Serial analysis of rRNA genes and the unexpected dominance of rare members of microbial communities
Serial analysis of rRNA genes and the unexpected dominance of rare members of microbial communities
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DOI：
10.1128/aem.02956-06
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发表时间：
2007-07-01
影响因子：
4.4
通讯作者：
Dimster-Denk, Dago
中科院分区：
文献类型：
--
作者：
Ashby, Matthew N.;Rine, Jasper;Dimster-Denk, Dago
准确描述微生物群落是了解其组成部分在生态系统功能中作用的重要第一步。本文介绍了一种用于微生物群落调查的rRNA基因系列分析方法。通过一系列分子克隆步骤，从微生物群落的原核16S rRNA基因的第五可变区（V5）回收短DNA序列标签。将这些标签连接以形成由20至40个标签组成的多联体，将其克隆并通过DNA测序鉴定。四个农业土壤样品与SARD分析，以评估该方法的实用性。鉴定了总共37，008个SARD标签，其包含3，127个独特序列。从一个土壤基因组DNA制备的重复配置文件的比较表明，该方法是高度可重复的。大量的单例标签，连同非参数丰富度估计，表明大量的序列标签多样性仍未检测到这种水平的采样。所观察到的标签的丰度类是无标度的，并符合幂律分布。从数字上看，观察到的大部分总标签属于丰度类，每个丰度类在群落中的比例不到1%。超过99%的独特标签只占社区的不到1%。因此，无论是从数量或多样性的角度来看，低丰度的类群包括一个显着比例的微生物群落检查，并可能作出巨大贡献的生态系统功能。SARD可能提供一种手段，探索这些稀有的微生物群落成员的生态作用，在定性和定量方面。
The accurate description of a microbial community is an important first step in understanding the roles of its components in ecosystem function. A method for surveying microbial communities termed serial analysis of rRNA genes (SARD) is described here. Through a series of molecular cloning steps, short DNA sequence tags are recovered from the fifth variable (V5) region of the prokaryotic 16S rRNA genes from microbial communities. These tags are ligated to form concatemers comprised of 20 to 40 tags which are cloned and identified by DNA sequencing. Four agricultural soil samples were profiled with SARD to assess the method's utility. A total of 37,008 SARD tags comprising 3,127 unique sequences were identified. A comparison of duplicate profiles from one soil genomic DNA preparation revealed that the method was highly reproducible. The large numbers of singleton tags, together with nonparametric richness estimates, indicated that a significant amount of sequence tag diversity remained undetected with this level of sampling. The abundance classes of the observed tags were scale-free and conformed to a power law distribution. Numerically, the majority of the total tags observed belonged to abundance classes that were each present at less than 1% of the community. Over 99% of the unique tags individually made up less than 1% of the community. Therefore, from either a numerical or diversity standpoint, taxa with low abundance comprised a significant proportion of the microbial communities examined and could potentially make a large contribution to ecosystem function. SARD may provide a means to explore the ecological roles of these rare members of microbial communities in qualitative and quantitative terms.