Direction Etudes et Recherches, Office National de la Chasse et de la Faune Sauvage, Kourou, French Guiana, France.
PLoS One. 2013;8(4):e60799. doi: 10.1371/journal.pone.0060799. Epub 2013 Apr 1.
Characterizing the trophic relationships between large herbivores and the outstanding plant diversity in rainforest is a major challenge because of their elusiveness. This is crucial to understand the role of these herbivores in the functioning of the rainforest ecosystems. We tested a non-invasive approach based on the high-throughput sequencing of environmental samples using small plant plastid sequences (the trnL P6 loop) and ribosomal ITS1 primers, referred to as DNA metabarcoding, to investigate the diet of the largest neotropical herbivore, the lowland tapir. Sequencing was performed on plant DNA extracted from tapir faeces collected at the Nouragues station, a protected area of French Guiana. In spite of a limited sampling, our approach reliably provided information about the lowland tapir's diet at this site. Indeed, 95.1% and 74.4% of the plant families and genera identified thanks to the trnL P6 loop, respectively, matched with taxa already known to be consumed by tapirs. With this approach we were able to show that two families and eight new genera are also consumed by the lowland tapir. The taxonomic resolution of this method is limited to the plant family and genera. Complementary barcodes, such as a small portion of ITS1, can be used to efficiently narrow identifications down to the species in some problematic families. We will discuss the remaining limitations of this approach and how useful it is at this stage to unravel the diet of elusive rainforest herbivores and better understand their role as engineers of the ecosystem.
描述大型食草动物与热带雨林中突出植物多样性之间的营养关系是一项重大挑战，因为它们难以捉摸。这对于了解这些食草动物在热带雨林生态系统功能中的作用至关重要。我们测试了一种非侵入性方法，该方法基于使用小植物质体序列（trnL P6 环）和核糖体 ITS1 引物对环境样本进行高通量测序，称为 DNA 代谢组学，以调查最大的新热带食草动物——低地貘的饮食。在法属圭亚那的一个保护区 Nouragues 站收集的貘粪便中提取植物 DNA 后进行了测序。尽管采样有限，但我们的方法可靠地提供了有关该地点低地貘饮食的信息。实际上，通过 trnL P6 环分别鉴定出的 95.1％和 74.4％的植物科和属与已知被貘消耗的分类群相匹配。通过这种方法，我们能够证明两种科和八种新属也被低地貘消耗。该方法的分类分辨率仅限于植物科和属。补充条形码，例如一小部分 ITS1，可以有效地将鉴定缩小到某些有问题的科的物种。我们将讨论该方法的剩余局限性以及在现阶段解开难以捉摸的雨林食草动物的饮食并更好地了解它们作为生态系统工程师的作用方面的有用性。
