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利用沉积物DNA和RNA的宏条形码技术对深海群落进行时空监测。

Spatio-temporal monitoring of deep-sea communities using metabarcoding of sediment DNA and RNA.

作者信息

Guardiola Magdalena, Wangensteen Owen S, Taberlet Pierre, Coissac Eric, Uriz María Jesús, Turon Xavier

机构信息

Department of Marine Ecology, Centre for Advanced Studies of Blanes (CEAB-CSIC) , Blanes , Spain.

Department of Animal Biology and Biodiversity Research Institute (IRBIO), University of Barcelona, Barcelona, Spain; Ecosystems & Environment Research Centre, School of Environment & Life Sciences, University of Salford, Salford, United Kingdom.

出版信息

PeerJ. 2016 Dec 21;4:e2807. doi: 10.7717/peerj.2807. eCollection 2016.

DOI:10.7717/peerj.2807
PMID:28028473
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC5180584/
Abstract

We assessed spatio-temporal patterns of diversity in deep-sea sediment communities using metabarcoding. We chose a recently developed eukaryotic marker based on the v7 region of the 18S rRNA gene. Our study was performed in a submarine canyon and its adjacent slope in the Northwestern Mediterranean Sea, sampled along a depth gradient at two different seasons. We found a total of 5,569 molecular operational taxonomic units (MOTUs), dominated by Metazoa, Alveolata and Rhizaria. Among metazoans, Nematoda, Arthropoda and Annelida were the most diverse. We found a marked heterogeneity at all scales, with important differences between layers of sediment and significant changes in community composition with zone (canyon vs slope), depth, and season. We compared the information obtained from metabarcoding DNA and RNA and found more total MOTUs and more MOTUs per sample with DNA (ca. 20% and 40% increase, respectively). Both datasets showed overall similar spatial trends, but most groups had higher MOTU richness with the DNA template, while others, such as nematodes, were more diverse in the RNA dataset. We provide metabarcoding protocols and guidelines for biomonitoring of these key communities in order to generate information applicable to management efforts.

摘要

我们使用宏条形码技术评估了深海沉积物群落多样性的时空模式。我们基于18S rRNA基因的v7区域选择了一种最近开发的真核生物标记。我们的研究在地中海西北部的一个海底峡谷及其相邻斜坡进行，在两个不同季节沿深度梯度进行采样。我们共发现了5569个分子操作分类单元（MOTUs），以后生动物、囊泡虫和根足虫为主。在后生动物中，线虫、节肢动物和环节动物最为多样。我们发现在所有尺度上都存在明显的异质性，沉积物层之间存在重要差异，群落组成随区域（峡谷与斜坡）、深度和季节发生显著变化。我们比较了从宏条形码DNA和RNA获得的信息，发现DNA的总MOTUs和每个样本的MOTUs更多（分别增加约20%和40%）。两个数据集总体上显示出相似的空间趋势，但大多数类群在DNA模板上具有更高的MOTU丰富度，而其他类群，如线虫，在RNA数据集中更加多样。我们提供了用于这些关键群落生物监测的宏条形码方案和指南，以便生成适用于管理工作的信息。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6dd3/5180584/d63c915141f9/peerj-04-2807-g009.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6dd3/5180584/c6d2733c9503/peerj-04-2807-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6dd3/5180584/6216e33a909c/peerj-04-2807-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6dd3/5180584/a880d8869fe2/peerj-04-2807-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6dd3/5180584/5b35e21ca167/peerj-04-2807-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6dd3/5180584/71adc5d0ce10/peerj-04-2807-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6dd3/5180584/3cac839dcdbb/peerj-04-2807-g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6dd3/5180584/46a38ce8ff2b/peerj-04-2807-g007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6dd3/5180584/8418a72ba279/peerj-04-2807-g008.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6dd3/5180584/d63c915141f9/peerj-04-2807-g009.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6dd3/5180584/c6d2733c9503/peerj-04-2807-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6dd3/5180584/6216e33a909c/peerj-04-2807-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6dd3/5180584/a880d8869fe2/peerj-04-2807-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6dd3/5180584/5b35e21ca167/peerj-04-2807-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6dd3/5180584/71adc5d0ce10/peerj-04-2807-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6dd3/5180584/3cac839dcdbb/peerj-04-2807-g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6dd3/5180584/46a38ce8ff2b/peerj-04-2807-g007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6dd3/5180584/8418a72ba279/peerj-04-2807-g008.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6dd3/5180584/d63c915141f9/peerj-04-2807-g009.jpg

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