Effects of Reclaimed Wastewater Containing Pharmaceutical Active Compounds (PhACs) and Tomato–Wheat Crop Succession on Soil Microbial Communities and Crop Productivity

Water scarcity is driving increased use of treated wastewater in agriculture while also leading to an increase in concerns about the presence of active pharmaceutical active compounds (PhACs) and their impact on soil ecosystems. This study provides novel field-scale evidence on the combined impact of tertiary-treated wastewater (TWW) irrigation and short-term tomato/wheat crop succession on soil microbial communities, nitrogen-cycling functional groups, and crop productivity. Over two consecutive years in southern Italy, TWW was compared with freshwater (FW) using integrated chemical, microbiological, and metagenomic approaches. TWW irrigation significantly increased tomato and wheat yields (+14% and +20%, respectively) without negatively affecting crop quality. Several PhACs were detected in soil and showed moderate accumulation under TWW, particularly sitagliptin and flecainide, which reached 10 ng/g. However, limited effects were observed in terms of total microbial abundance, nitrogen-cycle gene markers, or overall microbiome structure. The fungal population of Bionectria was found to be a potential biomarker since it was negatively affected by TWW (−56%). In contrast, time and crop succession emerged as the primary driver of microbial dynamics, inducing marked shifts in bacterial and fungal community composition and diversity, with wheat promoting higher diversity than tomato. Nitrogen-fixing bacteria were higher in tomato crop seasons. Ammonia oxidizing increased in the wheat crop season, while denitrifiers were more influenced by sampling time. These findings demonstrate that, under compliant treatment conditions, TWW reuse can enhance crop productivity with limited short-term ecological risks, supporting sustainable agricultural water management.