Navigating Past Oceans: Comparing Metabarcoding and Metagenomics of Marine Ancient Sediment Environmental DNA.

IF 5.5 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY
Luke E Holman, Giulia Zampirolo, Richard Gyllencreutz, James Scourse, Tobias Frøslev, Christian Carøe, Shyam Gopalakrishnan, Mikkel Winther Pedersen, Kristine Bohmann
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引用次数: 0

Abstract

The condition of ancient marine ecosystems provides context for contemporary biodiversity changes in human-impacted oceans. Sequencing sedimentary ancient DNA (sedaDNA) is an emerging method for generating high-resolution biodiversity time-series data, offering insights into past ecosystems. However, few studies directly compare the two predominant sedaDNA sequencing approaches: metabarcoding and shotgun-metagenomics, and it remains unclear if these methodological differences affect diversity metrics. We compared these methods using sedaDNA from an archived marine sediment record sampled in the Skagerrak, North Sea, spanning almost 8000 years. We performed metabarcoding of a eukaryotic 18S rRNA region (V9) and sequenced 153-229 million metagenomic reads per sample. Our results show limited overlap between metabarcoding and metagenomics, with only three metazoan genera detected by both methods. For overlapping taxa, metabarcoding detections became inconsistent for samples older than 2000 years, while metagenomics detected taxa throughout the time series. We observed divergent patterns of alpha diversity, with metagenomics indicating decreased richness towards the present and metabarcoding showing an increase. However, beta diversity patterns were similar between methods, with discrepancies only in metazoan data comparisons. Our findings demonstrate that the choice of sequencing method significantly impacts detected biodiversity in an ancient marine sediment record. While we stress that studies with limited variation in DNA degradation among samples may not be strongly affected, researchers should exonerate methodological explanations for observed biodiversity changes in marine sediment cores, particularly when considering alpha diversity, before making ecological interpretations.

导航过去的海洋:比较海洋古代沉积物环境DNA的元条形码和宏基因组学。
古代海洋生态系统的状况为人类影响的海洋中当代生物多样性的变化提供了背景。沉积古DNA测序(sedaDNA)是一种生成高分辨率生物多样性时间序列数据的新兴方法,可以深入了解过去的生态系统。然而,很少有研究直接比较两种主要的sedaDNA测序方法:元条形码和散弹-宏基因组学,并且尚不清楚这些方法差异是否会影响多样性指标。我们使用来自北海Skagerrak近8000年的海洋沉积物记录的sedaDNA来比较这些方法。我们对真核生物18S rRNA区域(V9)进行了元条形码编码,并对每个样本进行了1.53 - 2.29亿元基因组测序。我们的研究结果显示元条形码和元基因组学之间的重叠有限,两种方法仅检测到三个后生动物属。对于重叠的分类群,元条形码检测在2000年以上的样本中变得不一致,而元基因组学在整个时间序列中检测分类群。我们观察到不同的α多样性模式,宏基因组学表明丰富度向现在减少,而元条形码显示增加。然而,不同方法之间的β多样性模式相似,只有在后生动物数据比较中存在差异。我们的研究结果表明,测序方法的选择显著影响了古代海洋沉积物记录中检测到的生物多样性。虽然我们强调,样品中DNA降解变化有限的研究可能不会受到强烈影响,但研究人员应该在做出生态学解释之前,对海洋沉积物岩心中观察到的生物多样性变化进行方法学解释,特别是在考虑α多样性时。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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来源期刊
Molecular Ecology Resources
Molecular Ecology Resources 生物-进化生物学
CiteScore
15.60
自引率
5.20%
发文量
170
审稿时长
3 months
期刊介绍: Molecular Ecology Resources promotes the creation of comprehensive resources for the scientific community, encompassing computer programs, statistical and molecular advancements, and a diverse array of molecular tools. Serving as a conduit for disseminating these resources, the journal targets a broad audience of researchers in the fields of evolution, ecology, and conservation. Articles in Molecular Ecology Resources are crafted to support investigations tackling significant questions within these disciplines. In addition to original resource articles, Molecular Ecology Resources features Reviews, Opinions, and Comments relevant to the field. The journal also periodically releases Special Issues focusing on resource development within specific areas.
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