Suppressive composts represent a sustainable approach to combat soilborne plant pathogens and an alternative to the ineffective chemical fungicides used against those. Nevertheless, suppressiveness to plant pathogens and reliability of composts are often inconsistent with unpredictable effects. While suppressiveness is usually attributed to the compost’s microorganisms, the mechanisms governing microbial recruitment by the roots and the composition of selected microbial communities are not fully elucidated. Herein, the purpose of the study was to evaluate the impact of a compost on tomato plant growth and its suppressiveness against Fusarium oxysporum f. sp. lycopersici (Foxl) and Verticillium dahliae (Vd). First, growth parameters of tomato plants grown in sterile peat-based substrates including 20 and 30% sterile compost (80P/20C-ST and 70P/30C-ST) or non-sterile compost (80P/20C and 70P/30C) were evaluated in a growth room experiment. Plant height, total leaf surface, and fresh and dry weight of plants grown in the non-sterile compost mixes were increased compared to the plants grown in the sterile compost substrates, indicating the plant growth promoting activity of the compost’s microorganisms. Subsequently, compost’s suppressiveness against Foxl and Vd was evaluated with pathogenicity experiments on tomato plants grown in 70P/30C-ST and 70P/30C substrates. Disease intensity was significantly less in plants grown in the non-sterile compost than in those grown in the sterile compost substrate; AUDPC was 2.3- and 1.4-fold less for Foxl and Vd, respectively. Moreover, fungal quantification in planta demonstrated reduced colonization in plants grown in the non-sterile mixture. To further investigate these findings, we characterized the culturable microbiome attracted by the roots compared to the unplanted compost. Bacteria and fungi isolated from unplanted compost and the rhizosphere of plants were sequence-identified. Community-level analysis revealed differential microbial communities between the compost and the rhizosphere, suggesting a clear effect of the plant in the microbiome assembly. Proteobacteria and Actinobacteria were highly enriched in the rhizosphere whereas Firmicutes were strongly represented in both compartments with Bacillus being the most abundant species. Our results shed light on the composition of a microbial consortium that could protect plants against the wilt pathogens of tomato and improve plant overall health.

Composts represent a sustainable way to suppress diseases and improve plant growth. Identification of compost-derived microbial communities enriched in the rhizosphere of plants and characterization of their traits, could facilitate the design of microbial synthetic communities (SynComs) that upon soil inoculation could yield consistent beneficial effects towards plants. Here, we characterized a collection of compost-derived bacteria, previously isolated from tomato rhizosphere, for in vitro antifungal activity against soil-borne fungal pathogens and for their potential to change growth parameters in Arabidopsis. We further assessed root-competitive traits in the dominant rhizospheric genus Bacillus. Certain isolated rhizobacteria displayed antifungal activity against the tested pathogens and affected growth of Arabidopsis, and Bacilli members possessed several enzymatic activities. Subsequently, we designed two SynComs with different composition and tested their effect on Arabidopsis and tomato growth and health. SynCom1, consisting of different bacterial genera, displayed negative effect on Arabidopsis in vitro, but promoted tomato growth in pots. SynCom2, consisting of Bacilli, didn't affect Arabidopsis growth, enhanced tomato growth and suppressed Fusarium wilt symptoms. Overall, we found selection of compost-derived microbes with beneficial properties in the rhizosphere of tomato plants, and observed that application of SynComs on poor substrates can yield reproducible plant phenotypes.

It has been suggested that some microorganisms, including plant growth–promoting rhizobacteria, manipulate the level of ethylene in plants by degrading 1-aminocyclopropane-1-carboxylic acid (ACC), an ethylene precursor, into α-ketobutyrate and ammonia, using ACC deaminase (ACCd). Here, we investigated whether ACCd of Verticillium dahliae, a soil-borne fungal pathogen of many important crops, is involved in causing vascular wilt disease. Overexpression of the V. dahliae gene encoding this enzyme, labeled as ACCd, significantly increased virulence in both tomato and eggplant, while disruption of ACCd reduced virulence. Both types of mutant produced more ethylene than a wild-type (70V-WT) strain, although they significantly differed in ACC content. Overexpression strains lowered ACC levels in the roots of infected plants, while the amount of ACC in the roots of plants infected with deletion mutants increased. To test the hypothesis that ACC acts as a signal for controlling defense, roots of WT and Never-ripe (Nr) tomato plants were treated with ACC before V. dahliae inoculation. Plants pretreated with ACC displayed less severe symptoms than untreated controls. Collectively, our results suggest a novel role of ACC as a regulator of both plant defense and pathogen virulence.