Soil Biodiversity Reshapes Nutrient Processing through Microbial Interactions in Degraded Tropical Soils

Soil biodiversity plays a central role in regulating organic matter dynamics and ecosystem health, particularly in highly weathered tropical soils. Amazonian Dark Earths (ADEs), enriched in stable organic matter and diverse microbial communities, provide a unique opportunity to examine how microbial diversity and interactions shape soil functioning. In this study, we assessed whether small inputs of ADE (2% w/w), alone or combined with Urochloa brizantha-Conditioned Soil (CS; 20%), could alter soil biodiversity, organic matter-related processes, and early tree establishment in a pasture-degraded Oxisol. Using a greenhouse experiment with four tree species (Cecropia pachystachya, Schizolobium amazonicum, Handroanthus avellanedae, and Acacia mangium), we evaluated plant performance, prokaryotic community structure (16S rRNA gene sequencing), soil enzyme activity, predicted microbial functions, and co-occurrence networks. While neither ADE nor CS significantly increased plant growth or microbial alpha diversity, marked shifts in microbial community composition and interaction patterns were observed. The combined CS+ADE treatment reduced aerobic Gram-positive taxa and the nitrogen-fixing bacterium Herbaspirillum, while substantially strengthening microbial network connectivity, particularly in the Cecropia and Acacia rhizospheres. Despite stable predicted functional profiles, a 70% reduction in β-glucosidase activity under CS+ADE in Acacia indicated altered carbon processing linked to microbial structure reorganization rather than biomass loss. Overall, our findings show that soil biodiversity can reshape organic matter dynamics primarily through changes in microbial interactions and network structure, even when diversity and plant responses remain unchanged. These results emphasize microbial resilience and legacy effects as key determinants of ecosystem health and soil organic matter stability in tropical restoration contexts.