Short-read assembly of full-length 16S amplicons reveals bacterial diversity in subsurface sediments.
Short-read assembly of full-length 16S amplicons reveals bacterial diversity in subsurface sediments.
复制标题
DOI：
10.1371/journal.pone.0056018
复制
发表时间：
2013
期刊：
影响因子：
3.7
通讯作者：
Banfield JF
中科院分区：
文献类型：
--
作者：
Miller CS;Handley KM;Wrighton KC;Frischkorn KR;Thomas BC;Banfield JF
在微生物生态学中，一个基本的问题涉及群落多样性和组成如何随着扰动的变化而变化。大多数研究对群落结构的深入采样能力有限(例如，Sanger测序的16S rRNA文库)，或者分类分辨率有限(例如，基于16S rRNA高变区测序的研究)。在这里，我们将近全长16S rRNA基因扩增的较高分类分辨率与短读测序的经济性和敏感性相结合，以分析仅占沉积物细菌群落0.01%的生物体的丰度和特性。我们使用了一种针对大数据量进行优化的新版本的EMIRGE，从剪除的扩增片段中重建了接近全长的16S rRNA基因，并用Illumina技术进行了测序。该方法使我们能够区分在扰动之前、在醋酸盐修正将主要代谢转移到铁还原之后、以及一旦硫酸盐还原开始时获得的样本中的群落组成。结果在技术重复上具有高度的重复性，并确定了对扰动做出反应的特定分类群。所有样本都含有非常高的阿尔法多样性和丰富的生物门，没有培养的代表性。令人惊讶的是，在测量的时间点，尽管醋酸酯修饰的选择性压力和末端电子接受过程的变化，但没有强烈的均匀性损失。然而，社区成员身份发生了重大变化。该方法可以灵敏、准确地描绘存在于许多微生物群落中的低丰度生物体的“长尾”，并可以解决因环境变化而产生的种群动态。
In microbial ecology, a fundamental question relates to how community diversity and composition change in response to perturbation. Most studies have had limited ability to deeply sample community structure (e.g. Sanger-sequenced 16S rRNA libraries), or have had limited taxonomic resolution (e.g. studies based on 16S rRNA hypervariable region sequencing). Here, we combine the higher taxonomic resolution of near-full-length 16S rRNA gene amplicons with the economics and sensitivity of short-read sequencing to assay the abundance and identity of organisms that represent as little as 0.01% of sediment bacterial communities. We used a new version of EMIRGE optimized for large data size to reconstruct near-full-length 16S rRNA genes from amplicons sheared and sequenced with Illumina technology. The approach allowed us to differentiate the community composition among samples acquired before perturbation, after acetate amendment shifted the predominant metabolism to iron reduction, and once sulfate reduction began. Results were highly reproducible across technical replicates, and identified specific taxa that responded to the perturbation. All samples contain very high alpha diversity and abundant organisms from phyla without cultivated representatives. Surprisingly, at the time points measured, there was no strong loss of evenness, despite the selective pressure of acetate amendment and change in the terminal electron accepting process. However, community membership was altered significantly. The method allows for sensitive, accurate profiling of the “long tail” of low abundance organisms that exist in many microbial communities, and can resolve population dynamics in response to environmental change.
登录
查看更多内容
DOI：
10.1038/ismej.2012.8
发表时间：
2012-08
期刊：
The ISME journal
影响因子：
--
作者：
通讯作者：
--
DOI：
10.1073/pnas.1002601107
发表时间：
2010-06-29
影响因子：
11.1
作者：
Dominguez-Bello, Maria G.;Costello, Elizabeth K.;Knight, Rob
通讯作者：
Knight, Rob
影响因子：
4.4
作者：
Bartram, Andrea K.;Lynch, Michael D. J.;Neufeld, Josh D.
通讯作者：
Neufeld, Josh D.
影响因子：
11
作者：
Degnan, Patrick H.;Ochman, Howard
通讯作者：
Ochman, Howard
影响因子：
4.4
作者：
Goltsman, Daniela S. Aliaga;Denef, Vincent J.;Banfield, Jillian F.
通讯作者：
Banfield, Jillian F.