Contrasting Microbial Persistence of Industrial and Long-Matured Compost in Soil- and Root-Associated Microbiomes of Pepper and Onion

Compost application can improve soil properties while introducing complex microbial communities, yet the persistence of compost-associated microorganisms in soil and plant roots remains poorly understood. We compared industrial compost (IC) and long-matured compost (LMC) with contrasting production and maturation histories in a two-season field experiment with pepper followed by onion, using mineral fertilization at an equivalent nitrogen input as a reference. The composts differed markedly in physicochemical properties, biological activity, and prokaryotic community structure. Compost application caused transient changes in soil pH and dehydrogenase activity, while LMC produced more persistent increases in microbial biomass carbon and glucose-induced respiration. Soil prokaryotic communities were strongly affected by sampling time, treatment, and their interaction. SourceTracker estimated similar initial contributions of IC and LMC to soil communities approximately six weeks after application, but their subsequent trajectories differed: the IC-associated signature declined from about 12% to below 1%, whereas the LMC-associated signature remained detectable approximately one year later. Root-associated communities also responded to treatment, although direct compost contributions were limited. Crop yield was unaffected. These results show that compost effects in horticultural systems extend beyond nutrient supply and yield, affecting soil biological activity and microbial community trajectories over time.