International audienceBiocontrol 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
Protective effect of organic substrates against soil-borne pathogens in soilless cucumber crops. Scientia Horticulturae, Elsevier, 2016, 206, pp.62-70. 10.1016/j.scienta.2016.04.035. hal-01523673 Scientia Horticulturae 206 (2016 Contents lists available at ScienceDirect Scientia Horticulturae j o u r n a l h o m e p a g e : w w w . e l s e v i e r . c o m / l o c a t e / s c i h o r t i
a b s t r a c tThe development of sustainable crop protection is expected by vegetable producers and highly encouraged by authorities. For crops grown in soilless systems, vegetable fibers are relevant for both agronomical and plant protection purposes. This work examines their potential against the soil-borne pathogen Fusarium oxysporum f. sp. radicis-cucumerinum. Wood fiber, coir fiber and peat were tested over two cucumber cropping periods. Fusarium blight symptoms were monitored on cucumber, and fungal community structure (PCR-TTGE) in substrates. Substrate sterilization and bio-augmentation with antagonistic strains were also studied; they did not modify protection. Compared to the other substrates, wood fiber increased protection at the end of the first assay, but did not during the second assay. Differences in crop season and plant density may have impacted on cucumber physiology and may have indirectly modified rhizosphere fungal community structure.The sole determination of microbial activity in substrates is not sufficient to predict protection. Growth conditions, substrate type and the microbiome altogether impacted on the protection of cucumber.
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