High-throughput environmental DNA analysis informs a biological assessment of an urban stream
High-throughput environmental DNA analysis informs a biological assessment of an urban stream
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DOI：
10.1016/j.ecolind.2019.04.088
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发表时间：
2019-09-01
影响因子：
6.9
通讯作者：
Banerji, Aabir
中科院分区：
文献类型：
--
作者：
Bagley, Mark;Pilgrim, Erik;Banerji, Aabir
人们对使用DNA条形码和元条形码方法来协助水体的生物评估和监测越来越感兴趣。虽然生物多样性的形态和DNA测量往往已被发现相关，很少有研究比较DNA数据的损害，如许多生物评估计划使用的多度量污染耐受指数建立措施。我们将环境DNA（eDNA）元编码悬浮物到一个严格的流域尺度的生物评估的城市流，研究在何种程度上eDNA的丰富性和多样性模式与多指标和生态损害状态指定。我们还评估了不同的过滤方法和分类学分类，以确定环境评估的最佳实践。Seston eDNA揭示了真核生物类群的广泛多样性，但以硅藻为主（36%）。在阿尔法和β多样性的网站之间的分化是更大的操作分类单位（OTUs）进行分类，但粗分辨率分类（界）比细分辨率分类（科，属）的信息。鱼类和大型无脊椎动物的DNA丰富度和多样性与多指标指数的相关性普遍较弱，可能是因为后生动物在我们的DNA数据集中没有很高的代表性。尽管如此，网站可以区分的基础上，生态损害的状态，更受损的网站具有较低的eDNA多样性的香农指数，但较高的分类丰富度。从约束排序分析中推断，群落结构的重要环境驱动因素在eDNA数据集内的王国之间以及鱼类和大型底栖动物之间存在差异，这表明eDNA提供了新的环境信息。这些结果表明，即使是一个简单的悬浮物eDNA过滤协议可以提供生物多样性信息的价值流生物评估计划。该方法作为一种可能有用的快速评估议定书，以补充更密集的实地采样工作，值得进一步研究。
There is growing interest in the use of DNA barcoding and metabarcoding approaches to aid biological assessments and monitoring of waterbodies. While biodiversity measured by morphology and by DNA often has been found correlated, few studies have compared DNA data to established measures of impairment such as multimetric pollution tolerance indices used by many bioassessment programs. We incorporated environmental DNA (eDNA) metabarcoding of seston into a rigorous watershed-scale biological assessment of an urban stream to examine the extent to which eDNA richness and diversity patterns were correlated with multimetric indices and ecological impairment status designations. We also evaluated different filtering approaches and taxonomic classifications to identify best practices for environmental assessments. Seston eDNA revealed a wide diversity of eukaryotic taxa but was dominated by diatoms (36%). Differentiation among sites in alpha and beta diversity was greater when operational taxonomic units (OTUs) were classified taxonomically, but coarse resolution taxonomy (kingdom) was more informative than finer resolution taxonomy (family, genus). Correlations of DNA richness and diversity with multimetric indices for fish and macroinvertebrates were generally weak, possibly because Metazoa were not highly represented in our DNA dataset. Nonetheless, sites could be differentiated based on ecological impairment status, with more impaired sites having lower eDNA diversity as measured by the Shannon index, but higher taxonomic richness. Significant environmental drivers of community structure, as inferred from constrained ordination analyses, differed among kingdoms within the eDNA dataset, as well as from fish and macrobenthos, suggesting that eDNA provides novel environmental information. These results suggest that even a simple seston eDNA filtering protocol can provide biodiversity information of value to stream bioassessment programs. The approach bears further investigation as a potentially useful rapid assessment protocol to supplement more intensive field sampling efforts.