Comparison of DNA metabarcoding and morphological identification for stream macroinvertebrate biodiversity assessment and monitoring
Comparison of DNA metabarcoding and morphological identification for stream macroinvertebrate biodiversity assessment and monitoring
复制标题
DOI：
10.1016/j.ecolind.2019.02.008
复制
发表时间：
2019-06-01
影响因子：
6.9
通讯作者：
Watanabe, Kozo
中科院分区：
文献类型：
--
作者：
Serrana, Joeselle M.;Miyake, Yo;Watanabe, Kozo
常规的基于形态学的识别通常用于淡水生态系统的常规评估。然而，成本和时间有效的技术，如基于高通量测序（HTS）的方法可以解决在进行基于形态学的调查中遇到的限制。在这里，我们的特点是流大型无脊椎动物的物种多样性和群落组成，通过元条形码和形态分析从重延河流域在日本爱媛县，收集的环境样品。我们比较了多样性指标，并评估了两种方法的能力，以评估大型无脊椎动物群落和环境变量之间的关系。我们总共从10个研究地点收集了8，276个个体，从形态学上鉴定了45个分类群（3科，6亚科，31属和5种）。我们检测到44种元巴编码，35种崩溃成11组匹配的形态学鉴定的类群。记录的深度（HTS读数的数量）和丰富的形态类群之间的显着正相关性进行了观察，这意味着定量数据可用于后续分析。我们恢复了相当高的相对丰度检测率的形态学鉴定的样品。通过发病率或存在/不存在计数回收的样品相当低，特别是对于在社区样品中具有稀缺代表性的物种，假阴性检测率很高。鉴于本研究中形态分配的分类分辨率较低，我们报告称，元条形码不能反映我们网站中自然发生的大多数物种，这可以通过对样品进行精细的形态评估来进一步证明。然而，基于丰度的检测被证明是有效的，92%的个体被正确证明。我们的结论是，DNA metabarcoding提供了一个实用的和具有成本效益的方法，特别是快速的淡水大型无脊椎动物群落的生物监测，但进一步改善稀缺的样品的检测应考虑增加检测的灵敏度，如果不是所有的，在环境中存在的物种。
Conventional morphology-based identification is commonly used for routine assessment of freshwater ecosystems. However, cost and time efficient techniques such as high-throughput sequencing (HTS) based approaches may resolve the constraints encountered in conducting morphology-based surveys. Here, we characterized stream macroinvertebrate species diversity and community composition via metabarcoding and morphological analysis from environmental samples collected from the Shigenobu River Basin in Ehime Prefecture, Japan. We compared diversity metrics and assessed both approaches' ability to evaluate the relationship between macroinvertebrate community and environmental variables. In total, we morphologically identified 45 taxa (3 families, six subfamilies, 31 genera, and five species) from 8,276 collected individuals from ten study sites. We detected 44 species by metabarcoding, with 35 species collapsed into 11 groups matching the morphologically identified taxa. A significant positive correlation between logged depth (number of HTS reads) and abundance of morphological taxa was observed, which implied that quantitative data could be used for subsequent analyses. We recovered a considerably high rate of relative abundance detection of the morphologically identified samples. Recovery of samples by incidence or presence/absence count were considerably low, with a high rate of false-negative detection specifically for species with scarce representation in the community sample. Given the low taxonomic resolution of the morphological assignment in this study, we report that metabarcoding does not reflect the majority of the species naturally occurring in our site, which could further be proven by performing refined morphological assessment of the samples. However, abundance-based detection proved to be efficient with 92% of the individuals correctly demonstrated. We conclude that DNA metabarcoding provides a practical and cost-effective approach especially for rapid biological monitoring of freshwater macroinvertebrate communities, but further improvements in the detection of scarce samples should be considered to increase the sensitivity of detecting most, if not all, of the species present in the environment.