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

Montagne, Virginie, Capiaux, Hervé, Barret, Matthieu, Cannavo, Patrice, Charpentier, Sylvain, Grosbellet, Claire, Lebeau, Thierry
Environmental chemistry letters 2017 v.15 no.3 pp. 537-545
Eurotiomycetes, Flavobacteria, Fusarium oxysporum, Fusarium wilt, Leotiomycetes, Trichoderma, bacteria, biological control, biological control agents, coir, crops, cucumbers, fungal communities, fungi, gamma-Proteobacteria, genes, internal transcribed spacers, pathogens, peat, ribosomal RNA, soil, transcription (genetics), wood, wood fibers
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.