Ultra-deep sequencing of foraminiferal microbarcodes unveils hidden richness of early monothalamous lineages in deep-sea sediments
Ultra-deep sequencing of foraminiferal microbarcodes unveils hidden richness of early monothalamous lineages in deep-sea sediments
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DOI：
10.1073/pnas.1018426108
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发表时间：
2011-08-09
影响因子：
11.1
通讯作者：
Pawlowski, Jan
中科院分区：
文献类型：
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作者：
Lecroq, Beatrice;Lejzerowicz, Franck;Pawlowski, Jan
深海海底是地球上最大和最复杂的生态系统之一，但基本上尚未开发。这一生态系统的广阔和偏远使深海取样变得困难，妨碍了传统的分类观察和多样性评估。这一问题在深海小型底栖生物方面尤其严重，因为它们主要是小型、脆弱和难以识别的后生动物和原生生物。在这里，我们介绍了一个超深测序为基础的宏成方法来检查底栖有孔虫，深海小型底栖生物的主要组成部分的丰富性。我们使用Illumina测序技术评估了来自五个不同海洋区域的31个未筛分深海沉积物样品中的有孔虫丰度。我们测序了小亚基核糖体DNA高变区37 f的一个极短片段（36个碱基），该片段已被证明可以准确区分有孔虫物种。我们总共获得了495，978个独特的序列，这些序列被分为1，643个操作分类单位，其中大约一半（841个）可以可靠地分配给有孔虫。绝大多数的操作分类单位（近90%）被分配到早期（古老）谱系的软壁，单室（monothalamous）有孔虫或仍然未定，但可能属于未知的早期谱系。对比与多室类群占主导地位的有孔虫组合的经典观点，我们的工作反映了一个意想不到的多样性monothalamous血统，是迄今为止未知的使用传统的微体古生物学观测。虽然我们只能推测它们的形态，但这项研究揭示的深海底栖生物类型的巨大丰富性表明，超深测序可以提高对深海底栖生物多样性的理解，根据传统的分类方法，深海底栖生物多样性迄今仍被认为是不可知的。
Deep-sea floors represent one of the largest and most complex ecosystems on Earth but remain essentially unexplored. The vastness and remoteness of this ecosystem make deep-sea sampling difficult, hampering traditional taxonomic observations and diversity assessment. This problem is particularly true in the case of the deep-sea meiofauna, which largely comprises small-sized, fragile, and difficult-to-identify metazoans and protists. Here, we introduce an ultra-deep sequencing-based metagenetic approach to examine the richness of benthic foraminifera, a principal component of deep-sea meiofauna. We used Illumina sequencing technology to assess foraminiferal richness in 31 unsieved deep-sea sediment samples from five distinct oceanic regions. We sequenced an extremely short fragment (36 bases) of the small subunit ribosomal DNA hypervariable region 37f, which has been shown to accurately distinguish foraminiferal species. In total, we obtained 495,978 unique sequences that were grouped into 1,643 operational taxonomic units, of which about half (841) could be reliably assigned to foraminifera. The vast majority of the operational taxonomic units (nearly 90%) were either assigned to early (ancient) lineages of soft-walled, single-chambered (monothalamous) foraminifera or remained undetermined and yet possibly belong to unknown early lineages. Contrasting with the classical view of multichambered taxa dominating foraminiferal assemblages, our work reflects an unexpected diversity of monothalamous lineages that are as yet unknown using conventional micropaleontological observations. Although we can only speculate about their morphology, the immense richness of deep-sea phylotypes revealed by this study suggests that ultra-deep sequencing can improve understanding of deep-sea benthic diversity considered until now as unknowable based on a traditional taxonomic approach.