The taxonomic and functional diversity of microbes at a temperate coastal site: a 'multi-omic' study of seasonal and diel temporal variation.
The taxonomic and functional diversity of microbes at a temperate coastal site: a 'multi-omic' study of seasonal and diel temporal variation.
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DOI：
10.1371/journal.pone.0015545
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发表时间：
2010-11-29
期刊：
影响因子：
3.7
通讯作者：
Mühling M
中科院分区：
文献类型：
--
作者：
Gilbert JA;Field D;Swift P;Thomas S;Cummings D;Temperton B;Weynberg K;Huse S;Hughes M;Joint I;Somerfield PJ;Mühling M
人们对微生物群落如何随时间变化以适应环境的情况知之甚少。此前，来自西英吉利海峡的 16S rRNA V6 数据的六年时间序列证明了细菌群落内强大的季节性结构，其多样性与日长呈负相关。在这里，我们确定宏基因组和宏转录组是否遵循相似的模式。我们为 2008 年采样的另外 8 个时间点生成了 16S rRNA 数据集、宏基因组 (1.2 GB) 和元转录组 (157 MB)，代表三个季节（冬季、春季、夏季），包括白天和夜间样本。这是第一个将 16S rRNA 扩增子测序与宏基因组和宏转录组分析相结合的微生物“多组学”研究。对这些数据的分析可以得出五个主要结论：1）古细菌遵循与细菌相同的季节模式，但相对多样性较低； 2）较高的16S rRNA多样性也反映了较高的转录本多样性； 3）冬季和夜间多样性最高； 4) 基于 16S 的多样性和宏基因组谱的群落水平变化可以通过季节性模式更好地解释（时间上最接近的样本最相似），而元转录组谱可以通过昼夜模式和基因特定类别（即功能组）的变化更好地解释； 5）关键基因在季节和昼夜之间发生变化（即光合作用）；但这些样本包含大量没有已知同源物的孤儿基因，正是这些未知的基因组似乎对定义不同时间之间观察到的差异做出了最大贡献。尽管这些微生物群落具有巨大的多样性，但随着时间的推移，有明显的可预测模式和可检测稳定性的迹象。需要重新加强努力来揭示最复杂的微生物群落的基本确定性模式。此外，相当大比例的孤儿序列的存在强调需要确定目前未知功能的序列的基因产物。
How microbial communities change over time in response to the environment is poorly understood. Previously a six-year time series of 16S rRNA V6 data from the Western English Channel demonstrated robust seasonal structure within the bacterial community, with diversity negatively correlated with day-length. Here we determine whether metagenomes and metatranscriptomes follow similar patterns. We generated 16S rRNA datasets, metagenomes (1.2 GB) and metatranscriptomes (157 MB) for eight additional time points sampled in 2008, representing three seasons (Winter, Spring, Summer) and including day and night samples. This is the first microbial ‘multi-omic’ study to combine 16S rRNA amplicon sequencing with metagenomic and metatranscriptomic profiling. Five main conclusions can be drawn from analysis of these data: 1) Archaea follow the same seasonal patterns as Bacteria, but show lower relative diversity; 2) Higher 16S rRNA diversity also reflects a higher diversity of transcripts; 3) Diversity is highest in winter and at night; 4) Community-level changes in 16S-based diversity and metagenomic profiles are better explained by seasonal patterns (with samples closest in time being most similar), while metatranscriptomic profiles are better explained by diel patterns and shifts in particular categories (i.e., functional groups) of genes; 5) Changes in key genes occur among seasons and between day and night (i.e., photosynthesis); but these samples contain large numbers of orphan genes without known homologues and it is these unknown gene sets that appear to contribute most towards defining the differences observed between times. Despite the huge diversity of these microbial communities, there are clear signs of predictable patterns and detectable stability over time. Renewed and intensified efforts are required to reveal fundamental deterministic patterns in the most complex microbial communities. Further, the presence of a substantial proportion of orphan sequences underscores the need to determine the gene products of sequences with currently unknown function.
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