ARC Centre for Mine Site Restoration, School of Molecular and Life Sciences, Curtin University, Perth, WA, Australia.
Trace and Environmental DNA Laboratory, School of Life and Molecular Sciences, Curtin University, Perth, WA, Australia.
Mol Ecol Resour. 2020 May;20(3). doi: 10.1111/1755-0998.13148. Epub 2020 Mar 6.
Biological surveys based on visual identification of the biota are challenging, expensive and time consuming, yet crucial for effective biomonitoring. DNA metabarcoding is a rapidly developing technology that can also facilitate biological surveys. This method involves the use of next generation sequencing technology to determine the community composition of a sample. However, it is uncertain as to what biological substrate should be the primary focus of metabarcoding surveys. This study aims to test multiple sample substrates (soil, scat, plant material and bulk arthropods) to determine what organisms can be detected from each and where they overlap. Samples (n = 200) were collected in the Pilbara (hot desert climate) and Swan Coastal Plain (hot Mediterranean climate) regions of Western Australia. Soil samples yielded little plant or animal DNA, especially in the Pilbara, probably due to conditions not conducive to long-term preservation. In contrast, scat samples contained the highest overall diversity with 131 plant, vertebrate and invertebrate families detected. Invertebrate and plant sequences were detected in the plant (86 families), pitfall (127 families) and vane trap (126 families) samples. In total, 278 families were recovered from the survey, 217 in the Swan Coastal Plain and 156 in the Pilbara. Aside from soil, 22%-43% of the families detected were unique to the particular substrate, and community composition varied significantly between substrates. These results demonstrate the importance of selecting appropriate metabarcoding substrates when undertaking terrestrial surveys. If the aim is to broadly capture all biota then multiple substrates will be required.
基于生物区系的视觉识别的生物调查具有挑战性、昂贵且耗时，但对于有效的生物监测至关重要。 DNA 代谢组学是一种快速发展的技术，也可以促进生物调查。该方法涉及使用下一代测序技术来确定样品的群落组成。然而，对于代谢组学调查应该主要关注哪种生物基质，还存在不确定性。本研究旨在测试多种样品基质（土壤、粪便、植物材料和大型节肢动物），以确定从每种基质中可以检测到哪些生物，以及它们的重叠程度。在西澳大利亚的皮尔巴拉（炎热的沙漠气候）和斯旺沿海平原（炎热的地中海气候）地区采集了 200 个样本。土壤样本几乎没有植物或动物 DNA，尤其是在皮尔巴拉地区，可能是由于不适合长期保存的条件。相比之下，粪便样本的总体多样性最高，共检测到 131 种植物、脊椎动物和无脊椎动物科。在植物（86 科）、陷坑（127 科）和风标陷阱（126 科）样本中检测到无脊椎动物和植物序列。总共从调查中回收了 278 个科，斯旺沿海平原有 217 个，皮尔巴拉有 156 个。除了土壤之外，22%-43%的科是特定基质特有的，而且基质之间的群落组成差异显著。这些结果表明，在进行陆地调查时，选择合适的代谢组学基质非常重要。如果目的是广泛捕获所有生物，则需要多种基质。
