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Capture by hybridization for full-length barcode-based eukaryotic and prokaryotic biodiversity inventories of deep sea ecosystems
Molecular Ecology Resources ( IF 7.7 ) Pub Date : 2021-09-06 , DOI: 10.1111/1755-0998.13500
Babett Günther 1 , Sophie Marre 2 , Clémence Defois 2 , Thomas Merzi 3 , Philippe Blanc 3 , Pierre Peyret 2 , Sophie Arnaud-Haond 1
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Biodiversity inventory of marine systems remains limited due to unbalanced access to the three ocean dimensions. The use of environmental DNA (eDNA) for metabarcoding allows fast and effective biodiversity inventory and is forecast as a future biodiversity research and biomonitoring tool. However, in poorly understood ecosystems, eDNA results remain difficult to interpret due to large gaps in reference databases and PCR bias limiting the detection of some major phyla. Here, we aimed to circumvent these limitations by avoiding PCR and recollecting larger DNA fragments to improve assignment of detected taxa through phylogenetic reconstruction. We applied capture by hybridization (CBH) to enrich DNA from deep-sea sediment samples and compared the results with those obtained through an up-to-date metabarcoding PCR-based approach (MTB). Originally developed for bacterial communities and targeting 16S rDNA, the CBH approach was applied to 18S rDNA to improve the detection of species forming benthic communities of eukaryotes, with a particular focus on metazoans. The results confirmed the possibility of extending CBH to metazoans with two major advantages: (i) CBH revealed a broader spectrum of prokaryotic, eukaryotic, and particularly metazoan diversity, and (ii) CBH allowed much more robust phylogenetic reconstructions of full-length barcodes with up to 1900 base pairs. This is particularly important for taxa whose assignment is hampered by gaps in reference databases. This study provides a database and probes to apply 18S CBH to diverse marine systems, confirming this promising new tool to improve biodiversity assessments in data-poor ecosystems such as those in the deep sea.

中文翻译:

通过杂交捕获基于全长条形码的深海生态系统真核和原核生物多样性清单

由于对三个海洋维度的访问不平衡,海洋系统的生物多样性清单仍然有限。使用环境 DNA (eDNA) 进行元条形码编码可以快速有效地进行生物多样性清单,并被预测为未来的生物多样性研究和生物监测工具。然而,在知之甚少的生态系统中,由于参考数据库中的巨大差距和 PCR 偏差限制了某些主要门的检测,eDNA 结果仍然难以解释。在这里,我们旨在通过避免 PCR 和重新收集更大的 DNA 片段来规避这些限制,以通过系统发育重建改进检测到的分类群的分配。我们应用杂交捕获 (CBH) 从深海沉积物样品中富集 DNA,并将结果与​​通过最新的基于元条形码 PCR 的方法 (MTB) 获得的结果进行比较。最初为细菌群落开发并针对 16S rDNA,CBH 方法应用于 18S rDNA,以改进对形成真核生物底栖群落的物种的检测,特别关注后生动物。结果证实了将 CBH 扩展到后生动物的可能性有两个主要优点:(i) CBH 揭示了更广泛的原核生物、真核生物,特别是后生动物多样性,以及 (ii) CBH 允许对全长条形码进行更稳健的系统发育重建多达 1900 个碱基对。这对于因参考数据库中的空白而受阻的分类群尤其重要。这项研究提供了一个数据库和探针,以将 18S CBH 应用于不同的海洋系统,证实了这一有前途的新工具可以改善数据匮乏的生态系统(如深海生态系统)的生物多样性评估。
更新日期:2021-09-06
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