ITS fungal barcoding primers versus 18S AMF-specific primers reveal similar AMF-based diversity patterns in roots and soils of three mountain vineyards
ITS fungal barcoding primers versus 18S AMF-specific primers reveal similar AMF-based diversity patterns in roots and soils of three mountain vineyards
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DOI：
10.1111/1758-2229.12574
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发表时间：
2017-10-01
影响因子：
3.3
通讯作者：
Bonfante, Paola
中科院分区：
文献类型：
--
作者：
Berruti, Andrea;Desiro, Alessandro;Bonfante, Paola
通常用于描述土壤真菌的 ITS 引物在 AMF 方面存在缺陷，尽管尚不清楚它们在多大程度上扭曲了群落模式的解释。在这里，我们重点关注与 18S 上的新型 AMF 特异性方法相比，使用偏向 AMF 的特定 ITS2 真菌条形码引物对如何改变对三个山地葡萄园 AMF 群落模式的解释。我们发现，尽管两个结果数据集的分类组成存在差异，但 AMF 群落多样性模式的估计是相似的，并且导致两个引物系统能够正确评估位置、区室（根与土壤）和环境的群落结构效应。两种方法都可以在所研究的位置之间检测到相同的α多样性趋势，但不能在根部和土壤横断面之间检测到相同的α多样性趋势。我们表明，用于真菌条形码的 ITS2 引物系统可以很好地估计 AMF 群落结构以及与环境变量的关系。然而，该引物系统不适合跨区室调查（根与土壤），因为它可能低估土壤样品中的 AMF 多样性。当专门关注 AMF 时，18S 引物系统可实现广泛的覆盖范围和边缘非目标扩增。
ITS primers commonly used to describe soil fungi are flawed for AMF although it is unknown the extent to which they distort the interpretation of community patterns. Here, we focus on how the use of a specific ITS2 fungal barcoding primer pair biased for AMF changes the interpretation of AMF community patterns from three mountain vineyards compared to a novel AMF-specific approach on the 18S. We found that although discrepancies were present in the taxonomic composition of the two resulting datasets, the estimation of diversity patterns among AMF communities was similar and resulted in both primer systems being able to correctly assess the community-structuring effect of location, compartment (root vs. soil) and environment. Both methodologies made it possible to detect the same alpha-diversity trend among the locations under study but not between root and soil transects. We show that the ITS2 primer system for fungal barcoding provides a good estimate of both AMF community structure and relation to environmental variables. However, this primer system does not fit in with cross-compartment surveys (roots vs. soil) as it can underestimate AMF diversity in soil samples. When specifically focusing on AMF, the 18S primer system resulted in wide coverage and marginal non-target amplification.