Advancing the use of molecular methods for routine freshwater macroinvertebrate biomonitoring - the need for calibration experiments
Advancing the use of molecular methods for routine freshwater macroinvertebrate biomonitoring - the need for calibration experiments
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DOI：
10.3897/mbmg.3.34735
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发表时间：
2019-01-01
影响因子：
--
通讯作者：
Deiner, Kristy
中科院分区：
文献类型：
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作者：
Blackman, Rosetta C.;Maechler, Elvira;Deiner, Kristy
在过去十年中，在使用基于DNA的方法检测各种生态系统中的物种方面取得了稳步进展。这一进展最终导致分子监测方法被用于检测几个物种，用于全球濒危，入侵和非法捕捞物种的可执行管理目的。然而，为评估生态系统状况而例行应用基于DNA的方法来监测整个群落（通常是元条码方法）的做法仍然有限。在水生生态系统中，对大型无脊椎动物群落的限制使用尤其如此。作为DNAqua-Net联盟的一部分，发起了一次结构化讨论，目的是确定淡水大型无脊椎动物群落评估的潜在分子方法，并确定其日常应用的重要知识差距。我们专注于三个互补的DNA来源，可以metabarcoded：1）DNA均质样品（散装DNA），2）DNA提取的样品防腐剂（固定DNA），和3）环境DNA（eDNA）从水或沉积物。我们提供了一个简要的概述metabarcoding大型无脊椎动物社区从每个DNA来源，并确定其应用程序的挑战，以常规监测。为了推进利用基于DNA的大型无脊椎动物的监测，我们提出了一系列的方法校准测试的实验设计模板。模板比较DNA来源，目的是确定分子加工步骤对精密度和准确度的影响。此外，将对相同的样品进行形态分析，这将使分子加工方法与传统加工方法的基准化成为可能。在这样做的时候，我们希望突出的途径，为发展基于DNA的方法，用于监测淡水大型无脊椎动物。
Over the last decade, steady advancements have been made in the use of DNA-based methods for detection of species in a wide range of ecosystems. This progress has culminated in molecular monitoring methods being employed for the detection of several species for enforceable management purposes of endangered, invasive, and illegally harvested species worldwide. However, the routine application of DNA-based methods to monitor whole communities (typically a metabarcoding approach) in order to assess the status of ecosystems continues to be limited. In aquatic ecosystems, the limited use is particularly true for macroinvertebrate communities. As part of the DNAqua-Net consortium, a structured discussion was initiated with the aim to identify potential molecular methods for freshwater macroinvertebrate community assessment and identify important knowledge gaps for their routine application. We focus on three complementary DNA sources that can be metabarcoded: 1) DNA from homogenised samples (bulk DNA), 2) DNA extracted from sample preservative (fixative DNA), and 3) environmental DNA (eDNA) from water or sediment. We provide a brief overview of metabarcoding macroinvertebrate communities from each DNA source and identify challenges for their application to routine monitoring. To advance the utilisation of DNA-based monitoring for macroinvertebrates, we propose an experimental design template for a series of methodological calibration tests. The template compares sources of DNA with the goal of identifying the effects of molecular processing steps on precision and accuracy. Furthermore, the same samples will be morphologically analysed, which will enable the benchmarking of molecular to traditional processing approaches. In doing so we hope to highlight pathways for the development of DNA-based methods for the monitoring of freshwater macroinvertebrates.