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Evaluation of primer pairs for studying arbuscular mycorrhizal fungal community compositions using a MiSeq platform

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Abstract

Although many primers have been proposed for arbuscular mycorrhizal fungi (AMF)–specific sequencing, only a few studies have evaluated suitable primer pairs for MiSeq analysis. Here, we analyzed AMF community compositions using several primer pairs and evaluated which pair can detect a more diverse AMF community. Three AMF-specific primer pairs targeting the 18S and 28S rRNA genes and a fungal universal primer pair targeting the ITS region were examined using soil DNA as the template. The effect of nested PCR was also evaluated. Only a few AMF sequences were obtained from a fungal universal primer targeting the ITS region. On the other hand, use of AMF-specific primers improved AMF detection rates (35–98%). Particularly, almost all of the sequences obtained with the nested PCR were AMF-related sequences. However, the AMF community compositions were differentiated among the primer pairs. In addition, the number of AMF taxa and diversity decreased with the nested PCR, suggesting that it affected AMF community analysis.

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Author notes

  1. Kazuki Suzuki and Kohei Takahashi contributed equally to this work.

Authors and Affiliations

  1. Center for Transdisciplinary Research, Institute for Research Promotion, Niigata University, 8050 Ikarashi-2, Nishi-ku, Niigata, 950-2181, Japan

    Kazuki Suzuki

  2. Graduate School of Science and Technology, Niigata University, 8050 Ikarashi-2, Nishi-ku, Niigata, 950-2181, Japan

    Kohei Takahashi

  3. Institute of Science and Technology, Niigata University, 8050 Ikarashi-2, Nishi-ku, Niigata, 950-2181, Japan

    Naoki Harada

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  1. Kazuki Suzuki
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  2. Kohei Takahashi
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  3. Naoki Harada
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Correspondence to Kazuki Suzuki.

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Suzuki, K., Takahashi, K. & Harada, N. Evaluation of primer pairs for studying arbuscular mycorrhizal fungal community compositions using a MiSeq platform. Biol Fertil Soils 56, 853–858 (2020). https://doi.org/10.1007/s00374-020-01431-6

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  • DOI: https://doi.org/10.1007/s00374-020-01431-6

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