Contrasting effects of treated wastewater irrigation and Trichoderma inoculation on tomato soil microbiomes

Agricultural water reuse is expanding to mitigate freshwater scarcity, yet its effects on soil microbial ecology remain unclear, particularly when combined with biological inoculants. In a controlled greenhouse setting, we examined how municipal treated wastewater (TW), chlorinated treated wastewater (TW Cl ), and tap water (TapW) interact with Trichoderma afroharzianum T-22 inoculation to shape soil bacterial communities, rhizosphere potential pathobiomes, and class 1 integron abundance. Prolonged (till harvest) watering with TW Cl significantly reduced bacterial community richness compared to TapW in not inoculated samples. Chlorination did not significantly lower potential pathobiome richness; however, in TW Cl treatment, there was a trend for potentially pathogenic bacteria to accumulate. Trichoderma colonized the roots and reshaped the rhizosphere communities, increasing the potential pathobiome richness at intermediate stages, yet reducing the overall bacterial diversity at harvest. To note that, even if not significant, class 1 integron abundance tended to decrease in Trichoderma -associated soils, suggesting a potential beneficial effect on anthropogenic pollution markers. These findings, although based on a limited number of samples, highlight the interacting effects of irrigation water quality and microbial inoculation on soil microbial structure and potential pathobiome. This information supports the need for systematic microbial monitoring to develop sustainable water reuse strategies.