Extensive Phylogenetic Analysis of a Soil Bacterial Community Illustrates Extreme Taxon Evenness and the Effects of Amplicon Length, Degree of Coverage, and DNA Fractionation on Classification and Ecological Parameters
Extensive Phylogenetic Analysis of a Soil Bacterial Community Illustrates Extreme Taxon Evenness and the Effects of Amplicon Length, Degree of Coverage, and DNA Fractionation on Classification and Ecological Parameters
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DOI：
10.1128/aem.01757-08
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发表时间：
2009-02-01
影响因子：
4.4
通讯作者：
Holben, William E.
中科院分区：
文献类型：
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作者：
Morales, Sergio E.;Cosart, Theodore F.;Holben, William E.
为了深入研究农业土壤单个复合样品中细菌群落的多样性，并检验数据采集和分析方法产生的潜在偏差，我们研究了G+C DNA百分比、序列长度和细菌多样性的覆盖程度对几个常用生态参数(物种估计、多样性指数和均匀度)的影响。我们还考察了基于多种常用方法(ARB比对和多种RDP工具)在系统发育定位方面的差异。结果表明，该土壤细菌群落具有高度的多样性，根据16S rRNA基因的序列相似性，有1,714个可操作的分类单位和3,555个(基于Chao1丰富度估计)。研究结果还显示了一种基本缺乏优势度的现象(即高度的均衡性)，82%的系统类型出现三次或更少。数据还表明，被普遍接受的门水平分类的分界值可能不像之前假设的那样适用或一般，而且这些值可能在原核门或组之间有所不同。
To thoroughly investigate the bacterial community diversity present in a single composite sample from an agricultural soil and to examine potential biases resulting from data acquisition and analytical approaches, we examined the effects of percent G+C DNA fractionation, sequence length, and degree of coverage of bacterial diversity on several commonly used ecological parameters (species estimation, diversity indices, and evenness). We also examined variation in phylogenetic placement based on multiple commonly used approaches (ARB alignments and multiple RDP tools). The results demonstrate that this soil bacterial community is highly diverse, with 1,714 operational taxonomic units demonstrated and 3,555 estimated (based on the Chao1 richness estimation) at 97% sequence similarity using the 16S rRNA gene. The results also demonstrate a fundamental lack of dominance (i.e., a high degree of evenness), with 82% of phylotypes being encountered three times or less. The data also indicate that generally accepted cutoff values for phylum-level taxonomic classification might not be as applicable or as general as previously assumed and that such values likely vary between prokaryotic phyla or groups.