Soil microbiome responses to organic fertilization in a subtropical banana agroecosystem

Summary

Organic fertilizers are increasingly applied in intensive banana production to improve soil fertility and support sustainable crop management. However, their long-term effects on soil microbial communities in subtropical systems remain poorly characterized. In this study, we evaluated the impact of four organic amendments commonly used in the Canary Islands—chicken manure, cow manure, compost, and pelletised compost—on soil bacterial and fungal communities during a banana pot experiment spanning almost two years and covering a complete crop cycle.
Microbial community dynamics were assessed using long-read amplicon sequencing of bacterial 16S rRNA genes and fungal ITS regions. The different amendments produced distinct microbial responses over time. Chicken manure caused the strongest shifts in both bacterial and fungal community composition and was associated with increased soil electrical conductivity and reduced soil pH. In contrast, compost-based amendments and cow manure promoted more progressive changes in microbial structure and were linked to higher organic matter content and nutrient availability throughout the experiment.
Differential abundance analyses identified amendment-specific microbial responses, including reductions in several bacterial taxa under chicken manure treatment and an enrichment of saprotrophic fungi in compost-amended soils. Comparisons between culture-dependent methods and sequencing data revealed strong consistency for bacterial communities but lower agreement for fungal taxa.
These findings highlight the importance of fertilizer composition and nutrient release patterns in shaping soil microbial communities in banana production systems. Understanding these microbial responses can support the development of more sustainable fertilization strategies for subtropical agriculture.