Mills DeEtta K, Entry James A, Voss Joshua D, Gillevet Patrick M, Mathee Kalai
Department of Biological Sciences, Florida International University, Miami, FL 33199, USA.
FEMS Microbiol Ecol. 2006 Sep;57(3):496-503. doi: 10.1111/j.1574-6941.2006.00135.x.
Amplicon length heterogeneity PCR (LH-PCR) was investigated for its ability to distinguish between microbial community patterns from the same soil type under different land management practices. Natural sagebrush and irrigated mouldboard-ploughed soils from Idaho were queried as to which hypervariable domains, or combinations of 16S rRNA gene domains, were the best molecular markers. Using standard ecological indices to measure richness, diversity and evenness, the combination of three domains, V1, V3 and V1+V2, or the combined V1 and V3 domains were the markers that could best distinguish the undisturbed natural sagebrush communities from the mouldboard-ploughed microbial communities. Bray-Curtis similarity and multidimensional scaling were found to be better metrics to ordinate and cluster the LH-PCR community profiling data. The use/misuse of traditional ecological indices such as diversity and evenness to study microbial community profiles will remain a major point to consider when performing metagenomic studies.
研究了扩增子长度异质性PCR（LH-PCR）区分不同土地管理方式下相同土壤类型微生物群落模式的能力。对来自爱达荷州的天然山艾树土壤和灌溉后的铧式犁耕土壤进行了调查，以确定哪些高变区或16S rRNA基因区域的组合是最佳分子标记。使用标准生态指数来衡量丰富度、多样性和均匀度，三个区域（V1、V3和V1+V2）的组合，或V1和V3区域的组合是最能区分未受干扰的天然山艾树群落和铧式犁耕微生物群落的标记。发现Bray-Curtis相似度和多维尺度分析是对LH-PCR群落分析数据进行排序和聚类的更好指标。在进行宏基因组研究时，使用/误用传统生态指数（如多样性和均匀度）来研究微生物群落图谱仍是一个需要重点考虑的问题。
