Single cell genomics yields a wide diversity of small planktonic protists across major ocean ecosystems
Single cell genomics yields a wide diversity of small planktonic protists across major ocean ecosystems
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DOI：
10.1038/s41598-019-42487-1
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发表时间：
2019-04
影响因子：
4.6
通讯作者：
M. Sieracki;N. Poulton;O. Jaillon;P. Wincker;C. Vargas;Laura Rubinat-Ripoll;R. Stepanauskas;R. Logares;R. Massana
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文献类型：
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作者：
M. Sieracki;N. Poulton;O. Jaillon;P. Wincker;C. Vargas;Laura Rubinat-Ripoll;R. Stepanauskas;R. Logares;R. Massana
海洋浮游原生生物是海洋生态系统的重要组成部分，具有高度多样性。分子测序方法正被用来描述这种多样性，并揭示新的协会和代谢是重要的，这些生态系统的功能。我们在这里描述了使用单细胞基因组学的方法来采样和询问的多样性较小的（皮科和纳米大小）原生生物从一系列的海洋样品。我们从印度洋和地中海的8个TaraOcean样本中创建了900多个单扩增基因组（SAG）。我们表明，流式细胞仪分选的单细胞有效地区分质体和无质体细胞类型，同意我们的理解原生动物的胚胎发育。产量的基因组DNA与PCR可识别的18S rRNA基因序列的单细胞是低的（15%的无质体细胞的种类，和7%的质体的种类）和测试与备用引物和比较metabarcoding没有显示系统发育的偏见，在主要的原生生物群体。几乎没有证据表明存在明显的偏见，反对或支持任何预期或已知的系统发育组。印度洋上的四个开阔洋观测站尽管分布在北纬14°至南纬20°之间，但群落相似，与地中海观测站不同。原生生物的单细胞基因组学研究表明，仅在几百微升的表层海水中发现的优势类群的分类多样性与在分子调查中发现的相似，在分子调查中发现的是升的样品被过滤。
Marine planktonic protists are critical components of ocean ecosystems and are highly diverse. Molecular sequencing methods are being used to describe this diversity and reveal new associations and metabolisms that are important to how these ecosystems function. We describe here the use of the single cell genomics approach to sample and interrogate the diversity of the smaller (pico- and nano-sized) protists from a range of oceanic samples. We created over 900 single amplified genomes (SAGs) from 8TaraOcean samples across the Indian Ocean and the Mediterranean Sea. We show that flow cytometric sorting of single cells effectively distinguishes plastidic and aplastidic cell types that agree with our understanding of protist phylogeny. Yields of genomic DNA with PCR-identifiable 18S rRNA gene sequence from single cells was low (15% of aplastidic cell sorts, and 7% of plastidic sorts) and tests with alternate primers and comparisons to metabarcoding did not reveal phylogenetic bias in the major protist groups. There was little evidence of significant bias against or in favor of any phylogenetic group expected or known to be present. The four open ocean stations in the Indian Ocean had similar communities, despite ranging from 14°N to 20°S latitude, and they differed from the Mediterranean station. Single cell genomics of protists suggests that the taxonomic diversity of the dominant taxa found in only several hundreds of microliters of surface seawater is similar to that found in molecular surveys where liters of sample are filtered.