Long–term agricultural amendments are widely employed to enhance soil quality and ecological sustainability. However, their effects on the assembly processes of bacterial sub–communities and on multispecies biofilm development remain poorly understood. In a seven–year field experiment, we investigated the impact of lime (L) and organic fertilizer (OF) amendments on the assembly mechanisms of abundant, moderate, and rare bacterial taxa in paddy soil, as well as on the formation and growth of multispecies biofilms. Our results demonstrated that both amendments significantly increased biofilm biomass, enhancing biofilm thickness by 0.72– to 1.33–fold, and shifted microbial niche adaptation. Assembly processes, assessed via the Normalized Stochasticity Ratio (NST), exhibited contrasting patterns among taxa: for the whole and rare bacterial communities, NST increased from 45.3 % to 68.9 % and from 48.3 % to 71.3 % under OF, and from 44.3 % to 55.7 % and from 47.8 % to 57.2 % under L, indicating a shift from deterministic toward stochastic process. In contrast, moderate taxa showed decreased stochasticity, with NST declining from 70.0 % to 43.2 % under OF and from 77.4 % to 58.3 % under L. Organic fertilization also enhanced soil multifunctionality by 2.37–fold and increased bacterial network complexity by 77 %. Soil pH was identified as the key driver governing both bacterial community assembly and multispecies biofilm growth. These findings provide novel insights into how long–term agricultural amendments modulate biofilm dynamics and bacterial assembly processes in soil ecosystems.
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