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Bacterial and fungal communities vary with the type of organic substrate: implications for biocontrol of soilless crops

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Abstract

Biocontrol strategies using organic substrates such as wood fibers and biocontrol agents such as Trichoderma are currently developed to control soil pathogens such as Fusarium oxysporum. Nonetheless, such biocontrol methods give discording results, notably because microbial communities of organic substrates actually are not taken into account. Therefore, there is a lack of information concerning the variability of microbial composition related to the organic substrate type. Here we studied peat, wood and coir fibers, that are substrates known for their different biocontrol efficiency against Fusarium wilt of cucumber. We analyzed in microcosms the microbial composition of wood fibers, coir fibers and peat, incubated up to 60 days, by using an amplicon-sequencing approach based on 16S rRNA gene for bacteria and the internal transcribed spacer (ITS) for fungi. Diversity was assessed by sequencing the 16S rRNA for bacteria and ITS2 region for fungi. Results showed that bacterial richness was threefold higher for coir fiber and peat than for wood fiber. Fungal richness was three times higher for wood and coir fibers compared to peat. Bacterial and fungal patterns showed a dominance of α- and γ- Proteobacteria and Sordariomycetes for coir fiber; β- and γ-Proteobacteria and Eurotiomycetes for wood fibers; Flavobacteria, Leotiomycetes and Sordariomycetes for peat. In conclusion, results show that substrates have different microbial composition. Finally, for a proper use of a biocontrol strategy is important to take into account the type of substrate.

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Acknowledgements

We wish to thank the Florentaise firm, the ANRT (Association Nationale de la Recherche et de la Technologie—CIFRE convention No. 2012/1062) for funding this work. We are particularly grateful to the NED team (UMR1289 TANDEM) and the GeT-PLaGE plateform in Toulouse using Illumina Miseq technology (Génopole Toulouse-Midi-pyrénées, INRA Auzeville, 24 Chemin de Borde Rouge-Auzeville, CS52627, 31326 Castanet-Tolosan, France).

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Authors and Affiliations

  1. INRA, UMR Agroecologie, 21065, Dijon, France

    Virginie Montagne

  2. Plateforme d’Analyse Moléculaire Biodiversité-Environnement, IUT, 85035, La Roche sur Yon, France

    Hervé Capiaux

  3. UMR 6112 CNRS, LPG, 44322, Nantes, France

    Hervé Capiaux & Thierry Lebeau

  4. IRHS-INRA, 49071, Beaucouzé, France

    Matthieu Barret

  5. AGROCAMPUS OUEST, UP EPHOR, 49042, Angers, France

    Patrice Cannavo & Sylvain Charpentier

  6. Université Bretagne Loire, 35044, Rennes, France

    Patrice Cannavo & Sylvain Charpentier

  7. FLORENTAISE Firm, 44850, Saint-Mars du Désert, France

    Claire Grosbellet

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  1. Virginie Montagne
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  2. Hervé Capiaux
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  3. Matthieu Barret
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  4. Patrice Cannavo
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  5. Sylvain Charpentier
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  6. Claire Grosbellet
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  7. Thierry Lebeau
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Correspondence to Virginie Montagne.

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Montagne, V., Capiaux, H., Barret, M. et al. Bacterial and fungal communities vary with the type of organic substrate: implications for biocontrol of soilless crops. Environ Chem Lett 15, 537–545 (2017). https://doi.org/10.1007/s10311-017-0628-0

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  • DOI: https://doi.org/10.1007/s10311-017-0628-0

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