Unveiling the diet of elusive rainforest herbivores in next generation sequencing era? The tapir as a case study.
Unveiling the diet of elusive rainforest herbivores in next generation sequencing era? The tapir as a case study.
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DOI：
10.1371/journal.pone.0060799
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发表时间：
2013
期刊：
影响因子：
3.7
通讯作者：
Richard-Hansen C
中科院分区：
文献类型：
--
作者：
Hibert F;Taberlet P;Chave J;Scotti-Saintagne C;Sabatier D;Richard-Hansen C
大型食草动物和热带雨林中杰出的植物多样性之间的营养关系的特点是一个重大的挑战，因为他们的难以捉摸。这对于了解这些食草动物在雨林生态系统中的作用至关重要。我们测试了一种非侵入性的方法的基础上的高通量测序的环境样品，使用小植物质体序列（的trnL P6环）和核糖体ITS1引物，被称为DNA metabarcoding，调查的饮食最大的新热带区食草动物，低地貘。对从法属圭亚那保护区Nouragues站收集的貘粪便中提取的植物DNA进行测序。尽管取样有限，我们的方法可靠地提供了有关该地点低地貘饮食的信息。事实上，95.1%和74.4%的植物科和属鉴定感谢trnL P6环，分别与已知被貘消耗的分类群相匹配。通过这种方法，我们能够证明两个科和八个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。互补条形码，如ITS1的一小部分，可用于有效地将鉴定范围缩小到一些有问题的科中的物种。我们将讨论这种方法的剩余局限性，以及在这个阶段如何解开难以捉摸的热带雨林食草动物的饮食，更好地了解它们作为生态系统工程师的作用。
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.
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影响因子：
3.7
作者：
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