Taxonomic Composition and Predicted Functional Potential of a Commercial Microbiome-Based Fertilizer Additive and Agricultural Soils in Eastern Paraguay

Abstract

Anthropogenic soil degradation is a major challenge for sustainable food production, particularly in tropical agricultural systems where excessive fertilizer use contributes to soil deterioration and greenhouse gas emissions. Microbiome-based agricultural technologies offer a potential strategy to improve fertilizer-use efficiency while maintaining crop productivity. Here, we characterized the taxonomic composition and predicted functional potential of a commercial microbiome-based fertilizer additive (humus) deployed across more than 1.4 million hectares in Paraguay and Uruguay, and compared it with root-associated microbiomes. In parallel, we evaluated agricultural and forest soil microbiomes from eastern Paraguay. Microbial communities were analyzed using 16S rRNA gene sequencing and PICRUSt2-based functional prediction. The humus microbiome displayed enrichment of pathways associated with degradation of organic compounds, nutrient cycling, and plant-growth-promoting activities. Furthermore, humus and root-associated microbiomes shared over 350 predicted microbial pathways, indicating substantial functional overlap despite differences in specific bacterial taxa, and suggesting that the consortium may function as a rhizosphere-like microbial community capable of providing functions commonly associated with plant-associated microbiomes. In agricultural soils, significant taxonomic differences were observed between high- and low-productivity fields, whereas predicted functional profiles remained largely conserved, consistent with functional redundancy within soil microbial communities. Productive soils were enriched in the superpathway of demethylmenaquinol-6 biosynthesis II, a microbial vitamin K2-related pathway involved in respiratory metabolism. Together, these findings provide the first detailed taxonomic and predicted functional characterization of a large-scale commercial microbiome-based fertilizer additive and establish a baseline for understanding microbial diversity and functional potential across productive agricultural soils in Paraguay. ImportanceSoil degradation and inefficient fertilizer use are major constraints to sustainable agriculture, particularly in tropical systems where nutrient losses and greenhouse gas emissions are high. Microbiome-based agricultural inputs are increasingly proposed as tools to enhance soil functioning and improve nutrient cycling efficiency, yet their ecological characteristics and functional potential remain poorly understood. This study provides the first detailed taxonomic and predicted functional characterization of a large-scale commercial microbiome-based fertilizer additive deployed in South American agriculture, and places it in the context of native forest and agricultural soil microbiomes. By integrating 16S rRNA gene sequencing with predictive functional profiling, this work reveals substantial functional overlap between the microbial consortium and plant-associated microbiomes, suggesting ecological convergence toward rhizosphere-like functions. In addition, the identification of conserved functional profiles across soils with contrasting productivity highlights the potential role of functional redundancy in maintaining ecosystem processes under different management regimes. Together, these findings provide a foundational framework for understanding microbiome-based agricultural inputs and soil microbial functional stability in subtropical agroecosystems, specifically Paraguay, contributing to the development of more sustainable agricultural practices.