Microbial fertilizer enhanced root-rot resistance and improved yield and processing-related fruit quality of tomato under deficit irrigation

In arid and hot areas, excessive water and fertilizer inputs in tomato ( Solanum lycopersicum L.) production can aggravate soil-borne diseases such as root rot and limit yield improvement. Microbial fertilizer has considerable potential to enhance plant resistance and water productivity, but its synergistic effects with deficit irrigation in tomato remain unclear. This study evaluated the effects of three irrigation levels and four microbial fertilizer levels on tomato growth, root-rot resistance, yield, and quality. A randomized block design with 12 treatments and three replicates was used, and PLS-SEM was applied to analyze the pathways among factors. Results from the 2023 and 2025 growing seasons showed that mild and severe root rot incidence decreased by 23.81%-40.0% and 45.46%-60.0%, respectively. The W 2 M 2 treatment produced the highest yield in both years, reaching 155,931.11 ± 3801.25 and 121,452.18 ± 3867.54 kg/ha, respectively. Lycopene ranged from 2.41 to 4.83 μg/g and from 2.26 to 3.93 μg/g, with an average increase of 38.30%. In conclusion, an appropriate combination of deficit irrigation and microbial fertilizer improved plant growth, disease resistance, yield, and fruit quality. In addition, the improvement in lycopene and nutrient-related quality traits suggests potential processing-related value of tomato fruits for tomato-based products and lycopene-oriented value-added utilization. This strategy provides a practical basis for improving water-fertilizer management in arid seasonal areas. ● Microbial fertilizer promoted tomato growth under moderate water deficit irrigation, increasing yield by 15.60%-28.65%. ● Microbial fertilizer raised microbial diversity by 6.83%-32.17% and cut root rot by 21.43%-51.27% under deficit irrigation. ● W 2 M 2 was optimal, reducing root rot and increasing lycopene by 15.93%-65.82% for tomato processing and lycopene-based valorization.