Evaluating the congruence between DNA-based and morphological taxonomic approaches in water and sediment trap samples: Analyses of a 36-month time series from a temperate monomictic lake
Evaluating the congruence between DNA-based and morphological taxonomic approaches in water and sediment trap samples: Analyses of a 36-month time series from a temperate monomictic lake
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DOI：
10.1002/lno.11856
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发表时间：
2021-06-02
影响因子：
4.5
通讯作者：
Gregory-Eaves, Irene
中科院分区：
文献类型：
--
作者：
Gauthier, Joanna;Walsh, David;Gregory-Eaves, Irene
古湖沼学研究是确定长期变化的核心，但许多研究依赖于生物指标，存款可检测的亚化石沉积物，如硅藻和枝角类。新兴的基于DNA的方法正在扩大可以调查的分类多样性。然而，由于沉积DNA为基础的方法正在迅速扩大，校准工作需要确定这些技术的优点和局限性。在这项研究中，我们评估了形态和DNA为基础的方法应用于沉积物陷阱样品的硅藻和甲壳类动物使用细胞内和细胞外的DNA之间的一致性。我们还评估了哪些类群沉积在沉积物陷阱从水柱，以确定潜在的环境变化的古湖沼生物指标。基于18S rRNA基因扩增子，我们开发和分析了一个微型真核生物，每月的时间序列，跨越3年，是由成对的水柱和沉积物陷阱样本Cultus湖，不列颠哥伦比亚省，加拿大。来自我们的遗传和形态分析RV系数组合的比较显示硅藻的显着相关性，但甲壳类动物的相关性较弱。细胞内DNA读数与硅藻形态相关性更强，而细胞外DNA读数与甲壳类形态相关性更强。水和沉积物陷阱样品之间共享的扩增子序列变体的额外分析揭示了在古湖泊学研究的分类群的广泛多样性，包括纤毛门，甲藻门，壶菌门，蓝藻门和隐藻门。部分RDA确定了这些共享的组合的重要环境预测。总的来说，我们的研究表明了基于DNA的方法来跟踪沉积物样品的群落动态的有效性，这是成功进行古湖泊学研究的重要一步。
Paleolimnological studies are central for identifying long-term changes, yet many studies rely on bioindicators that deposit detectable subfossils in sediments, such as diatoms and cladocerans. Emerging DNA-based approaches are expanding the taxonomic diversity that can be investigated. However, as sedimentary DNA-based approaches are expanding rapidly, calibration work is required to determine the advantages and limitations of these techniques. In this study, we assessed the congruence between morphological and DNA-based approaches applied to sediment trap samples for diatoms and crustaceans using both intracellular and extracellular DNA. We also evaluated which taxa are deposited in sediment traps from the water column to identify potential paleolimnological bioindicators of environmental variations. Based on 18S rRNA gene amplicons, we developed and analyzed a micro-eukaryotic, monthly time series that spanned 3 years and was comprised of paired water column and sediment trap samples from Cultus Lake, British Columbia, Canada. Comparisons of assemblages derived from our genetic and morphological analyses using RV coefficients revealed significant correlations for diatoms, but weaker correlations for crustaceans. Intracellular DNA reads correlated more strongly with diatom morphology, while extracellular DNA reads correlated more strongly with crustacean morphology. Additional analyses of amplicon sequence variants shared between water and sediment trap samples revealed a wide diversity of taxa to study in paleolimnology, including Ciliophora, Dinoflagellata, Chytridiomycota, Chrysophyceae, and Cryptophyceae. Partial RDAs identified significant environmental predictors of these shared assemblages. Overall, our study demonstrates the effectiveness of DNA-based approaches to track community dynamics from sediment samples, an essential step for successful paleolimnological studies.