Environmental DNA enables detection of terrestrial mammals from forest pond water
Environmental DNA enables detection of terrestrial mammals from forest pond water
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DOI：
10.1111/1755-0998.12690
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发表时间：
2017-11-01
影响因子：
7.7
通讯作者：
Miya, Masaki
中科院分区：
文献类型：
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作者：
Ushio, Masayuki;Fukuda, Hisato;Miya, Masaki
陆地动物必须经常与水接触才能生存，这意味着来自这些动物的环境DNA（eDNA）应该可以从陆地生态系统中的含水场所检测到。为了利用森林水样检测陆生哺乳动物的存在，我们应用了一组通用PCR引物（MiMammal，鱼类通用引物的修改版本）用于元巴编码哺乳动物eDNA。通过计算机模拟和扩增从组织中提取的DNA来测试MiMammal引物的通用性。结果表明，MiMammal引物能够扩增和区分不同的哺乳动物物种。此外，从动物园笼子里的哺乳动物与已知的物种组成的水样分析表明，MiMammal引物可以成功地检测在该领域的水样中的哺乳动物物种。然后，我们进行了一项实验，以检测哺乳动物从自然生态系统中收集5个500毫升的水样，从池塘中的两个冷温带森林在北海道，北方日本。使用从水样中提取的eDNA构建MiMammal扩增子文库，并对Illumina MiSeq产生的序列进行数据处理和分类学分配。因此，我们检测到采样区常见的多种哺乳动物，包括鹿（Cervus nippon）、小鼠（Mus musculus）、田鼠（Myodes rufocanus）、浣熊（Procyon lotor）、大鼠（Rattus norvegicus）和鼩 鼱（Sorex unguiculatus）。许多以前的应用程序的eDNA元条码的方法已被限制到水生/半水生系统，但这里提出的结果表明，该方法也是有前途的，即使是森林哺乳动物生物多样性调查。
Terrestrial animals must have frequent contact with water to survive, implying that environmental DNA (eDNA) originating from those animals should be detectable from places containing water in terrestrial ecosystems. Aiming to detect the presence of terrestrial mammals using forest water samples, we applied a set of universal PCR primers (MiMammal, a modified version of fish universal primers) for metabarcoding mammalian eDNA. The versatility of MiMammal primers was tested in silico and by amplifying DNAs extracted from tissues. The results suggested that MiMammal primers are capable of amplifying and distinguishing a diverse group of mammalian species. In addition, analyses of water samples from zoo cages of mammals with known species composition suggested that MiMammal primers could successfully detect mammalian species from water samples in the field. Then, we performed an experiment to detect mammals from natural ecosystems by collecting five 500-ml water samples from ponds in two cool-temperate forests in Hokkaido, northern Japan. MiMammal amplicon libraries were constructed using eDNA extracted from water samples, and sequences generated by Illumina MiSeq were subjected to data processing and taxonomic assignment. We thereby detected multiple species of mammals common to the sampling areas, including deer (Cervus nippon), mouse (Mus musculus), vole (Myodes rufocanus), raccoon (Procyon lotor), rat (Rattus norvegicus) and shrew (Sorex unguiculatus). Many previous applications of the eDNA metabarcoding approach have been limited to aquatic/semiaquatic systems, but the results presented here show that the approach is also promising even for forest mammal biodiversity surveys.