Metagenome-assembled genomes (MAGs) revealed a functionally stratified microbiome in Jeevamrit, enabling co-operative nutrient cycling and rhizospheric growth promotion in the natural farming practices

Abstract

Jeevamrit, a fermented liquid microbial bioinoculant, is increasingly recognized as a soil and plant growth enhancer in sustainable agricultural practices such as zero-budget natural farming; however, the genetic pool attributed to the functionality by microbial constituents remained poorly resolved. In this study, we reconstructed 16 high-quality metagenome-assembled genomes (MAGs) from Jeevamrit under two critical mixing regimes to elucidate the contributions of key taxa affiliated with Pseudomonadota, Bacillota, and Bacteroidota to nutrient cycling and plant growth promotion. Functional annotation revealed a stratified (upper-middle-lower) metabolic organization with interdependent interactions driving combinatorial functionality. Upper-layer MAGs, including Klebsiella and Pseudaeromonas exhibited organic polymer degradation, glycolytic and oxidative carbon metabolism, respiratory versatility with nutrient acquisition traits such as nitrogen fixation and phosphate/iron solubilization. In middle and lower-layer, Trichococcus, Clostridium, and Veillonella displayed fermentative and reductive metabolisms that facilitate the turnover of partially degraded organic matter and production of organic acids, nitrogen transformations, and metabolic cross-feeding under fluctuating redox conditions. Phylogenetic and taxono-genomic analyses support the designation of eight MAGs as novel species (sp. nov.), for which new names are proposed. A consensus genetic map deciphered traits linked to phytohormone biosynthesis (IAA, cytokinins), quorum-sensing-mediated rhizosphere colonization, and abiotic stress tolerance. Ultimately, this culture-independent metagenome study underpins field-relevant mechanistic insights into an indigenous microbial inoculant, highlighting its potential as a locally adapted solution for sustainable agriculture. ImportanceMicrobial bioinoculants such as Jeevamrit are increasingly used in sustainable agriculture, yet their functional basis remains insufficiently understood due to the limited genome-level resolution of constituent microbiota. This study addresses this gap by applying genome-resolved metagenomics to connect microbial diversity with agriculture-associated ecological functions in a complex fermented local formulation. By integrating metabolic reconstruction with plant-associated functional traits, this study advances understanding of how microbial consortia contribute to nutrient mobilization, rhizosphere competence, and environmental adaptability. This highlights the contribution of yet-to-be-cultivated but metabolically versatile taxa, which are important to the functions of agricultural ecosystems. By uncovering the roles of key microbes and their cooperative metabolic interactions, this work provides a scientific basis for improving Jeevamrit formulations through informed selection or enrichment of functionally important microbes to enhance nutrient delivery and plant growth performance.