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

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. This suggests 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.