Scratching the surface of the rare biosphere with ribosomal sequence tag primers
Scratching the surface of the rare biosphere with ribosomal sequence tag primers
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DOI：
10.1111/j.1574-6968.2008.01124.x
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发表时间：
2008-06-01
影响因子：
2.1
通讯作者：
Mohn, William W.
中科院分区：
文献类型：
--
作者：
Neufeld, Josh D.;Li, Jason;Mohn, William W.
越来越大的 16S rRNA 基因序列数据集揭示了有关微生物多样性程度和稀有生物圈令人惊讶的范围的新信息。目前，许多最大的数据集都由短且可变的核糖体序列标签（RST）表示，这些标签准确地将序列分配给大规模系统发育树的能力受到限制。在本研究中，我们从现有序列数据集中选择了 30 个罕见的 RST，并设计了引物来扩增 c。 16S rRNA 基因的 1400 个碱基，以确定这些序列是否由现有数据库代表，或者它们是否可能揭示细菌内的新谱系。大约三分之一的 RST 引物以特定方式成功扩增了这些低丰度 16S rRNA 基因的较长部分。随后的系统发育分析表明，大多数这些序列（1）与现有的培养微生物关系较远，（2）与最近存放在 GenBank 中的未培养克隆序列密切相关。现有数据库中存在如此多的最近收集的 16S rRNA 基因参考序列，表明微生物普查正在迅速取得进展，这一普查已经开始触及“稀有生物圈”的表面。
Increasingly large datasets of 16S rRNA gene sequences reveal new information about the extent of microbial diversity and the surprising extent of the rare biosphere. Currently, many of the largest datasets are represented by short and variable ribosomal sequence tags (RSTs) that are limited in their ability to accurately assign sequences to broad-scale phylogenetic trees. In this study, we selected 30 rare RSTs from existing sequence datasets and designed primers to amplify c. 1400 bases of the 16S rRNA gene to determine whether these sequences were represented by existing databases or if they might reveal new lineages within the Bacteria. Approximately one-third of the RST primers successfully amplified longer portions of these low-abundance 16S rRNA genes in a specific manner. Subsequent phylogenetic analysis demonstrated that most of these sequences were (1) distantly related to existing cultivated microorganisms and (2) closely related to uncultivated clone sequences that were recently deposited in GenBank. The presence of so many recently collected 16S rRNA gene reference sequences in existing databases suggests that progress is being made quickly towards a microbial census, one which has begun scratching the surface of the 'rare biosphere'.