Functional and Structural Shifts in the Rhizosphere and Tuberosphere of Potato Under Combined Microbial Inoculation and Reduced Fertilization

Background Potato is a globally significant crop, but its intensive cultivation depends heavily on mineral fertilizers, leading to soil degradation, water pollution, increased production costs, and environmental harm. Microbial inoculants, composed of beneficial bacteria and fungi, provide a sustainable alternative enhancing nutrient availability, promoting plant health, and promoting growth. However, the specific mechanisms of action of these microorganisms and their effects on soil microbial communities and soil functionality remain insufficiently understood. Methods This study aimed to evaluate how microbial inoculants affect prokaryotic and fungal community composition, diversity, functionality, and pathogen suppression in the rhizosphere and tuberosphere of a potato crop throughout its full growing cycle. We investigated the temporal changes of the potato microbiome (in the rhizosphere and tuberosphere) under different fertilization strategies: full mineral fertilization (F100), 50% reduced mineral fertilization (F50), and two treatments combining F50 with a microbial inoculant consisting of Azospirillum , Bacillus and Pseudomonas (F50 + BA), or a microbial inoculant containing Azotobacter , Bacillus and non-mycorrhizal fungi (F50 + BAFU). Using the estimated absolute abundance approach, which infers quantitative measurements from sequencing data, we monitored microbial shifts throughout the cropping cycle. Results In the rhizosphere, bioinoculated soils showed an increase in beneficial bacteria and fungi, along with a decline in pathogens, without compromising potato yield. F50 + BAFU promoted bacterial taxa involved in plant growth, resistance, and pathogen suppression ( Allorhizobium , Devosia , Bacillus , Lysobacter , Massilia , Paenibacillus , Sphingomonas , Streptomyces ). F50 + BA significantly reduced fungal pathogens such as Verticillium , Gibellulopsis , and Phialophora , while promoting Clonostachys , a biocontrol fungus with mycoparasitic properties. Microbial inoculants also enhanced key soil functions such as nitrogen fixation, ammonification, denitrification, cellulose degradation, and CO₂ fixation, contributing to improved soil fertility. Conclusion Our findings demonstrate the potential of microbial inoculants to enrich soil with plant growth-promoting microorganisms, suppress pathogens, and sustain plant growth under reduced fertilization. This highlights their value as a promising strategy for more sustainable potato production systems.