Conditionally rare taxa disproportionately contribute to temporal changes in microbial diversity.
Conditionally rare taxa disproportionately contribute to temporal changes in microbial diversity.
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DOI：
10.1128/mbio.01371-14
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发表时间：
2014-07-15
期刊：
影响因子：
6.4
通讯作者：
Gilbert JA
中科院分区：
文献类型：
--
作者：
Shade A;Jones SE;Caporaso JG;Handelsman J;Knight R;Fierer N;Gilbert JA
微生物群落通常包含许多稀有类群，占观察到的成员的大多数，但这种微生物的“稀有生物圈”的贡献社区动态尚不清楚。使用16 S rRNA扩增子对来自9个不同生态系统的42个时间序列微生物群落的3，237个样品进行测序（空气;海洋;湖泊;溪流;成人皮肤、舌头和肠道;婴儿肠道;和啤酒废水处理），我们引入了一种新的方法来检测偶尔变得非常丰富的典型稀有微生物类群，（条件稀有类群[CRT]），然后量化其贡献的时间变化的社区结构。我们发现CRT占群落成员的1.5%至28%，代表了细菌和古细菌谱系的广泛多样性，并解释了大量的时间群落差异（即，高达Bray-Curtis相异度的97%）。大多数CRT是在多个时间点检测到的，尽管我们也发现了仅在一个时间点观察到的“一次性奇迹”CRT。从温带湖泊的案例研究，我们获得了额外的见解CRT的生态比较常规的社区时间序列大的干扰事件。我们的研究结果表明，许多罕见的类群贡献了更大的金额比从他们的低比例丰度的微生物群落动态。这一观察结果在广泛的生态系统中都是真实的，表明这些罕见的类群对于了解群落随时间的变化至关重要。微生物群落及其过程是生态系统的基础。稀有微生物的生态作用在很大程度上是未知的，但人们认为，它们作为一个水库，可以迅速应对环境变化，有助于社区的稳定。我们调查了典型的罕见类群的发生，非常偶尔成为他们的社区更突出（“条件罕见”）。我们从各种各样的生态系统中量化了时间序列中的条件稀有类群，发现不仅条件稀有类群存在于所有的例子中，而且它们在最丰富的时候也对多样性的时间变化做出了不成比例的贡献。这一结果表明，一个重要的和一般的作用，罕见的微生物类群在其社区。
Microbial communities typically contain many rare taxa that make up the majority of the observed membership, yet the contribution of this microbial “rare biosphere” to community dynamics is unclear. Using 16S rRNA amplicon sequencing of 3,237 samples from 42 time series of microbial communities from nine different ecosystems (air; marine; lake; stream; adult human skin, tongue, and gut; infant gut; and brewery wastewater treatment), we introduce a new method to detect typically rare microbial taxa that occasionally become very abundant (conditionally rare taxa [CRT]) and then quantify their contributions to temporal shifts in community structure. We discovered that CRT made up 1.5 to 28% of the community membership, represented a broad diversity of bacterial and archaeal lineages, and explained large amounts of temporal community dissimilarity (i.e., up to 97% of Bray-Curtis dissimilarity). Most of the CRT were detected at multiple time points, though we also identified “one-hit wonder” CRT that were observed at only one time point. Using a case study from a temperate lake, we gained additional insights into the ecology of CRT by comparing routine community time series to large disturbance events. Our results reveal that many rare taxa contribute a greater amount to microbial community dynamics than is apparent from their low proportional abundances. This observation was true across a wide range of ecosystems, indicating that these rare taxa are essential for understanding community changes over time. Microbial communities and their processes are the foundations of ecosystems. The ecological roles of rare microorganisms are largely unknown, but it is thought that they contribute to community stability by acting as a reservoir that can rapidly respond to environmental changes. We investigated the occurrence of typically rare taxa that very occasionally become more prominent in their communities (“conditionally rare”). We quantified conditionally rare taxa in time series from a wide variety of ecosystems and discovered that not only were conditionally rare taxa present in all of the examples, but they also contributed disproportionately to temporal changes in diversity when they were most abundant. This result indicates an important and general role for rare microbial taxa within their communities.