Modulation of the soil microbiome by long-term Ca-based soil amendments boosts soil organic carbon and physicochemical quality in a tropical no-till crop rotation system

Unsustainable agricultural management practices such as non-conservationist tillage and overuse of fertilizers result in soil acidity and, in turn, soil degradation due to reduced carbon (C) concentrations and nutrient availability and increased aluminum toxicity. Application of lime (L) and phosphogypsum (PG) can overcome these constraints and improve soil quality, but the long-term effects of these amendments on both abiotic and biotic soil properties are not known, particularly when applied in combination. Here, we evaluated the effects of L (acidity corrective), PG (soil conditioner), and their combination (LPG) on soil organic matter (SOM) transformations, soil chemical and physical properties, and microbiome assembly in a long-term experiment under a no-till crop rotation system in a tropical soil. The Ca-based soil amendments increased C concentrations (labile and stable fractions), improved soil physicochemical properties, and changed the associations between several bacterial and fungal groups. Contrary to expectations, the acidic soil amended with PG exhibited greater number of significant shifts in the bacterial community than soil amended with L or LPG, as well as higher soil bulk density. By contrast, the fungal community underwent greater shifts in soil amended with L or LPG, which had higher macroporosity. L and LPG amendment shaped the fungal community and rearranged the SOM fractions at similar rates, suggesting an essential role of the altered fungi in SOM transformation. In addition, combining L with PG increased the relevance of many low-abundance microorganisms, especially fungi, compared with the control, indicating an increase in their ecological role in the soil. Finally, by applying general joint attribute modeling and sensitivity analysis, we determined that soil fertility increased most in LPG-amended soil, as the ensuing changes in the bacterial and fungal communities resulted in improved SOM fractions, soil physical characteristics and, ultimately, soil quality.