Organic amendments drive bacterial and fungal soil microbiomes over time in a subtropical banana agroecosystem

Summary

Organic amendments are increasingly promoted as sustainable alternatives to intensive fertilization in banana production, yet their long-term effects on soil microbiome assembly remain poorly understood in subtropical systems. Here, we investigated how four commonly used organic amendments (chicken manure, cow manure, compost, and pelletised compost) in Canary Island influence bacterial (16S rRNA) and fungal (ITS) communities over a 20.8-month controlled banana pot experiment under subtropical conditions. Amplicon sequencing combined with multivariate analyses revealed that amendment identity, rather than organic input per se, was the primary driver of microbiome restructuring. Chicken manure induced the strongest and most persistent divergence in both bacterial and fungal communities, closely associated with increased soil conductivity and phosphorus availability. In contrast, cow manure and compost amendments promoted more gradual and progressive shifts, linked to higher organic matter and nitrogen levels. Bacterial richness increased over time under manure and compost treatments before declining towards the final sampling point, whereas fungal richness exhibited more variable temporal dynamics, particularly under compost. Redundancy analyses indicated that amendment-driven physicochemical changes acted as major ecological filters shaping community trajectories. Differential abundance analyses further highlighted amendment-specific microbial responses. Overall, our findings show that amendment quality determines the magnitude and direction of soil microbiome reassembly, with nutrient-rich inputs acting as strong ecological pulses and more balanced amendments promoting progressive community diversification in subtropical banana systems.