Rhizosphere microbiome-mediated adaptation to soil nutrient stress under organic substitution: implications for kiwifruit productivity and metabolic quality

Introduction Intensive perennial orchards frequently suffer from soil nutrient imbalance marked by accumulated legacy nutrients and insufficient bioavailable nutrient pools, which acts as a major abiotic stress limiting kiwifruit productivity. In this study, we adopted an isosynthetic-nutrient experimental design with rapeseed-cake substitution gradients to disentangle organic carbon effects from macronutrient inputs, and investigate how organic amendments remodel rhizosphere microbiomes in association with kiwifruit acclimation to soil nutrient stress. We hypothesized that suitable organic substitution would reshape rhizosphere microbial composition and co-occurrence patterns linked to balanced soil nutrient supply and enhanced fruit performance, without inferring causal microbial functions. Methods Based on a five-year field trial involving two commercial kiwifruit cultivars (‘Donghong’ and ‘Jinyan’), we implemented equal-nutrient fertilization treatments with 25%, 50%, and 100% rapeseed cake replacing mineral fertilizer. By combining high-throughput amplicon sequencing and PLS-SEM modeling, we uncovered correlative, non-causal pathways within the “soil-microbe-fruit” continuum. Results The 100% rapeseed-cake treatment (T1) showed the best overall performance among the tested treatments, depleting legacy soil N and P. This treatment enriched key microbial taxa including Steroidobacter , Lysobacter , Mortierella , and Nitrospira , and generated more resilient microbial co-occurrence networks. While such microbial community shifts were significantly associated with better fruit performance, their precise biological functions remain unvalidated via manipulative experiments. Discussion Collectively, our field-based correlative findings show that rational rapeseed-cake substitution remodels rhizosphere microbiome assembly associated with optimized soil nutrient status and improved kiwifruit output. This work provides field-scale insights into microbiome-fruit relationships under nutrient stress and delivers practical references for chemical-fertilizer reduction in sustainable kiwifruit production.