Synthetic Rhizosphere Communities as Scalable Enhancers of Fertilizer Efficiency for Climate-Smart Agriculture

Anthropogenic soil degradation is a major barrier to sustainable food production. It impairs soil biological and chemical properties through the disruption of microbial communities, resulting in reduced agricultural productivity. Excessive use of synthetic fertilizers, while increasing yields, often leads to soil compaction, salinization, and greenhouse gas emissions. Latin America is especially vulnerable to these impacts. To address this, we have previously developed a microbiome-based fertilizer additive that allows increased crop yields with lower fertilizer input. Despite its commercial application on over 1.4 million hectares in Paraguay and Uruguay, its predicted microbial functions were previously unstudied. Furthermore, Paraguayan arable and forest soil microbiomes have not been studied in detail. Here, we used 16S rRNA gene sequencing and PICRUSt2-based functional prediction to assess the additive’s microbial functional potential, and differences in soil microbial diversity, structure, and function. The additive contained high abundance of nutrient cycling related microbial pathways. A subsequent multivariable association analysis revealed higher abundances of Pseudomonas , Hamadaea , Reyranella , and Lyzobacter in forest, additive-treated, and untreated high-productivity soils. These taxa are linked to nutrient cycling and biocontrol, suggesting their potential as soil health indicators. Our findings highlight the importance of microbiome-centered strategies for regenerative agriculture, supporting food security and sustainable development.