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Soil drying procedure affects the DNA quantification of Lactarius vinosus but does not change the fungal community composition

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Abstract

Drying soil samples before DNA extraction is commonly used for specific fungal DNA quantification and metabarcoding studies, but the impact of different drying procedures on both the specific fungal DNA quantity and the fungal community composition has not been analyzed. We tested three different drying procedures (freeze-drying, oven-drying, and room temperature) on 12 different soil samples to determine (a) the soil mycelium biomass of the ectomycorrhizal species Lactarius vinosus using qPCR with a specifically designed TaqMan® probe and (b) the fungal community composition and diversity using the PacBio® RS II sequencing platform. Mycelium biomass of L. vinosus was significantly greater in the freeze-dried soil samples than in samples dried at oven and room temperature. However, drying procedures had no effect on fungal community composition or on fungal diversity. In addition, there were no significant differences in the proportions of fungi according to their functional roles (moulds vs. mycorrhizal species) in response to drying procedures. Only six out of 1139 operational taxonomic units (OTUs) had increased their relative proportions after soil drying at room temperature, with five of these OTUs classified as mould or yeast species. However, the magnitude of these changes was small, with an overall increase in relative abundance of these OTUs of approximately 2 %. These results suggest that DNA degradation may occur especially after drying soil samples at room temperature, but affecting equally nearly all fungi and therefore causing no significant differences in diversity and community composition. Despite the minimal effects caused by the drying procedures at the fungal community composition, freeze-drying resulted in higher concentrations of L. vinosus DNA and prevented potential colonization from opportunistic species.

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Acknowledgments

The authors are very grateful to the PNIN of Poblet for its strong help in the installation and maintenance process of the experimental plots, and the Department of the Forest Mycology and Plant Pathology from SLU (Uppsala) for providing us the lab facilities. We are in debt with Björn Lindahl for the outstanding technical assistance in the DNA sequencing, and with Diem Nguyen for helping us with the statistical analysis of the fungal community. We are grateful for the critical review of the manuscript from Christine Fischer and the constructive comments and suggestions from two anonymous reviewers, which improved the quality of this manuscript.

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Authors and Affiliations

  1. Forest Bioengineering Solutions S.A., Ctra. de Sant Llorenç de Morunys, Km. 2, 25280, Solsona, Spain

    Carles Castaño

  2. Departament de Producció Vegetal i Ciència Forestal, Universitat de Lleida-AGROTECNIO, Av. Rovira Roure, 191, 25198, Lleida, Spain

    Carles Castaño, Josu G. Alday & José Antonio Bonet

  3. Protecció Vegetal Sostenible, IRTA, Centre de Cabrils, Ctra. Cabrils Km. 2, 08348, Cabrils, Barcelona, Spain

    Javier Parladé & Joan Pera

  4. Centre Tecnològic Forestal de Catalunya, CTFC-CEMFOR, Ctra. de Sant. Llorenç de Morunys Km. 2, 25280, Solsona, Spain

    Juan Martínez de Aragón & José Antonio Bonet

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  1. Carles Castaño
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  2. Javier Parladé
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  3. Joan Pera
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Correspondence to Carles Castaño.

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Funding

This work was supported by a STSM Grant from COST Action FP1203 and by the Spanish Ministry of Economy and Competitivity (MINECO) through the project AGL 2012-40035-C03. Carles Castaño received support from the Secretaria d’Universitats i Recerca del Departament d’Economia i Coneixement de la Generalitat de Catalunya through the program of Doctorats Industrials, funded by the European Union and the European Social Fund. Josu G. Alday was supported by Juan de la Cierva fellowships (IJCI-2014-21393).

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Castaño, C., Parladé, J., Pera, J. et al. Soil drying procedure affects the DNA quantification of Lactarius vinosus but does not change the fungal community composition. Mycorrhiza 26, 799–808 (2016). https://doi.org/10.1007/s00572-016-0714-3

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