Bacterial Succession, Pesticide Removal and Proliferation of Halotolerant Antagonists Against Soil-Borne Phytopathogens Are Driven by the Saline–Alkaline Conditions of Mineral-Rich Compost from Greenhouse Tomato Residues

Greenhouse cultivation generates large quantities of plant residues, whose untreated disposal may pose a risk of phytopathogen proliferation and pesticide dispersal into agricultural soils. In this work, composting of greenhouse tomato plant and fruit residues was assessed as a sustainable bioeconomy treatment approach. The composting process progressed through two active thermophilic phases and a three-month maturation period, over which organic matter declined from 84.6% to 68.9% and soluble phenolics from 16.91 to 2.71 mg/g d.w., while ash content increased from 15.4% to 31.1% owing to organic matter loss. Mineralization raised electrical conductivity (EC) from 5.37 to 7.87 mS/cm and stabilized pH at 9.0, generating a mineral-rich, saline–alkaline environment enriched in Ca, K and Mg. High-throughput amplicon sequencing revealed pronounced bacterial succession, with the relative abundance of the lignocellulose-degrading Nocardiopsis decreasing from 37.93% to 2.46%, whereas halotolerant and alkalitolerant genera, i.e., Halomonas (10.10%), Marinimicrobium (6.01%), Salinicoccus (6.28%), Truepera (3.27%) and Salinimicrobium (1.84%), were enriched during maturation. Enterobacteriaceae and Enterococcus relative abundances also decreased, indicating effective sanitization. Regarding the 21 pesticides detected by LC-MS/MS in the initial mixture, the total pesticide load decreased from 2929 to 1129 ng/g d.w. Extracts of mature compost at 5–10% w/v appeared to enhance germination of Solanum lycopersicum and Lepidium sativum seeds, whereas inhibition of the germination was observed at 20% w/v or above, which may be attributed to salinity rather than residual phytotoxicity. Moreover, application of compost extract resulted in the suppression of Fusarium oxysporum f. sp. radicis-lycopersici in a dose-dependent manner. Of 55 bacterial strains isolated from the mature compost, five antagonized F. oxysporum f. sp. radicis-lycopersici and seven antagonized Phytophthora nicotianae, with isolate KGA-18, related to Ornithinimicrobium murale, inhibiting both phytopathogens. These in vitro antagonistic candidates were halotolerant and predominantly alkalitolerant or alkaliphilic. Composting of greenhouse tomato residues thus yields a detoxified, nutrient-rich amendment harboring candidate biocontrol-competent halotolerant and alkalitolerant bacteria, supporting more sustainable nutrient management and plant protection in greenhouse agriculture.