Intra-host symbiont diversity in eastern Pacific cold seep tubeworms identified by the 16S-V6 region, but undetected by the 16S-V4 region
Intra-host symbiont diversity in eastern Pacific cold seep tubeworms identified by the 16S-V6 region, but undetected by the 16S-V4 region
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DOI：
10.1371/journal.pone.0227053
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发表时间：
2020-01-15
期刊：
影响因子：
3.7
通讯作者：
Young, Curtis Robert
中科院分区：
文献类型：
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作者：
Breusing, Corinna;Franke, Maximilian;Young, Curtis Robert
Vestimentiferan管虫是全世界深海化学合成生境的关键类群。作为成年人，它们通过从环境中获得的硫化物氧化细菌内共生体获得营养。虽然水平传播应该有利于各种共生微生物的感染，但目前的范式认为，每种管虫都只有一种内共生16 S rRNA基因型。虽然以前的研究传统的桑格测序的基础上质疑这些发现，人口水平的高通量分析的共生体16 S多样性仍然缺失。为了进一步深入了解共生体的遗传变异和发现迄今隐藏的多样性，我们采用了最先进的16 S-V4扩增子测序的共同发生的管虫物种Lamellibrachia barhami和Escarpia spicata，收集在E/V鹦鹉螺和R/V西方传单巡航冷渗漏在东太平洋的人口。与先前的工作一致，我们的序列数据表明，L。barhami和E.穗花针茅属共有一种单形共生类型。然而，针对16 S-V6区域的互补CARD-FISH分析暗示L. barhami。我们的研究结果表明，V4区可能没有足够的变量，调查多样性的宿主内共生体人口至少在分析的样本集。这是一个重要的发现，因为该区域已成为高通量微生物组分析的标准分子标记。进一步的宏基因组研究将是必要的，以解决这些问题，并揭示共生体的多样性，隐藏在16 S rRNA水平。
Vestimentiferan tubeworms are key taxa in deep-sea chemosynthetic habitats worldwide. As adults they obtain their nutrition through their sulfide-oxidizing bacterial endosymbionts, which are acquired from the environment. Although horizontal transmission should favor infections by various symbiotic microbes, the current paradigm holds that every tubeworm harbors only one endosymbiotic 16S rRNA phylotype. Although previous studies based on traditional Sanger sequencing have questioned these findings, population level high-throughput analyses of the symbiont 16S diversity are still missing. To get further insights into the symbiont genetic variation and uncover hitherto hidden diversity we applied state-of-the-art 16S-V4 amplicon sequencing to populations of the co-occurring tubeworm species Lamellibrachia barhami and Escarpia spicata that were collected during E/V Nautilus and R/V Western Flyer cruises to cold seeps in the eastern Pacific Ocean. In agreement with earlier work our sequence data indicated that L. barhami and E. spicata share one monomorphic symbiont phylotype. However, complementary CARD-FISH analyses targeting the 16S-V6 region implied the existence of an additional phylotype in L. barhami. Our results suggest that the V4 region might not be sufficiently variable to investigate diversity in the intra-host symbiont population at least in the analyzed sample set. This is an important finding given that this region has become the standard molecular marker for high-throughput microbiome analyses. Further metagenomic research will be necessary to solve these issues and to uncover symbiont diversity that is hidden below the 16S rRNA level.