Ultradeep 16S rRNA sequencing analysis of geographically similar but diverse unexplored marine samples reveal varied bacterial community composition.
Ultradeep 16S rRNA sequencing analysis of geographically similar but diverse unexplored marine samples reveal varied bacterial community composition.
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DOI：
10.1371/journal.pone.0076724
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发表时间：
2013
期刊：
影响因子：
3.7
通讯作者：
Karutha Pandian S
中科院分区：
文献类型：
--
作者：
Aravindraja C;Viszwapriya D;Karutha Pandian S
海洋环境中的细菌群落组成因地理位置而异。描述地理位置相似的不同海洋样品的细菌多样性的报告有限。本研究旨在了解不同海洋样品的细菌群落组成是否具有相似的细菌多样性，因为它们在地理上彼此相关。本研究采用Illumina条形码测序技术对靶向V3区的16S rRNA进行深度测序分析。从海洋沉积物、根际沉积物、海水的宏基因组DNA以及海藻和海草的表细菌DNA中共获得2244万个对端读。多样性指数分析表明，海洋沉积物细菌多样性最高，根际沉积物细菌多样性最低。所有海洋样品中均以变形菌门、放线菌门和拟杆菌门为优势分类群。在所有样品中鉴定出的珍稀物种接近62-71%，而且这些珍稀物种大多是特定样品所特有的。进一步在门和属水平上的分类鉴定表明，不同样品的细菌群落组成存在差异。这是第一个支持这一事实的报告，即细菌群落组成对特定样品是特定的，而不考虑其相似的地理位置。每个样品中特定细菌群落的存在可能导致每个样品中细菌结构组成的整体差异。进一步的研究，如全宏基因组测序，将为关键的石头参与者及其相互关联的代谢途径提供更多的见解。此外，这是使用下一代测序技术描述印度Palk湾未表征的沿海地区较高深度海洋样本（海洋沉积物、根际沉积物、海水）和宿主相关海洋样本（海藻和海草）中未探索的细菌多样性的极少数报告之一。
Bacterial community composition in the marine environment differs from one geographical location to another. Reports that delineate the bacterial diversity of different marine samples from geographically similar location are limited. The present study aims to understand whether the bacterial community compositions from different marine samples harbour similar bacterial diversity since these are geographically related to each other. In the present study, 16S rRNA deep sequencing analysis targeting V3 region was performed using Illumina bar coded sequencing. A total of 22.44 million paired end reads were obtained from the metagenomic DNA of Marine sediment, Rhizosphere sediment, Seawater and the epibacterial DNA of Seaweed and Seagrass. Diversity index analysis revealed that Marine sediment has the highest bacterial diversity and the least bacterial diversity was observed in Rhizosphere sediment. Proteobacteria, Actinobacteria and Bacteroidetes were the dominant taxa present in all the marine samples. Nearly 62–71% of rare species were identified in all the samples and most of these rare species were unique to a particular sample. Further taxonomic assignment at the phylum and genus level revealed that the bacterial community compositions differ among the samples. This is the first report that supports the fact that, bacterial community composition is specific for specific samples irrespective of its similar geographical location. Existence of specific bacterial community for each sample may drive overall difference in bacterial structural composition of each sample. Further studies like whole metagenomic sequencing will throw more insights to the key stone players and its interconnecting metabolic pathways. In addition, this is one of the very few reports that depicts the unexplored bacterial diversity of marine samples (Marine sediment, Rhizosphere sediment, Seawater) and the host associated marine samples (Seaweed and Seagrass) at higher depths from uncharacterised coastal region of Palk Bay, India using next generation sequencing technology.
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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：
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影响因子：
4.2
作者：
Nithyanand, Paramasivam;Pandian, Shunmugiah Karutha
通讯作者：
Pandian, Shunmugiah Karutha
影响因子：
3.4
作者：
Austen, MC;Lambshead, PJD;Smith, C
通讯作者：
Smith, C
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