以纳入广泛的分类范围的潜在猎物。设计了三十四个生态分支特异性引物组，以覆盖欧洲河流生态系统中发现的大部分猎物物种。选定的引物组在分离的动物、藻类或植物组织上进行测试，然后使用巢式 PCR 在鱼类粪便上进行测试，以提高 DNA 检测灵敏度。对 PCR 产物进行测序和分析，以确认分类单元的身份并验证该方法。这里开发的方法应用于对三种淡水鲤鱼物种的饮食分析，这些物种被认为具有相似的摄食行为[Chondrostoma toxostoma toxostoma (Vallot 1837)、Chondrostoma nasus nasus (Linnaeus, 1758) 和 Barbus barbus (Linneaus 1758)]。这三个物种是在四个不同的水文盆地中取样的。基于猎物比例的主成分分析确定了不同的石周食草和底栖行为。此外，我们的结果与有关这些鱼摄食行为的现有文献一致。基于 PCR 的方法的简单性及其对其他淡水生物的潜在推广可能会为食物网生态学开辟新的视角。
The development of DNA barcoding from faeces represents a promising method for animal diet analysis. However, current studies mainly rely on prior knowledge of prey diversity for a specific predator rather than on a range of its potential prey species. Considering that the feeding behaviour of teleosts may evolve with their environment, it could prove difficult to establish an exhaustive listing of their prey. In this article, we extend the DNA barcoding approach to diet analysis to allow the inclusion of a wide taxonomic range of potential prey items. Thirty-four ecological clade-specific primer sets were designed to cover a large proportion of prey species found in European river ecosystems. Selected primers sets were tested on isolated animal, algal or plant tissues and thereafter on fish faeces using nested PCR to increase DNA detection sensitivity. The PCR products were sequenced and analysed to confirm the identity of the taxa and to validate the method. The methodology developed here was applied to a diet analysis of three freshwater cyprinid species that are assumed to have similar feeding behaviour [Chondrostoma toxostoma toxostoma (Vallot 1837), Chondrostoma nasus nasus (Linnaeus, 1758) and Barbus barbus, (Linneaus 1758)]. These three species were sampled in four different hydrographic basins. Principal Component Analysis based on prey proportions identified distinct perilithon grazer and benthophagous behaviours. Furthermore, our results were consistent with the available literature on feeding behaviour in these fish. The simplicity of the PCR-based method and its potential generalization to other freshwater organisms may open new perspectives in food web ecology.